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A

Aa - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Aa() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
 
aa - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
abMax - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
abMax - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
absolute - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
 
absolute - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
 
absolute - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
 
AbstractContactType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A contact is either a person or an organization.
AbstractContactType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractContactType
 
AbstractContactType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A contact is either a person or an organization.
AbstractContactType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractContactType
 
AbstractFile - Class in umich.ms.fileio.filetypes.util
Author: Dmitry Avtonomov (dmitriya) Email: dmitriy.avtonomov@gmail.com Date: 2/18/13 Time: 11:01 AM
AbstractFile(String) - Constructor for class umich.ms.fileio.filetypes.util.AbstractFile
 
AbstractLCMSDataSource<T extends Index<?>> - Class in umich.ms.fileio.filetypes
Provides some basic defaults for simple LCMSFile interface methods.
AbstractLCMSDataSource(String) - Constructor for class umich.ms.fileio.filetypes.AbstractLCMSDataSource
Create a new source with autoload of spectra disabled.
AbstractParamType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Abstract entity allowing either cvParam or userParam to be referenced in other schemas.
AbstractParamType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
 
AbstractParamType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Abstract entity allowing either cvParam or userParam to be referenced in other schemas.
AbstractParamType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
 
AbstractScan - Class in umich.ms.datatypes.scan
The most general representation of a Scan.
AbstractScan(int) - Constructor for class umich.ms.datatypes.scan.AbstractScan
Creates a scan with STRONG storage strategy.
AbstractSpectrum - Class in umich.ms.datatypes.spectrum
Author: Dmitry Avtonomov (dmitriya) Email: dmitriy.avtonomov@gmail.com Date: 3/1/13 Time: 2:04 PM
AbstractSpectrum() - Constructor for class umich.ms.datatypes.spectrum.AbstractSpectrum
 
AbstractXMLBasedDataSource<E extends XMLBasedIndexElement,I extends Index<E>> - Class in umich.ms.fileio.filetypes.xmlbased
 
AbstractXMLBasedDataSource(String) - Constructor for class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
AbstractXMLBasedIndexElement - Class in umich.ms.fileio.filetypes.xmlbased
 
AbstractXMLBasedIndexElement(int, int, OffsetLength) - Constructor for class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedIndexElement
 
abTot - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
abTot - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
ACC_NUMPRESS_LINEAR - Static variable in class umich.ms.external.msnumpress.MSNumpress
 
ACC_NUMPRESS_PIC - Static variable in class umich.ms.external.msnumpress.MSNumpress
 
ACC_NUMPRESS_SLOF - Static variable in class umich.ms.external.msnumpress.MSNumpress
 
accepts(Path) - Method in interface umich.ms.fileio.filetypes.LCMSDataSourceDetector
 
accession - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CVParamType
 
accession - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
 
accession - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CVParamType
 
accession - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
 
accession - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
 
accession - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
accession - Variable in class umich.ms.fileio.filetypes.mzml.util.CVTerm
 
accession - Variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
accession - Variable in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
 
act - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
activateObject(PooledObject<ByteArrayHolder>) - Method in class umich.ms.util.ByteArrayHolderFactory
 
activation - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
 
ActivationCVTerm - Class in umich.ms.fileio.filetypes.mzml.util
 
ActivationCVTerm(String, String, String, String) - Constructor for class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
 
ActivationCVTerm(String, String, String) - Constructor for class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
 
ActivationInfo - Class in umich.ms.datatypes.scan.props
 
ActivationInfo() - Constructor for class umich.ms.datatypes.scan.props.ActivationInfo
 
activationMethod - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
 
activationMethod - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
activationMethod - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
activationMethod - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
activationMethodFromAccession(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
Returns the possible shortest abbreviation for a given activation method.
activationMethodFromAccession(CharArray) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
Returns the possible shortest abbreviation for a given activation method.
ActivationMethodType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for activationMethodType.
ActivationMethodType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for activationMethodType.
ActivationMethodType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for activationMethodType.
activityDate - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProtocolApplicationType
 
activityDate - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProtocolApplicationType
 
Adapter1 - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
 
Adapter1() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.Adapter1
 
Adapter1 - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
 
Adapter1() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.Adapter1
 
Adapter1 - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
 
Adapter1() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.Adapter1
 
Adapter1 - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
 
Adapter1() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.Adapter1
 
Adapter1 - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
 
Adapter1() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Adapter1
 
Adapter1 - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
 
Adapter1() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Adapter1
 
Adapter1 - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
 
Adapter1() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Adapter1
 
Adapter1 - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
 
Adapter1() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.Adapter1
 
Adapter2 - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
 
Adapter2() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.Adapter2
 
Adapter2 - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
 
Adapter2() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.Adapter2
 
Adapter2 - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
 
Adapter2() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.Adapter2
 
Adapter2 - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
 
Adapter2() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.Adapter2
 
Adapter2 - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
 
Adapter2() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Adapter2
 
Adapter2 - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
 
Adapter2() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Adapter2
 
Adapter2 - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
 
Adapter2() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Adapter2
 
Adapter2 - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
 
Adapter2() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.Adapter2
 
add(T) - Method in class umich.ms.datatypes.index.impl.IndexDefault
Add a IndexElement to the index.
Don't use this method, unless you're building a new index.
add(T) - Method in interface umich.ms.datatypes.index.Index
Add a new index element to this index.
add(LCMSRange) - Method in class umich.ms.datatypes.LCMSRangeSet
This add method gradually removes scan-ranges from the input range as it descends down the hierarchy.
add(IScan) - Method in class umich.ms.datatypes.scancollection.ScanIndex
Adds a scan to the index.
add(IScan) - Method in class umich.ms.datatypes.scancollection.ScanIndexRoot
 
add(AgilentMSPeak) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
add(AgilentCompound) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
 
addAll(Collection<? extends AgilentMSPeak>) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
addCurScanAndFlushVars() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
addCurScanAndFlushVars() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
addIndexElement(T) - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
 
addInstrument(Instrument, String) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
If only one instrument is added, it will be set as the default instrument, all the scans, that you add to the ScanCollection will implicitly refer to this one instrument.
additionalSearchParams - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
additionalSearchParams - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
addScan(IScan) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Adds a new scan to this collection, maintains all the proper inside mappings.
addScan(IScan) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Adds a new scan to this collection, maintains all the proper inside mappings.
adduct - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
addUnfinishedIndexElement(T) - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
 
adjRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
 
adjRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
 
adjRatioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
 
adjRatioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
 
affectedChannel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel
 
AffectedChannel - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AffectedChannel() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AffectedChannel
 
affectedChannel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ContributingChannel
 
AffectedChannel - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AffectedChannel() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AffectedChannel
 
affectedChannel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ContributingChannel
 
AffectedChannel - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
AffectedChannel() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AffectedChannel
 
affectedChannel - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ContributingChannel
 
AffectedChannel - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
AffectedChannel() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.AffectedChannel
 
affectedChannel - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ContributingChannel
 
affiliation - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
 
affiliation - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
 
AffiliationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Java class for AffiliationType complex type.
AffiliationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AffiliationType
 
AffiliationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Java class for AffiliationType complex type.
AffiliationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AffiliationType
 
AgilentCefFile - Class in umich.ms.fileio.filetypes.agilent.cef.example
Factory for features detected by Agilent MassHunter, stored as .cef files.
AgilentCefFile(Path) - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
 
AgilentCefTest - Class in umich.ms.fileio.filetypes.agilent.cef.example
Created by Dmitry Avtonomov on 2015-09-22.
AgilentCefTest() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefTest
 
AgilentCompound - Class in umich.ms.fileio.filetypes.agilent.cef.example
One entry in Agilent .cef file, created by Molecular Feature Extractor algorithm.
AgilentCompound() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
AgilentCompounds - Class in umich.ms.fileio.filetypes.agilent.cef.example
All compounds from an Agilent .cef file.
AgilentCompounds() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
 
AgilentCompounds(int) - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
 
AgilentMSPeak - Class in umich.ms.fileio.filetypes.agilent.cef.example
 
AgilentMSPeak() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
algo - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Compound
 
allNttProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult
 
allNttProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
 
allNttProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetResult
 
allNttProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
 
allNttProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetResult
 
allNttProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
 
alternativeProtein - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
AlternativeProtein - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AlternativeProtein() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
 
alternativeProtein - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
AlternativeProtein - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AlternativeProtein() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
 
alternativeProtein - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
altPosToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
 
altPosToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
 
altPosToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
 
altPosToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
 
altPosToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
 
altPosToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
 
ambiguousResidue - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MassTableType
 
ambiguousResidue - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MassTableType
 
AmbiguousResidueType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Ambiguous residues e.g.
AmbiguousResidueType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AmbiguousResidueType
 
AmbiguousResidueType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Ambiguous residues e.g.
AmbiguousResidueType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AmbiguousResidueType
 
aminoacid - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
aminoacid - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
 
aminoacid - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
 
aminoacidModification - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
AminoacidModification - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AminoacidModification() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
 
aminoacidModification - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
AminoacidModification - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AminoacidModification() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
 
aminoacidModification - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
amu2ppm(double, double) - Static method in class umich.ms.util.SpectrumUtils
Given an absolute m/z difference (amu parameter), find out how much ppm that is.
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisResult
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisResult
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
 
analysis - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
 
analysis - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisResult
 
analysis - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
 
analysis - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
 
analysis - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisResult
 
analysis - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
 
analysis - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
 
analysisCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
analysisCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
AnalysisCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The analyses performed to get the results, which map the input and output data sets.
AnalysisCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisCollectionType
 
AnalysisCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The analyses performed to get the results, which map the input and output data sets.
AnalysisCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisCollectionType
 
analysisData - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DataCollectionType
 
analysisData - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DataCollectionType
 
AnalysisDataType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Data sets generated by the analyses, including peptide and protein lists.
AnalysisDataType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisDataType
 
AnalysisDataType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Data sets generated by the analyses, including peptide and protein lists.
AnalysisDataType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisDataType
 
analysisDistributionFile - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
 
analysisDistributionFile - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
 
analysisParams - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionProtocolType
 
analysisParams - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionProtocolType
 
analysisProtocolCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
analysisProtocolCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
AnalysisProtocolCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The collection of protocols which include the parameters and settings of the performed analyses.
AnalysisProtocolCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisProtocolCollectionType
 
AnalysisProtocolCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The collection of protocols which include the parameters and settings of the performed analyses.
AnalysisProtocolCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisProtocolCollectionType
 
analysisResult - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
AnalysisResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AnalysisResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisResult
 
analysisResult - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
AnalysisResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AnalysisResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisResult
 
analysisResult - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
AnalysisResult - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
AnalysisResult() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisResult
 
analysisResult - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
AnalysisResult - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
AnalysisResult() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisResult
 
analysisResult - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
analysisSampleCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
analysisSampleCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
AnalysisSampleCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The samples analysed can optionally be recorded using CV terms for descriptions.
AnalysisSampleCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSampleCollectionType
 
AnalysisSampleCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The samples analysed can optionally be recorded using CV terms for descriptions.
AnalysisSampleCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSampleCollectionType
 
analysisSoftware - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareListType
 
analysisSoftware - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareListType
 
analysisSoftwareList - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
analysisSoftwareList - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
AnalysisSoftwareListType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The software packages used to perform the analyses.
AnalysisSoftwareListType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareListType
 
AnalysisSoftwareListType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The software packages used to perform the analyses.
AnalysisSoftwareListType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareListType
 
analysisSoftwareRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionProtocolType
 
analysisSoftwareRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProviderType
 
analysisSoftwareRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
analysisSoftwareRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionProtocolType
 
analysisSoftwareRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProviderType
 
analysisSoftwareRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
AnalysisSoftwareType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The software used for performing the analyses.
AnalysisSoftwareType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
 
AnalysisSoftwareType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The software used for performing the analyses.
AnalysisSoftwareType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
 
analysisSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
 
AnalysisSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
 
analysisSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
 
AnalysisSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
 
analysisSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
 
AnalysisSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
AnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
 
analysisSummary - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
 
AnalysisSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
AnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
 
analysisSummary - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
 
analysisTimestamp - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
AnalysisTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AnalysisTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
 
analysisTimestamp - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
AnalysisTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AnalysisTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
 
analysisTimestamp - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
analyzer - Variable in class umich.ms.datatypes.scan.props.Instrument
 
analyzer - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentListType
 
AnalyzerComponentType - Class in umich.ms.fileio.filetypes.mzml.jaxb
This element must be used to describe an Analyzer Component Type.
AnalyzerComponentType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.AnalyzerComponentType
 
annotation - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
 
annotation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishableProtein
 
annotation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishableProtein
 
any - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
 
any - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
 
any - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
 
any - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisResult
 
any - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
 
any - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisResult
 
any - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
 
any - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisResult
 
any - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
 
any - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
 
any - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisResult
 
any - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
 
any - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
 
area - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
 
area - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
 
area - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
 
area - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
 
area - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
 
area - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
 
areaError - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
 
areaError - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
 
areaError - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
 
areaError - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
 
areaError - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
 
areaError - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
 
areaFlag - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
 
areaFlag - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
 
areaFlag - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
 
areaFlag - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
 
areaFlag - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
 
areaFlag - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
 
arrayLength - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
 
ASAPDta - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ASAPDta() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPDta
 
asapDta - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
ASAPDta - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ASAPDta() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPDta
 
asapDta - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
ASAPPeak - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ASAPPeak() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
asapPeak - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
ASAPPeak - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ASAPPeak() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
asapPeak - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
ASAPProtAnalysisSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ASAPProtAnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
 
ASAPProtAnalysisSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ASAPProtAnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
 
asapProtId - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
 
asapProtId - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
 
ASAPPvalueAnalysisModel - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ASAPPvalueAnalysisModel() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisModel
 
ASAPPvalueAnalysisModel - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ASAPPvalueAnalysisModel() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisModel
 
ASAPPvalueAnalysisSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ASAPPvalueAnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
 
ASAPPvalueAnalysisSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ASAPPvalueAnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
 
ASAPRatio - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ASAPRatio() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
 
ASAPRatio - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ASAPRatio() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
 
AsapratioContribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
AsapratioContribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
 
asapratioContribution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
 
AsapratioContribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AsapratioContribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
 
asapratioContribution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
 
AsapratioContribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AsapratioContribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
 
asapratioContribution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
 
asapratioId - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
 
asapratioId - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
 
asapratioLcHeavypeak - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
 
AsapratioLcHeavypeak - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
AsapratioLcHeavypeak() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
 
asapratioLcHeavypeak - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
 
AsapratioLcHeavypeak - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AsapratioLcHeavypeak() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
 
asapratioLcHeavypeak - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
 
AsapratioLcHeavypeak - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AsapratioLcHeavypeak() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
 
asapratioLcLightpeak - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
 
AsapratioLcLightpeak - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
AsapratioLcLightpeak() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
 
asapratioLcLightpeak - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
 
AsapratioLcLightpeak - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AsapratioLcLightpeak() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
 
asapratioLcLightpeak - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
 
AsapratioLcLightpeak - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AsapratioLcLightpeak() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
 
AsapratioPeptideData - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
AsapratioPeptideData() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
 
asapratioPeptideData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
 
AsapratioPeptideData - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AsapratioPeptideData() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
 
asapratioPeptideData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
 
AsapratioPeptideData - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AsapratioPeptideData() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
 
asapratioPeptideData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
 
ASAPRatioPvalue - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ASAPRatioPvalue() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
 
ASAPRatioPvalue - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ASAPRatioPvalue() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
 
AsapratioResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
AsapratioResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
 
AsapratioResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AsapratioResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
 
AsapratioResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AsapratioResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
 
AsapratioSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
AsapratioSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
 
AsapratioSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AsapratioSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
 
AsapratioSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AsapratioSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
 
AsapratioTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
AsapratioTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioTimestamp
 
AsapratioTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
AsapratioTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioTimestamp
 
AsapratioTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
AsapratioTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioTimestamp
 
asapSeq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
 
ASAPSeq - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ASAPSeq() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
asapSeq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
 
ASAPSeq - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ASAPSeq() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
assumedCharge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
assumedCharge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
assumedCharge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
at - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
 
ATTR_OFFSET_ID - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
ATTR_OFFSET_ID - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
Attribute - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Attribute() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Attribute
 
attribute - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
 
auditCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
auditCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
AuditCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The complete set of Contacts (people and organisations) for this file.
AuditCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AuditCollectionType
 
AuditCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The complete set of Contacts (people and organisations) for this file.
AuditCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AuditCollectionType
 
author - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
 
author - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
 
author - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
 
author - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
 
author - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
 
author - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
author - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
 
author - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
 
author - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
authors - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
authors - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 
available() - Method in class umich.ms.util.base64.Base64Context
Returns the amount of buffered data available for reading.
avgMassDelta - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
 
avgMassDelta - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
 
avgMassDelta - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
 
avgMassDelta - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
 

B

background - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
 
background - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
 
background - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
 
background - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
 
background - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
 
background - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
 
backgroundFittingError - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
 
backgroundFittingError - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
 
backgroundRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
 
backgroundRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
 
backgroundRatioStdev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
 
backgroundRatioStdev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
 
Base64 - Class in umich.ms.util.base64
Follows implementation from Apache Commons Codec (org.apache.commons.codec.binary.Base64).
Base64() - Constructor for class umich.ms.util.base64.Base64
Creates a Base64 codec used for decoding (all modes) and encoding in URL-unsafe mode.
Base64(int) - Constructor for class umich.ms.util.base64.Base64
 
Base64(int, byte[], boolean) - Constructor for class umich.ms.util.base64.Base64
Creates a Base64 codec used for decoding (all modes) and encoding in URL-unsafe mode.
base64Chars - Static variable in class umich.ms.util.base64.Base64Slow
Table of the sixty-four characters that are used as the Base64 alphabet: [a-z0-9A-Z+/]
Base64Context - Class in umich.ms.util.base64
 
Base64Context() - Constructor for class umich.ms.util.base64.Base64Context
 
Base64ContextPooled - Class in umich.ms.util.base64
 
Base64ContextPooled() - Constructor for class umich.ms.util.base64.Base64ContextPooled
 
Base64DecodingException - Exception in umich.ms.util.base64
Exception that is thrown when an unexpected character is encountered during Base64 decoding.
Base64DecodingException(String, char) - Constructor for exception umich.ms.util.base64.Base64DecodingException
Construct an new exception.
Base64Slow - Class in umich.ms.util.base64
Implements Base64 encoding and decoding as defined by RFC 2045: "Multi-purpose Internet Mail Extensions (MIME) Part One: Format of Internet Message Bodies" page 23.
baseName - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
baseName - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
baseName - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
baseName - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
baseName - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
baseName - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
basePeakIntensity - Variable in class umich.ms.datatypes.scan.AbstractScan
Intensity of the most intense peak
basePeakIntensity - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
basePeakMz - Variable in class umich.ms.datatypes.scan.AbstractScan
m/z of the most intense peak
basePeakMz - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
bibliographicReference - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
bibliographicReference - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
BibliographicReferenceType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Represents bibliographic references.
BibliographicReferenceType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
BibliographicReferenceType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Represents bibliographic references.
BibliographicReferenceType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 
binary - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
 
binary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
binary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
 
binary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
 
binaryDataArray - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayListType
 
binaryDataArrayList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
 
binaryDataArrayList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
BinaryDataArrayListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List of binary data arrays.
BinaryDataArrayListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayListType
 
BinaryDataArrayType - Class in umich.ms.fileio.filetypes.mzml.jaxb
The structure into which encoded binary data goes.
BinaryDataArrayType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
 
binaryRefFiles - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
 
binaryRefFiles - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
 
binNo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
 
binNo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
 
binNo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
 
binNo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
 
binNo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
 
binNo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
 
Bioml - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Bioml() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Bioml
 
bIons - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
bScore - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
buf - Variable in class umich.ms.util.ByteArrayHolder
The buffer where data is stored.
BUF_SIZE - Static variable in class umich.ms.fileio.filetypes.util.AbstractFile
 
BufferedRandomAccessFile - Class in umich.ms.external.apache.cassandra.io
A BufferedRandomAccessFile is like a RandomAccessFile, but it uses a private buffer so that most operations do not require a disk access.
BufferedRandomAccessFile(File, String) - Constructor for class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
Open a new BufferedRandomAccessFile on file in mode mode, which should be "r" for reading only, or "rw" for reading and writing.
BufferedRandomAccessFile(File, String, int) - Constructor for class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
BufferedRandomAccessFile(String, String) - Constructor for class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
Open a new BufferedRandomAccessFile on the file named name in mode mode, which should be "r" for reading only, or "rw" for reading and writing.
BufferedRandomAccessFile(String, String, int) - Constructor for class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
BufferedRandomAccessFile - Class in umich.ms.external
This is an optimized version of the BufferedRandomAccessFile class as described by Nick Zhang on JavaWorld.com.
BufferedRandomAccessFile(String, String, int) - Constructor for class umich.ms.external.BufferedRandomAccessFile
Creates a new instance of the BufferedRandomAccessFile.
BufferedRandomAccessFile(File, String, int) - Constructor for class umich.ms.external.BufferedRandomAccessFile
 
BuffSz_ - Static variable in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
buildIndex(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
For use with Executors, consider using instead of calling this method directly.
buildIndex(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.MZMLIndexBuilder
 
buildIndex(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
For use with Executors, consider using instead of calling this method directly.
buildIndex(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.MZXMLIndexBuilder
 
buildIndex(I) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
Be careful with this method, it will go over the whole file, building index from scans that it can find.
buildIndex(IndexBuilder.Info) - Method in interface umich.ms.fileio.filetypes.xmlbased.IndexBuilder
 
ByteArrayHolder - Class in umich.ms.util
Auto-growing array of bytes, with access to the underlying data.
ByteArrayHolder(int) - Constructor for class umich.ms.util.ByteArrayHolder
Creates a new byte array output stream, with a buffer capacity of the specified size, in bytes.
ByteArrayHolder() - Constructor for class umich.ms.util.ByteArrayHolder
Creates a new byte array output stream.
ByteArrayHolder(byte[]) - Constructor for class umich.ms.util.ByteArrayHolder
 
ByteArrayHolderFactory - Class in umich.ms.util
 
ByteArrayHolderFactory() - Constructor for class umich.ms.util.ByteArrayHolderFactory
 
ByteArrayHolderFactory(int) - Constructor for class umich.ms.util.ByteArrayHolderFactory
 
byteorder - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
 
byteOrder - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
 

C

CACHE - Static variable in class umich.ms.fileio.util.jaxb.JaxbUtils
Cache.
calcNeutralPepMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
calcNeutralPepMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
calcNeutralPepMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
calcNeutralPepMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
 
calcNeutralPepMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
 
calcNeutralPepMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
calcNeutralPepMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
 
calcNeutralPepMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
 
calcNeutralPepMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
calcPI - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
calcPI - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
calcPI - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
calculatedMassToCharge - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
calculatedMassToCharge - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
calculatedPI - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
calculatedPI - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
call() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
call() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.MZMLIndexBuilder
 
call() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
call() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.MZXMLIndexBuilder
 
category - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.OntologyEntryType
 
CEF - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
CEF() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.CEF
 
centroided - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
 
centroided - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
centroidingPreference - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
 
centroidingPreference - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
 
centroidingPreference - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
 
centroidingPreference - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
centroidingPreference - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.FragmentMasses
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AffectedChannel
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ContributingChannel
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.FragmentMasses
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AffectedChannel
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ContributingChannel
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.FragmentMasses
 
channel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
 
channel - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AffectedChannel
 
channel - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ContributingChannel
 
channel - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FragmentMasses
 
channel - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AffectedChannel
 
channel - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ContributingChannel
 
channel - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FragmentMasses
 
channelCode - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
 
channelCode - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
 
channelCode - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
 
channelCode - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
channelCode - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
charArray - Variable in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.TAG
 
charge - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IonTypeType
 
charge - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IonTypeType
 
charge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
 
charge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
 
charge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
 
charge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
 
charge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
 
charge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
 
charge - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
 
charge - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
 
charge - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
charge - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
 
charge - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
 
charge - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
CHARGE_UNKNOWN - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
CHARGE_UNKNOWN - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
chargeDeconvoluted - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
 
chargeDeconvoluted - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
chargeEstCorrect - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
 
chargeEstCorrect - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
 
chargeEstCorrect - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
 
chargeState - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
chargeState - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
check() - Method in class umich.ms.util.IntervalST
Check integrity of subtree count fields.
childScans - Variable in class umich.ms.datatypes.scan.AbstractScan
A list of MS/MS scans, that originated from this one
chromatogram - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramListType
 
chromatogramList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
 
ChromatogramListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List of chromatograms.
ChromatogramListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramListType
 
ChromatogramType - Class in umich.ms.fileio.filetypes.mzml.jaxb
A single chromatogram.
ChromatogramType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
 
ChunkedFile - Class in umich.ms.fileio.chunk
 
ChunkedFile(Path) - Constructor for class umich.ms.fileio.chunk.ChunkedFile
 
ChunkedFile(Path, int, int) - Constructor for class umich.ms.fileio.chunk.ChunkedFile
 
cidGasPressure - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
cidIndex - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
 
cidIndex - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
 
cidIndex - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
 
ClassFactory - Class in umich.ms.fileio.filetypes.thermo.raw.com4j
Defines methods to create COM objects
clear() - Method in class umich.ms.util.ByteArrayHolder
 
clear() - Method in class umich.ms.util.StrongReference
 
cloneWithoutPeaks() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
close() - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
close() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method Close
close() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method Close
close() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirUV
method Close
close() - Method in class umich.ms.fileio.filetypes.util.AbstractFile
 
close() - Method in class umich.ms.util.base64.Base64Context
should be called when context becomes useless
close() - Method in class umich.ms.util.base64.Base64ContextPooled
 
close() - Method in class umich.ms.util.ByteArrayHolder
Closing a ByteArrayOutputStream has no effect.
code - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AmbiguousResidueType
 
code - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ResidueType
 
code - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AmbiguousResidueType
 
code - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ResidueType
 
collisionEnergy - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
collisionEnergy - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
collisionEnergy - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
collisionEnergy - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
collisionGas - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
 
comEnumValue() - Method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0001
 
comEnumValue() - Method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0002
 
comEnumValue() - Method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0003
 
comEnumValue() - Method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0004
 
comEnumValue() - Method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_MSOrder
 
comments - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
 
comments - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
 
comments - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
 
compareTo(AgilentMSPeak) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
compareTo(Interval1D<V>) - Method in class umich.ms.util.Interval1D
 
compensationVoltage - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
compensationVoltage - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
compensationVoltage - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
compensationVoltage - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
completionTime - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
 
componentList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
 
ComponentListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List with the different components used in the mass spectrometer.
ComponentListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ComponentListType
 
ComponentType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Java class for ComponentType complex type.
ComponentType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ComponentType
 
Compound - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
Compound() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.Compound
 
compound - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.CompoundList
 
compoundList - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.CEF
 
CompoundList - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
CompoundList() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.CompoundList
 
compressedLen - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
 
compressedLen - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
 
compressionType - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
 
compressionType - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
 
confidence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
confidence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
configureJavaUtilLogging() - Static method in class umich.ms.logging.LogHelper
Configures JUL (java.util.logging) using the logging.properties file located in this package.
contact - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.FileDescriptionType
 
contactRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ContactRoleType
 
contactRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ContactRoleType
 
contactRole - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
 
contactRole - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProviderType
 
contactRole - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SampleType
 
contactRole - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
 
contactRole - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProviderType
 
contactRole - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SampleType
 
ContactRoleType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The role that a Contact plays in an organization or with respect to the associating class.
ContactRoleType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ContactRoleType
 
ContactRoleType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The role that a Contact plays in an organization or with respect to the associating class.
ContactRoleType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ContactRoleType
 
contains(LCMSDataSubset) - Method in class umich.ms.datatypes.LCMSDataSubset
Checks if data ranges described by this subset fully contain ranges specified in another set.
According to this definition, for example LCMSDataSubset.WHOLE_RUN contains any other subset, including itself.
contains(V) - Method in class umich.ms.util.Interval1D
Does this interval contain a point?
contains(Interval1D<K>) - Method in class umich.ms.util.IntervalST
Check if the tree contains this exact interval.
containsAlphabetOrPad(byte[]) - Method in class umich.ms.util.base64.Base64
Tests a given byte array to see if it contains any characters within the alphabet or PAD.
content - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Note
 
content - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
 
contentType - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
 
contributingChannel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions
 
ContributingChannel - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
ContributingChannel() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ContributingChannel
 
contributingChannel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.IsotopicContributions
 
ContributingChannel - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
ContributingChannel() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ContributingChannel
 
contributingChannel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.IsotopicContributions
 
ContributingChannel - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ContributingChannel() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ContributingChannel
 
contributingChannel - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IsotopicContributions
 
ContributingChannel - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ContributingChannel() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ContributingChannel
 
contributingChannel - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IsotopicContributions
 
convertJAXBObjectToDomain(Class<T>, Object) - Method in class umich.ms.fileio.filetypes.gpmdb.GPMDBFile
 
convertJAXBObjectToDomain(Class<T>, Object) - Method in class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
convertJAXBObjectToDomain(Class<T>, Object) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser
 
convertJAXBObjectToDomain(Class<T>, Object) - Method in class umich.ms.fileio.filetypes.mzxml.XmlBasedRunHeaderParser
 
correction - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
 
correction - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AffectedChannel
 
correction - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AffectedChannel
 
correction - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AffectedChannel
 
correction - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AffectedChannel
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ProductListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SampleListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanWindowListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SelectedIonListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileRefListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumListType
 
count - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.TargetListType
 
count - Variable in class umich.ms.util.ByteArrayHolder
The number of valid bytes in the buffer.
cpdAlgo - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
 
create() - Static method in class umich.ms.datatypes.LCMSRange
A range that will contain all the scans in an LCMS run, no filters applied.
create(Range<Integer>) - Static method in class umich.ms.datatypes.LCMSRange
A range that will contain all scans within the specified scan number range.
create(Range<Integer>, Integer) - Static method in class umich.ms.datatypes.LCMSRange
A range that will contain all scans with the scan number range, but only at a specific MS-Level.
create(Range<Integer>, Integer, DoubleRange) - Static method in class umich.ms.datatypes.LCMSRange
A range, containing all scans within the scan number range at a specific MS-Level and a specific precursor range.
create() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
 
create(Path) - Static method in class umich.ms.fileio.filetypes.LCMSDataSourceFactory
Try and create a data source from a given file path.
create(String) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method Create
create(String) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirUV
method Create
create() - Method in class umich.ms.fileio.filetypes.xmlbased.XMLStreamReaderFactory
 
create() - Method in class umich.ms.util.ByteArrayHolderFactory
 
createAa() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Aa
createAffectedChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AffectedChannel
createAffectedChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AffectedChannel
createAffectedChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of AffectedChannel
createAffectedChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of AffectedChannel
createAffiliationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of AffiliationType
createAffiliationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of AffiliationType
createAlternativeProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AlternativeProtein
createAlternativeProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AlternativeProtein
createAmbiguousResidueType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of AmbiguousResidueType
createAmbiguousResidueType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of AmbiguousResidueType
createAminoacidModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AminoacidModification
createAminoacidModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AminoacidModification
createAnalysisCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisCollectionType
createAnalysisCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of AnalysisCollectionType
createAnalysisDataType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisDataType
createAnalysisDataType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of AnalysisDataType
createAnalysisProtocolCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisProtocolCollectionType
createAnalysisProtocolCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of AnalysisProtocolCollectionType
createAnalysisResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisResult
createAnalysisResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AnalysisResult
createAnalysisResult() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisResult
createAnalysisResult() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of AnalysisResult
createAnalysisSampleCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisSampleCollectionType
createAnalysisSampleCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of AnalysisSampleCollectionType
createAnalysisSoftwareListType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisSoftwareListType
createAnalysisSoftwareListType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of AnalysisSoftwareListType
createAnalysisSoftwareType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisSoftwareType
createAnalysisSoftwareType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of AnalysisSoftwareType
createAnalysisSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisSummary
createAnalysisSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AnalysisSummary
createAnalysisSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisSummary
createAnalysisSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of AnalysisSummary
createAnalysisTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AnalysisTimestamp
createAnalysisTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AnalysisTimestamp
createAnalyzerComponentType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of AnalyzerComponentType
createASAPDta() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ASAPDta
createASAPDta() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ASAPDta
createASAPPeak() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ASAPPeak
createASAPPeak() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ASAPPeak
createASAPProtAnalysisSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ASAPProtAnalysisSummary
createASAPProtAnalysisSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ASAPProtAnalysisSummary
createASAPPvalueAnalysisModel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ASAPPvalueAnalysisModel
createASAPPvalueAnalysisModel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ASAPPvalueAnalysisModel
createASAPPvalueAnalysisSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ASAPPvalueAnalysisSummary
createASAPPvalueAnalysisSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ASAPPvalueAnalysisSummary
createASAPRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ASAPRatio
createASAPRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ASAPRatio
createAsapratioContribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of AsapratioContribution
createAsapratioContribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AsapratioContribution
createAsapratioContribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AsapratioContribution
createAsapratioLcHeavypeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of AsapratioLcHeavypeak
createAsapratioLcHeavypeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AsapratioLcHeavypeak
createAsapratioLcHeavypeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AsapratioLcHeavypeak
createAsapratioLcLightpeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of AsapratioLcLightpeak
createAsapratioLcLightpeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AsapratioLcLightpeak
createAsapratioLcLightpeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AsapratioLcLightpeak
createAsapratioPeptideData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of AsapratioPeptideData
createAsapratioPeptideData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AsapratioPeptideData
createAsapratioPeptideData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AsapratioPeptideData
createASAPRatioPvalue() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ASAPRatioPvalue
createASAPRatioPvalue() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ASAPRatioPvalue
createAsapratioResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of AsapratioResult
createAsapratioResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AsapratioResult
createAsapratioResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AsapratioResult
createAsapratioSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of AsapratioSummary
createAsapratioSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AsapratioSummary
createAsapratioSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AsapratioSummary
createAsapratioTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of AsapratioTimestamp
createAsapratioTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of AsapratioTimestamp
createAsapratioTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of AsapratioTimestamp
createASAPSeq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ASAPSeq
createASAPSeq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ASAPSeq
createAttribute() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Attribute
createAuditCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of AuditCollectionType
createAuditCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of AuditCollectionType
createBibliographicReferenceType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of BibliographicReferenceType
createBibliographicReferenceType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of BibliographicReferenceType
createBinaryDataArrayListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of BinaryDataArrayListType
createBinaryDataArrayType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of BinaryDataArrayType
createBioml() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Bioml
createCEF() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of CEF
createChromatogramListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ChromatogramListType
createChromatogramType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ChromatogramType
createCollectionElement(String, Collection<T>) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Create a JAXBElement containing a JAXBCollection.
createComponentListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ComponentListType
createComponentType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ComponentType
createCompound() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of Compound
createCompoundList() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of CompoundList
createContactRoleType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ContactRoleType
createContactRoleType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ContactRoleType
createContributingChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of ContributingChannel
createContributingChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of ContributingChannel
createContributingChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ContributingChannel
createContributingChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ContributingChannel
createCVListType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of CVListType
createCVListType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of CVListType
createCVListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of CVListType
createCVParamType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of CVParamType
createCVParamType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of CVParamType
createCVParamType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of CVParamType
createCvType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of CvType
createCvType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of CvType
createCVType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of CVType
createDatabaseFiltersType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of DatabaseFiltersType
createDatabaseFiltersType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of DatabaseFiltersType
createDatabaseRefreshTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of DatabaseRefreshTimestamp
createDatabaseRefreshTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of DatabaseRefreshTimestamp
createDatabaseRefreshTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of DatabaseRefreshTimestamp
createDatabaseTranslationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of DatabaseTranslationType
createDatabaseTranslationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of DatabaseTranslationType
createDataCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of DataCollectionType
createDataCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of DataCollectionType
createDataFilter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of DataFilter
createDataFilter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of DataFilter
createDataFilter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of DataFilter
createDataFilter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of DataFilter
createDataProcessingListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of DataProcessingListType
createDataProcessingType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of DataProcessingType
createDatasetDerivation() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of DatasetDerivation
createDatasetDerivation() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of DatasetDerivation
createDatasetDerivation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of DatasetDerivation
createDatasetDerivation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of DatasetDerivation
createDBSequenceType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of DBSequenceType
createDBSequenceType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of DBSequenceType
createDetectorComponentType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of DetectorComponentType
createDevice() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of Device
createDistributionPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of DistributionPoint
createDistributionPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of DistributionPoint
createDomain() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Domain
createEmpty() - Static method in class umich.ms.fileio.filetypes.mzml.MZMLPeaksDecoder.DecodedData
 
createEmpty() - Static method in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
createEnzymaticSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of EnzymaticSearchConstraint
createEnzymaticSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of EnzymaticSearchConstraint
createEnzymesType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of EnzymesType
createEnzymesType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of EnzymesType
createEnzymeType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of EnzymeType
createEnzymeType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of EnzymeType
createErrorPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of ErrorPoint
createErrorPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of ErrorPoint
createExternalDataType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ExternalDataType
createExternalDataType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ExternalDataType
createFile() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of File
createFileDescriptionType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of FileDescriptionType
createFileFormatType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of FileFormatType
createFileFormatType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of FileFormatType
createFilterType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of FilterType
createFilterType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of FilterType
createFpkmDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of FpkmDistribution
createFpkmDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of FpkmDistribution
createFpkmInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of FpkmInformation
createFpkmInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of FpkmInformation
createFragmentArrayType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of FragmentArrayType
createFragmentArrayType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of FragmentArrayType
createFragmentationTableType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of FragmentationTableType
createFragmentationTableType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of FragmentationTableType
createFragmentationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of FragmentationType
createFragmentationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of FragmentationType
createFragmentMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of FragmentMasses
createFragmentMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of FragmentMasses
createFragmentMasses() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of FragmentMasses
createFragmentMasses() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of FragmentMasses
createGAMLValues() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of GAMLValues
createGroup() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Group
createIndistinguishablePeptide() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of IndistinguishablePeptide
createIndistinguishablePeptide() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of IndistinguishablePeptide
createIndistinguishableProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of IndistinguishableProtein
createIndistinguishableProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of IndistinguishableProtein
createInputFileType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of InputFileType
createInputFileType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of InputFileType
createInputFileType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of InputFileType
createInputSpectraType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of InputSpectraType
createInputSpectraType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of InputSpectraType
createInputSpectrumIdentificationsType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of InputSpectrumIdentificationsType
createInputSpectrumIdentificationsType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of InputSpectrumIdentificationsType
createInputsType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of InputsType
createInputsType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of InputsType
createInstrumentConfigurationListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of InstrumentConfigurationListType
createInstrumentConfigurationType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of InstrumentConfigurationType
createIntensity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of Intensity
createIntensity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of Intensity
createIntensity() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of Intensity
createIntensity() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of Intensity
createInteractSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of InteractSummary
createInteractSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of InteractSummary
createInteractSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of InteractSummary
createInterprophetResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of InterprophetResult
createInterprophetResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of InterprophetResult
createInterprophetResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of InterprophetResult
createInterprophetResultSearchScoreSummaryIProphet() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createInterprophetSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of InterprophetSummary
createInterprophetSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of InterprophetSummary
createInterprophetSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of InterprophetSummary
createIonTypeType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of IonTypeType
createIonTypeType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of IonTypeType
createIsotopicContributions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of IsotopicContributions
createIsotopicContributions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of IsotopicContributions
createIsotopicContributions() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of IsotopicContributions
createIsotopicContributions() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of IsotopicContributions
createLibraResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of LibraResult
createLibraResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of LibraResult
createLibraResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of LibraResult
createLibraResult() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of LibraResult
createLibraResult() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of LibraResult
createLibraResultIntensity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of LibraResult.Intensity
createLibraSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of LibraSummary
createLibraSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of LibraSummary
createLibraSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of LibraSummary
createLibraSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of LibraSummary
createLibraSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of LibraSummary
createLibraSummaryFragmentMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of LibraSummary.FragmentMasses
createLibraSummaryIsotopicContributions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createLibraSummaryIsotopicContributionsContributingChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createLibraSummaryIsotopicContributionsContributingChannelAffectedChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createLocation() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of Location
createMassTableType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of MassTableType
createMassTableType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of MassTableType
createMeasureType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of MeasureType
createMeasureType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of MeasureType
createMixturemodel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of Mixturemodel
createMixturemodel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of Mixturemodel
createMixturemodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of MixturemodelDistribution
createMixturemodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of MixturemodelDistribution
createMixtureModelling() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of MixtureModelling
createMixtureModelling() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of MixtureModelling
createMixtureModelPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of MixtureModelPoint
createMixtureModelPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of MixtureModelPoint
createMixtureModelType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of MixtureModelType
createMixtureModelType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of MixtureModelType
createMixtureModelType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of MixtureModelType
createMixtureModelTypeMixtureModelPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMod() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of Mod
createMod() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of Mod
createModAminoacidMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of ModAminoacidMass
createModAminoacidMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of ModAminoacidMass
createModAminoacidMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ModAminoacidMass
createModAminoacidMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ModAminoacidMass
createModificationInfo() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of ModificationInfo
createModificationInfo() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of ModificationInfo
createModificationInfo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ModificationInfo
createModificationInfo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ModificationInfo
createModificationParamsType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ModificationParamsType
createModificationParamsType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ModificationParamsType
createModificationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ModificationType
createModificationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ModificationType
createMSDetails() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of MSDetails
createMSFileReader_XRawfile() - Static method in class umich.ms.fileio.filetypes.thermo.raw.com4j.ClassFactory
MSFileReader XRawfile Class
createMSFileReader_XVirMS() - Static method in class umich.ms.fileio.filetypes.thermo.raw.com4j.ClassFactory
MSFileReader XVirMS Class
createMSFileReader_XVirUV() - Static method in class umich.ms.fileio.filetypes.thermo.raw.com4j.ClassFactory
MSFileReader XVirUV Class
createMsmsPipelineAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of MsmsPipelineAnalysis
createMsmsPipelineAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of MsmsPipelineAnalysis
createMsmsPipelineAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of MsmsPipelineAnalysis
createMsmsPipelineAnalysisAnalysisSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisDatasetDerivation() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisDatasetDerivationDataFilter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummaryAnalysisTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySampleEnzyme() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySampleEnzymeSpecificity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummaryAminoacidModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummaryEnzymaticSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummarySearchDatabase() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummarySequenceSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySearchSummaryTerminalModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuery() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHit() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitAlternativeProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitAnalysisResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitModificationInfo() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsPipelineAnalysisMsmsRunSummarySpectrumQuerySearchResultSearchHitModificationInfoModAminoacidMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createMsmsRunSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of MsmsRunSummary
createMsmsRunSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of MsmsRunSummary
createMSPeaks() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of MSPeaks
createMsRun() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun
createMsRunDataProcessing() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.DataProcessing
createMsRunMsInstrument() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.MsInstrument
createMsRunMsInstrumentMsManufacturer() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.MsInstrument.MsManufacturer
createMsRunMsInstrumentMsMassAnalyzer() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.MsInstrument.MsMassAnalyzer
createMsRunParentFile() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.ParentFile
createMsRunSeparation() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.Separation
createMsRunSpotting() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.Spotting
createMsRunSpottingPlate() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.Spotting.Plate
createMsRunSpottingPlatePattern() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.Spotting.Plate.Pattern
createMsRunSpottingPlatePatternOrientation() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
createMsRunSpottingPlateSpot() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.Spotting.Plate.Spot
createMsRunSpottingRobot() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of MsRun.Spotting.Robot
createMzIdentML(MzIdentMLType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of JAXBElement<MzIdentMLType>}
createMzIdentML(MzIdentMLType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of JAXBElement<MzIdentMLType>}
createMzIdentMLType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of MzIdentMLType
createMzIdentMLType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of MzIdentMLType
createMzML(MzMLType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of JAXBElement<MzMLType>}
createMzMLType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of MzMLType
createNamevalueType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of NamevalueType
createNameValueType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of NameValueType
createNameValueType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of NameValueType
createNameValueType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of NameValueType
createNameValueType() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of NameValueType
createNameValueType() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of NameValueType
createNegmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of NegmodelDistribution
createNegmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of NegmodelDistribution
createNiDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of NiDistribution
createNiDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of NiDistribution
createNiInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of NiInformation
createNiInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of NiInformation
createNote() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Note
createNspDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of NspDistribution
createNspDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of NspDistribution
createNspInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of NspInformation
createNspInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of NspInformation
createOntologyEntryType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of OntologyEntryType
createOperator() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of Operator
createOrganizationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of OrganizationType
createOrganizationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of OrganizationType
createP() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of P
createParamGroupType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ParamGroupType
createParamListType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ParamListType
createParamListType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ParamListType
createParamType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ParamType
createParamType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ParamType
createParentOrganizationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ParentOrganizationType
createParentOrganizationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ParentOrganizationType
createPeptide() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Peptide
createPeptide() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of Peptide
createPeptide() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of Peptide
createPeptideEvidenceRefType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of PeptideEvidenceRefType
createPeptideEvidenceRefType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of PeptideEvidenceRefType
createPeptideEvidenceType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of PeptideEvidenceType
createPeptideEvidenceType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of PeptideEvidenceType
createPeptideHypothesisType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of PeptideHypothesisType
createPeptideHypothesisType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of PeptideHypothesisType
createPeptideParentProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of PeptideParentProtein
createPeptideParentProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of PeptideParentProtein
createPeptideprophetResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of PeptideprophetResult
createPeptideprophetResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of PeptideprophetResult
createPeptideprophetResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of PeptideprophetResult
createPeptideprophetResultSearchScoreSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createPeptideprophetSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of PeptideprophetSummary
createPeptideprophetSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of PeptideprophetSummary
createPeptideprophetSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of PeptideprophetSummary
createPeptideprophetSummaryDistributionPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createPeptideprophetSummaryMixtureModelling() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createPeptideprophetSummaryMixtureModellingMixturemodel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createPeptideprophetSummaryMixtureModellingMixturemodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createPeptideprophetSummaryMixtureModellingMixturemodelDistributionNegmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createPeptideprophetSummaryMixtureModellingMixturemodelDistributionPosmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createPeptideprophetSummaryMixtureModellingMixturemodelPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
createPeptideType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of PeptideType
createPeptideType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of PeptideType
createPersonType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of PersonType
createPersonType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of PersonType
createPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of Point
createPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of Point
createPoint() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of Point
createPoint() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of Point
createPosmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of PosmodelDistribution
createPosmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of PosmodelDistribution
createPrecursorListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of PrecursorListType
createPrecursorType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of PrecursorType
createProcessingMethodType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ProcessingMethodType
createProductListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ProductListType
createProductType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ProductType
createProgramDetails() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ProgramDetails
createProgramDetails() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ProgramDetails
createProtein() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Protein
createProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of Protein
createProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of Protein
createProteinAmbiguityGroupType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ProteinAmbiguityGroupType
createProteinAmbiguityGroupType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ProteinAmbiguityGroupType
createProteinAnnotation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ProteinAnnotation
createProteinAnnotation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ProteinAnnotation
createProteinDetectionHypothesisType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ProteinDetectionHypothesisType
createProteinDetectionHypothesisType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ProteinDetectionHypothesisType
createProteinDetectionListType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ProteinDetectionListType
createProteinDetectionListType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ProteinDetectionListType
createProteinDetectionProtocolType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ProteinDetectionProtocolType
createProteinDetectionProtocolType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ProteinDetectionProtocolType
createProteinDetectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ProteinDetectionType
createProteinDetectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ProteinDetectionType
createProteinGroup() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ProteinGroup
createProteinGroup() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ProteinGroup
createProteinprophetDetails() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ProteinprophetDetails
createProteinprophetDetails() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ProteinprophetDetails
createProteinSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ProteinSummary
createProteinSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ProteinSummary
createProteinSummaryDataFilter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ProteinSummaryDataFilter
createProteinSummaryDataFilter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ProteinSummaryDataFilter
createProteinSummaryHeader() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of ProteinSummaryHeader
createProteinSummaryHeader() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of ProteinSummaryHeader
createProviderType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ProviderType
createProviderType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ProviderType
createReferenceableParamGroupListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ReferenceableParamGroupListType
createReferenceableParamGroupRefType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ReferenceableParamGroupRefType
createReferenceableParamGroupType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ReferenceableParamGroupType
createResidueType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ResidueType
createResidueType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ResidueType
createRocDataPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of RocDataPoint
createRocDataPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of RocDataPoint
createRocErrorDataType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of RocErrorDataType
createRocErrorDataType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of RocErrorDataType
createRocErrorDataType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of RocErrorDataType
createRocErrorDataTypeErrorPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of RocErrorDataType.ErrorPoint
createRocErrorDataTypeRocDataPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of RocErrorDataType.RocDataPoint
createRoleType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of RoleType
createRoleType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of RoleType
createRTRange() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of RTRange
createRTRanges() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of RTRanges
createRunType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of RunType
createSampleEnzyme() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of SampleEnzyme
createSampleEnzyme() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of SampleEnzyme
createSampleListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SampleListType
createSampleType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SampleType
createSampleType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SampleType
createSampleType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SampleType
createScan() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of Scan
createScanListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ScanListType
createScanMaldi() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of Scan.Maldi
createScanPeaks() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of Scan.Peaks
createScanPrecursorMz() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of Scan.PrecursorMz
createScanScanOrigin() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of Scan.ScanOrigin
createScanSettingsListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ScanSettingsListType
createScanSettingsType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ScanSettingsType
createScanStub(int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
createScanStub(int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Creates a scan stub, using the right StorageStrategy.
createScanType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ScanType
createScanWindowListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of ScanWindowListType
createSearchDatabase() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of SearchDatabase
createSearchDatabase() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of SearchDatabase
createSearchDatabaseRefType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SearchDatabaseRefType
createSearchDatabaseRefType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SearchDatabaseRefType
createSearchDatabaseType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SearchDatabaseType
createSearchDatabaseType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SearchDatabaseType
createSearchHit() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of SearchHit
createSearchHit() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of SearchHit
createSearchModificationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SearchModificationType
createSearchModificationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SearchModificationType
createSearchResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of SearchResult
createSearchResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of SearchResult
createSearchScoreSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of SearchScoreSummary
createSearchScoreSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of SearchScoreSummary
createSearchScoreSummaryIProphet() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of SearchScoreSummaryIProphet
createSearchScoreSummaryIProphet() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of SearchScoreSummaryIProphet
createSearchSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of SearchSummary
createSearchSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of SearchSummary
createSelectedIonListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SelectedIonListType
createSeparationTechnique(SeparationTechniqueType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of JAXBElement<SeparationTechniqueType>}
createSeparationTechniqueType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of SeparationTechniqueType
createSequenceCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SequenceCollectionType
createSequenceCollectionType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SequenceCollectionType
createSequenceSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of SequenceSearchConstraint
createSequenceSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of SequenceSearchConstraint
createSoftware() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create an instance of Software
createSoftwareListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SoftwareListType
createSoftwareRefType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SoftwareRefType
createSoftwareType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SoftwareType
createSourceComponentType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SourceComponentType
createSourceFileListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SourceFileListType
createSourceFileRefListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SourceFileRefListType
createSourceFileRefType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SourceFileRefType
createSourceFileType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SourceFileType
createSourceFileType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SourceFileType
createSourceFileType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SourceFileType
createSpecificity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of Specificity
createSpecificity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of Specificity
createSpecificityRulesType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SpecificityRulesType
createSpecificityRulesType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SpecificityRulesType
createSpectraDataType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SpectraDataType
createSpectraDataType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SpectraDataType
createSpectrum() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create an instance of Spectrum
createSpectrumIdentificationItemRefType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SpectrumIdentificationItemRefType
createSpectrumIdentificationItemRefType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SpectrumIdentificationItemRefType
createSpectrumIdentificationItemType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SpectrumIdentificationItemType
createSpectrumIdentificationItemType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SpectrumIdentificationItemType
createSpectrumIdentificationListType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SpectrumIdentificationListType
createSpectrumIdentificationListType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SpectrumIdentificationListType
createSpectrumIdentificationProtocolType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
createSpectrumIdentificationProtocolType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
createSpectrumIdentificationResultType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SpectrumIdentificationResultType
createSpectrumIdentificationResultType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SpectrumIdentificationResultType
createSpectrumIdentificationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SpectrumIdentificationType
createSpectrumIdentificationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SpectrumIdentificationType
createSpectrumIDFormatType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SpectrumIDFormatType
createSpectrumIDFormatType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SpectrumIDFormatType
createSpectrumListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SpectrumListType
createSpectrumQuery() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of SpectrumQuery
createSpectrumQuery() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of SpectrumQuery
createSpectrumType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of SpectrumType
createSubSampleType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SubSampleType
createSubSampleType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SubSampleType
createSubstitutionModificationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of SubstitutionModificationType
createSubstitutionModificationType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of SubstitutionModificationType
createTargetListType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of TargetListType
createTerminalModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of TerminalModification
createTerminalModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of TerminalModification
createToleranceType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of ToleranceType
createToleranceType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of ToleranceType
createTrace() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Trace
createTranslationTableType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of TranslationTableType
createTranslationTableType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of TranslationTableType
createUserParamType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create an instance of UserParamType
createUserParamType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create an instance of UserParamType
createUserParamType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create an instance of UserParamType
createValues() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Values
createXdata() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Xdata
createXmlStreamReader(Path, boolean) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Creates an XMLStreamReader based on a file path.
createXmlStreamReader(InputStream, boolean) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Creates an XMLStreamReader based on an input stream.
createXmlStreamReader(Reader, boolean) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Creates an XMLStreamReader based on a Reader.
createXPressAnalysisSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create an instance of XPressAnalysisSummary
createXPressAnalysisSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create an instance of XPressAnalysisSummary
createXpressratioResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of XpressratioResult
createXpressratioResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of XpressratioResult
createXpressratioResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of XpressratioResult
createXpressratioSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of XpressratioSummary
createXpressratioSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of XpressratioSummary
createXpressratioSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of XpressratioSummary
createXpressratioTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create an instance of XpressratioTimestamp
createXpressratioTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create an instance of XpressratioTimestamp
createXpressratioTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create an instance of XpressratioTimestamp
createYdata() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create an instance of Ydata
creationDate - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
creationDate - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
cTermGain - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
 
cTermGain - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
 
curScan - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
 
customizations - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
 
customizations - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
 
cut - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
 
cut - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
 
cut - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
 
cv - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CVListType
 
cv - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CVListType
 
cv - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVListType
 
cvList - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
cvList - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
cvList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
CVListType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The list of controlled vocabularies used in the file.
CVListType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CVListType
 
CVListType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The list of controlled vocabularies used in the file.
CVListType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CVListType
 
CVListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Container for one or more controlled vocabulary definitions.
CVListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.CVListType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FileFormatType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IonTypeType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MeasureType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParamType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.RoleType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpecificityRulesType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIDFormatType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ToleranceType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.TranslationTableType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FileFormatType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IonTypeType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MeasureType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParamType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.RoleType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpecificityRulesType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIDFormatType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ToleranceType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.TranslationTableType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ParamGroupType
 
cvParam - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupType
 
CVParamType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A single entry from an ontology or a controlled vocabulary.
CVParamType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CVParamType
 
CVParamType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A single entry from an ontology or a controlled vocabulary.
CVParamType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CVParamType
 
CVParamType - Class in umich.ms.fileio.filetypes.mzml.jaxb
This element holds additional data or annotation.
CVParamType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
 
cvRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CVParamType
 
cvRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CVParamType
 
cvRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
 
CVTerm - Class in umich.ms.fileio.filetypes.mzml.util
Just the most generic representation of a CV term.
CVTerm(String, String) - Constructor for class umich.ms.fileio.filetypes.mzml.util.CVTerm
 
CvType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A source controlled vocabulary from which cvParams will be obtained.
CvType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
 
CvType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A source controlled vocabulary from which cvParams will be obtained.
CvType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
 
CVType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Information about an ontology or CV source and a short 'lookup' tag to refer to.
CVType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.CVType
 

D

DATA_FACTORY - Static variable in class umich.ms.fileio.filetypes.util.MultiSpectraParser
 
database - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.DatabaseRefreshTimestamp
 
database - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatabaseRefreshTimestamp
 
database - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatabaseRefreshTimestamp
 
databaseFilters - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
databaseFilters - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
DatabaseFiltersType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The specification of filters applied to the database searched.
DatabaseFiltersType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DatabaseFiltersType
 
DatabaseFiltersType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The specification of filters applied to the database searched.
DatabaseFiltersType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DatabaseFiltersType
 
databaseName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
 
databaseName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
 
databaseName - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
databaseName - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
 
databaseName - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
 
DatabaseRefreshTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
DatabaseRefreshTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.DatabaseRefreshTimestamp
 
DatabaseRefreshTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
DatabaseRefreshTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatabaseRefreshTimestamp
 
DatabaseRefreshTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
DatabaseRefreshTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatabaseRefreshTimestamp
 
databaseReleaseDate - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
databaseReleaseDate - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
 
databaseReleaseDate - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
 
databaseReleaseIdentifier - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
databaseReleaseIdentifier - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
 
databaseReleaseIdentifier - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
 
databaseTranslation - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
databaseTranslation - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
DatabaseTranslationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A specification of how a nucleic acid sequence database was translated for searching.
DatabaseTranslationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DatabaseTranslationType
 
DatabaseTranslationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A specification of how a nucleic acid sequence database was translated for searching.
DatabaseTranslationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DatabaseTranslationType
 
dataCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
dataCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
DataCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The collection of input and output data sets of the analyses.
DataCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DataCollectionType
 
DataCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The collection of input and output data sets of the analyses.
DataCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DataCollectionType
 
dataFilter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation
 
DataFilter - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
DataFilter() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
 
dataFilter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatasetDerivation
 
DataFilter - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
DataFilter() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
 
dataFilter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatasetDerivation
 
DataFilter - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
DataFilter() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
 
dataFilter - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DatasetDerivation
 
DataFilter - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
DataFilter() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
 
dataFilter - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DatasetDerivation
 
datanum - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
datanum - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
datanum - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
datanum - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
dataProcessing - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingListType
 
dataProcessing - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
dataProcessingList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
DataProcessingListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List and descriptions of data processing applied to this data.
DataProcessingListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingListType
 
dataProcessingRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
 
dataProcessingRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
 
dataProcessingRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
DataProcessingType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Description of the way in which a particular software was used.
DataProcessingType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingType
 
datasetDerivation - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
 
DatasetDerivation - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
DatasetDerivation() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatasetDerivation
 
datasetDerivation - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
 
DatasetDerivation - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
DatasetDerivation() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatasetDerivation
 
datasetDerivation - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
 
DatasetDerivation - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
DatasetDerivation() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DatasetDerivation
 
datasetDerivation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
 
DatasetDerivation - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
DatasetDerivation() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.DatasetDerivation
 
datasetDerivation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
 
date - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
date - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
 
date - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
 
date - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
 
dbSequence - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SequenceCollectionType
 
dbSequence - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SequenceCollectionType
 
dbSequenceRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
dbSequenceRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
 
dbSequenceRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
dbSequenceRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
 
DBSequenceType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
DBSequenceType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
 
DBSequenceType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A database sequence from the specified SearchDatabase (nucleic acid or amino acid).
DBSequenceType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
 
deadVolume - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
 
DEBUG - Static variable in class umich.ms.fileio.Opts
 
decimalPvalue - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
 
decimalPvalue - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
 
decimalRatio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
decimalRatio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
decimalRatio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
decode(String, byte[], int) - Static method in class umich.ms.external.msnumpress.MSNumpress
Convenience function for decoding binary data encoded by MSNumpress.
decode(byte[], int, Integer, int, EnumSet<PeaksCompression>) - Static method in class umich.ms.fileio.filetypes.mzml.MZMLPeaksDecoder
Converts a base64 encoded mz or intensity string used in mzML files to an array of doubles.
decode(byte[], int, PeaksCompression) - Static method in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder
Convenience shortcut, which assumes the whole bytesIn array is useful data.
decode(byte[], int, int, PeaksCompression) - Static method in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder
Converts a base64 encoded mz-intensity string from used in mzXML and mzML files to an array of doubles.
decode(byte[], Base64Context) - Method in class umich.ms.util.base64.Base64
Decodes a byte[] containing characters in the Base-N alphabet.
decode(byte[], int, int, Base64Context) - Method in class umich.ms.util.base64.Base64
Decodes a byte[] containing characters in the Base-N alphabet.
decode(char[], Base64Context) - Method in class umich.ms.util.base64.Base64
Decodes a char[] containing characters in the Base-N alphabet.
decode(char[], int, int, Base64Context) - Method in class umich.ms.util.base64.Base64
Decodes a char[] containing characters in the Base-N alphabet.
decode(String) - Static method in class umich.ms.util.base64.Base64Slow
Decode a Base64 encoded String.
decode(String, String) - Static method in class umich.ms.util.base64.Base64Slow
Decode a Base64 encoded String.
decode(String, String, String) - Static method in class umich.ms.util.base64.Base64Slow
Decode a Base64 encoded String.
decode(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded bytes.
decode(byte[], OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded bytes to the an OutputStream.
decode(InputStream, OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded data from the InputStream to the OutputStream.
decode(InputStream, OutputStream, boolean) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded data from the InputStream to the OutputStream.
decodeFixedPoint(byte[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
 
decodeLinear(byte[], int, double[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
Decodes data encoded by encodeLinear.
decodePic(byte[], int, double[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
Decodes data encoded by encodePic

result vector guaranteed to be shorter of equal to |data| * 2

Note that this method may throw a ArrayIndexOutOfBoundsException if it deems the input data to be corrupt, i.e.

decodeSlof(byte[], int, double[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
Decodes data encoded by encodeSlof

The result vector will be exactly (|data| - 8) / 2 doubles.

decodeToBytes(String) - Static method in class umich.ms.util.base64.Base64Slow
Decode a Base64 encoded String.
decodeToBytes(String, String) - Static method in class umich.ms.util.base64.Base64Slow
Decode a Base64 encoded String.
decodeToBytes(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded bytes.
decodeToBytes(InputStream) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded data from the InputStream to a byte array.
decodeToStream(String, OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
Decode a Base64 encoded String to an OutputStream.
decodeToStream(String, String, OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
Decode a Base64 encoded String to an OutputStream.
decodeToStream(byte[], OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded bytes to the an OutputStream.
decodeToString(String) - Static method in class umich.ms.util.base64.Base64Slow
Decode a Base64 encoded String.
decodeToString(String, String) - Static method in class umich.ms.util.base64.Base64Slow
Decode a Base64 encoded String.
decodeToString(String, String, String) - Static method in class umich.ms.util.base64.Base64Slow
Decode a Base64 encoded String.
decodeToString(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded bytes.
decodeToString(byte[], String) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded bytes.
decodeToString(InputStream) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded data from the InputStream to a String.
decodeToString(InputStream, String) - Static method in class umich.ms.util.base64.Base64Slow
Decode Base64 encoded data from the InputStream to a String.
DEFAULT_BUFFER_RESIZE_FACTOR - Static variable in class umich.ms.util.base64.Base64
 
DEFAULT_BUFFER_SIZE - Static variable in class umich.ms.util.base64.Base64
 
DEFAULT_STORAGE_STRATEGY - Static variable in interface umich.ms.datatypes.scancollection.IScanCollection
The storage strategy, that should be used by default by all implementations of this interface.
defaultArrayLength - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
 
defaultArrayLength - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
defaultDataProcessingRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramListType
 
defaultDataProcessingRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumListType
 
defaultInstrumentConfigurationRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
 
defaultInstrumentID - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
defaultSize - Variable in class umich.ms.util.ByteArrayHolderFactory
 
defaultSize - Variable in class umich.ms.util.PooledByteArrayHolders
 
defaultSourceFileRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
 
defaultStorageStrategy - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
defaultStringRepresentation - Variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
degenFlag - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
degenFlag - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
deisotoped - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
 
deisotoped - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
delta - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
description - Variable in class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
 
description - Variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
 
description - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
 
description - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
 
description - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
 
description - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
 
description - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
 
detector - Variable in class umich.ms.datatypes.scan.props.Instrument
 
detector - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentListType
 
DetectorComponentType - Class in umich.ms.fileio.filetypes.mzml.jaxb
This element must be used to describe a Detector Component Type.
DetectorComponentType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.DetectorComponentType
 
Device - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
Device() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.Device
 
device - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
 
directory - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InteractSummary
 
directory - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InputFileType
 
directory - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InteractSummary
 
directory - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InputFileType
 
directory - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InteractSummary
 
distributeParseLoad(int, ArrayList<OffsetLength>) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
distributionPoint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
 
DistributionPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
DistributionPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
distributionPoint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
 
DistributionPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
DistributionPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
distributionPoint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
 
doesNeedSpectrumParsing(IScan) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
doesNeedSpectrumParsing(IScan) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
doi - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
doi - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 
Domain - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Domain() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
domain - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Peptide
 
DoubleRange - Class in umich.ms.util
Represents a range of doubles, e.g.
DoubleRange(Double, Double) - Constructor for class umich.ms.util.DoubleRange
 

E

editor - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
editor - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 
elution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
 
elution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
 
elution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
 
email - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
 
encode(String) - Static method in class umich.ms.util.base64.Base64Slow
Encode a String in Base64.
encode(String, String) - Static method in class umich.ms.util.base64.Base64Slow
Encode a String in Base64.
encode(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
Encode bytes in Base64.
encode(byte[], boolean) - Static method in class umich.ms.util.base64.Base64Slow
Encode bytes in Base64.
encode(InputStream, OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
Encode data from the InputStream to the OutputStream in Base64.
encode(InputStream, OutputStream, boolean) - Static method in class umich.ms.util.base64.Base64Slow
Encode data from the InputStream to the OutputStream in Base64.
encodedLength - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
 
encodeFixedPoint(double, byte[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
 
encodeInt(long, byte[], int) - Static method in class umich.ms.external.msnumpress.MSNumpress
This encoding works on a 4 byte integer, by truncating initial zeros or ones.
encodeLinear(double[], int, byte[], double) - Static method in class umich.ms.external.msnumpress.MSNumpress
Encodes the doubles in data by first using a - lossy conversion to a 4 byte 5 decimal fixed point repressentation - storing the residuals from a linear prediction after first to values - encoding by encodeInt (see above)

The resulting binary is maximally 8 + dataSize * 5 bytes, but much less if the data is reasonably smooth on the first order.

encodePic(double[], int, byte[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
Encodes ion counts by simply rounding to the nearest 4 byte integer, and compressing each integer with encodeInt.
encodeSlof(double[], int, byte[], double) - Static method in class umich.ms.external.msnumpress.MSNumpress
Encodes ion counts by taking the natural logarithm, and storing a fixed point representation of this.
encodeToString(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
Encode bytes in Base64.
encodeToString(byte[], boolean) - Static method in class umich.ms.util.base64.Base64Slow
Encode bytes in Base64.
end - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
end - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Peptide
 
end - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
end - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
endElement(String, String, String) - Method in class umich.ms.fileio.util.jaxb.NamespaceFilter
 
endMz - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
endScan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
endScan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
endScan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
endTime - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
EngineType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for engineType.
EngineType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for engineType.
EngineType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for engineType.
enqueue() - Method in class umich.ms.util.StrongReference
 
ensemblName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
 
ensemblName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
 
ensureBufferHasCapacityLeft(int) - Method in class umich.ms.util.base64.Base64Context
Ensure, that the output data buffer has enough space left for size mode bytes.
ensureBufferHasCapacityLeft(int) - Method in class umich.ms.util.base64.Base64ContextPooled
 
ensureCapacity(int) - Method in class umich.ms.util.ByteArrayHolder
Increases the capacity if necessary to ensure that it can hold at least the number of elements specified by the minimum capacity argument.
ensureCapacity(int, boolean) - Method in class umich.ms.util.ByteArrayHolder
 
ensureHasSpace(int) - Method in class umich.ms.util.ByteArrayHolder
Checks if there is enough space in the buffer to write N additional bytes.
enzymaticSearchConstraint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
EnzymaticSearchConstraint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
EnzymaticSearchConstraint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EnzymaticSearchConstraint
 
enzymaticSearchConstraint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
EnzymaticSearchConstraint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
EnzymaticSearchConstraint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.EnzymaticSearchConstraint
 
enzymaticSearchConstraint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
enzyme - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymesType
 
enzyme - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymesType
 
enzyme - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
 
enzyme - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EnzymaticSearchConstraint
 
enzyme - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.EnzymaticSearchConstraint
 
enzymeName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
 
enzymeName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
 
enzymes - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
enzymes - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
EnzymesType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The list of enzymes used in experiment
EnzymesType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymesType
 
EnzymesType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The list of enzymes used in experiment
EnzymesType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymesType
 
EnzymeType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The details of an individual cleavage enzyme should be provided by giving a regular expression or a CV term if a "standard" enzyme cleavage has been performed.
EnzymeType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
 
EnzymeType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The details of an individual cleavage enzyme should be provided by giving a regular expression or a CV term if a "standard" enzyme cleavage has been performed.
EnzymeType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
 
equals(Object) - Method in class umich.ms.datatypes.LCMSDataSubset
 
equals(Object) - Method in class umich.ms.datatypes.scan.props.Instrument
 
equals(Object) - Method in class umich.ms.fileio.chunk.FileChunk
 
equals(Object) - Method in class umich.ms.util.Interval1D
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
 
error - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
 
error - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Intensity
 
error - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Intensity
 
errorCode() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
property ErrorCode
errorCode() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirUV
property ErrorCode
errorPoint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
 
ErrorPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
ErrorPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
 
errorPoint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
 
ErrorPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
ErrorPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
 
errorPoint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
 
estTotCorrect - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
 
estTotCorrect - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
 
estTotCorrect - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
 
estTotNumCorrect - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
 
estTotNumCorrect - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
 
estTotNumCorrect - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
 
estTotNumCorrectPep - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
 
estTotNumCorrectPep - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
 
estTotNumCorrectPsm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
 
estTotNumCorrectPsm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
 
Example - Class in umich.ms.fileio.filetypes.mzxml.example
 
Example() - Constructor for class umich.ms.fileio.filetypes.mzxml.example.Example
 
Example2 - Class in umich.ms.fileio.filetypes.mzxml.example
Created by Dmitry Avtonomov on 2016-04-18.
Example2() - Constructor for class umich.ms.fileio.filetypes.mzxml.example.Example2
 
Example3 - Class in umich.ms.fileio.filetypes.mzxml.example
Created by Dmitry Avtonomov on 2016-04-18.
Example3() - Constructor for class umich.ms.fileio.filetypes.mzxml.example.Example3
 
Example4 - Class in umich.ms.fileio.filetypes.mzxml.example
Created by Dmitry Avtonomov on 2016-04-18.
Example4() - Constructor for class umich.ms.fileio.filetypes.mzxml.example.Example4
 
exclude - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FilterType
 
exclude - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FilterType
 
excludeEmptyScans - Variable in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
When set to true, will discard scans with no m/z values.
expect - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
expect - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
expect - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
 
experimentalMassToCharge - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
experimentalMassToCharge - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
expSiblingIonBin - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
expSiblingIonBin - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
expSiblingIonInstances - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
expSiblingIonInstances - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
expTotInstances - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
expTotInstances - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
ExternalDataType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Data external to the XML instance document.
ExternalDataType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ExternalDataType
 
ExternalDataType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Data external to the XML instance document.
ExternalDataType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ExternalDataType
 
externalFormatDocumentation - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ExternalDataType
 
externalFormatDocumentation - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ExternalDataType
 
externalSpectrumID - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
 
externalSpectrumID - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
 
extractInstMethodFromRaw(String) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method ExtractInstMethodFromRaw

F

factory - Variable in class umich.ms.util.PooledByteArrayHolders
 
falsePositiveErrorRate - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
 
falsePositiveErrorRate - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
 
fetchAttribute(Attributes, MZXMLMultiSpectraParser.ATTR) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
fetchIndex() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Returns the index, or parses it from the original file and caches for future reuse.
If you don't want the index to be cached, you can call LCMSDataSource.parseIndex() instead.
fetchIndex() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
fetchIndex() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
fetchIndex() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
fetchRunInfo() - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
 
fetchRunInfo() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Gets the run info, parsing it if it yet hasn't been, and caches for reuse.
fetchSpectrum() - Method in class umich.ms.datatypes.scan.impl.ScanDefault
 
fetchSpectrum() - Method in interface umich.ms.datatypes.scan.IScan
Get the spectrum, possibly preloading it from disk.
fetchXrawfile() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
fi - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
fidelity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
fidelity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
 
fidelity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
 
File - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
File() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.File
 
file - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
 
FILE_TYPE_NAME - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
FILE_TYPE_NAME - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
FileChunk - Class in umich.ms.fileio.chunk
 
FileChunk(int, long, int) - Constructor for class umich.ms.fileio.chunk.FileChunk
 
FileChunkSource - Interface in umich.ms.fileio.chunk
Supplies chunks of raw bytes from a file.
fileContent - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.FileDescriptionType
 
fileDescription - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
FileDescriptionType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Information pertaining to the entire mzML file (i.e.
FileDescriptionType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.FileDescriptionType
 
fileFormat - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ExternalDataType
 
fileFormat - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ExternalDataType
 
FileFormatType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The format of the ExternalData file, for example "tiff" for image files.
FileFormatType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FileFormatType
 
FileFormatType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The format of the ExternalData file, for example "tiff" for image files.
FileFormatType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FileFormatType
 
FileListing - Class in umich.ms.fileio.util
Created by Dmitry Avtonomov on 2015-10-21.
FileListing(Path, String) - Constructor for class umich.ms.fileio.util.FileListing
 
fileName - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
 
filename - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InteractSummary
 
filename - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InteractSummary
 
filename - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InteractSummary
 
FileParsingException - Exception in umich.ms.fileio.exceptions
Is thrown when anything bad happens during parsing LC/MS files.
FileParsingException() - Constructor for exception umich.ms.fileio.exceptions.FileParsingException
 
FileParsingException(String) - Constructor for exception umich.ms.fileio.exceptions.FileParsingException
 
FileParsingException(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.FileParsingException
 
FileParsingException(Throwable) - Constructor for exception umich.ms.fileio.exceptions.FileParsingException
 
fileSha1 - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
 
fileType - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
 
filter - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DatabaseFiltersType
 
filter - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DatabaseFiltersType
 
filter - Variable in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawIndexElement
 
filterLine - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
FilterType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Filters applied to the search database.
FilterType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FilterType
 
filterType - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FilterType
 
FilterType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Filters applied to the search database.
FilterType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FilterType
 
filterType - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FilterType
 
finalizePrecursorWindows(IScanCollection) - Static method in class umich.ms.datatypes.scancollection.ScanCollectionHelper
Calling this method only makes sense if the whole LC/MS structure has been parsed.
finalizeReferent() - Method in class umich.ms.datatypes.LCMSData.User
 
finalizeScanCollection(IScanCollection) - Static method in class umich.ms.datatypes.scancollection.ScanCollectionHelper
Sets relationships between parent/child scans based on scan numbering.
finalPeptideWtIters - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
finalPeptideWtIters - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
findClosestMzIdx(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
findClosestMzIdx(double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
 
findFiles() - Method in class umich.ms.fileio.util.FileListing
 
findIndexOffset(RandomAccessFile) - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
Reads the last several kB of the file, looking for MZMLIndexParser.TAG_INDEXOFFSET tag.
findIndexOffset(RandomAccessFile) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
Reads the last few kB of the file, looking for MZXMLIndexParser.TAG_INDEXOFFSET tag.
findMzIdxCeiling(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
findMzIdxCeiling(double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
Finds the idx of MZ that is equal or greater than the provided one.
findMzIdxFloor(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
findMzIdxFloor(double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
Finds the idx of MZ that is equal or less than the provided one.
findMzIdxs(double, double) - Method in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
 
findMzIdxs(double, double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
Finds indexes of MZs that are within a tolerance window (inclusive)
findMzIdxsWithinPpm(double, double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
findMzIdxsWithinPpm(double, double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
Finds indexes of MZs that are within a PPM tolerance window (inclusive)
findPrecursorMassInFullScan(int, Holder<Integer>, Holder<Double>, Holder<Double>, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method FindPrecursorMassInFullScan
findPrevLine() - Method in class umich.ms.fileio.util.ReverseLineInputStream
 
findScanLength(long) - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
Finds the length of a scan entry in the original file by reading it, starting at the provided offset and looking for an "end of scan" tag.
findScanLength(long) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
Finds the length of a scan entry in the original file by reading it, starting at the provided offset and looking for an "end of scan" tag.
findThisStreamFirstScanLen() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
Intended use: find the length of the last scan entry in the file.
findThisStreamFirstScanLen() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
Intended use: find the length of the last scan entry in the file.
findTypes(Collection<T>) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Discovers all the classes in the given Collection.
first - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
 
firstName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
 
firstName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
 
firstSpotID - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern.Orientation
 
fixedMod - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
 
fixedMod - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
 
fixIndex(MZXMLIndex) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
fixIndex(I) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
The index as it is built by index builder contains offsets of "scan" tags, and their lengths.
flush() - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
Flush any bytes in the file's buffer that have not yet been written to disk.
flushVars() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
 
flushVarsIfNoCurScan() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
If the current vars variable doesn't contain a scan, that we've started processing, then flushes all the fields in vars and returns true, otherwise does nothing and returns false.
flybase - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
 
flybase - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
 
FMT_DOUBLE_2_DIGITS_AFTER_DOT - Static variable in class umich.ms.datatypes.scan.AbstractScan
 
format - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
 
fpkmAdjustedProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
fpkmAdjustedProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
fpkmBin - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
fpkmBin - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
FpkmDistribution - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
FpkmDistribution() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
 
fpkmDistribution - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmInformation
 
FpkmDistribution - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
FpkmDistribution() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
 
fpkmDistribution - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmInformation
 
fpkmFlag - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
fpkmFlag - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
FpkmInformation - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
FpkmInformation() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmInformation
 
fpkmInformation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
FpkmInformation - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
FpkmInformation() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmInformation
 
fpkmInformation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
fpkmLowerBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
 
fpkmLowerBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
 
fpkmLowerBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
 
fpkmLowerBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
 
fpkmUpperBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
 
fpkmUpperBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
 
fpkmUpperBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
 
fpkmUpperBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
 
fragmentArray - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IonTypeType
 
fragmentArray - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IonTypeType
 
FragmentArrayType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
An array of values for a given type of measure and for a particular ion type, in parallel to the index of ions identified.
FragmentArrayType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentArrayType
 
FragmentArrayType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
An array of values for a given type of measure and for a particular ion type, in parallel to the index of ions identified.
FragmentArrayType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentArrayType
 
fragmentation - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
fragmentation - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
fragmentationTable - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
 
fragmentationTable - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
 
FragmentationTableType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Contains the types of measures that will be reported in generic arrays for each SpectrumIdentificationItem e.g.
FragmentationTableType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentationTableType
 
FragmentationTableType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Contains the types of measures that will be reported in generic arrays for each SpectrumIdentificationItem e.g.
FragmentationTableType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentationTableType
 
FragmentationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The product ions identified in this result.
FragmentationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentationType
 
FragmentationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The product ions identified in this result.
FragmentationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentationType
 
fragmentMasses - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
 
FragmentMasses - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
FragmentMasses() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.FragmentMasses
 
fragmentMasses - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
 
FragmentMasses - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
FragmentMasses() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.FragmentMasses
 
fragmentMasses - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
 
FragmentMasses - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
FragmentMasses() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FragmentMasses
 
fragmentMasses - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
FragmentMasses - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
FragmentMasses() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.FragmentMasses
 
fragmentMasses - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
fragmentMassType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
fragmentMassType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
fragmentMassType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
fragmentTolerance - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
fragmentTolerance - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
frame - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
frame - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
frames - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DatabaseTranslationType
 
frames - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DatabaseTranslationType
 
fromAccession(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
fromAccession(CharArray) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
fromInterval1D(Interval1D<Double>) - Static method in class umich.ms.util.DoubleRange
 
fromPSIMSOntology(String) - Static method in enum umich.ms.datatypes.scan.props.ScanType
Get enum value from PSI-MS ontology terms.
fromString(String) - Static method in enum umich.ms.datatypes.scan.props.ScanType
Case-insensitive conversion from a string representation to values of this Enum.
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.ActivationMethodType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.EngineType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.MassType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.ModelDisType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ActivationMethodType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EngineType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MassType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModelDisType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.ActivationMethodType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.EngineType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.MassType
 
fromValue(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModelDisType
 
FRQ - Static variable in class umich.ms.datatypes.LCMSData
 
FULL_SCAN_RANGE - Static variable in class umich.ms.datatypes.LCMSRange
Represents the whole range of scans by number in any LCMS run.
fullAnalysisDistributionFile - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
 
fullAnalysisDistributionFile - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
 
fullName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
 
fullName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
 
fullName - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
 
fv - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
 
fvalue - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
fvalue - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
fvalue - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 

G

GAMLValues - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for GAML.values complex type.
GAMLValues() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.GAMLValues
 
generationNo - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation
 
generationNo - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatasetDerivation
 
generationNo - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatasetDerivation
 
generationNo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DatasetDerivation
 
generationNo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DatasetDerivation
 
get(Interval1D<K>) - Method in class umich.ms.util.IntervalST
Get the value associated with the given key (Interval).
get() - Method in class umich.ms.util.StrongReference
 
getAa() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the aa property.
getAbMax() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
getAbMax() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
getAbsolute() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
Gets the value of the absolute property.
getAbsolute() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
Gets the value of the absolute property.
getAbsolute() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
Gets the value of the absolute property.
getAbstractFile() - Method in class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
getAbstractFile() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser
 
getAbstractFile() - Method in class umich.ms.fileio.filetypes.mzxml.XmlBasedRunHeaderParser
 
getAbTot() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
getAbTot() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
getAccession() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CVParamType
Gets the value of the accession property.
getAccession() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
Gets the value of the accession property.
getAccession() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CVParamType
Gets the value of the accession property.
getAccession() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
Gets the value of the accession property.
getAccession() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Gets the value of the accession property.
getAccession() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the accession property.
getAcquisitionDate(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetAcquisitionDate
getAcquisitionFileName(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetAcquisitionFileName
getAct() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the act property.
getActivation() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Gets the value of the activation property.
getActivationEnergyHi() - Method in class umich.ms.datatypes.scan.props.ActivationInfo
Either the end of the collision energy ramp or just the collision energy.
getActivationEnergyLo() - Method in class umich.ms.datatypes.scan.props.ActivationInfo
Either the beginning of the collision energy ramp or just the collision energy.
getActivationInfo() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
getActivationMethod() - Method in class umich.ms.datatypes.scan.props.ActivationInfo
 
getActivationMethod() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Gets the value of the activationMethod property.
getActivationMethod() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the activationMethod property.
getActivationMethod() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the activationMethod property.
getActivationMethod() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the activationMethod property.
getActivationTime() - Method in class umich.ms.datatypes.scan.props.ActivationInfo
This would mean different things for different activation methods and might not be present most of the time.
getActivationTypeForScanNum(int, int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetActivationTypeForScanNum
getActivityDate() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProtocolApplicationType
Gets the value of the activityDate property.
getActivityDate() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProtocolApplicationType
Gets the value of the activityDate property.
getAdditionalSearchParams() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the additionalSearchParams property.
getAdditionalSearchParams() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the additionalSearchParams property.
getAdduct() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
getAdjRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Gets the value of the adjRatioMean property.
getAdjRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Gets the value of the adjRatioMean property.
getAdjRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Gets the value of the adjRatioStandardDev property.
getAdjRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Gets the value of the adjRatioStandardDev property.
getAffectedChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel
Gets the value of the affectedChannel property.
getAffectedChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ContributingChannel
Gets the value of the affectedChannel property.
getAffectedChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ContributingChannel
Gets the value of the affectedChannel property.
getAffectedChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ContributingChannel
Gets the value of the affectedChannel property.
getAffectedChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ContributingChannel
Gets the value of the affectedChannel property.
getAffiliation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
Gets the value of the affiliation property.
getAffiliation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
Gets the value of the affiliation property.
getAlgo() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Compound
Gets the value of the algo property.
getAllMSOrderData(int, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetAllMSOrderData
getAllNttProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult
Gets the value of the allNttProb property.
getAllNttProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
Gets the value of the allNttProb property.
getAllNttProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetResult
Gets the value of the allNttProb property.
getAllNttProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
Gets the value of the allNttProb property.
getAllNttProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetResult
Gets the value of the allNttProb property.
getAllNttProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
Gets the value of the allNttProb property.
getAlternativeProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the alternativeProtein property.
getAlternativeProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the alternativeProtein property.
getAlternativeProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the alternativeProtein property.
getAltPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Gets the value of the altPosToNegRatio property.
getAltPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Gets the value of the altPosToNegRatio property.
getAltPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Gets the value of the altPosToNegRatio property.
getAltPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Gets the value of the altPosToNegRatio property.
getAltPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Gets the value of the altPosToNegRatio property.
getAltPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Gets the value of the altPosToNegRatio property.
getAmbiguousResidue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MassTableType
Gets the value of the ambiguousResidue property.
getAmbiguousResidue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MassTableType
Gets the value of the ambiguousResidue property.
getAminoacid() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Gets the value of the aminoacid property.
getAminoacid() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Gets the value of the aminoacid property.
getAminoacid() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Gets the value of the aminoacid property.
getAminoacidModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the aminoacidModification property.
getAminoacidModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the aminoacidModification property.
getAminoacidModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the aminoacidModification property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisResult
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisResult
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisResult
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisResult
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
Gets the value of the analysis property.
getAnalysis() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
Gets the value of the analysis property.
getAnalysisCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the analysisCollection property.
getAnalysisCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the analysisCollection property.
getAnalysisData() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DataCollectionType
Gets the value of the analysisData property.
getAnalysisData() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DataCollectionType
Gets the value of the analysisData property.
getAnalysisDistributionFile() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Gets the value of the analysisDistributionFile property.
getAnalysisDistributionFile() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Gets the value of the analysisDistributionFile property.
getAnalysisParams() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionProtocolType
Gets the value of the analysisParams property.
getAnalysisParams() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionProtocolType
Gets the value of the analysisParams property.
getAnalysisProtocolCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the analysisProtocolCollection property.
getAnalysisProtocolCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the analysisProtocolCollection property.
getAnalysisResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the analysisResult property.
getAnalysisResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the analysisResult property.
getAnalysisResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the analysisResult property.
getAnalysisResult() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the analysisResult property.
getAnalysisResult() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the analysisResult property.
getAnalysisSampleCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the analysisSampleCollection property.
getAnalysisSampleCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the analysisSampleCollection property.
getAnalysisSoftware() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareListType
Gets the value of the analysisSoftware property.
getAnalysisSoftware() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareListType
Gets the value of the analysisSoftware property.
getAnalysisSoftwareList() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the analysisSoftwareList property.
getAnalysisSoftwareList() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the analysisSoftwareList property.
getAnalysisSoftwareRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionProtocolType
Gets the value of the analysisSoftwareRef property.
getAnalysisSoftwareRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProviderType
Gets the value of the analysisSoftwareRef property.
getAnalysisSoftwareRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the analysisSoftwareRef property.
getAnalysisSoftwareRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionProtocolType
Gets the value of the analysisSoftwareRef property.
getAnalysisSoftwareRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProviderType
Gets the value of the analysisSoftwareRef property.
getAnalysisSoftwareRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the analysisSoftwareRef property.
getAnalysisSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
Gets the value of the analysisSummary property.
getAnalysisSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
Gets the value of the analysisSummary property.
getAnalysisSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
Gets the value of the analysisSummary property.
getAnalysisSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
Gets the value of the analysisSummary property.
getAnalysisSummary() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
Gets the value of the analysisSummary property.
getAnalysisTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the analysisTimestamp property.
getAnalysisTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the analysisTimestamp property.
getAnalysisTimestamp() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the analysisTimestamp property.
getAnalyzer() - Method in class umich.ms.datatypes.scan.props.Instrument
 
getAnalyzer() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentListType
Gets the value of the analyzer property.
getAnnotation() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Gets the value of the annotation property.
getAnnotation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishableProtein
Gets the value of the annotation property.
getAnnotation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishableProtein
Gets the value of the annotation property.
getAny() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisResult
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisResult
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisResult
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisResult
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
Gets the value of the any property.
getAny() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
Gets the value of the any property.
getArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Gets the value of the area property.
getArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Gets the value of the area property.
getArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Gets the value of the area property.
getArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Gets the value of the area property.
getArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Gets the value of the area property.
getArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Gets the value of the area property.
getAreaError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Gets the value of the areaError property.
getAreaError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Gets the value of the areaError property.
getAreaError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Gets the value of the areaError property.
getAreaError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Gets the value of the areaError property.
getAreaError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Gets the value of the areaError property.
getAreaError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Gets the value of the areaError property.
getAreaFlag() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Gets the value of the areaFlag property.
getAreaFlag() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Gets the value of the areaFlag property.
getAreaFlag() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Gets the value of the areaFlag property.
getAreaFlag() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Gets the value of the areaFlag property.
getAreaFlag() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Gets the value of the areaFlag property.
getAreaFlag() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Gets the value of the areaFlag property.
getArrayLength() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
Gets the value of the arrayLength property.
getASAPDta() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Gets the value of the asapDta property.
getASAPDta() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Gets the value of the asapDta property.
getASAPPeak() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Gets the value of the asapPeak property.
getASAPPeak() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Gets the value of the asapPeak property.
getAsapProtId() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Gets the value of the asapProtId property.
getAsapProtId() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Gets the value of the asapProtId property.
getAsapratioContribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Gets the value of the asapratioContribution property.
getAsapratioContribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Gets the value of the asapratioContribution property.
getAsapratioContribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Gets the value of the asapratioContribution property.
getAsapratioId() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Gets the value of the asapratioId property.
getAsapratioId() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Gets the value of the asapratioId property.
getAsapratioLcHeavypeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Gets the value of the asapratioLcHeavypeak property.
getAsapratioLcHeavypeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Gets the value of the asapratioLcHeavypeak property.
getAsapratioLcHeavypeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Gets the value of the asapratioLcHeavypeak property.
getAsapratioLcLightpeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Gets the value of the asapratioLcLightpeak property.
getAsapratioLcLightpeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Gets the value of the asapratioLcLightpeak property.
getAsapratioLcLightpeak() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Gets the value of the asapratioLcLightpeak property.
getAsapratioPeptideData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
Gets the value of the asapratioPeptideData property.
getAsapratioPeptideData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
Gets the value of the asapratioPeptideData property.
getAsapratioPeptideData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
Gets the value of the asapratioPeptideData property.
getASAPSeq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Gets the value of the asapSeq property.
getASAPSeq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Gets the value of the asapSeq property.
getAssumedCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the assumedCharge property.
getAssumedCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the assumedCharge property.
getAssumedCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the assumedCharge property.
getAt() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
Gets the value of the at property.
getAttribute() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Gets the value of the attribute property.
getAuditCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the auditCollection property.
getAuditCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the auditCollection property.
getAuthor() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Gets the value of the author property.
getAuthor() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Gets the value of the author property.
getAuthor() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Gets the value of the author property.
getAuthor() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Gets the value of the author property.
getAuthor() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Gets the value of the author property.
getAuthor() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Gets the value of the author property.
getAuthor() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Gets the value of the author property.
getAuthor() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Gets the value of the author property.
getAuthor() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Gets the value of the author property.
getAuthors() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Gets the value of the authors property.
getAuthors() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Gets the value of the authors property.
getAValueFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetAValueFromScanNum
getAveragedLabelData(Holder<Integer>, int, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetAveragedLabelData
getAveragedMassSpectrum(Holder<Integer>, int, boolean, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetAveragedMassSpectrum
getAverageMassList(Holder<Integer>, Holder<Integer>, Holder<Integer>, Holder<Integer>, Holder<Integer>, Holder<Integer>, String, int, int, int, int, Holder<Double>, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetAverageMassList
getAvgMassDelta() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
Gets the value of the avgMassDelta property.
getAvgMassDelta() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
Gets the value of the avgMassDelta property.
getAvgMassDelta() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
Gets the value of the avgMassDelta property.
getAvgMassDelta() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
Gets the value of the avgMassDelta property.
getBackground() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Gets the value of the background property.
getBackground() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Gets the value of the background property.
getBackground() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Gets the value of the background property.
getBackground() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Gets the value of the background property.
getBackground() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Gets the value of the background property.
getBackground() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Gets the value of the background property.
getBackgroundFittingError() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Gets the value of the backgroundFittingError property.
getBackgroundFittingError() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Gets the value of the backgroundFittingError property.
getBackgroundRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Gets the value of the backgroundRatioMean property.
getBackgroundRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Gets the value of the backgroundRatioMean property.
getBackgroundRatioStdev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Gets the value of the backgroundRatioStdev property.
getBackgroundRatioStdev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Gets the value of the backgroundRatioStdev property.
getBah() - Method in class umich.ms.fileio.chunk.FileChunk
 
getBaseName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the baseName property.
getBaseName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the baseName property.
getBaseName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the baseName property.
getBaseName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the baseName property.
getBaseName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the baseName property.
getBaseName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the baseName property.
getBasePeakIntensity() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getBasePeakIntensity() - Method in interface umich.ms.datatypes.scan.IScan
 
getBasePeakIntensity() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the basePeakIntensity property.
getBasePeakMz() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getBasePeakMz() - Method in interface umich.ms.datatypes.scan.IScan
 
getBasePeakMz() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the basePeakMz property.
getBibliographicReference() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the bibliographicReference property.
getBibliographicReference() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the bibliographicReference property.
getBinary() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
Gets the value of the binary property.
getBinary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Gets the value of the binary property.
getBinary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Gets the value of the binary property.
getBinary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Gets the value of the binary property.
getBinaryDataArray() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayListType
Gets the value of the binaryDataArray property.
getBinaryDataArrayList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Gets the value of the binaryDataArrayList property.
getBinaryDataArrayList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Gets the value of the binaryDataArrayList property.
getBinaryRefFiles() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Gets the value of the binaryRefFiles property.
getBinaryRefFiles() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Gets the value of the binaryRefFiles property.
getBinNo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Gets the value of the binNo property.
getBinNo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Gets the value of the binNo property.
getBinNo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Gets the value of the binNo property.
getBinNo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Gets the value of the binNo property.
getBinNo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Gets the value of the binNo property.
getBinNo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Gets the value of the binNo property.
getBIons() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the bIons property.
getBScore() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the bScore property.
getBufferedInputStream() - Method in class umich.ms.fileio.filetypes.util.AbstractFile
 
getBValueFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetBValueFromScanNum
getById(String) - Method in class umich.ms.datatypes.index.impl.IndexDefault
 
getById(String) - Method in interface umich.ms.datatypes.index.Index
Retrieves a value by the textual ID of a scan.
getByNum(int) - Method in class umich.ms.datatypes.index.impl.IndexDefault
 
getByNum(int) - Method in interface umich.ms.datatypes.index.Index
Retrieves a value by the internal scan number.
getByRawNum(int) - Method in class umich.ms.datatypes.index.impl.IndexDefault
 
getByRawNum(int) - Method in interface umich.ms.datatypes.index.Index
Retrieves a value by the raw scan number from the original file.
getByteorder() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
Gets the value of the byteorder property.
getByteOrder() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Gets the value of the byteOrder property.
getCalcNeutralPepMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the calcNeutralPepMass property.
getCalcNeutralPepMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the calcNeutralPepMass property.
getCalcNeutralPepMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the calcNeutralPepMass property.
getCalcNeutralPepMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
Gets the value of the calcNeutralPepMass property.
getCalcNeutralPepMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
Gets the value of the calcNeutralPepMass property.
getCalcNeutralPepMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the calcNeutralPepMass property.
getCalcNeutralPepMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
Gets the value of the calcNeutralPepMass property.
getCalcNeutralPepMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
Gets the value of the calcNeutralPepMass property.
getCalcNeutralPepMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the calcNeutralPepMass property.
getCalcPI() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the calcPI property.
getCalcPI() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the calcPI property.
getCalcPI() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the calcPI property.
getCalculatedMassToCharge() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the calculatedMassToCharge property.
getCalculatedMassToCharge() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the calculatedMassToCharge property.
getCalculatedPI() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the calculatedPI property.
getCalculatedPI() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the calculatedPI property.
getCapacity() - Method in class umich.ms.util.ByteArrayHolder
 
getCapacityLeft() - Method in class umich.ms.util.ByteArrayHolder
 
getCategory() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.OntologyEntryType
Gets the value of the category property.
getCentroided() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getCentroidingPreference() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Gets the value of the centroidingPreference property.
getCentroidingPreference() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Gets the value of the centroidingPreference property.
getCentroidingPreference() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Gets the value of the centroidingPreference property.
getCentroidingPreference() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Gets the value of the centroidingPreference property.
getCentroidingPreference() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Gets the value of the centroidingPreference property.
getChangelog() - Static method in class umich.ms.msfiletoolbox.MsftbxInfo
 
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.FragmentMasses
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AffectedChannel
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ContributingChannel
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.FragmentMasses
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AffectedChannel
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ContributingChannel
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.FragmentMasses
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AffectedChannel
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ContributingChannel
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FragmentMasses
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AffectedChannel
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ContributingChannel
Gets the value of the channel property.
getChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FragmentMasses
Gets the value of the channel property.
getChannelCode() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Gets the value of the channelCode property.
getChannelCode() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Gets the value of the channelCode property.
getChannelCode() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Gets the value of the channelCode property.
getChannelCode() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Gets the value of the channelCode property.
getChannelCode() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Gets the value of the channelCode property.
getChar() - Method in exception umich.ms.util.base64.Base64DecodingException
Get the character that caused this error.
getCharge() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
Precursor charge is optional in mzXML/mzML, so it can be null.
getCharge() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IonTypeType
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IonTypeType
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
Gets the value of the charge property.
getCharge() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the charge property.
getChargeEstCorrect() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
Gets the value of the chargeEstCorrect property.
getChargeEstCorrect() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
Gets the value of the chargeEstCorrect property.
getChargeEstCorrect() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
Gets the value of the chargeEstCorrect property.
getChargeState() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the chargeState property.
getChargeState() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the chargeState property.
getChildScans() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getChildScans() - Method in interface umich.ms.datatypes.scan.IScan
 
getChroByCompoundName(int, int, int, Object, String, String, double, Holder<Double>, Holder<Double>, int, int, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetChroByCompoundName
getChroData(int, int, int, String, String, String, double, Holder<Double>, Holder<Double>, int, int, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetChroData
getChromatogram() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramListType
Gets the value of the chromatogram property.
getChromatogramList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Gets the value of the chromatogramList property.
getChros(int, Holder<Double>, Holder<Double>, Object, Object, Object, Object) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetChros
getChunkBufferSize() - Method in class umich.ms.fileio.chunk.ChunkedFile
 
getChunkNum() - Method in class umich.ms.fileio.chunk.FileChunk
 
getChunkOverlap() - Method in class umich.ms.fileio.chunk.ChunkedFile
 
getChunks() - Method in class umich.ms.fileio.chunk.ChunkedFile
 
getChunkSize() - Method in class umich.ms.fileio.chunk.ChunkedFile
 
getCidGasPressure() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the cidGasPressure property.
getCidIndex() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Gets the value of the cidIndex property.
getCidIndex() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Gets the value of the cidIndex property.
getCidIndex() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Gets the value of the cidIndex property.
getCode() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AmbiguousResidueType
Gets the value of the code property.
getCode() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ResidueType
Gets the value of the code property.
getCode() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AmbiguousResidueType
Gets the value of the code property.
getCode() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ResidueType
Gets the value of the code property.
getCollisionEnergy() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the collisionEnergy property.
getCollisionEnergy() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the collisionEnergy property.
getCollisionEnergy() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the collisionEnergy property.
getCollisionEnergy() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the collisionEnergy property.
getCollisionEnergyForScanNum(int, int, Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetCollisionEnergyForScanNum
getComment1(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetComment1
getComment2(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetComment2
getComments() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Gets the value of the comments property.
getComments() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Gets the value of the comments property.
getComments() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Gets the value of the comments property.
getCompensationVoltage() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the compensationVoltage property.
getCompensationVoltage() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the compensationVoltage property.
getCompensationVoltage() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the compensationVoltage property.
getCompensationVoltage() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the compensationVoltage property.
getCompletionTime() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
Gets the value of the completionTime property.
getComponentList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
Gets the value of the componentList property.
getCompound() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.CompoundList
Gets the value of the compound property.
getCompoundList() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.CEF
Gets the value of the compoundList property.
getCompoundNameFromScanNum(int, Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetCompoundNameFromScanNum
getCompounds() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
 
getCompressedLen() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Gets the value of the compressedLen property.
getCompressionType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Gets the value of the compressionType property.
getConfidence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the confidence property.
getConfidence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the confidence property.
getContact() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.FileDescriptionType
Gets the value of the contact property.
getContactRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ContactRoleType
Gets the value of the contactRef property.
getContactRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ContactRoleType
Gets the value of the contactRef property.
getContactRole() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
Gets the value of the contactRole property.
getContactRole() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProviderType
Gets the value of the contactRole property.
getContactRole() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SampleType
Gets the value of the contactRole property.
getContactRole() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
Gets the value of the contactRole property.
getContactRole() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProviderType
Gets the value of the contactRole property.
getContactRole() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SampleType
Gets the value of the contactRole property.
getContent() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Note
Gets the value of the content property.
getContent() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
Gets the value of the content property.
getContentType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Gets the value of the contentType property.
getContributingChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions
Gets the value of the contributingChannel property.
getContributingChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.IsotopicContributions
Gets the value of the contributingChannel property.
getContributingChannel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.IsotopicContributions
Gets the value of the contributingChannel property.
getContributingChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IsotopicContributions
Gets the value of the contributingChannel property.
getContributingChannel() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IsotopicContributions
Gets the value of the contributingChannel property.
getControllerType(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetControllerType
getCorrection() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
Gets the value of the correction property.
getCorrection() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AffectedChannel
Gets the value of the correction property.
getCorrection() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AffectedChannel
Gets the value of the correction property.
getCorrection() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AffectedChannel
Gets the value of the correction property.
getCorrection() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AffectedChannel
Gets the value of the correction property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ProductListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SampleListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanWindowListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SelectedIonListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileRefListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumListType
Gets the value of the count property.
getCount() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.TargetListType
Gets the value of the count property.
getCpdAlgo() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Gets the value of the cpdAlgo property.
getCreationDate() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the creationDate property.
getCreationDate() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the creationDate property.
getCreatorID(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetCreatorID
getCTermGain() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Gets the value of the cTermGain property.
getCTermGain() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Gets the value of the cTermGain property.
getCurrentController(Holder<Integer>, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetCurrentController
getCustomizations() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
Gets the value of the customizations property.
getCustomizations() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
Gets the value of the customizations property.
getCut() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
Gets the value of the cut property.
getCut() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
Gets the value of the cut property.
getCut() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
Gets the value of the cut property.
getCv() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CVListType
Gets the value of the cv property.
getCv() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CVListType
Gets the value of the cv property.
getCv() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVListType
Gets the value of the cv property.
getCvList() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the cvList property.
getCvList() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the cvList property.
getCvList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the cvList property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FileFormatType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IonTypeType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MeasureType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParamType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.RoleType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpecificityRulesType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIDFormatType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ToleranceType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.TranslationTableType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FileFormatType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IonTypeType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MeasureType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParamType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.RoleType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpecificityRulesType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIDFormatType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ToleranceType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.TranslationTableType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ParamGroupType
Gets the value of the cvParam property.
getCvParam() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupType
Gets the value of the cvParam property.
getCvRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CVParamType
Gets the value of the cvRef property.
getCvRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CVParamType
Gets the value of the cvRef property.
getCvRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Gets the value of the cvRef property.
getCycleNumberFromScanNumber(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetCycleNumberFromScanNumber
getDatabase() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.DatabaseRefreshTimestamp
Gets the value of the database property.
getDatabase() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatabaseRefreshTimestamp
Gets the value of the database property.
getDatabase() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatabaseRefreshTimestamp
Gets the value of the database property.
getDatabaseFilters() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the databaseFilters property.
getDatabaseFilters() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the databaseFilters property.
getDatabaseName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Gets the value of the databaseName property.
getDatabaseName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Gets the value of the databaseName property.
getDatabaseName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Gets the value of the databaseName property.
getDatabaseName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Gets the value of the databaseName property.
getDatabaseName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Gets the value of the databaseName property.
getDatabaseReleaseDate() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Gets the value of the databaseReleaseDate property.
getDatabaseReleaseDate() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Gets the value of the databaseReleaseDate property.
getDatabaseReleaseDate() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Gets the value of the databaseReleaseDate property.
getDatabaseReleaseIdentifier() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Gets the value of the databaseReleaseIdentifier property.
getDatabaseReleaseIdentifier() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Gets the value of the databaseReleaseIdentifier property.
getDatabaseReleaseIdentifier() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Gets the value of the databaseReleaseIdentifier property.
getDatabaseTranslation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the databaseTranslation property.
getDatabaseTranslation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the databaseTranslation property.
getDataCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the dataCollection property.
getDataCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the dataCollection property.
getDataFilter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation
Gets the value of the dataFilter property.
getDataFilter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatasetDerivation
Gets the value of the dataFilter property.
getDataFilter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatasetDerivation
Gets the value of the dataFilter property.
getDataFilter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DatasetDerivation
Gets the value of the dataFilter property.
getDataFilter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DatasetDerivation
Gets the value of the dataFilter property.
getDatanum() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Gets the value of the datanum property.
getDatanum() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Gets the value of the datanum property.
getDatanum() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Gets the value of the datanum property.
getDatanum() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Gets the value of the datanum property.
getDataProcessing() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingListType
Gets the value of the dataProcessing property.
getDataProcessing() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Gets the value of the dataProcessing property.
getDataProcessingList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the dataProcessingList property.
getDataProcessingRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
Gets the value of the dataProcessingRef property.
getDataProcessingRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Gets the value of the dataProcessingRef property.
getDataProcessingRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Gets the value of the dataProcessingRef property.
getDatasetDerivation() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
Gets the value of the datasetDerivation property.
getDatasetDerivation() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
Gets the value of the datasetDerivation property.
getDatasetDerivation() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
Gets the value of the datasetDerivation property.
getDatasetDerivation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
Gets the value of the datasetDerivation property.
getDatasetDerivation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
Gets the value of the datasetDerivation property.
getDataSource() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
getDataSource() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
 
getDate() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
Gets the value of the date property.
getDate() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
Gets the value of the date property.
getDate() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
Gets the value of the date property.
getDBSequence() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SequenceCollectionType
Gets the value of the dbSequence property.
getDBSequence() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SequenceCollectionType
Gets the value of the dbSequence property.
getDBSequenceRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Gets the value of the dbSequenceRef property.
getDBSequenceRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
Gets the value of the dbSequenceRef property.
getDBSequenceRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Gets the value of the dbSequenceRef property.
getDBSequenceRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
Gets the value of the dbSequenceRef property.
getDeadVolume() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
Gets the value of the deadVolume property.
getDecimalPvalue() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Gets the value of the decimalPvalue property.
getDecimalPvalue() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Gets the value of the decimalPvalue property.
getDecimalRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the decimalRatio property.
getDecimalRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the decimalRatio property.
getDecimalRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the decimalRatio property.
getDefaultArrayLength() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Gets the value of the defaultArrayLength property.
getDefaultArrayLength() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Gets the value of the defaultArrayLength property.
getDefaultBufferSize() - Method in class umich.ms.util.base64.Base64
Get the default buffer size.
getDefaultDataProcessingRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramListType
Gets the value of the defaultDataProcessingRef property.
getDefaultDataProcessingRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumListType
Gets the value of the defaultDataProcessingRef property.
getDefaultInstrument() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
getDefaultInstrumentConfigurationRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Gets the value of the defaultInstrumentConfigurationRef property.
getDefaultInstrumentID() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
getDefaultSize() - Method in class umich.ms.util.ByteArrayHolderFactory
 
getDefaultSourceFileRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Gets the value of the defaultSourceFileRef property.
getDefaultStorageStrategy() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
getDefaultStorageStrategy() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
 
getDegenFlag() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the degenFlag property.
getDegenFlag() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the degenFlag property.
getDelta() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the delta property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Gets the value of the description property.
getDescription() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
Gets the value of the description property.
getDetector() - Method in class umich.ms.datatypes.scan.props.Instrument
 
getDetector() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentListType
Gets the value of the detector property.
getDetectorTypeForScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetDetectorTypeForScanNum
getDevice() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Gets the value of the device property.
getDirectory() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InteractSummary
Gets the value of the directory property.
getDirectory() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InputFileType
Gets the value of the directory property.
getDirectory() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InteractSummary
Gets the value of the directory property.
getDirectory() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InputFileType
Gets the value of the directory property.
getDirectory() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InteractSummary
Gets the value of the directory property.
getDistributionPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Gets the value of the distributionPoint property.
getDistributionPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Gets the value of the distributionPoint property.
getDistributionPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Gets the value of the distributionPoint property.
getDoi() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Gets the value of the doi property.
getDoi() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Gets the value of the doi property.
getDomain() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Peptide
 
getDummy() - Static method in class umich.ms.datatypes.scan.props.Instrument
Only to be used, when you need to construct a ScanCollection without any knowledge about the real run, so you have no idea about the instrument.
getDummyRunInfo() - Static method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
Only use if you can't get real run info.
getDuration() - Method in class umich.ms.datatypes.scan.props.InjectionInfo
 
getEditor() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Gets the value of the editor property.
getEditor() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Gets the value of the editor property.
getElution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Gets the value of the elution property.
getElution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Gets the value of the elution property.
getElution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Gets the value of the elution property.
getEmail() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Gets the value of the email property.
getEncodedLength() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
Gets the value of the encodedLength property.
getEnd() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the end property.
getEnd() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Peptide
Gets the value of the end property.
getEnd() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Gets the value of the end property.
getEnd() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Gets the value of the end property.
getEndMz() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the endMz property.
getEndScan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the endScan property.
getEndScan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the endScan property.
getEndScan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the endScan property.
getEndTime() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Gets the value of the endTime property.
getEndTime(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetEndTime
getEnsemblName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Gets the value of the ensemblName property.
getEnsemblName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Gets the value of the ensemblName property.
getEnumFromString(Class<T>, String) - Static method in class umich.ms.util.StringUtils
A common method for all enums since they can't have another base class
getEnzymaticSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the enzymaticSearchConstraint property.
getEnzymaticSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the enzymaticSearchConstraint property.
getEnzymaticSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the enzymaticSearchConstraint property.
getEnzyme() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymesType
Gets the value of the enzyme property.
getEnzyme() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymesType
Gets the value of the enzyme property.
getEnzyme() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
Gets the value of the enzyme property.
getEnzyme() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EnzymaticSearchConstraint
Gets the value of the enzyme property.
getEnzyme() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.EnzymaticSearchConstraint
Gets the value of the enzyme property.
getEnzymeName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Gets the value of the enzymeName property.
getEnzymeName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Gets the value of the enzymeName property.
getEnzymes() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the enzymes property.
getEnzymes() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the enzymes property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Intensity
Gets the value of the error property.
getError() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Intensity
Gets the value of the error property.
getErrorCode(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetErrorCode
getErrorFlag(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetErrorFlag
getErrorLogItem(int, Holder<Double>, Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetErrorLogItem
getErrorMessage(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetErrorMessage
getErrorPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
Gets the value of the errorPoint property.
getErrorPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
Gets the value of the errorPoint property.
getErrorPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
Gets the value of the errorPoint property.
getEstTotCorrect() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Gets the value of the estTotCorrect property.
getEstTotCorrect() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Gets the value of the estTotCorrect property.
getEstTotCorrect() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Gets the value of the estTotCorrect property.
getEstTotNumCorrect() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Gets the value of the estTotNumCorrect property.
getEstTotNumCorrect() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Gets the value of the estTotNumCorrect property.
getEstTotNumCorrect() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Gets the value of the estTotNumCorrect property.
getEstTotNumCorrectPep() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Gets the value of the estTotNumCorrectPep property.
getEstTotNumCorrectPep() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Gets the value of the estTotNumCorrectPep property.
getEstTotNumCorrectPsm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Gets the value of the estTotNumCorrectPsm property.
getEstTotNumCorrectPsm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Gets the value of the estTotNumCorrectPsm property.
getExclude() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FilterType
Gets the value of the exclude property.
getExclude() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FilterType
Gets the value of the exclude property.
getExpect() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the expect property.
getExpect() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the expect property.
getExpect() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Gets the value of the expect property.
getExpectedRunTime(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetExpectedRunTime
getExperimentalMassToCharge() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the experimentalMassToCharge property.
getExperimentalMassToCharge() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the experimentalMassToCharge property.
getExpSiblingIonBin() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the expSiblingIonBin property.
getExpSiblingIonBin() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the expSiblingIonBin property.
getExpSiblingIonInstances() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the expSiblingIonInstances property.
getExpSiblingIonInstances() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the expSiblingIonInstances property.
getExpTotInstances() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the expTotInstances property.
getExpTotInstances() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the expTotInstances property.
getExternalFormatDocumentation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ExternalDataType
Gets the value of the externalFormatDocumentation property.
getExternalFormatDocumentation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ExternalDataType
Gets the value of the externalFormatDocumentation property.
getExternalSpectrumID() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Gets the value of the externalSpectrumID property.
getExternalSpectrumID() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
Gets the value of the externalSpectrumID property.
getFactory() - Method in class umich.ms.fileio.chunk.ChunkedFile
 
getFalsePositiveErrorRate() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
Gets the value of the falsePositiveErrorRate property.
getFalsePositiveErrorRate() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
Gets the value of the falsePositiveErrorRate property.
getFI() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the fi property.
getFidelity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
Gets the value of the fidelity property.
getFidelity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
Gets the value of the fidelity property.
getFidelity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
Gets the value of the fidelity property.
getFile() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Gets the value of the file property.
getFileContent() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.FileDescriptionType
Gets the value of the fileContent property.
getFileDescription() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the fileDescription property.
getFileFormat() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ExternalDataType
Gets the value of the fileFormat property.
getFileFormat() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ExternalDataType
Gets the value of the fileFormat property.
getFileName() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
Gets the value of the fileName property.
getFilename() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InteractSummary
Gets the value of the filename property.
getFilename() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InteractSummary
Gets the value of the filename property.
getFilename() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InteractSummary
Gets the value of the filename property.
getFileName(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetFileName
getFileName(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method GetFileName
getFileName(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirUV
method GetFileName
getFilePointer() - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
getFilePointer() - Method in class umich.ms.external.BufferedRandomAccessFile
Returns the current position of the pointer in the file.
getFileSha1() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
Gets the value of the fileSha1 property.
getFileType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
Gets the value of the fileType property.
getFilter() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DatabaseFiltersType
Gets the value of the filter property.
getFilter() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DatabaseFiltersType
Gets the value of the filter property.
getFilter() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawIndexElement
The filter line string common to most Thermo instruments, looks like:
FTMS + p NSI Full ms [400.00-2000.00]
getFilterForScanNum(int, Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetFilterForScanNum
getFilterForScanRT(double, Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetFilterForScanRT
getFilterLine() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the filterLine property.
getFilterMassPrecision(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetFilterMassPrecision
getFilters(Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetFilters
getFilterType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FilterType
Gets the value of the filterType property.
getFilterType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FilterType
Gets the value of the filterType property.
getFinalPeptideWtIters() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the finalPeptideWtIters property.
getFinalPeptideWtIters() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the finalPeptideWtIters property.
getFirst() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Gets the value of the first property.
getFirstName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
Gets the value of the firstName property.
getFirstName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
Gets the value of the firstName property.
getFirstSpectrumNumber(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetFirstSpectrumNumber
getFirstSpotID() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern.Orientation
Gets the value of the firstSpotID property.
getFlags(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetFlags
getFlybase() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Gets the value of the flybase property.
getFlybase() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Gets the value of the flybase property.
getFormat() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
Gets the value of the format property.
getFpkmAdjustedProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the fpkmAdjustedProbability property.
getFpkmAdjustedProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the fpkmAdjustedProbability property.
getFpkmBin() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the fpkmBin property.
getFpkmBin() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the fpkmBin property.
getFpkmDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmInformation
Gets the value of the fpkmDistribution property.
getFpkmDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmInformation
Gets the value of the fpkmDistribution property.
getFpkmFlag() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the fpkmFlag property.
getFpkmFlag() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the fpkmFlag property.
getFpkmInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the fpkmInformation property.
getFpkmInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the fpkmInformation property.
getFpkmLowerBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Gets the value of the fpkmLowerBoundExcl property.
getFpkmLowerBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Gets the value of the fpkmLowerBoundExcl property.
getFpkmLowerBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Gets the value of the fpkmLowerBoundIncl property.
getFpkmLowerBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Gets the value of the fpkmLowerBoundIncl property.
getFpkmUpperBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Gets the value of the fpkmUpperBoundExcl property.
getFpkmUpperBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Gets the value of the fpkmUpperBoundExcl property.
getFpkmUpperBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Gets the value of the fpkmUpperBoundIncl property.
getFpkmUpperBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Gets the value of the fpkmUpperBoundIncl property.
getFragmentArray() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IonTypeType
Gets the value of the fragmentArray property.
getFragmentArray() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IonTypeType
Gets the value of the fragmentArray property.
getFragmentation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the fragmentation property.
getFragmentation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the fragmentation property.
getFragmentationTable() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
Gets the value of the fragmentationTable property.
getFragmentationTable() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
Gets the value of the fragmentationTable property.
getFragmentMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Gets the value of the fragmentMasses property.
getFragmentMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Gets the value of the fragmentMasses property.
getFragmentMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Gets the value of the fragmentMasses property.
getFragmentMasses() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Gets the value of the fragmentMasses property.
getFragmentMasses() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Gets the value of the fragmentMasses property.
getFragmentMassType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the fragmentMassType property.
getFragmentMassType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the fragmentMassType property.
getFragmentMassType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the fragmentMassType property.
getFragmentTolerance() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the fragmentTolerance property.
getFragmentTolerance() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the fragmentTolerance property.
getFrame() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Gets the value of the frame property.
getFrame() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Gets the value of the frame property.
getFrames() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DatabaseTranslationType
Gets the value of the frames property.
getFrames() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DatabaseTranslationType
Gets the value of the frames property.
getFullAnalysisDistributionFile() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Gets the value of the fullAnalysisDistributionFile property.
getFullAnalysisDistributionFile() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Gets the value of the fullAnalysisDistributionFile property.
getFullMSOrderPrecursorDataFromScanNum(int, int, Object) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetFullMSOrderPrecursorDataFromScanNum
getFullName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
Gets the value of the fullName property.
getFullName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
Gets the value of the fullName property.
getFullName() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
Gets the value of the fullName property.
getFv() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
Gets the value of the fv property.
getFvalue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the fvalue property.
getFvalue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the fvalue property.
getFvalue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the fvalue property.
getFValueFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetFValueFromScanNum
getGenerationNo() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation
Gets the value of the generationNo property.
getGenerationNo() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatasetDerivation
Gets the value of the generationNo property.
getGenerationNo() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatasetDerivation
Gets the value of the generationNo property.
getGenerationNo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DatasetDerivation
Gets the value of the generationNo property.
getGenerationNo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DatasetDerivation
Gets the value of the generationNo property.
getGroup() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Bioml
Gets the value of the group property.
getGroup() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the group property.
getGroupNumber() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
Gets the value of the groupNumber property.
getGroupNumber() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
Gets the value of the groupNumber property.
getGroupsFlag() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the groupsFlag property.
getGroupsFlag() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the groupsFlag property.
getGroupSiblingId() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the groupSiblingId property.
getGroupSiblingId() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the groupSiblingId property.
getHeavy2LightAdjRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Gets the value of the heavy2LightAdjRatioMean property.
getHeavy2LightAdjRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Gets the value of the heavy2LightAdjRatioMean property.
getHeavy2LightAdjRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Gets the value of the heavy2LightAdjRatioStandardDev property.
getHeavy2LightAdjRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Gets the value of the heavy2LightAdjRatioStandardDev property.
getHeavy2LightError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
Gets the value of the heavy2LightError property.
getHeavy2LightError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
Gets the value of the heavy2LightError property.
getHeavy2LightError() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
Gets the value of the heavy2LightError property.
getHeavy2LightMean() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
Gets the value of the heavy2LightMean property.
getHeavy2LightMean() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
Gets the value of the heavy2LightMean property.
getHeavy2LightMean() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
Gets the value of the heavy2LightMean property.
getHeavy2LightRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the heavy2LightRatio property.
getHeavy2LightRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the heavy2LightRatio property.
getHeavy2LightRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the heavy2LightRatio property.
getHeavy2LightRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Gets the value of the heavy2LightRatioMean property.
getHeavy2LightRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Gets the value of the heavy2LightRatioMean property.
getHeavy2LightRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Gets the value of the heavy2LightRatioMean property.
getHeavy2LightRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Gets the value of the heavy2LightRatioMean property.
getHeavy2LightRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Gets the value of the heavy2LightRatioMean property.
getHeavy2LightRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Gets the value of the heavy2LightRatioMean property.
getHeavy2LightRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Gets the value of the heavy2LightRatioStandardDev property.
getHeavy2LightRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Gets the value of the heavy2LightRatioStandardDev property.
getHeavy2LightRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Gets the value of the heavy2LightRatioStandardDev property.
getHeavy2LightRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Gets the value of the heavy2LightRatioStandardDev property.
getHeavy2LightRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Gets the value of the heavy2LightRatioStandardDev property.
getHeavy2LightRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Gets the value of the heavy2LightRatioStandardDev property.
getHeavyArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the heavyArea property.
getHeavyArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the heavyArea property.
getHeavyArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the heavyArea property.
getHeavyFirstscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the heavyFirstscan property.
getHeavyFirstscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the heavyFirstscan property.
getHeavyFirstscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the heavyFirstscan property.
getHeavyLastscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the heavyLastscan property.
getHeavyLastscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the heavyLastscan property.
getHeavyLastscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the heavyLastscan property.
getHeavyMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Gets the value of the heavyMass property.
getHeavyMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the heavyMass property.
getHeavyMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Gets the value of the heavyMass property.
getHeavyMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the heavyMass property.
getHeavyMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Gets the value of the heavyMass property.
getHeavyMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the heavyMass property.
getHi() - Method in class umich.ms.util.Interval1D
 
getHighMass(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetHighMass
getHighMz() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the highMz property.
getHitRank() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the hitRank property.
getHitRank() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the hitRank property.
getHitRank() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the hitRank property.
getHyperscore() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the hyperscore property.
getId() - Method in class umich.ms.datatypes.index.impl.IndexElementDefault
 
getId() - Method in interface umich.ms.datatypes.index.IndexElement
The textual representation of an ID of a scan.
getId() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IdentifiableType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IdentifiableType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SampleType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexElement
 
getId() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexElement
 
getId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisResult
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisResult
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisResult
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisResult
Gets the value of the id property.
getId() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
Gets the value of the id property.
getInclude() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FilterType
Gets the value of the include property.
getInclude() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FilterType
Gets the value of the include property.
getInclude() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPDta
Gets the value of the include property.
getInclude() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Gets the value of the include property.
getInclude() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Gets the value of the include property.
getInclude() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPDta
Gets the value of the include property.
getInclude() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Gets the value of the include property.
getInclude() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Gets the value of the include property.
getIndex() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Gets the index without an attempt to parse it.
getIndex() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IonTypeType
Gets the value of the index property.
getIndex() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IonTypeType
Gets the value of the index property.
getIndex() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Gets the value of the index property.
getIndex() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Gets the value of the index property.
getIndex() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
getIndex() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
getIndex() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the index property.
getIndex() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the index property.
getIndex() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the index property.
getIndex() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
getIndexBuilder(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
getIndexBuilder(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
getIndexBuilder(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
getIndexBuilder(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
getIndexBuilder(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
getIndexElements() - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
 
getIndistinguishablePeptide() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the indistinguishablePeptide property.
getIndistinguishablePeptide() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the indistinguishablePeptide property.
getIndistinguishableProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the indistinguishableProtein property.
getIndistinguishableProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the indistinguishableProtein property.
getInfo() - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
 
getInitialMinPeptideProb() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the initialMinPeptideProb property.
getInitialMinPeptideProb() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the initialMinPeptideProb property.
getInitialPeptideWtIters() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the initialPeptideWtIters property.
getInitialPeptideWtIters() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the initialPeptideWtIters property.
getInitialProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the initialProbability property.
getInitialProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the initialProbability property.
getInjectionAmountUnits(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInjectionAmountUnits
getInjectionInfo() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getInjectionInfo() - Method in interface umich.ms.datatypes.scan.IScan
 
getInjectionVolume(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInjectionVolume
getInletID(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInletID
getInputfile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InteractSummary
Gets the value of the inputfile property.
getInputfile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
Gets the value of the inputfile property.
getInputfile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Gets the value of the inputfile property.
getInputfile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InteractSummary
Gets the value of the inputfile property.
getInputfile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Gets the value of the inputfile property.
getInputfile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Gets the value of the inputfile property.
getInputfile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InteractSummary
Gets the value of the inputfile property.
getInputfile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Gets the value of the inputfile property.
getInputfile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Gets the value of the inputfile property.
getInputs() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DataCollectionType
Gets the value of the inputs property.
getInputs() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DataCollectionType
Gets the value of the inputs property.
getInputSpectra() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
Gets the value of the inputSpectra property.
getInputSpectra() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
Gets the value of the inputSpectra property.
getInputSpectrumIdentifications() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionType
Gets the value of the inputSpectrumIdentifications property.
getInputSpectrumIdentifications() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionType
Gets the value of the inputSpectrumIdentifications property.
getInstance() - Static method in class umich.ms.util.PooledByteArrayHolders
 
getInstChannelLabel(int, Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstChannelLabel
getInstFlags(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstFlags
getInstHardwareVersion(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstHardwareVersion
getInstMethod(int, Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstMethod
getInstMethodNames(Holder<Integer>, Object) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstMethodNames
getInstModel(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstModel
getInstName(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstName
getInstNumChannelLabels(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstNumChannelLabels
getInstrument(String) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
Get instrument by ID.
getInstrument() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getInstrument() - Method in interface umich.ms.datatypes.scan.IScan
 
getInstrumentConfiguration() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationListType
Gets the value of the instrumentConfiguration property.
getInstrumentConfigurationList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the instrumentConfigurationList property.
getInstrumentConfigurationRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
Gets the value of the instrumentConfigurationRef property.
getInstrumentDescription(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstrumentDescription
getInstrumentID(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstrumentID
getInstruments() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
getInstSerialNumber(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstSerialNumber
getInstSoftwareVersion(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetInstSoftwareVersion
getIntensities() - Method in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
 
getIntensities() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
Array of intensities.
getIntensity() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
getIntensity(int) - Method in interface umich.ms.datatypes.spectrum.IIndexedSpectrum
Deprecated.
 
getIntensity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult
Gets the value of the intensity property.
getIntensity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraResult
Gets the value of the intensity property.
getIntensity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraResult
Gets the value of the intensity property.
getIntensity() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraResult
Gets the value of the intensity property.
getIntensity() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraResult
Gets the value of the intensity property.
getIntensityCutoff() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Gets the value of the intensityCutoff property.
getInterval() - Method in class umich.ms.util.IntervalST.Node
 
getIonDescription() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
getIonId() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
getIonisation() - Method in class umich.ms.datatypes.scan.props.Instrument
 
getIonisationEnergy() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the ionisationEnergy property.
getIonType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentationType
Gets the value of the ionType property.
getIonType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentationType
Gets the value of the ionType property.
getIpiName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Gets the value of the ipiName property.
getIpiName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Gets the value of the ipiName property.
getIs() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
Gets the value of the is property.
getIsContributingEvidence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the isContributingEvidence property.
getIsContributingEvidence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the isContributingEvidence property.
getIsHeavy() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Gets the value of the isHeavy property.
getIsHeavy() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Gets the value of the isHeavy property.
getIsHeavy() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Gets the value of the isHeavy property.
getIsHeavy() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Gets the value of the isHeavy property.
getIsHeavy() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Gets the value of the isHeavy property.
getIsHeavy() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Gets the value of the isHeavy property.
getIsNondegenerateEvidence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the isNondegenerateEvidence property.
getIsNondegenerateEvidence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the isNondegenerateEvidence property.
getIsolationWidthForScanNum(int, int, Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetIsolationWidthForScanNum
getIsolationWindow() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Gets the value of the isolationWindow property.
getIsolationWindow() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ProductType
Gets the value of the isolationWindow property.
getIsotopeNumber() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
getIsotopicContributions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Gets the value of the isotopicContributions property.
getIsotopicContributions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Gets the value of the isotopicContributions property.
getIsotopicContributions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Gets the value of the isotopicContributions property.
getIsotopicContributions() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Gets the value of the isotopicContributions property.
getIsotopicContributions() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Gets the value of the isotopicContributions property.
getIsRejected() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the isRejected property.
getIsRejected() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the isRejected property.
getIsRejected() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the isRejected property.
getIssue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Gets the value of the issue property.
getIssue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Gets the value of the issue property.
getItems() - Method in class umich.ms.fileio.util.jaxb.JAXBCollection
 
getKValueFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetKValueFromScanNum
getLabel() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Bioml
Gets the value of the label property.
getLabel() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the label property.
getLabel() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Note
Gets the value of the label property.
getLabel() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Gets the value of the label property.
getLabel() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Gets the value of the label property.
getLabel() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Xdata
Gets the value of the label property.
getLabel() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Ydata
Gets the value of the label property.
getLabelData(Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile2
method GetLabelData
getLabeledResidues() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Gets the value of the labeledResidues property.
getLabeledResidues() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Gets the value of the labeledResidues property.
getLabeledResidues() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Gets the value of the labeledResidues property.
getLabeledResidues() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Gets the value of the labeledResidues property.
getLabeledResidues() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Gets the value of the labeledResidues property.
getLabeledResidues() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Gets the value of the labeledResidues property.
getLaserFrequency() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Gets the value of the laserFrequency property.
getLaserIntensity() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Gets the value of the laserIntensity property.
getLaserShootCount() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Gets the value of the laserShootCount property.
getLast() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Gets the value of the last property.
getLastName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
Gets the value of the lastName property.
getLastName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
Gets the value of the lastName property.
getLastSpectrumNumber(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetLastSpectrumNumber
getLeftValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Gets the value of the leftValley property.
getLeftValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Gets the value of the leftValley property.
getLeftValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Gets the value of the leftValley property.
getLeftValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Gets the value of the leftValley property.
getLeftValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Gets the value of the leftValley property.
getLeftValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Gets the value of the leftValley property.
getLength() - Method in class umich.ms.fileio.chunk.FileChunk
 
getLength() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
Gets the value of the length property.
getLength() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
Gets the value of the length property.
getLightArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the lightArea property.
getLightArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the lightArea property.
getLightArea() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the lightArea property.
getLightFirstscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the lightFirstscan property.
getLightFirstscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the lightFirstscan property.
getLightFirstscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the lightFirstscan property.
getLightLastscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the lightLastscan property.
getLightLastscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the lightLastscan property.
getLightLastscan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the lightLastscan property.
getLightMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Gets the value of the lightMass property.
getLightMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the lightMass property.
getLightMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Gets the value of the lightMass property.
getLightMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the lightMass property.
getLightMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Gets the value of the lightMass property.
getLightMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the lightMass property.
getLightSequence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Gets the value of the lightSequence property.
getLightSequence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Gets the value of the lightSequence property.
getLo() - Method in class umich.ms.util.Interval1D
 
getLocalPath() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Gets the value of the localPath property.
getLocalPath() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Gets the value of the localPath property.
getLocalPath() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Gets the value of the localPath property.
getLocation() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Compound
Gets the value of the location property.
getLocation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ExternalDataType
Gets the value of the location property.
getLocation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
Gets the value of the location property.
getLocation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
Gets the value of the location property.
getLocation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ExternalDataType
Gets the value of the location property.
getLocation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
Gets the value of the location property.
getLocation() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
Gets the value of the location property.
getLocation() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileType
Gets the value of the location property.
getLocusLinkName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Gets the value of the locusLinkName property.
getLocusLinkName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Gets the value of the locusLinkName property.
getLogratio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Point
Gets the value of the logratio property.
getLogratio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Point
Gets the value of the logratio property.
getLowMass(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetLowMass
getLowMz() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the lowMz property.
getM() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
Gets the value of the m property.
getMaldi() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the maldi property.
getMaldiMatrix() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
Gets the value of the maldiMatrix property.
getManufacturer() - Method in class umich.ms.datatypes.scan.props.Instrument
 
getMapById() - Method in class umich.ms.datatypes.index.impl.IndexDefault
 
getMapById() - Method in interface umich.ms.datatypes.index.Index
A mapping from textual scan IDs.
getMapByNum() - Method in class umich.ms.datatypes.index.impl.IndexDefault
 
getMapByNum() - Method in interface umich.ms.datatypes.index.Index
A mapping from internal scan numbers.
getMapByRawNum() - Method in class umich.ms.datatypes.index.impl.IndexDefault
 
getMapByRawNum() - Method in interface umich.ms.datatypes.index.Index
A mapping from original raw scan numbers (or "spectrum index" values in mzML).
getMapMsLevel2index() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Get a map which links MS Levels (starting from 1) to maps of (scanNum => scanObject).
getMapMsLevel2index() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Get a map which links MS Levels (starting from 1) to maps of (scanNum => scanObject)
getMapMsLevel2rangeGroups() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Get a map, holding spectra groupped by precursor m/z isolation window.
MS1 spectra are groupped by their overall m/z range.
getMapMsLevel2rangeGroups() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Get a map, holding spectra groupped by precursor m/z isolation window.
MS1 spectra are groupped by their overall m/z range.
getMapNum2scan() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Get a map which links actual scan numbers to instances of Scan objects.
getMapNum2scan() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Get a map which links actual scan numbers to instances of Scan objects
getMapRt2scan() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Maps retention time (in minutes) to lists of Scan objects.
getMapRt2scan() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Maps retention time (in minutes) to lists of Scan objects.
getMass() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
getMass() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ResidueType
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ResidueType
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModAminoacidMass
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModAminoacidMass
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModAminoacidMass
Gets the value of the mass property.
getMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModAminoacidMass
Gets the value of the mass property.
getMassAnalyzerTypeForScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetMassAnalyzerTypeForScanNum
getMassCalibrationValueFromScanNum(int, int, Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetMassCalibrationValueFromScanNum
getMassDelta() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
Gets the value of the massDelta property.
getMassDelta() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
Gets the value of the massDelta property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Gets the value of the massdiff property.
getMassdiff() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Gets the value of the massdiff property.
getMassListFromRT(Holder<Double>, String, int, int, int, int, Holder<Double>, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetMassListFromRT
getMassListFromScanNum(Holder<Integer>, String, int, int, int, int, Holder<Double>, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetMassListFromScanNum
getMassListRangeFromRT(Holder<Double>, String, int, int, int, int, Holder<Double>, Object, Object, String, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile3
method GetMassListRangeFromRT
getMassListRangeFromScanNum(Holder<Integer>, String, int, int, int, int, Holder<Double>, Object, Object, String, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile3
method GetMassListRangeFromScanNum
getMassPrecisionEstimate(int, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetMassPrecisionEstimate
getMassRangeFromScanNum(int, int, Holder<Double>, Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetMassRangeFromScanNum
getMassResolution(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetMassResolution
getMassTable() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the massTable property.
getMassTable() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the massTable property.
getMassTableRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the massTableRef property.
getMassTableRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the massTableRef property.
getMassTol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the massTol property.
getMasstol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Gets the value of the masstol property.
getMassTol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the massTol property.
getMasstol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Gets the value of the masstol property.
getMassTol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the massTol property.
getMasstol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Gets the value of the masstol property.
getMassTolerance() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Gets the value of the massTolerance property.
getMassTolerance() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Gets the value of the massTolerance property.
getMassTolerance() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Gets the value of the massTolerance property.
getMassTolerance() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Gets the value of the massTolerance property.
getMassTolerance() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Gets the value of the massTolerance property.
getMassTolerance(Holder<Integer>, Holder<Double>, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetMassTolerance
getMax() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRange
Gets the value of the max property.
getMaxFpkm() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the maxFpkm property.
getMaxFpkm() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the maxFpkm property.
getMaxI() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the maxI property.
getMaxInt() - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
getMaxInt() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
The highest intensity in the spectrumRef.
getMaxIntegratedIntensity(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetMaxIntegratedIntensity
getMaxIntensity(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetMaxIntensity
getMaxIntMz() - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
getMaxIntMz() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
The m/z value of the basepeak (i.e.
getMaxMZ() - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
getMaxMZ() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
The highest m/z value in the spectrumRef.
getMaxNumInternalCleavages() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
Gets the value of the maxNumInternalCleavages property.
getMaxNumInternalCleavages() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EnzymaticSearchConstraint
Gets the value of the maxNumInternalCleavages property.
getMaxNumInternalCleavages() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.EnzymaticSearchConstraint
Gets the value of the maxNumInternalCleavages property.
getmCount() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
getMean() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
Gets the value of the mean property.
getMean() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
Gets the value of the mean property.
getMean() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
Gets the value of the mean property.
getMeasure() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentationTableType
Gets the value of the measure property.
getMeasure() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentationTableType
Gets the value of the measure property.
getMeasureRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentArrayType
Gets the value of the measureRef property.
getMeasureRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentArrayType
Gets the value of the measureRef property.
getMh() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the mh property.
getMh() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the mh property.
getMidInitials() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
Gets the value of the midInitials property.
getMidInitials() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
Gets the value of the midInitials property.
getMin() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRange
Gets the value of the min property.
getMinDistance() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Gets the value of the minDistance property.
getMinDistance() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Gets the value of the minDistance property.
getMinInt() - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
getMinInt() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
The minimum intensity in the spectrumRef.
getMinIntNonZero() - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
getMinIntNonZero() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
The minimum intensity in the spectrumRef, but greater than zero.
It can still be zero, if there are only zero intensity peaks in the spectrumRef.
getMinMZ() - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
getMinMZ() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
The lowest m/z value in the spectrumRef.
getMinNumberTermini() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
Gets the value of the minNumberTermini property.
getMinNumberTermini() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EnzymaticSearchConstraint
Gets the value of the minNumberTermini property.
getMinNumberTermini() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.EnzymaticSearchConstraint
Gets the value of the minNumberTermini property.
getMinNumChromatogramPoints() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Gets the value of the minNumChromatogramPoints property.
getMinNumChromatogramPoints() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Gets the value of the minNumChromatogramPoints property.
getMinNumEnzTerm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.DatabaseRefreshTimestamp
Gets the value of the minNumEnzTerm property.
getMinNumEnzTerm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatabaseRefreshTimestamp
Gets the value of the minNumEnzTerm property.
getMinNumEnzTerm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatabaseRefreshTimestamp
Gets the value of the minNumEnzTerm property.
getMinNumIsotopePeaks() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Gets the value of the minNumIsotopePeaks property.
getMinNumIsotopePeaks() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Gets the value of the minNumIsotopePeaks property.
getMinPepProb() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Gets the value of the minPepProb property.
getMinPepProb() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Gets the value of the minPepProb property.
getMinPeptideProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Gets the value of the minPeptideProbability property.
getMinPeptideProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the minPeptideProbability property.
getMinPeptideProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
Gets the value of the minPeptideProbability property.
getMinPeptideProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Gets the value of the minPeptideProbability property.
getMinPeptideProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the minPeptideProbability property.
getMinPeptideProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
Gets the value of the minPeptideProbability property.
getMinPeptideWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Gets the value of the minPeptideWeight property.
getMinPeptideWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the minPeptideWeight property.
getMinPeptideWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
Gets the value of the minPeptideWeight property.
getMinPeptideWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Gets the value of the minPeptideWeight property.
getMinPeptideWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the minPeptideWeight property.
getMinPeptideWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
Gets the value of the minPeptideWeight property.
getMinPepWt() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Gets the value of the minPepWt property.
getMinPepWt() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Gets the value of the minPepWt property.
getMinProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Gets the value of the minProb property.
getMinProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
Gets the value of the minProb property.
getMinProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
Gets the value of the minProb property.
getMinProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
Gets the value of the minProb property.
getMinProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Gets the value of the minProb property.
getMinProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
Gets the value of the minProb property.
getMinProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
Gets the value of the minProb property.
getMinProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Gets the value of the minProb property.
getMinProb() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
Gets the value of the minProb property.
getMinProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
Gets the value of the minProbability property.
getMinProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
Gets the value of the minProbability property.
getMinProteinProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Gets the value of the minProteinProbability property.
getMinProteinProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
Gets the value of the minProteinProbability property.
getMinProteinProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Gets the value of the minProteinProbability property.
getMinProteinProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
Gets the value of the minProteinProbability property.
getMinProtProb() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Gets the value of the minProtProb property.
getMinProtProb() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Gets the value of the minProtProb property.
getMinSpacing() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
Gets the value of the minSpacing property.
getMinSpacing() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
Gets the value of the minSpacing property.
getMinSpacing() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
Gets the value of the minSpacing property.
getMissedCleavages() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the missedCleavages property.
getMissedCleavages() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Gets the value of the missedCleavages property.
getMissedCleavages() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Gets the value of the missedCleavages property.
getMixturemodel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
Gets the value of the mixturemodel property.
getMixtureModel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Gets the value of the mixtureModel property.
getMixturemodel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Gets the value of the mixturemodel property.
getMixtureModel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Gets the value of the mixtureModel property.
getMixturemodel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Gets the value of the mixturemodel property.
getMixtureModel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Gets the value of the mixtureModel property.
getMixturemodelDistributionOrMixturemodel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Gets the value of the mixturemodelDistributionOrMixturemodel property.
getMixturemodelDistributionOrMixturemodel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Gets the value of the mixturemodelDistributionOrMixturemodel property.
getMixturemodelDistributionOrMixturemodel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Gets the value of the mixturemodelDistributionOrMixturemodel property.
getMod() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
Gets the value of the mod property.
getMod() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
Gets the value of the mod property.
getModAminoacidMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
Gets the value of the modAminoacidMass property.
getModAminoacidMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
Gets the value of the modAminoacidMass property.
getModAminoacidMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
Gets the value of the modAminoacidMass property.
getModAminoacidMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
Gets the value of the modAminoacidMass property.
getModAminoacidMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
Gets the value of the modAminoacidMass property.
getModCtermMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
Gets the value of the modCtermMass property.
getModCtermMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
Gets the value of the modCtermMass property.
getModCtermMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
Gets the value of the modCtermMass property.
getModCtermMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
Gets the value of the modCtermMass property.
getModCtermMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
Gets the value of the modCtermMass property.
getModel() - Method in class umich.ms.datatypes.scan.props.Instrument
 
getModel1NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model1NegDistr property.
getModel1NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model1NegDistr property.
getModel1NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model1NegDistr property.
getModel1PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model1PosDistr property.
getModel1PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model1PosDistr property.
getModel1PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model1PosDistr property.
getModel2NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model2NegDistr property.
getModel2NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model2NegDistr property.
getModel2NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model2NegDistr property.
getModel2PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model2PosDistr property.
getModel2PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model2PosDistr property.
getModel2PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model2PosDistr property.
getModel3NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model3NegDistr property.
getModel3NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model3NegDistr property.
getModel3NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model3NegDistr property.
getModel3PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model3PosDistr property.
getModel3PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model3PosDistr property.
getModel3PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model3PosDistr property.
getModel4NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model4NegDistr property.
getModel4NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model4NegDistr property.
getModel4NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model4NegDistr property.
getModel4PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model4PosDistr property.
getModel4PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model4PosDistr property.
getModel4PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model4PosDistr property.
getModel5NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model5NegDistr property.
getModel5NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model5NegDistr property.
getModel5NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model5NegDistr property.
getModel5PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model5PosDistr property.
getModel5PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model5PosDistr property.
getModel5PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model5PosDistr property.
getModel6NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model6NegDistr property.
getModel6NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model6NegDistr property.
getModel6NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model6NegDistr property.
getModel6PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model6PosDistr property.
getModel6PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model6PosDistr property.
getModel6PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model6PosDistr property.
getModel7NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model7NegDistr property.
getModel7NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model7NegDistr property.
getModel7NegDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model7NegDistr property.
getModel7PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the model7PosDistr property.
getModel7PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the model7PosDistr property.
getModel7PosDistr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the model7PosDistr property.
getModelDistr() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Point
Gets the value of the modelDistr property.
getModelDistr() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Point
Gets the value of the modelDistr property.
getModification() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideType
Gets the value of the modification property.
getModification() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideType
Gets the value of the modification property.
getModificationInfo() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the modificationInfo property.
getModificationInfo() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the modificationInfo property.
getModificationInfo() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the modificationInfo property.
getModificationInfo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
Gets the value of the modificationInfo property.
getModificationInfo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the modificationInfo property.
getModificationInfo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
Gets the value of the modificationInfo property.
getModificationInfo() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the modificationInfo property.
getModificationParams() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the modificationParams property.
getModificationParams() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the modificationParams property.
getModified() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
Gets the value of the modified property.
getModifiedPeptide() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
Gets the value of the modifiedPeptide property.
getModifiedPeptide() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
Gets the value of the modifiedPeptide property.
getModifiedPeptide() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
Gets the value of the modifiedPeptide property.
getModifiedPeptide() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
Gets the value of the modifiedPeptide property.
getModifiedPeptide() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
Gets the value of the modifiedPeptide property.
getModNtermMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
Gets the value of the modNtermMass property.
getModNtermMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
Gets the value of the modNtermMass property.
getModNtermMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
Gets the value of the modNtermMass property.
getModNtermMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
Gets the value of the modNtermMass property.
getModNtermMass() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
Gets the value of the modNtermMass property.
getMolId() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
getMonoisotopicMassDelta() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
Gets the value of the monoisotopicMassDelta property.
getMonoisotopicMassDelta() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
Gets the value of the monoisotopicMassDelta property.
getMonoisotopicMassDelta() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
Gets the value of the monoisotopicMassDelta property.
getMonoisotopicMassDelta() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
Gets the value of the monoisotopicMassDelta property.
getMSDetails() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Gets the value of the msDetails property.
getMsDetector() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Gets the value of the msDetector property.
getMsDetector() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the msDetector property.
getMsDetector() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the msDetector property.
getMsDetector() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the msDetector property.
getMsInstrument() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Gets the value of the msInstrument property.
getMsInstrumentID() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Gets the value of the msInstrumentID property.
getMsInstrumentID() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the msInstrumentID property.
getMsIonisation() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Gets the value of the msIonisation property.
getMsIonization() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the msIonization property.
getMsIonization() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the msIonization property.
getMsIonization() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the msIonization property.
getMsLevel() - Method in class umich.ms.datatypes.LCMSRange
 
getMsLevel() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getMsLevel() - Method in interface umich.ms.datatypes.scan.IScan
 
getMsLevel() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MassTableType
Gets the value of the msLevel property.
getMsLevel() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MassTableType
Gets the value of the msLevel property.
getMsLevel() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the msLevel property.
getMsLvl2index() - Method in class umich.ms.datatypes.scancollection.ScanIndexRoot
 
getMsLvls() - Method in class umich.ms.datatypes.LCMSDataSubset
 
getMsManufacturer() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Gets the value of the msManufacturer property.
getMsManufacturer() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the msManufacturer property.
getMsManufacturer() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the msManufacturer property.
getMsManufacturer() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the msManufacturer property.
getMsMassAnalyzer() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Gets the value of the msMassAnalyzer property.
getMsMassAnalyzer() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the msMassAnalyzer property.
getMsMassAnalyzer() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the msMassAnalyzer property.
getMsMassAnalyzer() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the msMassAnalyzer property.
getMsModel() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Gets the value of the msModel property.
getMsModel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the msModel property.
getMsModel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the msModel property.
getMsModel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the msModel property.
getMsmsRunSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
Gets the value of the msmsRunSummary property.
getMsmsRunSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
Gets the value of the msmsRunSummary property.
getMsmsRunSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
Gets the value of the msmsRunSummary property.
getMSOrderForScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetMSOrderForScanNum
getMSPeaks() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Gets the value of the msPeaks property.
getMsResolution() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Gets the value of the msResolution property.
getMSXMultiplexValueFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetMSXMultiplexValueFromScanNum
getMz(int) - Method in interface umich.ms.datatypes.spectrum.IIndexedSpectrum
Deprecated.
 
getMz() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
getMz() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.FragmentMasses
Gets the value of the mz property.
getMz() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.FragmentMasses
Gets the value of the mz property.
getMz() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.FragmentMasses
Gets the value of the mz property.
getMz() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FragmentMasses
Gets the value of the mz property.
getMz() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Intensity
Gets the value of the mz property.
getMz() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FragmentMasses
Gets the value of the mz property.
getMz() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Intensity
Gets the value of the mz property.
getMzIntPair(int) - Method in interface umich.ms.datatypes.spectrum.IIndexedSpectrum
Deprecated.
Get one datapoint from the array
getMzRange() - Method in class umich.ms.datatypes.LCMSRange
 
getMzRange() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
TODO: might be better to treat null values as infinity and always return non-null DoubleRange.
getMzRangeEnd() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
The end of isolation window mz range
getMzRanges() - Method in class umich.ms.datatypes.LCMSDataSubset
 
getMzRangeStart() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
The beginning of isolation window mz range
getMZs() - Method in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
 
getMZs() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
Array of m/z values.
Might be of zero length, if the spectrumRef had no peaks in it.
getMzTarget() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
m/z of the precursor that was targeted.
getName() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Some identifier for the source, that can be used as its name.
getName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IdentifiableType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IdentifiableType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SampleType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InputFileType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InputFileType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixturemodelDistribution
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InputFileType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixturemodelDistribution
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
Gets the value of the name property.
getName() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
getName() - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
getNameValueAndComment() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Gets the value of the nameValueAndComment property.
getNameValueAndComment() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the nameValueAndComment property.
getNegBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
Gets the value of the negBandwidth property.
getNegBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
Gets the value of the negBandwidth property.
getNegBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
Gets the value of the negBandwidth property.
getNegBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
Gets the value of the negBandwidth property.
getNegBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
Gets the value of the negBandwidth property.
getNegBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
Gets the value of the negBandwidth property.
getNegDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
Gets the value of the negDens property.
getNegDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel.Point
Gets the value of the negDens property.
getNegDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
Gets the value of the negDens property.
getNegDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Point
Gets the value of the negDens property.
getNegDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
Gets the value of the negDens property.
getNegDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Point
Gets the value of the negDens property.
getNegFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Gets the value of the negFreq property.
getNegFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Gets the value of the negFreq property.
getNegFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Gets the value of the negFreq property.
getNegFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Gets the value of the negFreq property.
getNegFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Gets the value of the negFreq property.
getNegFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Gets the value of the negFreq property.
getNegmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution
Gets the value of the negmodelDistribution property.
getNegmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixturemodelDistribution
Gets the value of the negmodelDistribution property.
getNegmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixturemodelDistribution
Gets the value of the negmodelDistribution property.
getNegObsDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
Gets the value of the negObsDens property.
getNegObsDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
Gets the value of the negObsDens property.
getNegObsDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
Gets the value of the negObsDens property.
getNeighboringBinSmoothing() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmInformation
Gets the value of the neighboringBinSmoothing property.
getNeighboringBinSmoothing() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspInformation
Gets the value of the neighboringBinSmoothing property.
getNeighboringBinSmoothing() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmInformation
Gets the value of the neighboringBinSmoothing property.
getNeighboringBinSmoothing() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspInformation
Gets the value of the neighboringBinSmoothing property.
getNEnzymaticTermini() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the nEnzymaticTermini property.
getNEnzymaticTermini() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the nEnzymaticTermini property.
getNextLine() - Method in class umich.ms.external.BufferedRandomAccessFile
Returns the next line from the file.
getNextMassListFromScanNum(Holder<Integer>, String, int, int, int, int, Holder<Double>, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetNextMassListFromScanNum
getNextMassListRangeFromScanNum(Holder<Integer>, String, int, int, int, int, Holder<Double>, Object, Object, String, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile3
method GetNextMassListRangeFromScanNum
getNextScan(int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
getNextScan(int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Gets the next scan in the collection (by number).
getNextScanAtMsLevel(int, int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Finds the next scan at the same MS level, as the scan with scanNum.
getNextScanAtMsLevel(int, int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Finds the next scan at the same MS level, as the scan with scanNum.
getNextScanAtSameMsLevel(IScan) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Convenience method, calls ScanCollectionDefault.getNextScanAtMsLevel(int, int) internally
getNextScanAtSameMsLevel(IScan) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Convenience method, calls IScanCollection.getNextScanAtMsLevel(int, int) internally
getNextscore() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the nextscore property.
getNiAdjustedProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the niAdjustedProbability property.
getNiAdjustedProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the niAdjustedProbability property.
getNiDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiInformation
Gets the value of the niDistribution property.
getNiDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiInformation
Gets the value of the niDistribution property.
getNiInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the niInformation property.
getNiInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the niInformation property.
getNiLowerBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Gets the value of the niLowerBoundExcl property.
getNiLowerBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Gets the value of the niLowerBoundExcl property.
getNiLowerBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Gets the value of the niLowerBoundIncl property.
getNiLowerBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Gets the value of the niLowerBoundIncl property.
getNIndistinguishableProteins() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the nIndistinguishableProteins property.
getNIndistinguishableProteins() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the nIndistinguishableProteins property.
getNInstances() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the nInstances property.
getNInstances() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the nInstances property.
getNiUpperBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Gets the value of the niUpperBoundExcl property.
getNiUpperBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Gets the value of the niUpperBoundExcl property.
getNiUpperBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Gets the value of the niUpperBoundIncl property.
getNiUpperBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Gets the value of the niUpperBoundIncl property.
getNoCut() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
Gets the value of the noCut property.
getNoCut() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
Gets the value of the noCut property.
getNoCut() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
Gets the value of the noCut property.
getNoiseData(Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile2
method GetNoiseData
getNormalization() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Gets the value of the normalization property.
getNormalization() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Gets the value of the normalization property.
getNormalization() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Gets the value of the normalization property.
getNormalization() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Gets the value of the normalization property.
getNormalization() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Gets the value of the normalization property.
getNormalized() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
Gets the value of the normalized property.
getNormalized() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
Gets the value of the normalized property.
getNormalized() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
Gets the value of the normalized property.
getNote() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the note property.
getNote() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Gets the value of the note property.
getNSiblingPeptides() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the nSiblingPeptides property.
getNSiblingPeptides() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the nSiblingPeptides property.
getNSiblingPeptidesBin() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the nSiblingPeptidesBin property.
getNSiblingPeptidesBin() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the nSiblingPeptidesBin property.
getNspAdjustedProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the nspAdjustedProbability property.
getNspAdjustedProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the nspAdjustedProbability property.
getNspDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspInformation
Gets the value of the nspDistribution property.
getNspDistribution() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspInformation
Gets the value of the nspDistribution property.
getNspDistributionIters() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the nspDistributionIters property.
getNspDistributionIters() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the nspDistributionIters property.
getNspFlag() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the nspFlag property.
getNspFlag() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the nspFlag property.
getNspInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the nspInformation property.
getNspInformation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the nspInformation property.
getNspLowerBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Gets the value of the nspLowerBoundExcl property.
getNspLowerBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Gets the value of the nspLowerBoundExcl property.
getNspLowerBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Gets the value of the nspLowerBoundIncl property.
getNspLowerBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Gets the value of the nspLowerBoundIncl property.
getNspUpperBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Gets the value of the nspUpperBoundExcl property.
getNspUpperBoundExcl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Gets the value of the nspUpperBoundExcl property.
getNspUpperBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Gets the value of the nspUpperBoundIncl property.
getNspUpperBoundIncl() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Gets the value of the nspUpperBoundIncl property.
getNTermGain() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Gets the value of the nTermGain property.
getNTermGain() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Gets the value of the nTermGain property.
getNum() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getNum() - Method in interface umich.ms.datatypes.scan.IScan
Returns the internal scan number, which sometimes coincides with original scan numbers from raw mass-spec files.
getNum() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Device
Gets the value of the num property.
getNum() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the num property.
getNum() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.ScanOrigin
Gets the value of the num property.
getNum2scan() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Deprecated.
This is just a side effect of encapsulating the old Maps into the new ScanIndex. Use ScanCollectionDefault.getMapNum2scan() instead.
getNum2scan() - Method in class umich.ms.datatypes.scancollection.ScanIndex
 
getNumber() - Method in class umich.ms.datatypes.index.impl.IndexElementDefault
 
getNumber() - Method in interface umich.ms.datatypes.index.IndexElement
Internal scan number, starting from 1, incrementing by one for each consecutive scan.
This is the number you get from IScan.getNum()
getNumber() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
Gets the value of the number property.
getNumber() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
Gets the value of the number property.
getNumber() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
Gets the value of the number property.
getNumber() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
Gets the value of the number property.
getNumber() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraResult
Gets the value of the number property.
getNumber() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
Gets the value of the number property.
getNumber() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraResult
Gets the value of the number property.
getNumberOfControllers(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetNumberOfControllers
getNumberOfControllersOfType(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetNumberOfControllersOfType
getNumberOfMassCalibratorsFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetNumberOfMassCalibratorsFromScanNum
getNumberOfMassRangesFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetNumberOfMassRangesFromScanNum
getNumberOfMSOrdersFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetNumberOfMSOrdersFromScanNum
getNumberOfSourceFragmentationMassRangesFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetNumberOfSourceFragmentationMassRangesFromScanNum
getNumberOfSourceFragmentsFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetNumberOfSourceFragmentsFromScanNum
getNumCorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
Gets the value of the numCorr property.
getNumCorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
Gets the value of the numCorr property.
getNumCorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
Gets the value of the numCorr property.
getNumCorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
Gets the value of the numCorr property.
getNumCorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
Gets the value of the numCorr property.
getNumCorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
Gets the value of the numCorr property.
getNumDatabaseSequences() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Gets the value of the numDatabaseSequences property.
getNumDatabaseSequences() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Gets the value of the numDatabaseSequences property.
getNumErrorLog(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetNumErrorLog
getNumIncorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
Gets the value of the numIncorr property.
getNumIncorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
Gets the value of the numIncorr property.
getNumIncorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
Gets the value of the numIncorr property.
getNumIncorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
Gets the value of the numIncorr property.
getNumIncorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
Gets the value of the numIncorr property.
getNumIncorr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
Gets the value of the numIncorr property.
getNumInput1Spectra() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the numInput1Spectra property.
getNumInput1Spectra() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the numInput1Spectra property.
getNumInput2Spectra() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the numInput2Spectra property.
getNumInput2Spectra() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the numInput2Spectra property.
getNumInput3Spectra() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the numInput3Spectra property.
getNumInput3Spectra() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the numInput3Spectra property.
getNumInput4Spectra() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the numInput4Spectra property.
getNumInput4Spectra() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the numInput4Spectra property.
getNumInput5Spectra() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the numInput5Spectra property.
getNumInput5Spectra() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the numInput5Spectra property.
getNumInstMethods(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetNumInstMethods
getNumIterations() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Gets the value of the numIterations property.
getNumIterations() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Gets the value of the numIterations property.
getNumIterations() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Gets the value of the numIterations property.
getNumMatchedIons() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the numMatchedIons property.
getNumMatchedIons() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the numMatchedIons property.
getNumMatchedIons() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the numMatchedIons property.
getNumMatchedPeptides() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the numMatchedPeptides property.
getNumMatchedPeptides() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the numMatchedPeptides property.
getNumMatchedPeptides() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the numMatchedPeptides property.
getNumMissedCleavages() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the numMissedCleavages property.
getNumMissedCleavages() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the numMissedCleavages property.
getNumMissedCleavages() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the numMissedCleavages property.
getNumPredictedCorrectProts() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the numPredictedCorrectProts property.
getNumPredictedCorrectProts() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the numPredictedCorrectProts property.
getNumResidues() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Gets the value of the numResidues property.
getNumResidues() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Gets the value of the numResidues property.
getNumScansToProcess() - Method in class umich.ms.fileio.filetypes.util.MultiSpectraParser
 
getNumSequencesSearched() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
Gets the value of the numSequencesSearched property.
getNumSequencesSearched() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
Gets the value of the numSequencesSearched property.
getNumSpectra(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetNumSpectra
getNumStatusLog(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetNumStatusLog
getNumThreadsForParsing() - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
How many batches of scans will be processed in parallel.
getNumThreadsForParsing() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
How many batches of scans will be processed in parallel.
getNumTolTerm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Gets the value of the numTolTerm property.
getNumTolTerm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the numTolTerm property.
getNumTolTerm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Gets the value of the numTolTerm property.
getNumTolTerm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the numTolTerm property.
getNumTolTerm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Gets the value of the numTolTerm property.
getNumTolTerm() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the numTolTerm property.
getNumTotProteins() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the numTotProteins property.
getNumTotProteins() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the numTotProteins property.
getNumTotProteins() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the numTotProteins property.
getNumTrailerExtra(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetNumTrailerExtra
getNumTuneData(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetNumTuneData
getNumvalues() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
Gets the value of the numvalues property.
getObs1Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the obs1Distr property.
getObs1Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the obs1Distr property.
getObs1Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the obs1Distr property.
getObs2Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the obs2Distr property.
getObs2Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the obs2Distr property.
getObs2Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the obs2Distr property.
getObs3Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the obs3Distr property.
getObs3Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the obs3Distr property.
getObs3Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the obs3Distr property.
getObs4Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the obs4Distr property.
getObs4Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the obs4Distr property.
getObs4Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the obs4Distr property.
getObs5Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the obs5Distr property.
getObs5Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the obs5Distr property.
getObs5Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the obs5Distr property.
getObs6Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the obs6Distr property.
getObs6Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the obs6Distr property.
getObs6Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the obs6Distr property.
getObs7Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Gets the value of the obs7Distr property.
getObs7Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Gets the value of the obs7Distr property.
getObs7Distr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Gets the value of the obs7Distr property.
getObsDistr() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Point
Gets the value of the obsDistr property.
getObsDistr() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Point
Gets the value of the obsDistr property.
getOccamFlag() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the occamFlag property.
getOccamFlag() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the occamFlag property.
getOffset() - Method in class umich.ms.fileio.chunk.FileChunk
 
getOffset() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.FragmentMasses
Gets the value of the offset property.
getOffset() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.FragmentMasses
Gets the value of the offset property.
getOffset() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.FragmentMasses
Gets the value of the offset property.
getOffsetLength() - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedIndexElement
 
getOffsetLength() - Method in interface umich.ms.fileio.filetypes.xmlbased.XMLBasedIndexElement
 
getOperator() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Gets the value of the operator property.
getOperator(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetOperator
getOptions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
Gets the value of the options property.
getOptions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Gets the value of the options property.
getOptions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Gets the value of the options property.
getOptions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Gets the value of the options property.
getOptions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Gets the value of the options property.
getOptions() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Gets the value of the options property.
getOrder() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentType
Gets the value of the order property.
getOrder() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ProcessingMethodType
Gets the value of the order property.
getOrganism() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the organism property.
getOrganism() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the organism property.
getOrganizationRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AffiliationType
Gets the value of the organizationRef property.
getOrganizationRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParentOrganizationType
Gets the value of the organizationRef property.
getOrganizationRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AffiliationType
Gets the value of the organizationRef property.
getOrganizationRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParentOrganizationType
Gets the value of the organizationRef property.
getOrientation() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern
Gets the value of the orientation property.
getOrigDatabaseUrl() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Gets the value of the origDatabaseUrl property.
getOrigDatabaseUrl() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Gets the value of the origDatabaseUrl property.
getOrigDatabaseUrl() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Gets the value of the origDatabaseUrl property.
getOriginalFiles() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
getOriginalResidue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
Gets the value of the originalResidue property.
getOriginalResidue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
Gets the value of the originalResidue property.
getOutData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the outData property.
getOutData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the outData property.
getOutData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the outData property.
getOutDataType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the outDataType property.
getOutDataType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the outDataType property.
getOutDataType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the outDataType property.
getOutputType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Gets the value of the outputType property.
getOutputType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Gets the value of the outputType property.
getOutputType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Gets the value of the outputType property.
getOutputType() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Gets the value of the outputType property.
getOutputType() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Gets the value of the outputType property.
getP() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
Gets the value of the p property.
getP() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSPeaks
Gets the value of the p property.
getPages() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Gets the value of the pages property.
getPages() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Gets the value of the pages property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult.SearchScoreSummaryIProphet
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult.SearchScoreSummary
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.NegmodelDistribution
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.PosmodelDistribution
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NegmodelDistribution
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PosmodelDistribution
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchScoreSummary
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchScoreSummaryIProphet
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NegmodelDistribution
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PosmodelDistribution
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchScoreSummary
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchScoreSummaryIProphet
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishableProtein
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishableProtein
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the parameter property.
getParameter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the parameter property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractContactType
Attributes of this contact such as address, email, telephone etc.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AmbiguousResidueType
Parameters for capturing e.g.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
Additional descriptors for the sequence, such as taxon, description line etc.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MassTableType
Additional parameters or descriptors for the MassTable.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParamListType
Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Additional parameters or descriptors for the PeptideEvidence.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideType
Additional descriptors of this peptide sequence Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinAmbiguityGroupType
Scores or parameters associated with the ProteinAmbiguityGroup.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
Scores or parameters associated with this ProteinDetectionHypothesis e.g.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionListType
Scores or output parameters associated with the whole ProteinDetectionList Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SampleType
The characteristics of a Material.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SourceFileType
Any additional parameters description the source file.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Scores or attributes associated with the SpectrumIdentificationItem e.g.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
Scores or output parameters associated with the SpectrumIdentificationList.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
Scores or parameters associated with the SpectrumIdentificationResult (i.e the set of SpectrumIdentificationItems derived from one spectrum) e.g.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractContactType
Attributes of this contact such as address, email, telephone etc.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AmbiguousResidueType
Parameters for capturing e.g.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
Additional descriptors for the sequence, such as taxon, description line etc.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MassTableType
Additional parameters or descriptors for the MassTable.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParamListType
Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Additional parameters or descriptors for the PeptideEvidence.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideType
Additional descriptors of this peptide sequence Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinAmbiguityGroupType
Scores or parameters associated with the ProteinAmbiguityGroup.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
Scores or parameters associated with this ProteinDetectionHypothesis e.g.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionListType
Scores or output parameters associated with the whole ProteinDetectionList Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SampleType
The characteristics of a Material.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SourceFileType
Any additional parameters description the source file.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Scores or attributes associated with the SpectrumIdentificationItem e.g.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
Scores or output parameters associated with the SpectrumIdentificationList.Gets the value of the paramGroup property.
getParamGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
Scores or parameters associated with the SpectrumIdentificationResult (i.e the set of SpectrumIdentificationItems derived from one spectrum) e.g.
getParent() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.OrganizationType
Gets the value of the parent property.
getParent() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.OrganizationType
Gets the value of the parent property.
getParentFile() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Gets the value of the parentFile property.
getParentFile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
Gets the value of the parentFile property.
getParentFile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
Gets the value of the parentFile property.
getParentFile() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
Gets the value of the parentFile property.
getParentFile() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
Gets the value of the parentFile property.
getParentFile() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
Gets the value of the parentFile property.
getParentFileID() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.ScanOrigin
Gets the value of the parentFileID property.
getParentScanNum() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
Every scan can have a parent, if msLevel is > 1 type is Integer and not int, so we could use null for MS1 scans
getParentScanRefRaw() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
getParentTolerance() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the parentTolerance property.
getParentTolerance() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the parentTolerance property.
getParsingTimeout() - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
Timeout (in seconds) that worker threads are allowed for parsing one batch of spectra.
getParsingTimeout() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Timeout (in seconds) that worker threads are allowed for parsing one batch of spectra.
getPath() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
 
getPath() - Method in class umich.ms.fileio.filetypes.util.AbstractFile
Absolute normalized path to the file.
getPath() - Method in class umich.ms.fileio.util.FileListing
 
getPattern() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Gets the value of the pattern property.
getPattern() - Method in class umich.ms.fileio.util.FileListing
 
getPctSpectrumIds() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the pctSpectrumIds property.
getPctSpectrumIds() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the pctSpectrumIds property.
getPeaks() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
getPeaks() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the peaks property.
getPeaksCount() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the peaksCount property.
getPeptide() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Gets the value of the peptide property.
getPeptide() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SequenceCollectionType
Gets the value of the peptide property.
getPeptide() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SequenceCollectionType
Gets the value of the peptide property.
getPeptide() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the peptide property.
getPeptide() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the peptide property.
getPeptide() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the peptide property.
getPeptide() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the peptide property.
getPeptide() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the peptide property.
getPeptideBinaryInd() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Gets the value of the peptideBinaryInd property.
getPeptideBinaryInd() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Gets the value of the peptideBinaryInd property.
getPeptideEvidence() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SequenceCollectionType
Gets the value of the peptideEvidence property.
getPeptideEvidence() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SequenceCollectionType
Gets the value of the peptideEvidence property.
getPeptideEvidenceRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceRefType
Gets the value of the peptideEvidenceRef property.
getPeptideEvidenceRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideHypothesisType
Gets the value of the peptideEvidenceRef property.
getPeptideEvidenceRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the peptideEvidenceRef property.
getPeptideEvidenceRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceRefType
Gets the value of the peptideEvidenceRef property.
getPeptideEvidenceRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideHypothesisType
Gets the value of the peptideEvidenceRef property.
getPeptideEvidenceRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the peptideEvidenceRef property.
getPeptideGroupDesignator() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the peptideGroupDesignator property.
getPeptideGroupDesignator() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the peptideGroupDesignator property.
getPeptideHypothesis() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
Gets the value of the peptideHypothesis property.
getPeptideHypothesis() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
Gets the value of the peptideHypothesis property.
getPeptideIndex() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPDta
Gets the value of the peptideIndex property.
getPeptideIndex() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPDta
Gets the value of the peptideIndex property.
getPeptideInds() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Gets the value of the peptideInds property.
getPeptideInds() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Gets the value of the peptideInds property.
getPeptideNextAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Gets the value of the peptideNextAa property.
getPeptideNextAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the peptideNextAa property.
getPeptideNextAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Gets the value of the peptideNextAa property.
getPeptideNextAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the peptideNextAa property.
getPeptideNextAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Gets the value of the peptideNextAa property.
getPeptideNextAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the peptideNextAa property.
getPeptideParentProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the peptideParentProtein property.
getPeptideParentProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the peptideParentProtein property.
getPeptidePrevAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Gets the value of the peptidePrevAa property.
getPeptidePrevAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the peptidePrevAa property.
getPeptidePrevAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Gets the value of the peptidePrevAa property.
getPeptidePrevAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the peptidePrevAa property.
getPeptidePrevAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Gets the value of the peptidePrevAa property.
getPeptidePrevAa() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the peptidePrevAa property.
getPeptideRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Gets the value of the peptideRef property.
getPeptideRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the peptideRef property.
getPeptideRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Gets the value of the peptideRef property.
getPeptideRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the peptideRef property.
getPeptideSequence() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideType
Gets the value of the peptideSequence property.
getPeptideSequence() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideType
Gets the value of the peptideSequence property.
getPeptideSequence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
Gets the value of the peptideSequence property.
getPeptideSequence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
Gets the value of the peptideSequence property.
getPeptideSequence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the peptideSequence property.
getPeptideSequence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
Gets the value of the peptideSequence property.
getPeptideSequence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
Gets the value of the peptideSequence property.
getPeptideSequence() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the peptideSequence property.
getPeptideTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Gets the value of the peptideTerminus property.
getPeptideTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Gets the value of the peptideTerminus property.
getPeptideTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Gets the value of the peptideTerminus property.
getPercentCoverage() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the percentCoverage property.
getPercentCoverage() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the percentCoverage property.
getPersonOrOrganization() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AuditCollectionType
Gets the value of the personOrOrganization property.
getPersonOrOrganization() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AuditCollectionType
Gets the value of the personOrOrganization property.
getPhone() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Gets the value of the phone property.
getPlate() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting
Gets the value of the plate property.
getPlateID() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Gets the value of the plateID property.
getPlateID() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Gets the value of the plateID property.
getPlateManufacturer() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Gets the value of the plateManufacturer property.
getPlateModel() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Gets the value of the plateModel property.
getPm() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
Gets the value of the pm property.
getPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
Gets the value of the point property.
getPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
Gets the value of the point property.
getPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
Gets the value of the point property.
getPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
Gets the value of the point property.
getPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
Gets the value of the point property.
getPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
Gets the value of the point property.
getPoint() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisModel
Gets the value of the point property.
getPoint() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisModel
Gets the value of the point property.
getPolarity() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getPolarity() - Method in interface umich.ms.datatypes.scan.IScan
 
getPolarity() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the polarity property.
getPool() - Method in class umich.ms.fileio.chunk.ChunkedFile
 
getPool() - Method in class umich.ms.fileio.chunk.FileChunk
 
getPool() - Static method in class umich.ms.fileio.filetypes.util.ZlibInflater
The ByteArrayHolder pool, that this decoder is using.
getPool() - Method in class umich.ms.util.PooledByteArrayHolders
 
getPosBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
Gets the value of the posBandwidth property.
getPosBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
Gets the value of the posBandwidth property.
getPosBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
Gets the value of the posBandwidth property.
getPosBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
Gets the value of the posBandwidth property.
getPosBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
Gets the value of the posBandwidth property.
getPosBandwidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
Gets the value of the posBandwidth property.
getPosDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
Gets the value of the posDens property.
getPosDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel.Point
Gets the value of the posDens property.
getPosDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
Gets the value of the posDens property.
getPosDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Point
Gets the value of the posDens property.
getPosDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
Gets the value of the posDens property.
getPosDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Point
Gets the value of the posDens property.
getPosFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Gets the value of the posFreq property.
getPosFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Gets the value of the posFreq property.
getPosFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Gets the value of the posFreq property.
getPosFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Gets the value of the posFreq property.
getPosFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Gets the value of the posFreq property.
getPosFreq() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Gets the value of the posFreq property.
getPosition() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
Gets the value of the position property.
getPosition() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModAminoacidMass
Gets the value of the position property.
getPosition() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModAminoacidMass
Gets the value of the position property.
getPosition() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModAminoacidMass
Gets the value of the position property.
getPosition() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModAminoacidMass
Gets the value of the position property.
getPosition() - Method in class umich.ms.util.ByteArrayHolder
This is the position of the next write to the underlying buffer.
getPosmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution
Gets the value of the posmodelDistribution property.
getPosmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixturemodelDistribution
Gets the value of the posmodelDistribution property.
getPosmodelDistribution() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixturemodelDistribution
Gets the value of the posmodelDistribution property.
getPosObsDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
Gets the value of the posObsDens property.
getPosObsDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
Gets the value of the posObsDens property.
getPosObsDens() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
Gets the value of the posObsDens property.
getPossibleCharges() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Gets the value of the possibleCharges property.
getPost() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the post property.
getPost() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Gets the value of the post property.
getPost() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Gets the value of the post property.
getPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Gets the value of the posToNegRatio property.
getPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Gets the value of the posToNegRatio property.
getPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Gets the value of the posToNegRatio property.
getPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Gets the value of the posToNegRatio property.
getPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Gets the value of the posToNegRatio property.
getPosToNegRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Gets the value of the posToNegRatio property.
getPpmtol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Gets the value of the ppmtol property.
getPpmtol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Gets the value of the ppmtol property.
getPpmtol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Gets the value of the ppmtol property.
getPre() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the pre property.
getPre() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Gets the value of the pre property.
getPre() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Gets the value of the pre property.
getPrecision() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Gets the value of the precision property.
getPrecursor() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getPrecursor() - Method in interface umich.ms.datatypes.scan.IScan
 
getPrecursor() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Gets the value of the precursor property.
getPrecursor() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorListType
Gets the value of the precursor property.
getPrecursorCharge() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Gets the value of the precursorCharge property.
getPrecursorInfoFromScanNum(int, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile3
method GetPrecursorInfoFromScanNum
getPrecursorIntensity() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Gets the value of the precursorIntensity property.
getPrecursorIntensity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the precursorIntensity property.
getPrecursorIntensity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the precursorIntensity property.
getPrecursorIntensity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the precursorIntensity property.
getPrecursorIonCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Gets the value of the precursorIonCharge property.
getPrecursorIonCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Gets the value of the precursorIonCharge property.
getPrecursorIonCharge() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Gets the value of the precursorIonCharge property.
getPrecursorList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Gets the value of the precursorList property.
getPrecursorMassForScanNum(int, int, Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetPrecursorMassForScanNum
getPrecursorMassType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the precursorMassType property.
getPrecursorMassType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the precursorMassType property.
getPrecursorMassType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the precursorMassType property.
getPrecursorMz() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the precursorMz property.
getPrecursorNeutralMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the precursorNeutralMass property.
getPrecursorNeutralMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the precursorNeutralMass property.
getPrecursorNeutralMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the precursorNeutralMass property.
getPrecursorRangeForScanNum(int, int, Holder<Double>, Holder<Double>, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetPrecursorRangeForScanNum
getPrecursorScanNum() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Gets the value of the precursorScanNum property.
getPredictedNumCorrect() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
Gets the value of the predictedNumCorrect property.
getPredictedNumCorrect() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
Gets the value of the predictedNumCorrect property.
getPredictedNumIncorrect() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
Gets the value of the predictedNumIncorrect property.
getPredictedNumIncorrect() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
Gets the value of the predictedNumIncorrect property.
getPrevMassListFromScanNum(Holder<Integer>, String, int, int, int, int, Holder<Double>, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetPrevMassListFromScanNum
getPrevMassListRangeFromScanNum(Holder<Integer>, String, int, int, int, int, Holder<Double>, Object, Object, String, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile3
method GetPrevMassListRangeFromScanNum
getPrevScan(int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
getPrevScan(int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Gets the previous scan in the collection (by number).
getPrevScanAtMsLevel(int, int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Finds the next scan at the same MS level, as the scan with scanNum.
getPrevScanAtMsLevel(int, int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Finds the next scan at the same MS level, as the scan with scanNum.
getPrevScanAtSameMsLevel(IScan) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Convenience method, calls ScanCollectionDefault.getPrevScanAtMsLevel(int, int) internally
getPrevScanAtSameMsLevel(IScan) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Convenience method, calls IScanCollection.getPrevScanAtMsLevel(int, int) internally
getPriorProbability() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Gets the value of the priorProbability property.
getPriorProbability() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Gets the value of the priorProbability property.
getPriorProbability() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Gets the value of the priorProbability property.
getProbability() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult
Gets the value of the probability property.
getProbability() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
Gets the value of the probability property.
getProbability() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetResult
Gets the value of the probability property.
getProbability() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
Gets the value of the probability property.
getProbability() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetResult
Gets the value of the probability property.
getProbability() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
Gets the value of the probability property.
getProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the probability property.
getProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
Gets the value of the probability property.
getProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the probability property.
getProbability() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
Gets the value of the probability property.
getProcessingMethod() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingType
Gets the value of the processingMethod property.
getProcessingOperationAndComment() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Gets the value of the processingOperationAndComment property.
getProduct() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Gets the value of the product property.
getProduct() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ProductListType
Gets the value of the product property.
getProductList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Gets the value of the productList property.
getProgramDetails() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the programDetails property.
getProgramDetails() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the programDetails property.
getProtein() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the protein property.
getProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Gets the value of the protein property.
getProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the protein property.
getProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Gets the value of the protein property.
getProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the protein property.
getProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Gets the value of the protein property.
getProtein() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the protein property.
getProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
Gets the value of the protein property.
getProtein() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
Gets the value of the protein property.
getProteinAmbiguityGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionListType
Gets the value of the proteinAmbiguityGroup property.
getProteinAmbiguityGroup() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionListType
Gets the value of the proteinAmbiguityGroup property.
getProteinAnnotation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the proteinAnnotation property.
getProteinAnnotation() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the proteinAnnotation property.
getProteinDescr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Gets the value of the proteinDescr property.
getProteinDescr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the proteinDescr property.
getProteinDescr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Gets the value of the proteinDescr property.
getProteinDescr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the proteinDescr property.
getProteinDescr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Gets the value of the proteinDescr property.
getProteinDescr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the proteinDescr property.
getProteinDescription() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Gets the value of the proteinDescription property.
getProteinDescription() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Gets the value of the proteinDescription property.
getProteinDetection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisCollectionType
Gets the value of the proteinDetection property.
getProteinDetection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisCollectionType
Gets the value of the proteinDetection property.
getProteinDetectionHypothesis() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinAmbiguityGroupType
Gets the value of the proteinDetectionHypothesis property.
getProteinDetectionHypothesis() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinAmbiguityGroupType
Gets the value of the proteinDetectionHypothesis property.
getProteinDetectionList() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisDataType
Gets the value of the proteinDetectionList property.
getProteinDetectionList() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisDataType
Gets the value of the proteinDetectionList property.
getProteinDetectionListRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionType
Gets the value of the proteinDetectionListRef property.
getProteinDetectionListRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionType
Gets the value of the proteinDetectionListRef property.
getProteinDetectionProtocol() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisProtocolCollectionType
Gets the value of the proteinDetectionProtocol property.
getProteinDetectionProtocol() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisProtocolCollectionType
Gets the value of the proteinDetectionProtocol property.
getProteinDetectionProtocolRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionType
Gets the value of the proteinDetectionProtocolRef property.
getProteinDetectionProtocolRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionType
Gets the value of the proteinDetectionProtocolRef property.
getProteinGroup() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
Gets the value of the proteinGroup property.
getProteinGroup() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
Gets the value of the proteinGroup property.
getProteinMw() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Gets the value of the proteinMw property.
getProteinMw() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the proteinMw property.
getProteinMw() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Gets the value of the proteinMw property.
getProteinMw() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the proteinMw property.
getProteinMw() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Gets the value of the proteinMw property.
getProteinMw() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the proteinMw property.
getProteinName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishableProtein
Gets the value of the proteinName property.
getProteinName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.PeptideParentProtein
Gets the value of the proteinName property.
getProteinName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the proteinName property.
getProteinName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishableProtein
Gets the value of the proteinName property.
getProteinName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.PeptideParentProtein
Gets the value of the proteinName property.
getProteinName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the proteinName property.
getProteinSummaryDataFilter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the proteinSummaryDataFilter property.
getProteinSummaryDataFilter() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the proteinSummaryDataFilter property.
getProteinSummaryHeader() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
Gets the value of the proteinSummaryHeader property.
getProteinSummaryHeader() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
Gets the value of the proteinSummaryHeader property.
getProteinTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Gets the value of the proteinTerminus property.
getProteinTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Gets the value of the proteinTerminus property.
getProteinTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Gets the value of the proteinTerminus property.
getProteinTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Gets the value of the proteinTerminus property.
getProteinTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Gets the value of the proteinTerminus property.
getProvider() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the provider property.
getProvider() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the provider property.
getPseudoName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
Gets the value of the pseudoName property.
getPseudoName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
Gets the value of the pseudoName property.
getPublication() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Gets the value of the publication property.
getPublication() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Gets the value of the publication property.
getPublisher() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Gets the value of the publisher property.
getPublisher() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Gets the value of the publisher property.
getPvalue() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Gets the value of the pvalue property.
getPvalue() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Gets the value of the pvalue property.
getQuantLabelMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioTimestamp
Gets the value of the quantLabelMasses property.
getQuantLabelMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioTimestamp
Gets the value of the quantLabelMasses property.
getQuantLabelMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioTimestamp
Gets the value of the quantLabelMasses property.
getRandomAccessFile() - Method in class umich.ms.fileio.filetypes.util.AbstractFile
 
getRank() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the rank property.
getRank() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the rank property.
getRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Gets the value of the ratio property.
getRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Gets the value of the ratio property.
getRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Gets the value of the ratio property.
getRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Gets the value of the ratio property.
getRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Gets the value of the ratio property.
getRatio() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Gets the value of the ratio property.
getRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Intensity
Gets the value of the ratio property.
getRatio() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Intensity
Gets the value of the ratio property.
getRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Gets the value of the ratioMean property.
getRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Gets the value of the ratioMean property.
getRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Gets the value of the ratioMean property.
getRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Gets the value of the ratioMean property.
getRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Gets the value of the ratioMean property.
getRatioMean() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Gets the value of the ratioMean property.
getRatioNumberPeptides() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Gets the value of the ratioNumberPeptides property.
getRatioNumberPeptides() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Gets the value of the ratioNumberPeptides property.
getRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Gets the value of the ratioStandardDev property.
getRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Gets the value of the ratioStandardDev property.
getRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Gets the value of the ratioStandardDev property.
getRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Gets the value of the ratioStandardDev property.
getRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Gets the value of the ratioStandardDev property.
getRatioStandardDev() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Gets the value of the ratioStandardDev property.
getRawData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the rawData property.
getRawData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the rawData property.
getRawData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the rawData property.
getRawDataType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the rawDataType property.
getRawDataType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the rawDataType property.
getRawDataType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the rawDataType property.
getRawNumber() - Method in class umich.ms.datatypes.index.impl.IndexElementDefault
 
getRawNumber() - Method in interface umich.ms.datatypes.index.IndexElement
The scan number from the raw file.
getReaderPool() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
getReaderPool() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
getReaderPool() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
getRef(ISpectrum) - Method in enum umich.ms.datatypes.scan.StorageStrategy
 
getRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupRefType
Gets the value of the ref property.
getRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareRefType
Gets the value of the ref property.
getRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileRefType
Gets the value of the ref property.
getReferenceableParamGroup() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupListType
Gets the value of the referenceableParamGroup property.
getReferenceableParamGroupList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the referenceableParamGroupList property.
getReferenceableParamGroupRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ParamGroupType
Gets the value of the referenceableParamGroupRef property.
getReferenceDatabase() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the referenceDatabase property.
getReferenceDatabase() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the referenceDatabase property.
getReferenceIsotope() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Gets the value of the referenceIsotope property.
getReferenceIsotope() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
Gets the value of the referenceIsotope property.
getReferenceIsotope() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Gets the value of the referenceIsotope property.
getReferenceIsotope() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
Gets the value of the referenceIsotope property.
getRefseqName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Gets the value of the refseqName property.
getRefseqName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Gets the value of the refseqName property.
getReleaseDate() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Gets the value of the releaseDate property.
getReleaseDate() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Gets the value of the releaseDate property.
getReplacementResidue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
Gets the value of the replacementResidue property.
getReplacementResidue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
Gets the value of the replacementResidue property.
getResidue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MassTableType
Gets the value of the residue property.
getResidue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MassTableType
Gets the value of the residue property.
getResidues() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
Gets the value of the residues property.
getResidues() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
Gets the value of the residues property.
getResidues() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
Gets the value of the residues property.
getResidues() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
Gets the value of the residues property.
getResidueSubstitutionList() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the residueSubstitutionList property.
getResidueSubstitutionList() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the residueSubstitutionList property.
getRetentionTime() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the retentionTime property.
getRetentionTimeSec() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the retentionTimeSec property.
getRetentionTimeSec() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the retentionTimeSec property.
getRetentionTimeSec() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the retentionTimeSec property.
getRightValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Gets the value of the rightValley property.
getRightValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Gets the value of the rightValley property.
getRightValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Gets the value of the rightValley property.
getRightValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Gets the value of the rightValley property.
getRightValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Gets the value of the rightValley property.
getRightValley() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Gets the value of the rightValley property.
getRobot() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting
Gets the value of the robot property.
getRobotManufacturer() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
Gets the value of the robotManufacturer property.
getRobotModel() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
Gets the value of the robotModel property.
getRocDataPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
Gets the value of the rocDataPoint property.
getRocDataPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
Gets the value of the rocDataPoint property.
getRocDataPoint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
Gets the value of the rocDataPoint property.
getRocErrorData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
Gets the value of the rocErrorData property.
getRocErrorData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Gets the value of the rocErrorData property.
getRocErrorData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Gets the value of the rocErrorData property.
getRocErrorData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Gets the value of the rocErrorData property.
getRocErrorData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Gets the value of the rocErrorData property.
getRocErrorData() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Gets the value of the rocErrorData property.
getRole() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ContactRoleType
Gets the value of the role property.
getRole() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ContactRoleType
Gets the value of the role property.
getRt() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getRt() - Method in class umich.ms.datatypes.scan.impl.ScanDefault
 
getRt() - Method in interface umich.ms.datatypes.scan.IScan
 
getRt() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
getRt() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
getRt() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
Gets the value of the rt property.
getRt() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Gets the value of the rt property.
getRt() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the rt property.
getRt2scan() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Deprecated.
This is just a side effect of encapsulating the old Maps into the new ScanIndex. Use ScanCollectionDefault.getMapRt2scan() instead.
getRt2scan() - Method in class umich.ms.datatypes.scancollection.ScanIndex
 
getRtHi() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
getRtLo() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
getRtMax() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
RT of the last scan in this scan collection.
getRtMax() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
RT of the last scan in this scan collection.
getRtMin() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
RT of the first scan.
getRtMin() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
RT of the first scan.
getRTRange() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRanges
Gets the value of the rtRange property.
getRTRanges() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Gets the value of the rtRanges property.
getRun() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the run property.
getRunHeaderInputStream(OffsetLength) - Method in class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
getRunHeaderInputStream(OffsetLength) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser
Reads the whole msRun header portion from the file, appending a closing </msRun> tag to the end, so that it could be unmarshalled using JAXB without errors.
getRunHeaderInputStream(OffsetLength) - Method in class umich.ms.fileio.filetypes.mzxml.XmlBasedRunHeaderParser
Be sure to include all the correct tags in this stream.
getRunInfo() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
getRunInfo() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
 
getRunInfo() - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
 
getRunInfo() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Gets the run info, not attempting to parse it.
getRunOptions() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Gets the value of the runOptions property.
getRunOptions() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Gets the value of the runOptions property.
getRunStartTime() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
getRValueFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetRValueFromScanNum
getS() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Gets the value of the s property.
getSameScanRange() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Gets the value of the sameScanRange property.
getSameScanRange() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Gets the value of the sameScanRange property.
getSameScanRange() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Gets the value of the sameScanRange property.
getSample() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSampleCollectionType
Gets the value of the sample property.
getSample() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSampleCollectionType
Gets the value of the sample property.
getSample() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SampleListType
Gets the value of the sample property.
getSampleAmountUnits(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSampleAmountUnits
getSampleEnzyme() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the sampleEnzyme property.
getSampleEnzyme() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the sampleEnzyme property.
getSampleEnzyme() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the sampleEnzyme property.
getSampleEnzyme() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the sampleEnzyme property.
getSampleEnzyme() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the sampleEnzyme property.
getSampleList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the sampleList property.
getSampleRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the sampleRef property.
getSampleRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubSampleType
Gets the value of the sampleRef property.
getSampleRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the sampleRef property.
getSampleRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubSampleType
Gets the value of the sampleRef property.
getSampleRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Gets the value of the sampleRef property.
getSampleVolume(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSampleVolume
getSampleVolumeUnits(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSampleVolumeUnits
getSampleWeight(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSampleWeight
getSatLimit() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Gets the value of the satLimit property.
getScan() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanListType
Gets the value of the scan property.
getScan() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Gets the value of the scan property.
getScan() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the scan property.
getScanByNum(int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
The name says it all.
getScanByNum(int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
The name says it all.
getScanByNumClosest(int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Scan with the closest Number is returned.
getScanByNumClosest(int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Scan with the closest Number is returned.
getScanByNumLower(int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Scan with closest Number STRICTLY less than the provided one is returned.
getScanByNumLower(int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Scan with closest Number less or equal to the provided one is returned.
getScanByNumUpper(int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Scan with the closest Number greater or equal to the provided one is returned.
getScanByNumUpper(int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Scan with the closest Number greater or equal to the provided one is returned.
getScanCollection() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getScanCollection() - Method in interface umich.ms.datatypes.scan.IScan
 
getScanCount() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Get the total number of scans in this ScansCollection.
getScanCount() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Get the total number of scans in this ScansCollection.
getScanCount() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Gets the value of the scanCount property.
getScanCountAtMsLevel(int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
If the msLevel doesn't exist in this ScanCollectionDefault, returns null
getScanCountAtMsLevel(int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
If the msLevel doesn't exist in this ScanCollectionDefault, returns null
getScanEventForScanNum(int, Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile2
method GetScanEventForScanNum
getScanHeaderInfoForScanNum(int, Holder<Integer>, Holder<Double>, Holder<Double>, Holder<Double>, Holder<Double>, Holder<Double>, Holder<Double>, Holder<Integer>, Holder<Integer>, Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetScanHeaderInfoForScanNum
getScanList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Gets the value of the scanList property.
getScanMzWindowLower() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getScanMzWindowLower() - Method in interface umich.ms.datatypes.scan.IScan
 
getScanMzWindowUpper() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getScanMzWindowUpper() - Method in interface umich.ms.datatypes.scan.IScan
 
getScanNumHi() - Method in class umich.ms.datatypes.LCMSDataSubset
 
getScanNumLo() - Method in class umich.ms.datatypes.LCMSDataSubset
 
getScanOrigin() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the scanOrigin property.
getScanRange() - Method in class umich.ms.datatypes.LCMSRange
 
getScans() - Method in class umich.ms.datatypes.LCMSData
 
getScans() - Method in class umich.ms.datatypes.scan.impl.ScanDefault
 
getScansByNumSpan(int, int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
getScansByNumSpan(int, int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
 
getScansByNumSpanAtMsLevel(int, int, int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
A view(not a copy!) of the original scan map, containing only scans from numStart to numEnd (inclusive).
getScansByNumSpanAtMsLevel(int, int, int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
A view(not a copy!) of the original scan map, containing only scans from numStart to numEnd (inclusive).
getScansByRt(double) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Provided RT MUST be EXACT RT, existing in the map.
getScansByRt(double) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Provided RT MUST be EXACT RT, existing in the map.
getScansByRtClosest(double) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Scans with the closest RT are returned.
getScansByRtClosest(double) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Scans with the closest RT are returned.
getScansByRtLower(double) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Scan List with closest RT less or equal to the provided one are returned.
getScansByRtLower(double) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Scan List with closest RT less or equal to the provided one are returned.
getScansByRtSpan(double, double) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Returns a range of scans, whose RT is in the inclusive interval [rtStart; rtEnd].
getScansByRtSpan(double, double) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Returns a range of scans, whose RT is in the inclusive interval [rtStart; rtEnd].
getScansByRtSpanAtMsLevel(double, double, int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Same as ScanCollectionDefault.getScansByRtSpan(double, double), but only searches at one MS Level.
If it so happens, that the RTs are between just 2 consecutive scans, then null is returned.
You get a view of the original scan map, not a copy!
getScansByRtSpanAtMsLevel(double, double, int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Same as IScanCollection.getScansByRtSpan(double, double), but only searches at one MS Level
getScansByRtUpper(double) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Scan List with the closest RT greater or equal to the provided one are returned.
getScansByRtUpper(double) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Scan List with the closest RT greater or equal to the provided one are returned.
getScanSettings() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsListType
Gets the value of the scanSettings property.
getScanSettingsList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the scanSettingsList property.
getScanSettingsRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
Gets the value of the scanSettingsRef property.
getScanType() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getScanType() - Method in interface umich.ms.datatypes.scan.IScan
 
getScanType() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
Gets the value of the scanType property.
getScanType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the scanType property.
getScanTypeForScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetScanTypeForScanNum
getScanWindow() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanWindowListType
Gets the value of the scanWindow property.
getScanWindowList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
Gets the value of the scanWindowList property.
getSearchDatabase() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputsType
Gets the value of the searchDatabase property.
getSearchDatabase() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputsType
Gets the value of the searchDatabase property.
getSearchDatabase() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the searchDatabase property.
getSearchDatabase() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the searchDatabase property.
getSearchDatabase() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the searchDatabase property.
getSearchDatabaseRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
Gets the value of the searchDatabaseRef property.
getSearchDatabaseRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseRefType
Gets the value of the searchDatabaseRef property.
getSearchDatabaseRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
Gets the value of the searchDatabaseRef property.
getSearchDatabaseRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
Gets the value of the searchDatabaseRef property.
getSearchDatabaseRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseRefType
Gets the value of the searchDatabaseRef property.
getSearchDatabaseRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
Gets the value of the searchDatabaseRef property.
getSearchEngine() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the searchEngine property.
getSearchEngine() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the searchEngine property.
getSearchEngine() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the searchEngine property.
getSearchEngine() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the searchEngine property.
getSearchEngine() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the searchEngine property.
getSearchEngine() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the searchEngine property.
getSearchEngineVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the searchEngineVersion property.
getSearchEngineVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the searchEngineVersion property.
getSearchEngineVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the searchEngineVersion property.
getSearchHit() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
Gets the value of the searchHit property.
getSearchHit() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchResult
Gets the value of the searchHit property.
getSearchHit() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchResult
Gets the value of the searchHit property.
getSearchId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the searchId property.
getSearchId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
Gets the value of the searchId property.
getSearchId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchResult
Gets the value of the searchId property.
getSearchId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the searchId property.
getSearchId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchResult
Gets the value of the searchId property.
getSearchId() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the searchId property.
getSearchModification() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationParamsType
Gets the value of the searchModification property.
getSearchModification() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationParamsType
Gets the value of the searchModification property.
getSearchResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the searchResult property.
getSearchResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the searchResult property.
getSearchResult() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the searchResult property.
getSearchScore() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the searchScore property.
getSearchScore() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the searchScore property.
getSearchScore() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the searchScore property.
getSearchScoreSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult
Gets the value of the searchScoreSummary property.
getSearchScoreSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
Gets the value of the searchScoreSummary property.
getSearchScoreSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetResult
Gets the value of the searchScoreSummary property.
getSearchScoreSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
Gets the value of the searchScoreSummary property.
getSearchScoreSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetResult
Gets the value of the searchScoreSummary property.
getSearchScoreSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
Gets the value of the searchScoreSummary property.
getSearchSpecification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the searchSpecification property.
getSearchSpecification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the searchSpecification property.
getSearchSpecification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the searchSpecification property.
getSearchSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the searchSummary property.
getSearchSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the searchSummary property.
getSearchSummary() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the searchSummary property.
getSearchType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the searchType property.
getSearchType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the searchType property.
getSecondSpotID() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern.Orientation
Gets the value of the secondSpotID property.
getSegmentAndEventForScanNum(int, Holder<Integer>, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetSegmentAndEventForScanNum
getSegmentedMassListFromRT(Holder<Double>, String, int, int, int, int, Holder<Double>, Object, Object, Holder<Integer>, Object, Holder<Integer>, Object) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile2
method GetSegmentedMassListFromRT
getSegmentedMassListFromScanNum(Holder<Integer>, String, int, int, int, int, Holder<Double>, Object, Object, Holder<Integer>, Object, Holder<Integer>, Object) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile2
method GetSegmentedMassListFromScanNum
getSelectedIon() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SelectedIonListType
Gets the value of the selectedIon property.
getSelectedIonList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Gets the value of the selectedIonList property.
getSense() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
Gets the value of the sense property.
getSense() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
Gets the value of the sense property.
getSense() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
Gets the value of the sense property.
getSensitivity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
Gets the value of the sensitivity property.
getSensitivity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
Gets the value of the sensitivity property.
getSensitivity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
Gets the value of the sensitivity property.
getSensitivity() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
Gets the value of the sensitivity property.
getSensitivity() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
Gets the value of the sensitivity property.
getSeparation() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Gets the value of the separation property.
getSeparationTechnique() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Separation
Gets the value of the separationTechnique property.
getSeq() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the seq property.
getSeq() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
Gets the value of the seq property.
getSeq() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
Gets the value of the seq property.
getSeqRowBarcode(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile2
method GetSeqRowBarcode
getSeqRowBarcodeStatus(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile2
method GetSeqRowBarcodeStatus
getSeqRowCalibrationFile(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowCalibrationFile
getSeqRowComment(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowComment
getSeqRowDataPath(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowDataPath
getSeqRowDilutionFactor(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowDilutionFactor
getSeqRowInjectionVolume(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowInjectionVolume
getSeqRowInstrumentMethod(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowInstrumentMethod
getSeqRowISTDAmount(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowISTDAmount
getSeqRowLevelName(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowLevelName
getSeqRowNumber(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowNumber
getSeqRowProcessingMethod(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowProcessingMethod
getSeqRowRawFileName(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowRawFileName
getSeqRowSampleID(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowSampleID
getSeqRowSampleName(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowSampleName
getSeqRowSampleType(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowSampleType
getSeqRowSampleVolume(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowSampleVolume
getSeqRowSampleWeight(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowSampleWeight
getSeqRowUserLabel(int, Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowUserLabel
getSeqRowUserText(int, Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowUserText
getSeqRowUserTextEx(int, Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile2
method GetSeqRowUserTextEx
getSeqRowVial(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetSeqRowVial
getSequence() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint
Gets the value of the sequence property.
getSequence() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SequenceSearchConstraint
Gets the value of the sequence property.
getSequence() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SequenceSearchConstraint
Gets the value of the sequence property.
getSequenceCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the sequenceCollection property.
getSequenceCollection() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the sequenceCollection property.
getSequenceSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the sequenceSearchConstraint property.
getSequenceSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the sequenceSearchConstraint property.
getSequenceSearchConstraint() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the sequenceSearchConstraint property.
getSerialNumber() - Method in class umich.ms.datatypes.scan.props.Instrument
 
getSha1() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Gets the value of the sha1 property.
getShortName() - Method in class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
 
getSign() - Method in enum umich.ms.datatypes.scan.props.Polarity
 
getSiteRegexp() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Gets the value of the siteRegexp property.
getSiteRegexp() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Gets the value of the siteRegexp property.
getSizeInDbEntries() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Gets the value of the sizeInDbEntries property.
getSizeInDbEntries() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Gets the value of the sizeInDbEntries property.
getSizeInDbEntries() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Gets the value of the sizeInDbEntries property.
getSizeOfResidues() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Gets the value of the sizeOfResidues property.
getSizeOfResidues() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Gets the value of the sizeOfResidues property.
getSizeOfResidues() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Gets the value of the sizeOfResidues property.
getSoftware() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
getSoftware() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareListType
Gets the value of the software property.
getSoftware() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Software used to convert the data.
getSoftware() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Gets the value of the software property.
getSoftwareList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the softwareList property.
getSoftwareName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
Gets the value of the softwareName property.
getSoftwareName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
Gets the value of the softwareName property.
getSoftwareRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
Gets the value of the softwareRef property.
getSoftwareRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ProcessingMethodType
Gets the value of the softwareRef property.
getSource() - Method in class umich.ms.datatypes.LCMSData
 
getSource() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentListType
Gets the value of the source property.
getSource() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
getSource() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
getSource() - Method in class umich.ms.fileio.filetypes.util.MultiSpectraParser
 
getSourceFile() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputsType
Gets the value of the sourceFile property.
getSourceFile() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputsType
Gets the value of the sourceFile property.
getSourceFile() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileListType
Gets the value of the sourceFile property.
getSourceFileList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.FileDescriptionType
Gets the value of the sourceFileList property.
getSourceFileRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Gets the value of the sourceFileRef property.
getSourceFileRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
Gets the value of the sourceFileRef property.
getSourceFileRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileRefListType
Gets the value of the sourceFileRef property.
getSourceFileRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Gets the value of the sourceFileRef property.
getSourceFileRefList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsType
Gets the value of the sourceFileRefList property.
getSourceFiles() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the sourceFiles property.
getSourceFiles() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the sourceFiles property.
getSourceFilesAlt() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the sourceFilesAlt property.
getSourceFilesAlt() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the sourceFilesAlt property.
getSourceFileXtn() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the sourceFileXtn property.
getSourceFileXtn() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the sourceFileXtn property.
getSourceFragmentationMassRangeFromScanNum(int, int, Holder<Double>, Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetSourceFragmentationMassRangeFromScanNum
getSourceFragmentValueFromScanNum(int, int, Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetSourceFragmentValueFromScanNum
getSpecificity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
Gets the value of the specificity property.
getSpecificity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
Gets the value of the specificity property.
getSpecificity() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
Gets the value of the specificity property.
getSpecificityRules() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
Gets the value of the specificityRules property.
getSpecificityRules() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
Gets the value of the specificityRules property.
getSpecifiedResidueMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Gets the value of the specifiedResidueMasses property.
getSpecifiedResidueMasses() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Gets the value of the specifiedResidueMasses property.
getSpectraData() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputsType
Gets the value of the spectraData property.
getSpectraData() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputsType
Gets the value of the spectraData property.
getSpectraDataRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputSpectraType
Gets the value of the spectraDataRef property.
getSpectraDataRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
Gets the value of the spectraDataRef property.
getSpectraDataRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputSpectraType
Gets the value of the spectraDataRef property.
getSpectraDataRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
Gets the value of the spectraDataRef property.
getSpectraParser(InputStream, LCMSDataSubset, ObjectPool<XMLStreamReaderImpl>, Integer) - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
getSpectraParser(InputStream, LCMSDataSubset, ObjectPool<XMLStreamReaderImpl>, Integer) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
getSpectraParser(InputStream, LCMSDataSubset, ObjectPool<XMLStreamReaderImpl>, Integer) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
File type specific parser.
getSpectrum() - Method in class umich.ms.datatypes.scan.impl.ScanDefault
 
getSpectrum() - Method in interface umich.ms.datatypes.scan.IScan
Get the spectrum, not trying to loead it from disk, if it wasn't parsed.
getSpectrum() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Compound
Gets the value of the spectrum property.
getSpectrum() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumListType
Gets the value of the spectrumRef property.
getSpectrum() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the spectrum property.
getSpectrum() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the spectrum property.
getSpectrum() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the spectrum property.
getSpectrumID() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
Gets the value of the spectrumID property.
getSpectrumID() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
Gets the value of the spectrumID property.
getSpectrumIdentification() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisCollectionType
Gets the value of the spectrumIdentification property.
getSpectrumIdentification() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisCollectionType
Gets the value of the spectrumIdentification property.
getSpectrumIdentificationItem() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
Gets the value of the spectrumIdentificationItem property.
getSpectrumIdentificationItem() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
Gets the value of the spectrumIdentificationItem property.
getSpectrumIdentificationItemRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideHypothesisType
Gets the value of the spectrumIdentificationItemRef property.
getSpectrumIdentificationItemRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemRefType
Gets the value of the spectrumIdentificationItemRef property.
getSpectrumIdentificationItemRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideHypothesisType
Gets the value of the spectrumIdentificationItemRef property.
getSpectrumIdentificationItemRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemRefType
Gets the value of the spectrumIdentificationItemRef property.
getSpectrumIdentificationList() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisDataType
Gets the value of the spectrumIdentificationList property.
getSpectrumIdentificationList() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisDataType
Gets the value of the spectrumIdentificationList property.
getSpectrumIdentificationListRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputSpectrumIdentificationsType
Gets the value of the spectrumIdentificationListRef property.
getSpectrumIdentificationListRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
Gets the value of the spectrumIdentificationListRef property.
getSpectrumIdentificationListRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputSpectrumIdentificationsType
Gets the value of the spectrumIdentificationListRef property.
getSpectrumIdentificationListRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
Gets the value of the spectrumIdentificationListRef property.
getSpectrumIdentificationProtocol() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisProtocolCollectionType
Gets the value of the spectrumIdentificationProtocol property.
getSpectrumIdentificationProtocol() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisProtocolCollectionType
Gets the value of the spectrumIdentificationProtocol property.
getSpectrumIdentificationProtocolRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
Gets the value of the spectrumIdentificationProtocolRef property.
getSpectrumIdentificationProtocolRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
Gets the value of the spectrumIdentificationProtocolRef property.
getSpectrumIdentificationResult() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
Gets the value of the spectrumIdentificationResult property.
getSpectrumIdentificationResult() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
Gets the value of the spectrumIdentificationResult property.
getSpectrumIDFormat() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectraDataType
Gets the value of the spectrumIDFormat property.
getSpectrumIDFormat() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectraDataType
Gets the value of the spectrumIDFormat property.
getSpectrumList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Gets the value of the spectrumList property.
getSpectrumNativeID() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the spectrumNativeID property.
getSpectrumNativeID() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the spectrumNativeID property.
getSpectrumQuery() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Gets the value of the spectrumQuery property.
getSpectrumQuery() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Gets the value of the spectrumQuery property.
getSpectrumQuery() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Gets the value of the spectrumQuery property.
getSpectrumRef() - Method in class umich.ms.datatypes.scan.impl.ScanDefault
 
getSpectrumRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Gets the value of the spectrumRef property.
getSpectrumRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
Gets the value of the spectrumRef property.
getSpot() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Gets the value of the spot property.
getSpotDiameter() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
Gets the value of the spotDiameter property.
getSpotID() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Gets the value of the spotID property.
getSpotID() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
Gets the value of the spotID property.
getSpotID() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Gets the value of the spotID property.
getSpotting() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Gets the value of the spotting property.
getSpottingPattern() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern
Gets the value of the spottingPattern property.
getSpotXCount() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Gets the value of the spotXCount property.
getSpotXPosition() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
Gets the value of the spotXPosition property.
getSpotYCount() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Gets the value of the spotYCount property.
getSpotYPosition() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
Gets the value of the spotYPosition property.
getStart() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the start property.
getStart() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Peptide
Gets the value of the start property.
getStart() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Gets the value of the start property.
getStart() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Gets the value of the start property.
getStartMz() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the startMz property.
getStartScan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Gets the value of the startScan property.
getStartScan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Gets the value of the startScan property.
getStartScan() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Gets the value of the startScan property.
getStartTime() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Gets the value of the startTime property.
getStartTime(Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetStartTime
getStartTimeStamp() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Gets the value of the startTimeStamp property.
getStaticQuant() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Gets the value of the staticQuant property.
getStaticQuant() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Gets the value of the staticQuant property.
getStaticQuant() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Gets the value of the staticQuant property.
getStaticQuantLabel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioTimestamp
Gets the value of the staticQuantLabel property.
getStaticQuantLabel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioTimestamp
Gets the value of the staticQuantLabel property.
getStaticQuantLabel() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioTimestamp
Gets the value of the staticQuantLabel property.
getStatus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Gets the value of the status property.
getStatus() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Gets the value of the status property.
getStatusLogForPos(int, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetStatusLogForPos
getStatusLogForRT(Holder<Double>, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetStatusLogForRT
getStatusLogForScanNum(int, Holder<Double>, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetStatusLogForScanNum
getStatusLogLabelsForRT(Holder<Double>, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetStatusLogLabelsForRT
getStatusLogLabelsForScanNum(int, Holder<Double>, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetStatusLogLabelsForScanNum
getStatusLogPlottableIndex(Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetStatusLogAtIndex
getStatusLogValueForRT(Holder<Double>, String, Object) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetStatusLogValueForRT
getStatusLogValueForScanNum(int, String, Holder<Double>, Object) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetStatusLogValueForScanNum
getStorageStrategy() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getStorageStrategy() - Method in interface umich.ms.datatypes.scan.IScan
 
getStringInstrumentID() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
getSubSample() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SampleType
Gets the value of the subSample property.
getSubSample() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SampleType
Gets the value of the subSample property.
getSubstitutionModification() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideType
Gets the value of the substitutionModification property.
getSubstitutionModification() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideType
Gets the value of the substitutionModification property.
getSubsumingProteinEntry() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the subsumingProteinEntry property.
getSubsumingProteinEntry() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the subsumingProteinEntry property.
getSumI() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the sumI property.
getSumI() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Gets the value of the sumI property.
getSumInt() - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
getSumInt() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
The sum of all intensities.
getSummaryXml() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
Gets the value of the summaryXml property.
getSummaryXml() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
Gets the value of the summaryXml property.
getSummaryXml() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
Gets the value of the summaryXml property.
getSummaryXml() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
Gets the value of the summaryXml property.
getSummaryXml() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
Gets the value of the summaryXml property.
getSummedMassSpectrum(Holder<Integer>, int, boolean, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method GetSummedMassSpectrum
getSwissprotName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Gets the value of the swissprotName property.
getSwissprotName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Gets the value of the swissprotName property.
getSymbol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Gets the value of the symbol property.
getSymbol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Gets the value of the symbol property.
getSymbol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Gets the value of the symbol property.
getSymbol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Gets the value of the symbol property.
getSymbol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Gets the value of the symbol property.
getSymbol() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Gets the value of the symbol property.
getTarget() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.TargetListType
Gets the value of the target property.
getTargetList() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsType
Gets the value of the targetList property.
getTargetMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
Gets the value of the targetMass property.
getTargetMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
Gets the value of the targetMass property.
getTargetMass() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
Gets the value of the targetMass property.
getTasksPerCpuPerBatch() - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
How many spectra each CPU will be given in one batch.
getTasksPerCpuPerBatch() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
How many spectra each CPU will be given in one batch.
getTerminalModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Gets the value of the terminalModification property.
getTerminalModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Gets the value of the terminalModification property.
getTerminalModification() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Gets the value of the terminalModification property.
getTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Gets the value of the terminus property.
getTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Gets the value of the terminus property.
getTerminus() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Gets the value of the terminus property.
getThreshold() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionProtocolType
Gets the value of the threshold property.
getThreshold() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Gets the value of the threshold property.
getThreshold() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionProtocolType
Gets the value of the threshold property.
getThreshold() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Gets the value of the threshold property.
getTic() - Method in class umich.ms.datatypes.scan.AbstractScan
 
getTic() - Method in interface umich.ms.datatypes.scan.IScan
 
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
Gets the value of the time property.
getTime() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
Gets the value of the time property.
getTimePerSpot() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
Gets the value of the timePerSpot property.
getTimeWidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Gets the value of the timeWidth property.
getTimeWidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Gets the value of the timeWidth property.
getTimeWidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Gets the value of the timeWidth property.
getTimeWidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Gets the value of the timeWidth property.
getTimeWidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Gets the value of the timeWidth property.
getTimeWidth() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Gets the value of the timeWidth property.
getTitle() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Gets the value of the title property.
getTitle() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Gets the value of the title property.
getTotalNoSpectrumIds() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the totalNoSpectrumIds property.
getTotalNoSpectrumIds() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the totalNoSpectrumIds property.
getTotalNumberDistinctPeptides() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the totalNumberDistinctPeptides property.
getTotalNumberDistinctPeptides() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the totalNumberDistinctPeptides property.
getTotalNumberPeptides() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the totalNumberPeptides property.
getTotalNumberPeptides() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the totalNumberPeptides property.
getTotIonCurrent() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the totIonCurrent property.
getTotNumIons() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Gets the value of the totNumIons property.
getTotNumIons() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Gets the value of the totNumIons property.
getTotNumIons() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Gets the value of the totNumIons property.
getTotNumSpectra() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Gets the value of the totNumSpectra property.
getTotNumSpectra() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Gets the value of the totNumSpectra property.
getTotNumSpectra() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Gets the value of the totNumSpectra property.
getTrace() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the trace property.
getTrailerExtraForRT(Holder<Double>, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetTrailerExtraForRT
getTrailerExtraForScanNum(int, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetTrailerExtraForScanNum
getTrailerExtraLabelsForRT(Holder<Double>, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetTrailerExtraLabelsForRT
getTrailerExtraLabelsForScanNum(int, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetTrailerExtraLabelsForScanNum
getTrailerExtraValueForRT(Holder<Double>, String, Object) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetTrailerExtraValueForRT
getTrailerExtraValueForScanNum(int, String, Object) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetTrailerExtraValueForScanNum
getTranslationTable() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DatabaseTranslationType
Gets the value of the translationTable property.
getTranslationTable() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DatabaseTranslationType
Gets the value of the translationTable property.
getTranslationTableRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Gets the value of the translationTableRef property.
getTranslationTableRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Gets the value of the translationTableRef property.
getTremblName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Gets the value of the tremblName property.
getTremblName() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Gets the value of the tremblName property.
getTuneData(int, Object, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetTuneData
getTuneDataLabels(int, Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetTuneDataLabels
getTuneDataValue(int, String, Object) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetTuneDataValue
getType() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Device
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Attribute
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.File
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Note
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.UserParamType
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.UserParamType
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.NegmodelDistribution
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.PosmodelDistribution
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NegmodelDistribution
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PosmodelDistribution
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NegmodelDistribution
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PosmodelDistribution
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
Gets the value of the type property.
getType() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
Gets the value of the type property.
getUid() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Gets the value of the uid property.
getUnderlyingBytes() - Method in class umich.ms.util.ByteArrayHolder
 
getUnfinishedIndexElements() - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
 
getUniqueCompoundNames(Object, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetUniqueCompoundNames
getUniqueStrippedPeptides() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Gets the value of the uniqueStrippedPeptides property.
getUniqueStrippedPeptides() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Gets the value of the uniqueStrippedPeptides property.
getUnitAccession() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
Gets the value of the unitAccession property.
getUnitAccession() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
Gets the value of the unitAccession property.
getUnitAccession() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Gets the value of the unitAccession property.
getUnitAccession() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Gets the value of the unitAccession property.
getUnitCvRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
Gets the value of the unitCvRef property.
getUnitCvRef() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
Gets the value of the unitCvRef property.
getUnitCvRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Gets the value of the unitCvRef property.
getUnitCvRef() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Gets the value of the unitCvRef property.
getUnitName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
Gets the value of the unitName property.
getUnitName() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
Gets the value of the unitName property.
getUnitName() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Gets the value of the unitName property.
getUnitName() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Gets the value of the unitName property.
getUnits() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Xdata
Gets the value of the units property.
getUnits() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Ydata
Gets the value of the units property.
getUri() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
Gets the value of the uri property.
getUri() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
Gets the value of the uri property.
getUri() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
Gets the value of the uri property.
getUri() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
Gets the value of the uri property.
getURI() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
Gets the value of the uri property.
getURI() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Gets the value of the uri property.
getURL() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.File
Gets the value of the url property.
getURL() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Gets the value of the url property.
getURL() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Gets the value of the url property.
getURL() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Gets the value of the url property.
getUse() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Gets the value of the use property.
getUse() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Gets the value of the use property.
getUse() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Gets the value of the use property.
getUserParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParamType
Gets the value of the userParam property.
getUserParam() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParamType
Gets the value of the userParam property.
getUserParam() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ParamGroupType
Gets the value of the userParam property.
getUserParam() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupType
Gets the value of the userParam property.
getV() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
Gets the value of the v property.
getV() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Gets the value of the v property.
getValue() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Attribute
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InputFileType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel.Point
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InputFileType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Point
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InputFileType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Point
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
Gets the value of the value property.
getValue() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
Gets the value of the value property.
getValue() - Method in class umich.ms.util.IntervalST.Node
 
getValueNamevalueType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
Gets the value of the valueNamevalueType property.
getValueOntologyEntryType() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.OntologyEntryType
Gets the value of the valueOntologyEntryType property.
getValues() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.GAMLValues
Gets the value of the values property.
getValues() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentArrayType
Gets the value of the values property.
getValues() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentArrayType
Gets the value of the values property.
getValueStr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
Gets the value of the valueStr property.
getValueStr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
Gets the value of the valueStr property.
getValueStr() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
Gets the value of the valueStr property.
getValueStr() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
Gets the value of the valueStr property.
getValueStr() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
Gets the value of the valueStr property.
getVariable() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Gets the value of the variable property.
getVariable() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Gets the value of the variable property.
getVariable() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Gets the value of the variable property.
getVariable() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Gets the value of the variable property.
getVariable() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Gets the value of the variable property.
getVariable() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Gets the value of the variable property.
getVersion() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.CEF
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareType
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Gets the value of the version property.
getVersion() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
Gets the value of the version property.
getVersion() - Static method in class umich.ms.msfiletoolbox.MsftbxInfo
 
getVersionNumber(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetVersionNumber
getVialNumber(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetVialNumber
getVolume() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Gets the value of the volume property.
getVolume() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Gets the value of the volume property.
getVValueFromScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method GetVValueFromScanNum
getWarningMessage(Holder<String>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method GetWarningMessage
getWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Gets the value of the weight property.
getWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Gets the value of the weight property.
getWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Gets the value of the weight property.
getWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Gets the value of the weight property.
getWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Gets the value of the weight property.
getWeight() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Gets the value of the weight property.
getWinCygReferenceDatabase() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the winCygReferenceDatabase property.
getWinCygReferenceDatabase() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the winCygReferenceDatabase property.
getWinCygSourceFiles() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Gets the value of the winCygSourceFiles property.
getWinCygSourceFiles() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Gets the value of the winCygSourceFiles property.
getWindowsParent() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
Gets the value of the windowsParent property.
getWindowsParent() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
Gets the value of the windowsParent property.
getWindowsParent() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
Gets the value of the windowsParent property.
getWindowsParent() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
Gets the value of the windowsParent property.
getWindowsParent() - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
Gets the value of the windowsParent property.
getWindowWideness() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Gets the value of the windowWideness property.
getX() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Gets the value of the x property.
getXdata() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Gets the value of the xdata property.
getXmlInputFactory(boolean) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
 
getXpressLight() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Gets the value of the xpressLight property.
getXpressLight() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioTimestamp
Gets the value of the xpressLight property.
getXpressLight() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Gets the value of the xpressLight property.
getXpressLight() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioTimestamp
Gets the value of the xpressLight property.
getXpressLight() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Gets the value of the xpressLight property.
getXpressLight() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioTimestamp
Gets the value of the xpressLight property.
getY() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
Gets the value of the y property.
getY() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Gets the value of the y property.
getYdata() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Gets the value of the ydata property.
getYear() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Gets the value of the year property.
getYear() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Gets the value of the year property.
getYIons() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the yIons property.
getYScore() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Gets the value of the yScore property.
getZ() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
getZ() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
getZ() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Gets the value of the z property.
getZ() - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Gets the value of the z property.
getzCarrier() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
GPMDBFile - Class in umich.ms.fileio.filetypes.gpmdb
Data source for GPMDB XML files with identifications.
There is no corresponding data access API defined for such data yet.
GPMDBFile(String) - Constructor for class umich.ms.fileio.filetypes.gpmdb.GPMDBFile
 
GPMDBParser - Class in umich.ms.fileio.filetypes.gpmdb
A very simple parser for GPMDB XML files.
group - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Bioml
 
Group - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Group() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
group - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
groupNumber - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
 
groupNumber - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
 
groupsFlag - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
groupsFlag - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
groupSiblingId - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
groupSiblingId - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
GRP_ADDUCT - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
 
GRP_ADDUCT - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
GRP_ISOTOPE_NUM - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
 
GRP_ISOTOPE_NUM - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
GRP_M_COUNT - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
 
GRP_M_COUNT - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
GRP_MOL_IDENTITY - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
 
GRP_MOL_IDENTITY - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
GRP_Z_CARRIER - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
 
GRP_Z_CARRIER - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
GRP_Z_COUNT - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
 
GRP_Z_COUNT - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
GRP_Z_SIGN - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 

H

hasExpMethod(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method HasExpMethod
Hash - Class in umich.ms.datatypes.lcmsrun
 
Hash(String, Hash.TYPE) - Constructor for class umich.ms.datatypes.lcmsrun.Hash
 
hash - Variable in class umich.ms.datatypes.lcmsrun.OriginalFile
 
Hash.TYPE - Enum in umich.ms.datatypes.lcmsrun
 
hashCode() - Method in class umich.ms.datatypes.LCMSDataSubset
 
hashCode() - Method in class umich.ms.datatypes.scan.props.Instrument
 
hashCode() - Method in class umich.ms.fileio.chunk.FileChunk
 
hashCode() - Method in class umich.ms.util.Interval1D
 
heavy2LightAdjRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
 
heavy2LightAdjRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
 
heavy2LightAdjRatioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
 
heavy2LightAdjRatioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
 
heavy2LightError - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
 
heavy2LightError - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
 
heavy2LightError - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
 
heavy2LightMean - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
 
heavy2LightMean - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
 
heavy2LightMean - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
 
heavy2LightRatio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
heavy2LightRatio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
heavy2LightRatio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
heavy2LightRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
heavy2LightRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
 
heavy2LightRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
heavy2LightRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
heavy2LightRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
 
heavy2LightRatioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
heavy2LightRatioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
heavy2LightRatioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
 
heavy2LightRatioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
heavy2LightRatioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
heavy2LightRatioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
 
heavy2LightRatioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
heavyArea - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
heavyArea - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
heavyArea - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
heavyFirstscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
heavyFirstscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
heavyFirstscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
heavyLastscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
heavyLastscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
heavyLastscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
heavyMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
 
heavyMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
heavyMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
 
heavyMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
heavyMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
 
heavyMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
height() - Method in class umich.ms.util.IntervalST
 
hi - Variable in class umich.ms.util.Interval1D
 
highMz - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
hitRank - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
hitRank - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
hitRank - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
hyperscore - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 

I

id - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
 
id - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
id - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
id - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
 
id - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
 
id - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
 
id - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IdentifiableType
 
id - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
 
id - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IdentifiableType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SampleType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
id - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexElement
 
id - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser.OffsetId
 
id - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
 
id - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
 
id - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisResult
 
id - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
 
id - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisResult
 
id - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
 
id - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisResult
 
id - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
 
id - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisResult
 
id - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
 
ID_UNKNOWN - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
IdentifiableType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Other classes in the model can be specified as sub-classes, inheriting from Identifiable.
IdentifiableType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IdentifiableType
 
IdentifiableType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Other classes in the model can be specified as sub-classes, inheriting from Identifiable.
IdentifiableType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IdentifiableType
 
IIndexedSpectrum - Interface in umich.ms.datatypes.spectrum
Deprecated.
inAcquisition(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method InAcquisition
include - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FilterType
 
include - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FilterType
 
include - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPDta
 
include - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
include - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
include - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPDta
 
include - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
include - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
includeReferenceAndExceptionData(int) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method IncludeReferenceAndExceptionData
independent - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymesType
 
independent - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymesType
 
independent - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
independent - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
 
independent - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
 
Index<T extends IndexElement> - Interface in umich.ms.datatypes.index
 
index - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
index - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IonTypeType
 
index - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IonTypeType
 
index - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
 
index - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
index - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
index - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
index - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
index - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
index - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
index - Variable in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
INDEX_NAME - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
INDEX_NAME - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
INDEX_OFFSET_MIN_VALUE - Static variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
INDEX_OFFSET_MIN_VALUE - Static variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
IndexBrokenException - Exception in umich.ms.fileio.exceptions
 
IndexBrokenException() - Constructor for exception umich.ms.fileio.exceptions.IndexBrokenException
 
IndexBrokenException(String) - Constructor for exception umich.ms.fileio.exceptions.IndexBrokenException
 
IndexBrokenException(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.IndexBrokenException
 
IndexBrokenException(Throwable) - Constructor for exception umich.ms.fileio.exceptions.IndexBrokenException
 
IndexBrokenException(String, Throwable, boolean, boolean) - Constructor for exception umich.ms.fileio.exceptions.IndexBrokenException
 
IndexBuilder<T extends XMLBasedIndexElement> - Interface in umich.ms.fileio.filetypes.xmlbased
 
IndexBuilder.Info - Class in umich.ms.fileio.filetypes.xmlbased
 
IndexBuilder.Info(long, long, InputStream) - Constructor for class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
 
IndexBuilder.Result<T extends XMLBasedIndexElement> - Class in umich.ms.fileio.filetypes.xmlbased
 
IndexBuilder.Result(IndexBuilder.Info) - Constructor for class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
 
IndexDefault<T extends IndexElement> - Class in umich.ms.datatypes.index.impl
Raw and ID maps are lazily created on the first request for a search.
IndexDefault() - Constructor for class umich.ms.datatypes.index.impl.IndexDefault
 
IndexElement - Interface in umich.ms.datatypes.index
A mapping from internal scan numbers (which start at one) to scan numbering in the original files.
mzXML files are required to provide a scan number, those scan numbers are not always continuous, e.g.:
In mzXML data converted from AB Sciex raw files one might have the first scan number as 2037, the second as 4056 and so on, they are incrementing, but not incrementing by one.
IndexElementDefault - Class in umich.ms.datatypes.index.impl
 
IndexElementDefault(int, int) - Constructor for class umich.ms.datatypes.index.impl.IndexElementDefault
 
IndexNotFoundException - Exception in umich.ms.fileio.exceptions
Thrown when mzML/mzXML has no index.
IndexNotFoundException() - Constructor for exception umich.ms.fileio.exceptions.IndexNotFoundException
 
IndexNotFoundException(String) - Constructor for exception umich.ms.fileio.exceptions.IndexNotFoundException
 
IndexNotFoundException(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.IndexNotFoundException
 
IndexNotFoundException(Throwable) - Constructor for exception umich.ms.fileio.exceptions.IndexNotFoundException
 
IndexNotFoundException(String, Throwable, boolean, boolean) - Constructor for exception umich.ms.fileio.exceptions.IndexNotFoundException
 
IndistinguishablePeptide - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
IndistinguishablePeptide() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
 
indistinguishablePeptide - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
IndistinguishablePeptide - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
IndistinguishablePeptide() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
 
indistinguishablePeptide - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
IndistinguishableProtein - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
IndistinguishableProtein() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishableProtein
 
indistinguishableProtein - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
IndistinguishableProtein - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
IndistinguishableProtein() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishableProtein
 
indistinguishableProtein - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
init() - Method in class umich.ms.fileio.chunk.ChunkedFile
Check if the file is still valid.
initializeScanIndex(int, MS_PacketTypes) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method InitializeScanIndex
initialMinPeptideProb - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
initialMinPeptideProb - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
initialPeptideWtIters - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
initialPeptideWtIters - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
initialProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
initialProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
initMethodScanEvents() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method InitMethodScanEvents
injectionInfo - Variable in class umich.ms.datatypes.scan.AbstractScan
If a file contains injection information, it should be put here, otherwise this field might be null.
InjectionInfo - Class in umich.ms.datatypes.scan.props
Info about ion injection into the mass spectrometer.
InjectionInfo() - Constructor for class umich.ms.datatypes.scan.props.InjectionInfo
 
inMinutes(String, String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
Converts mzML representation of time into minutes.
inputfile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InteractSummary
 
inputfile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
 
inputfile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
 
inputfile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InteractSummary
 
inputfile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
 
inputfile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
 
inputfile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InteractSummary
 
inputfile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
 
inputfile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
 
InputFileType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Input file
InputFileType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InputFileType
 
InputFileType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Input file
InputFileType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InputFileType
 
InputFileType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Input file
InputFileType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InputFileType
 
inputs - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DataCollectionType
 
inputs - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DataCollectionType
 
inputSpectra - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
 
inputSpectra - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
 
InputSpectraType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The attribute referencing an identifier within the SpectraData section.
InputSpectraType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputSpectraType
 
InputSpectraType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The attribute referencing an identifier within the SpectraData section.
InputSpectraType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputSpectraType
 
inputSpectrumIdentifications - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionType
 
inputSpectrumIdentifications - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionType
 
InputSpectrumIdentificationsType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The lists of spectrum identifications that are input to the protein detection process.
InputSpectrumIdentificationsType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputSpectrumIdentificationsType
 
InputSpectrumIdentificationsType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The lists of spectrum identifications that are input to the protein detection process.
InputSpectrumIdentificationsType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputSpectrumIdentificationsType
 
InputsType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The inputs to the analyses including the databases searched, the spectral data and the source file converted to mzIdentML.
InputsType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputsType
 
InputsType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The inputs to the analyses including the databases searched, the spectral data and the source file converted to mzIdentML.
InputsType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputsType
 
instantiateReaderPool() - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
instrument - Variable in class umich.ms.datatypes.scan.AbstractScan
Should be a reference to one of the instruments listed in the ScanCollection
Instrument - Class in umich.ms.datatypes.scan.props
Author: Dmitry Avtonomov
Instrument() - Constructor for class umich.ms.datatypes.scan.props.Instrument
 
Instrument(String, String, String) - Constructor for class umich.ms.datatypes.scan.props.Instrument
 
Instrument(String, String, String, String, String) - Constructor for class umich.ms.datatypes.scan.props.Instrument
 
instrumentConfiguration - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationListType
 
instrumentConfigurationList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
InstrumentConfigurationListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List and descriptions of instrument configurations.
InstrumentConfigurationListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationListType
 
instrumentConfigurationRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
 
InstrumentConfigurationType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Description of a particular hardware configuration of a mass spectrometer.
InstrumentConfigurationType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
 
instrumentFromAccession(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
InstrumentModelCVTerm - Class in umich.ms.fileio.filetypes.mzml.util
 
InstrumentModelCVTerm(String, String, String, String) - Constructor for class umich.ms.fileio.filetypes.mzml.util.InstrumentModelCVTerm
 
instruments - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
intensities - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
intensity - Variable in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
 
intensity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult
 
Intensity - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
Intensity() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
 
intensity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraResult
 
Intensity - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
Intensity() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
 
intensity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraResult
 
Intensity - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
Intensity() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Intensity
 
intensity - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraResult
 
Intensity - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
Intensity() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.Intensity
 
intensity - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraResult
 
intensityCutoff - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
 
intensitySum - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
InteractSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
InteractSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InteractSummary
 
InteractSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
InteractSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InteractSummary
 
InteractSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
InteractSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InteractSummary
 
InterprophetResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
InterprophetResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult
 
InterprophetResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
InterprophetResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetResult
 
InterprophetResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
InterprophetResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetResult
 
InterprophetResult.SearchScoreSummaryIProphet - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
InterprophetResult.SearchScoreSummaryIProphet() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult.SearchScoreSummaryIProphet
 
InterprophetSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
InterprophetSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
 
InterprophetSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
InterprophetSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
 
InterprophetSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
InterprophetSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
 
intersects(Interval1D<V>) - Method in class umich.ms.util.Interval1D
Does this interval intersect that one?
Interval1D<V extends Comparable<V>> - Class in umich.ms.util
A generic 1D line segment (interval).
Interval1D(V, V) - Constructor for class umich.ms.util.Interval1D
Precondition: left <= right
IntervalST<K extends Comparable<K>,V> - Class in umich.ms.util
A generic Interval Search Tree.
IntervalST() - Constructor for class umich.ms.util.IntervalST
 
IntervalST.Node<U extends Comparable<U>,W> - Class in umich.ms.util
BST helper node data type.
ionDescription - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
IonId - Class in umich.ms.fileio.filetypes.agilent.cef.example
 
IonId() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
ionisation - Variable in class umich.ms.datatypes.scan.props.Instrument
 
ionisationEnergy - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
ionType - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentationType
 
ionType - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentationType
 
IonTypeType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
IonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g.
IonTypeType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IonTypeType
 
IonTypeType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
IonType defines the index of fragmentation ions being reported, importing a CV term for the type of ion e.g.
IonTypeType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IonTypeType
 
ipiName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
 
ipiName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
 
is - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
 
is - Variable in class umich.ms.fileio.filetypes.util.MultiSpectraParser
 
is - Variable in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
 
isAutoloadSpectra - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
isAutoloadSpectra() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
isAutoloadSpectra(boolean) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
isAutoloadSpectra() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Decides if spectra should be automatically loaded, when a spectrumRef is requested from a Scan, but there is no spectrumRef present.
isAutoloadSpectra(boolean) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Sets the new configuration for spectra autoloading.
isBase64(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
Determines if the byte array is in base64 format.
isBase64(String) - Static method in class umich.ms.util.base64.Base64Slow
Determines if the String is in base64 format.
isBase64(String, String) - Static method in class umich.ms.util.base64.Base64Slow
Determines if the String is in base64 format.
isBase64(File) - Static method in class umich.ms.util.base64.Base64Slow
Determines if the File is in base64 format.
isBase64(InputStream) - Static method in class umich.ms.util.base64.Base64Slow
Reads data from the stream and determines if it is in base64 format.
IScan - Interface in umich.ms.datatypes.scan
If you are ever writing a wrapper for 3rd party Scan implementations you must implement this interface Author: Dmitry Avtonomov (dmitriya) Email: dmitriy.avtonomov@gmail.com
IScanCollection - Interface in umich.ms.datatypes.scancollection
Manages scan meta-info and spectral data loading.
isCentroided - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
isCentroided() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
If any of data-processing entries in mzXML or a similar file has mentioned, that the files has been centroided.
isCentroided - Variable in class umich.ms.datatypes.scan.AbstractScan
Data might come already centroided out of the instrument or post-processing algorithms
isCentroided() - Method in class umich.ms.datatypes.scan.AbstractScan
 
isCentroided() - Method in interface umich.ms.datatypes.scan.IScan
 
isCentroided() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Gets the value of the centroided property.
isCentroided() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the centroided property.
isCentroidScanForScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method IsCentroidScanForScanNum
isChargeDeconvoluted() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Gets the value of the chargeDeconvoluted property.
isChargeDeconvoluted() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the chargeDeconvoluted property.
isCollisionGas() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Gets the value of the collisionGas property.
isContributingEvidence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
isContributingEvidence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
isDecoy - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
isDecoy - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
isDeisotoped() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Gets the value of the deisotoped property.
isDeisotoped() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Gets the value of the deisotoped property.
isEmpty() - Method in class umich.ms.datatypes.LCMSRangeSet
 
isEmpty() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
isEmpty() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Tells if the collection has at least one scan in it.
isEmpty() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
isEmpty() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
 
isEnqueued() - Method in class umich.ms.util.StrongReference
 
isError(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method IsError
isError() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
property IsError
isError() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirUV
property IsError
isExcludeEmptyScans() - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
Some ABSciex data has "peaks" tag empty and no "precursor" specified in such cases for MS2 - these are useless.
isExcludeEmptyScans() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
 
isFixedMod() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
Gets the value of the fixedMod property.
isFixedMod() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
Gets the value of the fixedMod property.
isFollowLinks() - Method in class umich.ms.fileio.util.FileListing
 
isHeavy - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
 
isHeavy - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
 
isHeavy - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
 
isHeavy - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
 
isHeavy - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
 
isHeavy - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
 
isInAlphabet(byte[], boolean) - Method in class umich.ms.util.base64.Base64
Tests a given byte array to see if it contains only valid characters within the alphabet.
isInAlphabet(byte) - Method in class umich.ms.util.base64.Base64
Returns whether or not the octet is in the Base64 alphabet.
isInAlphabet(String) - Method in class umich.ms.util.base64.Base64
Tests a given String to see if it contains only valid characters within the alphabet.
isIncludeDirectories() - Method in class umich.ms.fileio.util.FileListing
 
isIncludeFiles() - Method in class umich.ms.fileio.util.FileListing
 
isIndependent() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymesType
Gets the value of the independent property.
isIndependent() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymesType
Gets the value of the independent property.
isIndependent() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
Gets the value of the independent property.
isIndependent() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
Gets the value of the independent property.
isIndependent() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
Gets the value of the independent property.
isInSubset(IScan) - Method in class umich.ms.datatypes.LCMSDataSubset
In some cases we don't have the lower/upper mz window (for MS1 this requires either this data to be in scan meta info, or the spectrumRef to be parsed).
isIsDecoy() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Gets the value of the isDecoy property.
isIsDecoy() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Gets the value of the isDecoy property.
isIsRejected() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult
Gets the value of the isRejected property.
isIsRejected() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraResult
Gets the value of the isRejected property.
isIsRejected() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraResult
Gets the value of the isRejected property.
isLoaded(LCMSDataSubset) - Method in class umich.ms.datatypes.LCMSData
Checks among the loaded by all users if this particular subset has already been loaded by someone else.
isNewFile(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method IsNewFile
isNondegenerateEvidence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
isNondegenerateEvidence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
isolationWindow - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
 
isolationWindow - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ProductType
 
isotopicContributions - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
 
IsotopicContributions - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
IsotopicContributions() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.IsotopicContributions
 
isotopicContributions - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
 
IsotopicContributions - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
IsotopicContributions() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.IsotopicContributions
 
isotopicContributions - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
 
IsotopicContributions - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
IsotopicContributions() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IsotopicContributions
 
isotopicContributions - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
IsotopicContributions - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
IsotopicContributions() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.IsotopicContributions
 
isotopicContributions - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
isPassThreshold() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
Gets the value of the passThreshold property.
isPassThreshold() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Gets the value of the passThreshold property.
isPassThreshold() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
Gets the value of the passThreshold property.
isPassThreshold() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Gets the value of the passThreshold property.
isPeakPickingTerm(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
Checks if this accession maps to a known descendant of ["MS:1000035", "peak picking"] term.
isPeaksTagReached - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
 
ISpectrum - Interface in umich.ms.datatypes.spectrum
Author: Dmitry Avtonomov (dmitriya) Email: dmitriy.avtonomov@gmail.com
isPlatformSupported() - Static method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
Just checks if the OS is some flavor of windows.
isProfileScanForScanNum(int, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method IsProfileScanForScanNum
isQExactive(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile5
method IsQExactive
isRecursive() - Method in class umich.ms.fileio.util.FileListing
 
isReject() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
Gets the value of the reject property.
isReject() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
Gets the value of the reject property.
isReject() - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
Gets the value of the reject property.
isRejected - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult
 
isRejected - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
isRejected - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraResult
 
isRejected - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
isRejected - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraResult
 
isRejected - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
isReleasingMemory - Variable in class umich.ms.datatypes.LCMSData
 
isRequired - Variable in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.ATTR
 
isRequired - Variable in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.ATTR
 
isSat() - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Gets the value of the sat property.
isSemiSpecific() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Gets the value of the semiSpecific property.
isSemiSpecific() - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Gets the value of the semiSpecific property.
isSpotIntegration() - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Gets the value of the spotIntegration property.
issue - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
issue - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 
isThereMSData(Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method IsThereMSData
isThermoLibInstalled() - Static method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
Checks if the MSFileReader Type Library from Thermo is installed as a COM object.
We're using the latest IXrawfile5 interface, so if the machine has an older version of the library, which does not provide IXrawfile5, this method returns false.
isThermoSupportedHere() - Static method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
Checks if the particular machine the code runs on can read Thermo RAW files.
That is: The OS is Windows Thermo MSFileReader is installed
isUrlSafe() - Method in class umich.ms.util.base64.Base64
Returns our current encode mode.
isValid() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
property IsValid
isValid() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirUV
property IsValid
isWhiteSpace(byte) - Static method in class umich.ms.util.base64.Base64
Checks if a byte value is whitespace or not.
isWithinPpm(double, double, double) - Static method in class umich.ms.util.SpectrumUtils
Check if the 2nd m/z value is within some PPM distance from the 1st one.
iterator() - Method in class umich.ms.util.IntervalST
 
IXRawfile - Interface in umich.ms.fileio.filetypes.thermo.raw.com4j
IXRawfile Interface
IXRawfile2 - Interface in umich.ms.fileio.filetypes.thermo.raw.com4j
IXRawfile2 Interface
IXRawfile3 - Interface in umich.ms.fileio.filetypes.thermo.raw.com4j
IXRawfile3 Interface
IXRawfile4 - Interface in umich.ms.fileio.filetypes.thermo.raw.com4j
IXRawfile4 Interface
IXRawfile5 - Interface in umich.ms.fileio.filetypes.thermo.raw.com4j
IXRawfile5 Interface
IXVirMS - Interface in umich.ms.fileio.filetypes.thermo.raw.com4j
IXVirMS Interface
IXVirMS64 - Interface in umich.ms.fileio.filetypes.thermo.raw.com4j
IXVirMS64 Interface
IXVirUV - Interface in umich.ms.fileio.filetypes.thermo.raw.com4j
IXVirUV Interface

J

JAXBCollection<T> - Class in umich.ms.fileio.util.jaxb
Generic collection wrapper class.
JAXBCollection(Collection<T>) - Constructor for class umich.ms.fileio.util.jaxb.JAXBCollection
 
JAXBCollection() - Constructor for class umich.ms.fileio.util.jaxb.JAXBCollection
 
JaxbUtils - Class in umich.ms.fileio.util.jaxb
Generic serializer (marshaller/unmarshaller) class that uses JAXB.
JaxbUtils() - Constructor for class umich.ms.fileio.util.jaxb.JaxbUtils
 
JaxbUtils.Cache - Class in umich.ms.fileio.util.jaxb
To improve the performance, we'll cache the last JAXBContext used.
JaxbUtils.Cache(Class<?>) - Constructor for class umich.ms.fileio.util.jaxb.JaxbUtils.Cache
 
join(Iterable<?>, String) - Static method in class umich.ms.util.StringUtils
Join strings with a separator.
join(Iterator<?>, String) - Static method in class umich.ms.util.StringUtils
Join strings with a separator.

L

label - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Bioml
 
label - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
label - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Note
 
label - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
 
label - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
 
label - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Xdata
 
label - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Ydata
 
labeledResidues - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
 
labeledResidues - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
 
labeledResidues - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
 
labeledResidues - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
labeledResidues - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
 
labeledResidues - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
laserFrequency - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
 
laserIntensity - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
 
laserShootCount - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
 
last - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
 
lastName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
 
lastName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
 
LCMSData - Class in umich.ms.datatypes
A wrapper uniting a data source and a scan collection.
LCMSData(LCMSDataSource<?>) - Constructor for class umich.ms.datatypes.LCMSData
Will create LCMSData backed up by ScanCollectionDefault with spectra auto-loading turned off.
LCMSData(LCMSDataSource<?>, IScanCollection) - Constructor for class umich.ms.datatypes.LCMSData
You can pass you IScanCollection implementation, but you likely won't want to do that.
LCMSData.User - Class in umich.ms.datatypes
This is a PhantomRef for the object, that requests loading of data, so we could track it being garbage collected.
LCMSData.User(Object) - Constructor for class umich.ms.datatypes.LCMSData.User
 
LCMSDataSource<T extends Index<?>> - Interface in umich.ms.fileio.filetypes
Wrapper interface for working with all LC/MS files.
LCMSDataSourceDetector - Interface in umich.ms.fileio.filetypes
Implementations of this interface should be marked as Service Providers using @ProviderFor annotation.
LCMSDataSourceFactory - Class in umich.ms.fileio.filetypes
Factory for automatic detection of supported filetypes and creating corresponding LCMSDataSources.
LCMSDataSubset - Class in umich.ms.datatypes
Represents a subset of a ScanCollection.
LCMSDataSubset() - Constructor for class umich.ms.datatypes.LCMSDataSubset
 
LCMSDataSubset(Integer, Integer, Set<Integer>, List<DoubleRange>) - Constructor for class umich.ms.datatypes.LCMSDataSubset
 
LCMSRange - Class in umich.ms.datatypes
NOT IN USE YET, SUPPOSED TO REPLACE LCMSDataSubset Represents a subset of data in an LCMS run.
LCMSRange() - Constructor for class umich.ms.datatypes.LCMSRange
Creates a range, that includes the whole run.
LCMSRange(Range<Integer>, Integer, DoubleRange) - Constructor for class umich.ms.datatypes.LCMSRange
 
LCMSRangeSet - Class in umich.ms.datatypes
NOT IN USE YET, SUPPOSED TO REPLACE LCMSDataSubset A union of several LCMSRange objects.
LCMSRangeSet() - Constructor for class umich.ms.datatypes.LCMSRangeSet
 
LCMSRangeSet.MsLevelRangeSet - Class in umich.ms.datatypes
 
LCMSRangeSet.MsLevelRangeSet() - Constructor for class umich.ms.datatypes.LCMSRangeSet.MsLevelRangeSet
 
LCMSRunInfo - Class in umich.ms.datatypes.lcmsrun
Temporarily stores processed LC/MS file run header.
LCMSRunInfo() - Constructor for class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
leftValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
 
leftValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
 
leftValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
 
leftValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
 
leftValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
 
leftValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
 
length() - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
length - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
 
length - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
 
length - Variable in class umich.ms.fileio.filetypes.xmlbased.OffsetLength
The length of data entry in bytes
length() - Method in class umich.ms.util.DoubleRange
 
LibraResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
LibraResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult
 
LibraResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
LibraResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraResult
 
LibraResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
LibraResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraResult
 
LibraResult - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
LibraResult() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraResult
 
LibraResult - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
LibraResult() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraResult
 
LibraResult.Intensity - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
LibraResult.Intensity() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
 
LibraSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
LibraSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
 
LibraSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
LibraSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
 
LibraSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
LibraSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
 
LibraSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
LibraSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
LibraSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
LibraSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
LibraSummary.FragmentMasses - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
LibraSummary.FragmentMasses() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.FragmentMasses
 
LibraSummary.IsotopicContributions - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
LibraSummary.IsotopicContributions() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions
 
LibraSummary.IsotopicContributions.ContributingChannel - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
LibraSummary.IsotopicContributions.ContributingChannel() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel
 
LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
 
lightArea - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
lightArea - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
lightArea - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
lightFirstscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
lightFirstscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
lightFirstscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
lightLastscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
lightLastscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
lightLastscan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
lightMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
 
lightMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
lightMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
 
lightMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
lightMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
 
lightMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
lightSequence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
lightSequence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
lineLength - Variable in class umich.ms.util.base64.Base64
Chunksize for encoding.
lo - Variable in class umich.ms.util.Interval1D
 
load(LCMSDataSubset) - Method in class umich.ms.datatypes.LCMSData
Will load scan meta-info and spectra for the specified subset.
load(LCMSDataSubset, Object) - Method in class umich.ms.datatypes.LCMSData
Will load scan meta-info and spectra for the specified subset.
loadData(LCMSDataSubset) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
loadData(LCMSDataSubset, StorageStrategy) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
loadData(LCMSDataSubset, StorageStrategy) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
IMPLEMENTATIONS MUST BE SYNCHRONIZED
Loads spectra for a subset of scans, or all of them, depending on the configuration.
loadData(LCMSDataSubset) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
IMPLEMENTATIONS MUST BE SYNCHRONIZED
Loads spectra for a subset of scans, or all of them, depending on the configuration.
localPath - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
localPath - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
 
localPath - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
 
locateRunHeader(String, boolean, boolean, String, boolean, boolean) - Method in class umich.ms.fileio.filetypes.mzxml.XmlBasedRunHeaderParser
Reads the run header from the file, locating positions of <firstTag> and first <lastTag> tags.
location - Variable in class umich.ms.datatypes.lcmsrun.OriginalFile
 
location - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Compound
 
Location - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
Location() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
 
location - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ExternalDataType
 
location - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
 
location - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
 
location - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ExternalDataType
 
location - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
 
location - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
 
location - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileType
 
locusLinkName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
 
locusLinkName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
 
LogHelper - Class in umich.ms.logging
 
logratio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Point
 
logratio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Point
 
lowMz - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 

M

m - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
 
main(String[]) - Static method in class umich.ms.fileio.chunk.ChunkedFile
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefTest
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzidentml.example.MzIdentMlExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzxml.example.Example
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzxml.example.Example2
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzxml.example.Example3
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzxml.example.Example4
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
Use this for testing only
main(String[]) - Static method in class umich.ms.fileio.filetypes.pepxml.example.PepXmlExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.pepxml.example.PepXmlNestedExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.pepxml.example.PepXmlSimpleExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.pepxml.example.PepXmlWriteExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.protxml.example.ProtXmlJaxbExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.protxml.example.ProtXmlSimpleExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.thermo.raw.test.ThermoTest
 
main(String[]) - Static method in class umich.ms.util.Interval1D
 
main(String[]) - Static method in class umich.ms.util.IntervalST
test client
maldi - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
maldiMatrix - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
 
manufacturer - Variable in class umich.ms.datatypes.scan.props.Instrument
 
MAP_ANALYZER_TYPE - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MAP_INSTRUMENT_MODEL - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MAP_IONIZATION_TYPE - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MAP_PEAK_PICKING - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
mapById - Variable in class umich.ms.datatypes.index.impl.IndexDefault
 
mapByNum - Variable in class umich.ms.datatypes.index.impl.IndexDefault
 
mapByRawNum - Variable in class umich.ms.datatypes.index.impl.IndexDefault
 
mapCharArr2ActivationCVTerm - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
mapCharArr2PSIMSCV - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
mapIdRefToInternalScanNum(CharArray) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
Given a scan ID goes to the index and tries to find a mapping.
mapRawNumToInternalScanNum(int) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
Given a scan internal number (spectrum index) goes to the index and tries to find a mapping.
mapRawNumToInternalScanNum(int) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
Given a scan internal number (spectrum index) goes to the index and tries to find a mapping.
mapString2ActivationCVTerm - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
mapString2PSIMSCV - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
marshal(Integer) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Adapter1
 
marshal(Double) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Adapter2
 
marshal(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.Adapter1
 
marshal(Double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.Adapter2
 
marshal(Double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.Adapter1
 
marshal(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.Adapter2
 
marshal(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.Adapter1
 
marshal(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.Adapter2
 
marshal(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Adapter1
 
marshal(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Adapter2
 
marshal(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Adapter1
 
marshal(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Adapter2
 
marshal(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Adapter1
 
marshal(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Adapter2
 
marshal(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Adapter1
 
marshal(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Adapter2
 
marshal(T) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert an object to a string.
marshal(T, Writer) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert an object to a string and send it to a Writer.
marshal(T, File) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert an object to a string and save it to a File.
marshal(T, OutputStream) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert an object to a string and send it to an OutputStream.
marshal(String, Collection<T>) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert a collection to a string.
marshal(String, Collection<T>, Writer) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert a collection to a string and sends it to the Writer.
marshal(String, Collection<T>, File) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert a collection to a string and stores it in a File.
marshal(String, Collection<T>, OutputStream) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert a collection to a string and sends it to the OutputStream.
MASK_8BITS - Static variable in class umich.ms.util.base64.Base64
Mask used to extract 8 bits, used in decoding bytes
mass - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
mass - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ResidueType
 
mass - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ResidueType
 
mass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
mass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
mass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
 
mass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
 
mass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModAminoacidMass
 
mass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
 
mass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
 
mass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModAminoacidMass
 
mass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
 
mass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModAminoacidMass
 
mass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModAminoacidMass
 
massDelta - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
 
massDelta - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
 
massdiff - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
massTable - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
massTable - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
massTableRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
massTableRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
MassTableType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The masses of residues used in the search.
MassTableType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MassTableType
 
MassTableType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The masses of residues used in the search.
MassTableType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MassTableType
 
massTol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
masstol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
 
massTol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
masstol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
massTol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
masstol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
massTolerance - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
 
massTolerance - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
 
massTolerance - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
 
massTolerance - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
massTolerance - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
MassType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for massType.
MassType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for massType.
MassType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for massType.
MathHelper - Class in umich.ms.util
Math functions.
max - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRange
 
MAX_BYTES_FROM_END_TO_SEARCH_FOR_INDEX - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
MAX_BYTES_FROM_END_TO_SEARCH_FOR_INDEX - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
MAX_PRECURSOR_GROUP_SIZE_DIFF - Static variable in class umich.ms.datatypes.scancollection.ScanCollectionHelper
Defines the ratio of numbers of scans in the larges "precursor group" to the smallest "precursor group".
Formula used:
Math.abs(maxScansInGroup - minScansInGroup)) / minScansInGroup
A precursor group is a group of scans, which satisfy one of the two conditions:
precursor windows were not known for scans, but several scans had exactly the same precursor mass precursor windows were known and there was significant overlap between the precursor windows
There also must be more than one scan in EACH group, for a run to be auto-detected as a DIA run.
maxFpkm - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
maxFpkm - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
maxI - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
maxInt - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
maxIntensity - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
maxIntensityMz - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
maxIntensityPos - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
maxIntMz - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
maxMZ - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
maxNumInternalCleavages - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
 
maxNumInternalCleavages - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EnzymaticSearchConstraint
 
maxNumInternalCleavages - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.EnzymaticSearchConstraint
 
mCount - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
mean - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
 
mean - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
 
mean - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
 
measure - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentationTableType
 
measure - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentationTableType
 
measureRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentArrayType
 
measureRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentArrayType
 
MeasureType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
References to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem
MeasureType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MeasureType
 
MeasureType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
References to CV terms defining the measures about product ions to be reported in SpectrumIdentificationItem
MeasureType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MeasureType
 
merge(LCMSDataSubset) - Method in class umich.ms.datatypes.LCMSDataSubset
Doesn't modify original values, always returns a new one.
mh - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
mh - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
midInitials - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
 
midInitials - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
 
MIME_CHUNK_SIZE - Static variable in class umich.ms.util.base64.Base64
 
min - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRange
 
min(double...) - Static method in class umich.ms.util.MathHelper
Find the minimum in an array of numbers.
MIN_GROUP_OVERLAP - Static variable in interface umich.ms.datatypes.scancollection.IScanCollection
The minimum relative overlap between two spectra's MS1 ranges or MS2 isolation windows, for spectra to be considered as belonging to the same group.
minDistance - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
 
minDistance - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
 
minInt - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
minIntensity - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
minIntensityNonZero - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
minIntensityNonZeroPos - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
minIntensityPos - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
minIntNonZero - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
minMZ - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
minNumberTermini - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
 
minNumberTermini - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EnzymaticSearchConstraint
 
minNumberTermini - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.EnzymaticSearchConstraint
 
minNumChromatogramPoints - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
minNumChromatogramPoints - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
minNumEnzTerm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.DatabaseRefreshTimestamp
 
minNumEnzTerm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatabaseRefreshTimestamp
 
minNumEnzTerm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatabaseRefreshTimestamp
 
minNumIsotopePeaks - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
minNumIsotopePeaks - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
minPepProb - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
minPepProb - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
minPeptideProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
 
minPeptideProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
minPeptideProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
 
minPeptideProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
 
minPeptideProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
minPeptideProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
 
minPeptideWeight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
 
minPeptideWeight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
minPeptideWeight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
 
minPeptideWeight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
 
minPeptideWeight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
minPeptideWeight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
 
minPepWt - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
minPepWt - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
minProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
 
minProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
 
minProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
 
minProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
 
minProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
 
minProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
 
minProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
 
minProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
 
minProb - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
 
minProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
 
minProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
 
minProteinProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
 
minProteinProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
 
minProteinProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
 
minProteinProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
 
minProtProb - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
minProtProb - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
minSpacing - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
 
minSpacing - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
 
minSpacing - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
 
missedCleavages - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
missedCleavages - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
 
missedCleavages - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
 
mixturemodel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
 
mixtureModel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
 
mixturemodel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
 
Mixturemodel - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
Mixturemodel() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
 
mixtureModel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
 
mixturemodel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
 
Mixturemodel - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
Mixturemodel() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
 
mixtureModel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
 
MixturemodelDistribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
MixturemodelDistribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixturemodelDistribution
 
MixturemodelDistribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
MixturemodelDistribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixturemodelDistribution
 
mixturemodelDistributionOrMixturemodel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
 
mixturemodelDistributionOrMixturemodel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
 
mixturemodelDistributionOrMixturemodel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
 
MixtureModelling - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
MixtureModelling() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
 
MixtureModelling - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
MixtureModelling() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
 
MixtureModelPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
MixtureModelPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
 
MixtureModelPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
MixtureModelPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
 
MixtureModelType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for mixtureModelType complex type.
MixtureModelType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
 
MixtureModelType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for mixtureModelType complex type.
MixtureModelType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
 
MixtureModelType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for mixtureModelType complex type.
MixtureModelType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
 
MixtureModelType.MixtureModelPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MixtureModelType.MixtureModelPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
 
Mod - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
Mod() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
 
mod - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
 
Mod - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
Mod() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
 
mod - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
 
modAminoacidMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
 
ModAminoacidMass - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
ModAminoacidMass() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModAminoacidMass
 
modAminoacidMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
 
ModAminoacidMass - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
ModAminoacidMass() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModAminoacidMass
 
modAminoacidMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
 
modAminoacidMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
 
ModAminoacidMass - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ModAminoacidMass() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModAminoacidMass
 
modAminoacidMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
 
ModAminoacidMass - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ModAminoacidMass() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModAminoacidMass
 
modCtermMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
 
modCtermMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
 
modCtermMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
 
modCtermMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
 
modCtermMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
 
model - Variable in class umich.ms.datatypes.scan.props.Instrument
 
model - Variable in class umich.ms.fileio.filetypes.mzml.util.InstrumentModelCVTerm
 
model1NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model1NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model1NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model1PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model1PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model1PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model2NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model2NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model2NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model2PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model2PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model2PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model3NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model3NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model3NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model3PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model3PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model3PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model4NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model4NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model4NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model4PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model4PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model4PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model5NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model5NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model5NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model5PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model5PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model5PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model6NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model6NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model6NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model6PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model6PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model6PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model7NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model7NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model7NegDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
model7PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
model7PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
model7PosDistr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
modelDistr - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Point
 
modelDistr - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Point
 
ModelDisType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for model_dis_type.
ModelDisType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for model_dis_type.
ModelDisType - Enum in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for model_dis_type.
modification - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideType
 
modification - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideType
 
modificationInfo - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
ModificationInfo - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
ModificationInfo() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
 
modificationInfo - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
ModificationInfo - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
ModificationInfo() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
 
modificationInfo - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
modificationInfo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
 
ModificationInfo - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for modification_info complex type.
ModificationInfo() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
 
modificationInfo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
modificationInfo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
 
ModificationInfo - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for modification_info complex type.
ModificationInfo() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
 
modificationInfo - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
modificationParams - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
modificationParams - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
ModificationParamsType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The specification of static/variable modifications (e.g.
ModificationParamsType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationParamsType
 
ModificationParamsType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The specification of static/variable modifications (e.g.
ModificationParamsType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationParamsType
 
ModificationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A molecule modification specification.
ModificationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
 
ModificationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A molecule modification specification.
ModificationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
 
modified - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
 
modifiedPeptide - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
 
modifiedPeptide - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
 
modifiedPeptide - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
 
modifiedPeptide - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
 
modifiedPeptide - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
 
modNtermMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
 
modNtermMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
 
modNtermMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
 
modNtermMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
 
modNtermMass - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
 
molId - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
monoisotopicMassDelta - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
 
monoisotopicMassDelta - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
 
monoisotopicMassDelta - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
 
monoisotopicMassDelta - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
 
MS1_WITH_SPECTRA - Static variable in class umich.ms.datatypes.LCMSDataSubset
Sets up the parsing parameters to parse all scans, but spectra only for MS1 scans.
MS2_WITH_SPECTRA - Static variable in class umich.ms.datatypes.LCMSDataSubset
Sets up the parsing parameters to parse all scans, but spectra only for MS2 scans.
MS_Activations - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Corona - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_DataTypes - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Dep - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Detector - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_IonizationMode - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_MSOrder - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Multiplex - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_PacketTypes - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Param_A - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Param_B - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Param_F - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Param_K - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Param_R - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Param_V - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Polarity - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_PrecursorEnergy - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_ScanData - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_ScanType - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_SourceCID - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_SourceCIDType - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_TurboScan - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MS_Wideband - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
MSDetails - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
MSDetails() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
 
msDetails - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
 
msDetector - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
msDetector - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
msDetector - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
msDetector - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
MsftbxInfo - Class in umich.ms.msfiletoolbox
 
MsftbxInfo() - Constructor for class umich.ms.msfiletoolbox.MsftbxInfo
 
msInstrument - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
msInstrumentID - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Even though according to schema this must be an integer, we've seen cases, where ProteoWizard uses a String
msInstrumentID - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
msIonisation - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
msIonization - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
msIonization - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
msIonization - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
msLevel - Variable in class umich.ms.datatypes.scan.AbstractScan
 
msLevel - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MassTableType
 
msLevel - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MassTableType
 
msLevel - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
msLevel - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
 
msLevel2rangeGroups - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
msLvl2index - Variable in class umich.ms.datatypes.scancollection.ScanIndexRoot
 
msManufacturer - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
msManufacturer - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
msManufacturer - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
msManufacturer - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
msMassAnalyzer - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
msMassAnalyzer - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
msMassAnalyzer - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
msMassAnalyzer - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
msModel - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
msModel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
msModel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
msModel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
MsmsPipelineAnalysis - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
 
MsmsPipelineAnalysis - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
MsmsPipelineAnalysis() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
 
MsmsPipelineAnalysis - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
MsmsPipelineAnalysis() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
 
MsmsPipelineAnalysis.AnalysisSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.AnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
 
MsmsPipelineAnalysis.DatasetDerivation - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.DatasetDerivation() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation
 
MsmsPipelineAnalysis.DatasetDerivation.DataFilter - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.DatasetDerivation.DataFilter() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
 
MsmsPipelineAnalysis.MsmsRunSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
 
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint
 
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
 
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
 
msmsRunSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
 
msmsRunSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
 
MsmsRunSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
MsmsRunSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
msmsRunSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
 
MsmsRunSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
MsmsRunSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
MSNumpress - Class in umich.ms.external.msnumpress
 
MSNumpress() - Constructor for class umich.ms.external.msnumpress.MSNumpress
 
MSPeaks - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
MSPeaks() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSPeaks
 
msPeaks - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
 
msResolution - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
MsRun - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
MsRun.DataProcessing - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.DataProcessing() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
 
MsRun.MsInstrument - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.MsInstrument() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
MsRun.MsInstrument.MsManufacturer - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.MsInstrument.MsManufacturer() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument.MsManufacturer
 
MsRun.MsInstrument.MsMassAnalyzer - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.MsInstrument.MsMassAnalyzer() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument.MsMassAnalyzer
 
MsRun.ParentFile - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.ParentFile() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
 
MsRun.Separation - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.Separation() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Separation
 
MsRun.Spotting - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.Spotting() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting
 
MsRun.Spotting.Plate - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.Spotting.Plate() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
 
MsRun.Spotting.Plate.Pattern - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.Spotting.Plate.Pattern() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern
 
MsRun.Spotting.Plate.Pattern.Orientation - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.Spotting.Plate.Pattern.Orientation() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern.Orientation
 
MsRun.Spotting.Plate.Spot - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.Spotting.Plate.Spot() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
 
MsRun.Spotting.Robot - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
MsRun.Spotting.Robot() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
 
MsSoftware - Class in umich.ms.datatypes.lcmsrun
 
MsSoftware(String, String) - Constructor for class umich.ms.datatypes.lcmsrun.MsSoftware
 
MultiSpectraParser - Class in umich.ms.fileio.filetypes.util
Base class for parsers used by mzXML/mzML files.
MultiSpectraParser(InputStream, LCMSDataSubset) - Constructor for class umich.ms.fileio.filetypes.util.MultiSpectraParser
 
mz - Variable in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
 
mz - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
mz - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.FragmentMasses
 
mz - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.FragmentMasses
 
mz - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.FragmentMasses
 
mz - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FragmentMasses
 
mz - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Intensity
 
mz - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FragmentMasses
 
mz - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Intensity
 
MzIdentMlExample - Class in umich.ms.fileio.filetypes.mzidentml.example
As simple as it gets.
MzIdentMlExample() - Constructor for class umich.ms.fileio.filetypes.mzidentml.example.MzIdentMlExample
 
MzIdentMLParser - Class in umich.ms.fileio.filetypes.mzidentml
A very simple parser for MzIdentML.
MzIdentMLType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The upper-most hierarchy level of mzIdentML with sub-containers for example describing software, protocols and search results (spectrum identifications or protein detection results).
MzIdentMLType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
MzIdentMLType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The upper-most hierarchy level of mzIdentML with sub-containers for example describing software, protocols and search results (spectrum identifications or protein detection results).
MzIdentMLType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
MZMLFile - Class in umich.ms.fileio.filetypes.mzml
 
MZMLFile(String) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLFile
 
MZMLIndex - Class in umich.ms.fileio.filetypes.mzml
 
MZMLIndex() - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLIndex
 
MZMLIndexElement - Class in umich.ms.fileio.filetypes.mzml
 
MZMLIndexElement(int, int, String, OffsetLength) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLIndexElement
 
MZMLIndexParser - Class in umich.ms.fileio.filetypes.mzml
 
MZMLIndexParser(MZMLFile) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
MZMLIndexParser.OffsetId - Class in umich.ms.fileio.filetypes.mzml
 
MZMLIndexParser.OffsetId(long, String) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLIndexParser.OffsetId
 
MZMLMultiSpectraParser - Class in umich.ms.fileio.filetypes.mzml
Parses multiple spectra read from mzML file.
MZMLMultiSpectraParser(InputStream, LCMSDataSubset, MZMLFile) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
MZMLMultiSpectraParser.ATTR - Enum in umich.ms.fileio.filetypes.mzml
 
MZMLMultiSpectraParser.MZMLIndexBuilder - Class in umich.ms.fileio.filetypes.mzml
 
MZMLMultiSpectraParser.MZMLIndexBuilder(IndexBuilder.Info) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.MZMLIndexBuilder
 
MZMLMultiSpectraParser.TAG - Enum in umich.ms.fileio.filetypes.mzml
 
MZMLPeaksDecoder - Class in umich.ms.fileio.filetypes.mzml
 
MZMLPeaksDecoder() - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLPeaksDecoder
 
MZMLPeaksDecoder.DecodedData - Class in umich.ms.fileio.filetypes.mzml
 
MZMLPeaksDecoder.DecodedData(double[], double, int, double, int, double, int, double) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLPeaksDecoder.DecodedData
 
MZMLRunHeaderParser - Class in umich.ms.fileio.filetypes.mzml
Parses the run header of an mzML file.
MZMLRunHeaderParser(MZMLFile) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
MzMLType - Class in umich.ms.fileio.filetypes.mzml.jaxb
This is the root element for the Proteomics Standards Initiative (PSI) mzML schema, which is intended to capture the use of a mass spectrometer, the data generated, and the initial processing of that data (to the level of the peak list).
MzMLType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
mzs - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
MZXMLFile - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLFile(String) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
MZXMLFile(String, boolean) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLFile
MzXML file constructor.
MZXMLIndex - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLIndex() - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLIndex
 
MZXMLIndexElement - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLIndexElement(int, int, OffsetLength) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLIndexElement
 
MZXMLIndexParser - Class in umich.ms.fileio.filetypes.mzxml
Parses the index portion of an MZXML file.
MZXMLIndexParser(MZXMLFile) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
MZXMLMultiSpectraParser - Class in umich.ms.fileio.filetypes.mzxml
Parses several spectra using Javolution XML streaming parser.
MZXMLMultiSpectraParser(InputStream, LCMSDataSubset, MZXMLFile) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
MZXMLMultiSpectraParser.ATTR - Enum in umich.ms.fileio.filetypes.mzxml
 
MZXMLMultiSpectraParser.MZXMLIndexBuilder - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLMultiSpectraParser.MZXMLIndexBuilder(IndexBuilder.Info) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.MZXMLIndexBuilder
 
MZXMLMultiSpectraParser.TAG - Enum in umich.ms.fileio.filetypes.mzxml
 
MZXMLMultiSpectraParser.VarsHolder - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLMultiSpectraParser.VarsHolder() - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
Check MZXMLMultiSpectraParser.VarsHolder.flushVars() source for default values
MZXMLPeaksDecoder - Class in umich.ms.fileio.filetypes.mzxml
Author: Dmitry Avtonomov (dmitriya) Email: dmitriy.avtonomov@gmail.com Date: 2/21/13 Time: 10:24 AM
MZXMLPeaksDecoder.DecodedData - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLPeaksDecoder.DecodedData(double[], double[], int, double, int, double, int, double, double) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
MZXMLRunHeaderParser - Class in umich.ms.fileio.filetypes.mzxml
Parses the header of the file to get isntrument information.
MZXMLRunHeaderParser(MZXMLFile) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser
 

N

name - Variable in class umich.ms.datatypes.lcmsrun.MsSoftware
 
name - Variable in class umich.ms.datatypes.lcmsrun.OriginalFile
 
name - Variable in enum umich.ms.datatypes.scan.props.ScanType
 
name - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
 
name - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IdentifiableType
 
name - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
 
name - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IdentifiableType
 
name - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
 
name - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SampleType
 
name - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileType
 
name - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
 
name - Variable in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.ATTR
 
name - Variable in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.TAG
 
name - Variable in class umich.ms.fileio.filetypes.mzml.util.CVTerm
 
name - Variable in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
 
name - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
 
name - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
 
name - Variable in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.ATTR
 
name - Variable in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.TAG
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InputFileType
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InputFileType
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixturemodelDistribution
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InputFileType
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixturemodelDistribution
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
 
name - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
 
name - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
 
name - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
 
NamespaceFilter - Class in umich.ms.fileio.util.jaxb
Implementation of an XML filter that can add or remove namespaces from XML elements during parsing.
NamespaceFilter(String, boolean) - Constructor for class umich.ms.fileio.util.jaxb.NamespaceFilter
 
nameValueAndComment - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
nameValueAndComment - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
NamevalueType - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for namevalueType complex type.
NamevalueType() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
 
NameValueType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for nameValueType complex type.
NameValueType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
 
NameValueType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for nameValueType complex type.
NameValueType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
 
NameValueType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for nameValueType complex type.
NameValueType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
 
NameValueType - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for nameValueType complex type.
NameValueType() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
 
NameValueType - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for nameValueType complex type.
NameValueType() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
 
negBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
 
negBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
 
negBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
 
negBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
 
negBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
 
negBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
 
negDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
 
negDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel.Point
 
negDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
 
negDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Point
 
negDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
 
negDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Point
 
negFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
 
negFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
 
negFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
 
negFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
 
negFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
 
negFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
 
negmodelDistribution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution
 
negmodelDistribution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixturemodelDistribution
 
NegmodelDistribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
NegmodelDistribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NegmodelDistribution
 
negmodelDistribution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixturemodelDistribution
 
NegmodelDistribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
NegmodelDistribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NegmodelDistribution
 
negObsDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
 
negObsDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
 
negObsDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
 
neighboringBinSmoothing - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmInformation
 
neighboringBinSmoothing - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspInformation
 
neighboringBinSmoothing - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmInformation
 
neighboringBinSmoothing - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspInformation
 
nEnzymaticTermini - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
nEnzymaticTermini - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
next() - Method in class umich.ms.fileio.chunk.ChunkedFile
 
next() - Method in interface umich.ms.fileio.chunk.FileChunkSource
 
next(LCMSDataSubset, boolean) - Method in interface umich.ms.fileio.filetypes.SequentialScanReader
Gets the next scan.
nextscore - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
niAdjustedProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
niAdjustedProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
NiDistribution - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
NiDistribution() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
 
niDistribution - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiInformation
 
NiDistribution - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
NiDistribution() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
 
niDistribution - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiInformation
 
NiInformation - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
NiInformation() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiInformation
 
niInformation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
NiInformation - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
NiInformation() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiInformation
 
niInformation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
niLowerBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
 
niLowerBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
 
niLowerBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
 
niLowerBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
 
nIndistinguishableProteins - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
nIndistinguishableProteins - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
nInstances - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
nInstances - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
niUpperBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
 
niUpperBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
 
niUpperBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
 
niUpperBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
 
noCut - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
 
noCut - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
 
noCut - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
 
normalization - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
 
normalization - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
 
normalization - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
 
normalization - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
normalization - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
normalized - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
 
normalized - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
 
normalized - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
 
note - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
Note - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Note() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Note
 
note - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
 
nSiblingPeptides - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
nSiblingPeptides - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
nSiblingPeptidesBin - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
nSiblingPeptidesBin - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
nspAdjustedProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
nspAdjustedProbability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
NspDistribution - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
NspDistribution() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
 
nspDistribution - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspInformation
 
NspDistribution - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
NspDistribution() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
 
nspDistribution - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspInformation
 
nspDistributionIters - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
nspDistributionIters - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
nspFlag - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
nspFlag - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
NspInformation - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
NspInformation() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspInformation
 
nspInformation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
NspInformation - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
NspInformation() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspInformation
 
nspInformation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
nspLowerBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
 
nspLowerBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
 
nspLowerBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
 
nspLowerBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
 
nspUpperBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
 
nspUpperBoundExcl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
 
nspUpperBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
 
nspUpperBoundIncl - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
 
nTermGain - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
 
nTermGain - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
 
num - Variable in class umich.ms.datatypes.index.impl.IndexElementDefault
Internal scan number.
num - Variable in class umich.ms.datatypes.scan.AbstractScan
Serial number of this scan in an LC/MS run
num - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Device
 
num - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
num - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.ScanOrigin
 
num2scan - Variable in class umich.ms.datatypes.scancollection.ScanIndex
 
NUM_BYTES_TO_CHECK_INDEX - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
NUM_BYTES_TO_CHECK_INDEX - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
number - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
 
number - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
 
number - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
 
number - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
 
number - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraResult
 
number - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
 
number - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraResult
 
numCorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
 
numCorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
 
numCorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
 
numCorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
 
numCorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
 
numCorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
 
numDatabaseSequences - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
 
numDatabaseSequences - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
 
numIncorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
 
numIncorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
 
numIncorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
 
numIncorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
 
numIncorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
 
numIncorr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
 
numInput1Spectra - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
numInput1Spectra - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
numInput2Spectra - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
numInput2Spectra - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
numInput3Spectra - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
numInput3Spectra - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
numInput4Spectra - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
numInput4Spectra - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
numInput5Spectra - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
numInput5Spectra - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
numIterations - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
 
numIterations - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
 
numIterations - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
 
numMatchedIons - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
numMatchedIons - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
numMatchedIons - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
numMatchedPeptides - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
numMatchedPeptides - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
numMatchedPeptides - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
numMissedCleavages - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
numMissedCleavages - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
numMissedCleavages - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
numPredictedCorrectProts - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
numPredictedCorrectProts - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
numRaw - Variable in class umich.ms.datatypes.index.impl.IndexElementDefault
Raw scan number from raw file.
numResidues - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
 
numResidues - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
 
numScansToProcess - Variable in class umich.ms.fileio.filetypes.util.MultiSpectraParser
this will serve as a hint only, not required
numSequencesSearched - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
 
numSequencesSearched - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
 
numTolTerm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
numTolTerm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
numTolTerm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
 
numTolTerm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
numTolTerm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
 
numTolTerm - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
numTotProteins - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
numTotProteins - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
numTotProteins - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
numvalues - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
 

O

ObjectFactory - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
This object contains factory methods for each Java content interface and Java element interface generated in the umich.ms.fileio.filetypes.agilent.cef.jaxb package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.ms.fileio.filetypes.agilent.cef.jaxb
ObjectFactory - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
This object contains factory methods for each Java content interface and Java element interface generated in the umich.gpmdb.jaxb package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.gpmdb.jaxb
ObjectFactory - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
This object contains factory methods for each Java content interface and Java element interface generated in the umich.ms.fileio.filetypes.mzidentml.jaxb.primitive package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
ObjectFactory - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
This object contains factory methods for each Java content interface and Java element interface generated in the umich.ms.fileio.filetypes.mzidentml.jaxb.standard package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.ms.fileio.filetypes.mzidentml.jaxb.standard
ObjectFactory - Class in umich.ms.fileio.filetypes.mzml.jaxb
This object contains factory methods for each Java content interface and Java element interface generated in the umich.ms.fileio.filetypes.mzml.jaxb package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.ms.fileio.filetypes.mzml.jaxb
ObjectFactory - Class in umich.ms.fileio.filetypes.mzxml.jaxb
This object contains factory methods for each Java content interface and Java element interface generated in the umich.ms.fileio.filetypes.mzxml.jaxb package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.ms.fileio.filetypes.mzxml.jaxb
ObjectFactory - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
This object contains factory methods for each Java content interface and Java element interface generated in the umich.ms.fileio.filetypes.pepxml.jaxb.nested package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.ms.fileio.filetypes.pepxml.jaxb.nested
ObjectFactory - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
This object contains factory methods for each Java content interface and Java element interface generated in the umich.ms.fileio.filetypes.pepxml.jaxb.primitive package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.ms.fileio.filetypes.pepxml.jaxb.primitive
ObjectFactory - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
This object contains factory methods for each Java content interface and Java element interface generated in the umich.ms.fileio.filetypes.pepxml.jaxb.standard package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.ms.fileio.filetypes.pepxml.jaxb.standard
ObjectFactory - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
This object contains factory methods for each Java content interface and Java element interface generated in the umich.ms.fileio.filetypes.protxml.jaxb.primitive package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.ms.fileio.filetypes.protxml.jaxb.primitive
ObjectFactory - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
This object contains factory methods for each Java content interface and Java element interface generated in the umich.ms.fileio.filetypes.protxml.jaxb.standard package.
ObjectFactory() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ObjectFactory
Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: umich.ms.fileio.filetypes.protxml.jaxb.standard
obs1Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
obs1Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
obs1Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
obs2Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
obs2Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
obs2Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
obs3Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
obs3Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
obs3Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
obs4Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
obs4Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
obs4Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
obs5Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
obs5Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
obs5Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
obs6Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
obs6Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
obs6Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
obs7Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
obs7Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
 
obs7Distr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
 
obsDistr - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Point
 
obsDistr - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Point
 
occamFlag - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
occamFlag - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
offlen - Variable in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedIndexElement
The offset and length of scan entry in the XML file.
offset - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser.OffsetId
 
offset - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.FragmentMasses
 
offset - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.FragmentMasses
 
offset - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.FragmentMasses
 
offset - Variable in class umich.ms.fileio.filetypes.xmlbased.OffsetLength
Offset in bytes in a file (for use with RandomAccessFiles)
offsetInBuffer - Variable in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
Offset in the read-buffer (which is shared by multiple parsers), where this particular parser started parsing.
offsetInFile - Variable in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
Global offset of the read-buffer (which is shared by multiple parsers) relative to the start of the file.
OffsetLength - Class in umich.ms.fileio.filetypes.xmlbased
Simple holder for a byte offset in file and length of an entry.
OffsetLength(long, int) - Constructor for class umich.ms.fileio.filetypes.xmlbased.OffsetLength
 
ONTOLOGY - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
OntologyEntryType - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for ontologyEntryType complex type.
OntologyEntryType() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.OntologyEntryType
 
open(String) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method Open
operator - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
Operator - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
Operator() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
 
optimalLinearFixedPoint(double[], int) - Static method in class umich.ms.external.msnumpress.MSNumpress
 
optimalSlofFixedPoint(double[], int) - Static method in class umich.ms.external.msnumpress.MSNumpress
 
options - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
 
options - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
 
options - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
 
options - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
 
options - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
 
options - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
 
Opts - Class in umich.ms.fileio
Package options.
order - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentType
 
order - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ProcessingMethodType
 
organism - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
organism - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
organizationRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AffiliationType
 
organizationRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParentOrganizationType
 
organizationRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AffiliationType
 
organizationRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParentOrganizationType
 
OrganizationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Organizations are entities like companies, universities, government agencies.
OrganizationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.OrganizationType
 
OrganizationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Organizations are entities like companies, universities, government agencies.
OrganizationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.OrganizationType
 
orientation - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern
 
origDatabaseUrl - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
origDatabaseUrl - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
 
origDatabaseUrl - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
 
OriginalFile - Class in umich.ms.datatypes.lcmsrun
 
OriginalFile(String, String, Hash) - Constructor for class umich.ms.datatypes.lcmsrun.OriginalFile
 
originalFiles - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
originalResidue - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
 
originalResidue - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
 
outData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
outData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
outData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
outDataType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
outDataType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
outDataType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
OutOfMemoryException - Exception in umich.ms.fileio.exceptions
An indicator, that file parsing had troubles because of not enough memory.
OutOfMemoryException() - Constructor for exception umich.ms.fileio.exceptions.OutOfMemoryException
 
OutOfMemoryException(String) - Constructor for exception umich.ms.fileio.exceptions.OutOfMemoryException
 
OutOfMemoryException(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.OutOfMemoryException
 
OutOfMemoryException(Throwable) - Constructor for exception umich.ms.fileio.exceptions.OutOfMemoryException
 
OutOfMemoryException(String, Throwable, boolean, boolean) - Constructor for exception umich.ms.fileio.exceptions.OutOfMemoryException
 
outputType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
 
outputType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
 
outputType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
 
outputType - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
 
outputType - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
 
overlapAbsolute(DoubleRange) - Method in class umich.ms.util.DoubleRange
If the interval contains just a single point (i.e.
overlapRelative(DoubleRange) - Method in class umich.ms.util.DoubleRange
Relative overlap, that is the overlap, divided by the length of the largest interval.
If both intervals are single points and they're equal - returns 1

P

p - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
 
p - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSPeaks
 
P - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
P() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
 
PAD - Variable in class umich.ms.util.base64.Base64
 
PAD_DEFAULT - Static variable in class umich.ms.util.base64.Base64
Byte used to pad output.
pages - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
pages - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult.SearchScoreSummaryIProphet
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult.SearchScoreSummary
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.NegmodelDistribution
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.PosmodelDistribution
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NegmodelDistribution
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PosmodelDistribution
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchScoreSummary
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchScoreSummaryIProphet
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NegmodelDistribution
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PosmodelDistribution
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchScoreSummary
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchScoreSummaryIProphet
 
parameter - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
parameter - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishableProtein
 
parameter - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
parameter - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
parameter - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishableProtein
 
parameter - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
parameter - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractContactType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AmbiguousResidueType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MassTableType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParamListType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinAmbiguityGroupType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionListType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SampleType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SourceFileType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractContactType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AmbiguousResidueType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MassTableType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParamListType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinAmbiguityGroupType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionListType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SampleType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SourceFileType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
 
paramGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
 
ParamGroupType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Structure allowing the use of a controlled (cvParam) or uncontrolled vocabulary (userParam), or a reference to a predefined set of these in this mzML file (paramGroupRef).
ParamGroupType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ParamGroupType
 
ParamListType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Helper type to allow multiple cvParams or userParams to be given for an element.
ParamListType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParamListType
 
ParamListType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Helper type to allow multiple cvParams or userParams to be given for an element.
ParamListType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParamListType
 
ParamType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Helper type to allow either a cvParam or a userParam to be provided for an element.
ParamType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParamType
 
ParamType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Helper type to allow either a cvParam or a userParam to be provided for an element.
ParamType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParamType
 
parent - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.OrganizationType
 
parent - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.OrganizationType
 
parentFile - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
parentFile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
 
parentFile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
 
parentFile - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
 
parentFile - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
 
parentFile - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
 
parentFileID - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.ScanOrigin
 
ParentOrganizationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The containing organization (the university or business which a lab belongs to, etc.)
ParentOrganizationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParentOrganizationType
 
ParentOrganizationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The containing organization (the university or business which a lab belongs to, etc.)
ParentOrganizationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParentOrganizationType
 
parentTolerance - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
parentTolerance - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
parse(String) - Static method in enum umich.ms.datatypes.scan.props.Polarity
Parse Polarity from a string.
parse() - Method in class umich.ms.fileio.filetypes.gpmdb.GPMDBFile
 
parse(Path) - Static method in class umich.ms.fileio.filetypes.gpmdb.GPMDBParser
 
parse(LCMSDataSubset) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Parse a range of scan numbers.
parse(List<Integer>) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
The storage strategy should always be StorageStrategy.STRONG, the receiver then can set it to whatever it needs.
parse(Path) - Static method in class umich.ms.fileio.filetypes.mzidentml.MzIdentMLParser
Will parse the whole file.
parse() - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
parse() - Method in class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
parse() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
parse() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser
 
parse() - Method in class umich.ms.fileio.filetypes.mzxml.XmlBasedRunHeaderParser
 
parse(Path) - Static method in class umich.ms.fileio.filetypes.pepxml.PepXmlParser
 
parse(Path) - Static method in class umich.ms.fileio.filetypes.protxml.ProtXmlParser
 
parse(LCMSDataSubset) - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parse(List<Integer>) - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parse(LCMSDataSubset) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
parse(List<Integer>) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
Deprecated.
this method has not been updated to the new parsing version
parsedScans - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
parsedScans - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
parseHeaderWithJAXB(Class<T>, OffsetLength) - Method in class umich.ms.fileio.filetypes.mzxml.XmlBasedRunHeaderParser
 
parseIndex() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
 
parseIndex() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
parseIndex() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
parseIndex() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parseIndexEntries(byte[], TreeMap<Integer, MZMLIndexParser.OffsetId>) - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
parseIndexEntries(byte[], TreeMap<Integer, Long>) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
parseIonSignature() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
parseRunInfo() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
 
parseRunInfo() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
parseRunInfo() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
parseRunInfo() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parseScan(int, boolean) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Parse a single scan from file on disk by it's number.
Assuming every LCMS file interface must be able to do that.
The storage strategy should always be StorageStrategy.STRONG, the receiver then can set it to whatever it needs.
parseScan(int, boolean) - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parseScan(int, boolean) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
parseScanNumFromIndex(CharArray) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
parseSpectrum(int) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Parse a single spectrumRef from file on disk by it's number.
Assuming every LCMS file interface must be able to do that.
parseSpectrum(int) - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parseSpectrum(int) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
parsingTimeout - Variable in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
Timeout In seconds.
passivateObject(PooledObject<XMLStreamReaderImpl>) - Method in class umich.ms.fileio.filetypes.xmlbased.XMLStreamReaderFactory
 
passivateObject(PooledObject<ByteArrayHolder>) - Method in class umich.ms.util.ByteArrayHolderFactory
 
passThreshold - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
 
passThreshold - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
passThreshold - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
 
passThreshold - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
path - Variable in class umich.ms.fileio.filetypes.util.AbstractFile
 
path - Variable in class umich.ms.fileio.util.FileListing
 
pattern - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
 
pctSpectrumIds - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
pctSpectrumIds - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
peaks - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
PeaksCompression - Enum in umich.ms.datatypes.scan
Peaks (m/z and intensity) compression methods used in mzML and mzXML files.
peaksCount - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
peaksCount - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
 
PEM_CHUNK_SIZE - Static variable in class umich.ms.util.base64.Base64
 
Peptide - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Peptide() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Peptide
 
peptide - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
 
peptide - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SequenceCollectionType
 
peptide - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SequenceCollectionType
 
peptide - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
peptide - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
peptide - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
Peptide - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
Peptide() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
peptide - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
Peptide - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
Peptide() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
peptide - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
peptideBinaryInd - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
peptideBinaryInd - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
peptideEvidence - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SequenceCollectionType
 
peptideEvidence - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SequenceCollectionType
 
peptideEvidenceRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceRefType
 
peptideEvidenceRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideHypothesisType
 
peptideEvidenceRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
peptideEvidenceRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceRefType
 
peptideEvidenceRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideHypothesisType
 
peptideEvidenceRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
PeptideEvidenceRefType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Reference to the PeptideEvidence element identified.
PeptideEvidenceRefType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceRefType
 
PeptideEvidenceRefType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Reference to the PeptideEvidence element identified.
PeptideEvidenceRefType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceRefType
 
PeptideEvidenceType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
PeptideEvidence links a specific Peptide element to a specific position in a DBSequence.
PeptideEvidenceType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
PeptideEvidenceType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
PeptideEvidence links a specific Peptide element to a specific position in a DBSequence.
PeptideEvidenceType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
peptideGroupDesignator - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
peptideGroupDesignator - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
peptideHypothesis - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
 
peptideHypothesis - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
 
PeptideHypothesisType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Peptide evidence on which this ProteinHypothesis is based by reference to a PeptideEvidence element.
PeptideHypothesisType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideHypothesisType
 
PeptideHypothesisType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Peptide evidence on which this ProteinHypothesis is based by reference to a PeptideEvidence element.
PeptideHypothesisType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideHypothesisType
 
peptideIndex - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPDta
 
peptideIndex - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPDta
 
peptideInds - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
 
peptideInds - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
 
peptideNextAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
peptideNextAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
peptideNextAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
 
peptideNextAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
peptideNextAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
 
peptideNextAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
peptideParentProtein - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
PeptideParentProtein - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
PeptideParentProtein() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.PeptideParentProtein
 
peptideParentProtein - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
PeptideParentProtein - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
PeptideParentProtein() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.PeptideParentProtein
 
peptidePrevAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
peptidePrevAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
peptidePrevAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
 
peptidePrevAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
peptidePrevAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
 
peptidePrevAa - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
PeptideprophetResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
PeptideprophetResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
 
PeptideprophetResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
PeptideprophetResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
 
PeptideprophetResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
PeptideprophetResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
 
PeptideprophetResult.SearchScoreSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
PeptideprophetResult.SearchScoreSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult.SearchScoreSummary
 
PeptideprophetSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
PeptideprophetSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
 
PeptideprophetSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
PeptideprophetSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
 
PeptideprophetSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
PeptideprophetSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
 
PeptideprophetSummary.DistributionPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
PeptideprophetSummary.DistributionPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
 
PeptideprophetSummary.MixtureModelling - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
PeptideprophetSummary.MixtureModelling() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
 
PeptideprophetSummary.MixtureModelling.Mixturemodel - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
PeptideprophetSummary.MixtureModelling.Mixturemodel() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
 
PeptideprophetSummary.MixtureModelling.Mixturemodel.Point - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
PeptideprophetSummary.MixtureModelling.Mixturemodel.Point() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel.Point
 
PeptideprophetSummary.MixtureModelling.MixturemodelDistribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
PeptideprophetSummary.MixtureModelling.MixturemodelDistribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution
 
PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.NegmodelDistribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.NegmodelDistribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.NegmodelDistribution
 
PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.PosmodelDistribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.PosmodelDistribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.PosmodelDistribution
 
peptideRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
peptideRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
peptideRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
peptideRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
peptideSequence - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideType
 
peptideSequence - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideType
 
peptideSequence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
 
peptideSequence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
 
peptideSequence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
peptideSequence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
 
peptideSequence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
 
peptideSequence - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
peptideTerminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
peptideTerminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
 
peptideTerminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
 
PeptideType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
One (poly)peptide (a sequence with modifications).
PeptideType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideType
 
PeptideType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
One (poly)peptide (a sequence with modifications).
PeptideType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideType
 
PepXmlExample - Class in umich.ms.fileio.filetypes.pepxml.example
Simple parsing of all MsmsRunSummary entries in a pep.xml file.
PepXmlExample() - Constructor for class umich.ms.fileio.filetypes.pepxml.example.PepXmlExample
 
PepXmlNestedExample - Class in umich.ms.fileio.filetypes.pepxml.example
This is just a demo of how this auto-generated binding class can be used to get PSMs from a pep.xml file.
PepXmlNestedExample() - Constructor for class umich.ms.fileio.filetypes.pepxml.example.PepXmlNestedExample
 
PepXmlParser - Class in umich.ms.fileio.filetypes.pepxml
A very simple parser for PepXML files.
PepXmlSimpleExample - Class in umich.ms.fileio.filetypes.pepxml.example
Created by Dmitry Avtonomov on 2016-04-13.
PepXmlSimpleExample() - Constructor for class umich.ms.fileio.filetypes.pepxml.example.PepXmlSimpleExample
 
PepXmlWriteExample - Class in umich.ms.fileio.filetypes.pepxml.example
An example of how a pepxml file can be written using the provided bindings Created by Dmitry Avtonomov on 2015-10-17.
PepXmlWriteExample() - Constructor for class umich.ms.fileio.filetypes.pepxml.example.PepXmlWriteExample
 
percentCoverage - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
percentCoverage - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
personOrOrganization - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AuditCollectionType
 
personOrOrganization - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AuditCollectionType
 
PersonType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A person's name and contact details.
PersonType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
 
PersonType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A person's name and contact details.
PersonType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
 
phone - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
 
plate - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting
 
plateID - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
 
plateID - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
 
plateManufacturer - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
 
plateModel - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
 
pm - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
 
point - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
 
point - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
 
point - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
 
point - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
 
Point - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
Point() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Point
 
point - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
 
point - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
 
Point - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
Point() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Point
 
point - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisModel
 
Point - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
Point() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Point
 
point - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisModel
 
Point - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
Point() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.Point
 
polarity - Variable in class umich.ms.datatypes.scan.AbstractScan
 
Polarity - Enum in umich.ms.datatypes.scan.props
Author: Dmitry Avtonomov (dmitriya) Email: dmitriy.avtonomov@gmail.com Date: 3/25/13 Time: 5:11 PM
polarity - Variable in enum umich.ms.datatypes.scan.props.Polarity
 
polarity - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
pool - Variable in class umich.ms.util.base64.Base64ContextPooled
 
PooledByteArrayHolders - Class in umich.ms.util
A singleton pool of ByteArrayHolders.
posBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
 
posBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
 
posBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
 
posBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
 
posBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
 
posBandwidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
 
posDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
 
posDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel.Point
 
posDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
 
posDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Point
 
posDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
 
posDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Point
 
posFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
 
posFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
 
posFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
 
posFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
 
posFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
 
posFreq - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
 
position - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
 
position - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModAminoacidMass
 
position - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModAminoacidMass
 
position - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModAminoacidMass
 
position - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModAminoacidMass
 
posmodelDistribution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution
 
posmodelDistribution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixturemodelDistribution
 
PosmodelDistribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
PosmodelDistribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PosmodelDistribution
 
posmodelDistribution - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixturemodelDistribution
 
PosmodelDistribution - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
PosmodelDistribution() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PosmodelDistribution
 
posObsDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
 
posObsDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
 
posObsDens - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
 
possibleCharges - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
 
post - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
post - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
post - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
posToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
 
posToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
 
posToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
 
posToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
 
posToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
 
posToNegRatio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
 
ppm2amu(double, double) - Static method in class umich.ms.util.SpectrumUtils
Given an m/z value, calculates what a certain ppm accuracy converts to in terms of m/z.
ppmtol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
 
ppmtol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
ppmtol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
pre - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
pre - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
pre - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
precision - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
 
precisionInt - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
 
precisionMz - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
 
precursor - Variable in class umich.ms.datatypes.scan.AbstractScan
If this is an MS1 scan, this field is left null, indicating there was no precursor
precursor - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
 
precursor - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorListType
 
precursorCharge - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
 
PrecursorInfo - Class in umich.ms.datatypes.scan.props
Author: Dmitry Avtonomov (dmitriya) Email: dmitriy.avtonomov@gmail.com Date: 3/26/13 Time: 4:00 PM
PrecursorInfo() - Constructor for class umich.ms.datatypes.scan.props.PrecursorInfo
 
precursorIntensity - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
 
precursorIntensity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
precursorIntensity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
precursorIntensity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
precursorIonCharge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
 
precursorIonCharge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
 
precursorIonCharge - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
 
precursorList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
PrecursorListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List and descriptions of precursor isolations to the spectrumRef currently being described, ordered.
PrecursorListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorListType
 
precursorMassType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
precursorMassType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
precursorMassType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
precursorMz - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
precursorNeutralMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
precursorNeutralMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
precursorNeutralMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
precursorScanNum - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
 
PrecursorType - Class in umich.ms.fileio.filetypes.mzml.jaxb
The method of precursor ion selection and activation
PrecursorType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
 
predictedNumCorrect - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
 
predictedNumCorrect - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
 
predictedNumIncorrect - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
 
predictedNumIncorrect - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
 
prettyPrint() - Method in class umich.ms.util.IntervalST
Print out the current tree from left to right.
priorProbability - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
 
priorProbability - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
 
priorProbability - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
 
probability - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult
 
probability - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
 
probability - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetResult
 
probability - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
 
probability - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetResult
 
probability - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
 
probability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
probability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
 
probability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
probability - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
 
processingMethod - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingType
 
ProcessingMethodType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Java class for ProcessingMethodType complex type.
ProcessingMethodType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ProcessingMethodType
 
processingOperationAndComment - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
 
product - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
 
product - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ProductListType
 
productList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
ProductListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List and descriptions of product isolations to the spectrumRef currently being described, ordered.
ProductListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ProductListType
 
ProductType - Class in umich.ms.fileio.filetypes.mzml.jaxb
The method of product ion selection and activation in a precursor ion scan
ProductType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ProductType
 
ProgramDetails - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ProgramDetails() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
 
programDetails - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
ProgramDetails - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ProgramDetails() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
 
programDetails - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
protein - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
Protein - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Protein() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
 
protein - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
protein - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
protein - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
 
protein - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
protein - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
 
protein - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
Protein - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
Protein() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
protein - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
 
Protein - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
Protein() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
protein - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
 
proteinAmbiguityGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionListType
 
proteinAmbiguityGroup - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionListType
 
ProteinAmbiguityGroupType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.
ProteinAmbiguityGroupType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinAmbiguityGroupType
 
ProteinAmbiguityGroupType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A set of logically related results from a protein detection, for example to represent conflicting assignments of peptides to proteins.
ProteinAmbiguityGroupType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinAmbiguityGroupType
 
proteinAnnotation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
ProteinAnnotation - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for protein_annotation complex type.
ProteinAnnotation() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
 
proteinAnnotation - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
ProteinAnnotation - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for protein_annotation complex type.
ProteinAnnotation() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
 
proteinDescr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
proteinDescr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
proteinDescr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
 
proteinDescr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
proteinDescr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
 
proteinDescr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
proteinDescription - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
 
proteinDescription - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
 
proteinDetection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisCollectionType
 
proteinDetection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisCollectionType
 
proteinDetectionHypothesis - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinAmbiguityGroupType
 
proteinDetectionHypothesis - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinAmbiguityGroupType
 
ProteinDetectionHypothesisType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A single result of the ProteinDetection analysis (i.e.
ProteinDetectionHypothesisType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
 
ProteinDetectionHypothesisType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A single result of the ProteinDetection analysis (i.e.
ProteinDetectionHypothesisType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
 
proteinDetectionList - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisDataType
 
proteinDetectionList - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisDataType
 
proteinDetectionListRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionType
 
proteinDetectionListRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionType
 
ProteinDetectionListType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The protein list resulting from a protein detection process.
ProteinDetectionListType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionListType
 
ProteinDetectionListType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The protein list resulting from a protein detection process.
ProteinDetectionListType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionListType
 
proteinDetectionProtocol - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisProtocolCollectionType
 
proteinDetectionProtocol - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisProtocolCollectionType
 
proteinDetectionProtocolRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionType
 
proteinDetectionProtocolRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionType
 
ProteinDetectionProtocolType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The parameters and settings of a ProteinDetection process.
ProteinDetectionProtocolType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionProtocolType
 
ProteinDetectionProtocolType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The parameters and settings of a ProteinDetection process.
ProteinDetectionProtocolType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionProtocolType
 
ProteinDetectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
An Analysis which assembles a set of peptides (e.g.
ProteinDetectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionType
 
ProteinDetectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
An Analysis which assembles a set of peptides (e.g.
ProteinDetectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionType
 
ProteinGroup - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ProteinGroup() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
 
proteinGroup - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
 
ProteinGroup - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ProteinGroup() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
 
proteinGroup - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
 
proteinMw - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
 
proteinMw - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
proteinMw - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
 
proteinMw - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
proteinMw - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
 
proteinMw - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
proteinName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishableProtein
 
proteinName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.PeptideParentProtein
 
proteinName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
proteinName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishableProtein
 
proteinName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.PeptideParentProtein
 
proteinName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
ProteinprophetDetails - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ProteinprophetDetails() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
ProteinprophetDetails - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ProteinprophetDetails() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
ProteinSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ProteinSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
 
ProteinSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ProteinSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
 
proteinSummaryDataFilter - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
ProteinSummaryDataFilter - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ProteinSummaryDataFilter() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
 
proteinSummaryDataFilter - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
ProteinSummaryDataFilter - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ProteinSummaryDataFilter() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
 
proteinSummaryHeader - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
 
ProteinSummaryHeader - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
ProteinSummaryHeader() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
proteinSummaryHeader - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
 
ProteinSummaryHeader - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
ProteinSummaryHeader() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
proteinTerminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
proteinTerminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
 
proteinTerminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
 
proteinTerminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
 
proteinTerminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
 
ProtocolApplicationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The use of a protocol with the requisite Parameters and ParameterValues.
ProtocolApplicationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProtocolApplicationType
 
ProtocolApplicationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The use of a protocol with the requisite Parameters and ParameterValues.
ProtocolApplicationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProtocolApplicationType
 
ProtXmlJaxbExample - Class in umich.ms.fileio.filetypes.protxml.example
 
ProtXmlJaxbExample() - Constructor for class umich.ms.fileio.filetypes.protxml.example.ProtXmlJaxbExample
 
ProtXmlParser - Class in umich.ms.fileio.filetypes.protxml
A very simple parser for ProtXML files.
ProtXmlSimpleExample - Class in umich.ms.fileio.filetypes.protxml.example
 
ProtXmlSimpleExample() - Constructor for class umich.ms.fileio.filetypes.protxml.example.ProtXmlSimpleExample
 
provider - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
provider - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
ProviderType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The provider of the document in terms of the Contact and the software the produced the document instance.
ProviderType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProviderType
 
ProviderType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The provider of the document in terms of the Contact and the software the produced the document instance.
ProviderType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProviderType
 
pseudoName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
 
pseudoName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
 
PSIMSCV - Enum in umich.ms.fileio.filetypes.mzml.util
Commonly used Ontology terms in mzML files.
publication - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
publication - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 
publisher - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
publisher - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 
put(Interval1D<K>, V) - Method in class umich.ms.util.IntervalST
Insert a new node in the tree.
pvalue - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
 
pvalue - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
 

Q

quantLabelMasses - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioTimestamp
 
quantLabelMasses - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioTimestamp
 
quantLabelMasses - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioTimestamp
 

R

rank - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
rank - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
ratio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
 
ratio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
ratio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
 
ratio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
ratio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
 
ratio - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
ratio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Intensity
 
ratio - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Intensity
 
ratioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
ratioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
 
ratioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
ratioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
ratioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
 
ratioMean - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
ratioNumberPeptides - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
 
ratioNumberPeptides - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
 
ratioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
ratioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
 
ratioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
ratioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
ratioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
 
ratioStandardDev - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
rawData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
rawData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
rawData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
rawDataType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
rawDataType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
rawDataType - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
RE_END_OF_RUN - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
RE_END_OF_RUN - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
RE_INDEX_ENTRY - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
Not used since started using Javolution instead of regular expressions for parsing index
RE_INDEX_ENTRY_SIMPLE - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
RE_INDEX_ENTRY_SIMPLE - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
RE_INDEX_OFFSET - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
RE_INDEX_OFFSET - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
RE_PEAK_DESCRIPTION - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
read() - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
read(byte[]) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
read(byte[], int, int) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
read() - Method in class umich.ms.external.BufferedRandomAccessFile
Reads one byte form the current position
read(byte[], int, int) - Method in class umich.ms.external.BufferedRandomAccessFile
Reads the set number of bytes into the passed buffer.
read() - Method in class umich.ms.fileio.util.ReverseLineInputStream
 
readContinuousBatchOfSpectra(Iterator<? extends Map.Entry<Integer, ? extends XMLBasedIndexElement>>, RandomAccessFile, byte[], ArrayList<OffsetLength>, int) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
readerPool - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
readerPool - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
readerPool - Variable in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
readListOfSpectra(ListIterator<Integer>, int, ArrayList<OffsetLength>, NavigableMap<Integer, ? extends XMLBasedIndexElement>, RandomAccessFile, byte[]) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
Reads up to (@code maxScansToRead) scans from the iterator, checking for continuity of scans in the original file, so it could do sequential reads.
readResults() - Method in class umich.ms.util.base64.Base64Context
 
ref - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupRefType
 
ref - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareRefType
 
ref - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileRefType
 
referenceableParamGroup - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupListType
 
referenceableParamGroupList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
ReferenceableParamGroupListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Container for a list of referenceableParamGroups
ReferenceableParamGroupListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupListType
 
referenceableParamGroupRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ParamGroupType
 
ReferenceableParamGroupRefType - Class in umich.ms.fileio.filetypes.mzml.jaxb
A reference to a previously defined ParamGroup, which is a reusable container of one or more cvParams.
ReferenceableParamGroupRefType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupRefType
 
ReferenceableParamGroupType - Class in umich.ms.fileio.filetypes.mzml.jaxb
A collection of CVParam and UserParam elements that can be referenced from elsewhere in this mzML document by using the 'paramGroupRef' element in that location to reference the 'id' attribute value of this element.
ReferenceableParamGroupType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupType
 
referenceDatabase - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
referenceDatabase - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
referenceIsotope - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
 
referenceIsotope - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
 
referenceIsotope - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
 
referenceIsotope - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
 
refreshViewOfFile() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method RefreshViewOfFile
refseqName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
 
refseqName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
 
reject - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
 
reject - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
 
reject - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
 
releaseDate - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
 
releaseDate - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
 
releaseMemory() - Method in class umich.ms.datatypes.LCMSData
Releases all memory by calling LCMSDataSource.releaseMemory() and IScanCollection.reset().
releaseMemory() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
The intent is to be able to free the memory, e.g.
releaseMemory() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
releaseMemory() - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
releaseResources() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
releaseResources() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
releaseResources() - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
This method will be called by AbstractXMLBasedDataSource.releaseMemory() in addition to cleaning up resources, used by this abstract implementation.
remove(Interval1D<K>) - Method in class umich.ms.util.IntervalST
Remove and return value associated with given interval.
removeFromAll(LCMSRange) - Method in class umich.ms.datatypes.LCMSRangeSet.MsLevelRangeSet
Remove the range from all range sets in this ms level.
removeFromSpecific(LCMSRange) - Method in class umich.ms.datatypes.LCMSRangeSet.MsLevelRangeSet
Remove range from all specific precursor ranges at this ms level.
removeInstrument(String) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
removeInstrument(Instrument) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
replacementResidue - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
 
replacementResidue - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
 
reset() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
reset() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Bring the collection back to initial empty state.
reset() - Method in class umich.ms.util.ByteArrayHolder
Resets the count field of this byte array output stream to zero, so that all currently accumulated output in the output stream is discarded.
residue - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MassTableType
 
residue - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MassTableType
 
residues - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
 
residues - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
 
residues - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
 
residues - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
 
residueSubstitutionList - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
residueSubstitutionList - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
ResidueType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Java class for ResidueType complex type.
ResidueType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ResidueType
 
ResidueType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Java class for ResidueType complex type.
ResidueType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ResidueType
 
retentionTime - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
retentionTimeSec - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
retentionTimeSec - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
retentionTimeSec - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
reverseBase64Chars - Static variable in class umich.ms.util.base64.Base64Slow
Reverse lookup table for the Base64 alphabet.
ReverseLineInputStream - Class in umich.ms.fileio.util
 
ReverseLineInputStream(RandomAccessFile) - Constructor for class umich.ms.fileio.util.ReverseLineInputStream
 
rightValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
 
rightValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
 
rightValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
 
rightValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
 
rightValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
 
rightValley - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
 
robot - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting
 
robotManufacturer - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
 
robotModel - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
 
rocDataPoint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
 
RocDataPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
RocDataPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
 
rocDataPoint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
 
RocDataPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
RocDataPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
 
rocDataPoint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
 
rocErrorData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
 
rocErrorData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
 
rocErrorData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
 
rocErrorData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
 
rocErrorData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
 
rocErrorData - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
 
RocErrorDataType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Tag for encapsulating roc curves for pepXML
RocErrorDataType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
 
RocErrorDataType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Tag for encapsulating roc curves for pepXML
RocErrorDataType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
 
RocErrorDataType - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Tag for encapsulating roc curves for pepXML
RocErrorDataType() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
 
RocErrorDataType.ErrorPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
RocErrorDataType.ErrorPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
 
RocErrorDataType.RocDataPoint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
RocErrorDataType.RocDataPoint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
 
role - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ContactRoleType
 
role - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ContactRoleType
 
RoleType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The roles (lab equipment sales, contractor, etc.) the Contact fills.
RoleType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.RoleType
 
RoleType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The roles (lab equipment sales, contractor, etc.) the Contact fills.
RoleType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.RoleType
 
rt - Variable in class umich.ms.datatypes.scan.AbstractScan
Retention time in minutes
rt - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
RT in minutes.
rt - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
rt - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
 
rt - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
 
rt - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
rt2scan - Variable in class umich.ms.datatypes.scancollection.ScanIndex
 
rtFromScanNum(int, Holder<Double>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method RTFromScanNum
rtHi - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
rtLo - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
RTRange - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
RTRange() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRange
 
rtRange - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRanges
 
RTRanges - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
RTRanges() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRanges
 
rtRanges - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
 
run - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
RunHeaderBoundsNotFound - Exception in umich.ms.fileio.exceptions
Created by Dmitry Avtonomov on 2015-10-26.
RunHeaderBoundsNotFound() - Constructor for exception umich.ms.fileio.exceptions.RunHeaderBoundsNotFound
 
RunHeaderBoundsNotFound(String) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderBoundsNotFound
 
RunHeaderBoundsNotFound(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderBoundsNotFound
 
RunHeaderBoundsNotFound(Throwable) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderBoundsNotFound
 
RunHeaderParsingException - Exception in umich.ms.fileio.exceptions
Used in areas, where run header info is parsed.
RunHeaderParsingException() - Constructor for exception umich.ms.fileio.exceptions.RunHeaderParsingException
 
RunHeaderParsingException(String) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderParsingException
 
RunHeaderParsingException(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderParsingException
 
RunHeaderParsingException(Throwable) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderParsingException
 
runInfo - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
runInfo - Variable in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
 
runInfo - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
runInfo - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
runInfo - Variable in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
runOptions - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
 
runOptions - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
 
RunType - Class in umich.ms.fileio.filetypes.mzml.jaxb
A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.
RunType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.RunType
 

S

s - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
 
sameScanRange - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
 
sameScanRange - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
sameScanRange - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
sample - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSampleCollectionType
 
sample - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSampleCollectionType
 
sample - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SampleListType
 
sampleEnzyme - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
sampleEnzyme - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
SampleEnzyme - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
SampleEnzyme() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
 
sampleEnzyme - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
SampleEnzyme - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
SampleEnzyme() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
 
sampleEnzyme - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
sampleEnzyme - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
sampleList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
SampleListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List and descriptions of samples.
SampleListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SampleListType
 
sampleRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
sampleRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubSampleType
 
sampleRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
sampleRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubSampleType
 
sampleRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
 
SampleType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A description of the sample analysed by mass spectrometry using CVParams or UserParams.
SampleType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SampleType
 
SampleType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A description of the sample analysed by mass spectrometry using CVParams or UserParams.
SampleType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SampleType
 
SampleType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Expansible description of the sample used to generate the dataset, named in sampleName.
SampleType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SampleType
 
sat - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
 
satLimit - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
 
scan - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanListType
 
scan - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
Scan - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
Scan() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
scan - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
Scan.Maldi - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
Scan.Maldi() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
 
Scan.Peaks - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
Scan.Peaks() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
 
Scan.PrecursorMz - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
Scan.PrecursorMz() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
 
Scan.ScanOrigin - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
Scan.ScanOrigin() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.ScanOrigin
 
ScanCollectionDefault - Class in umich.ms.datatypes.scancollection.impl
The default implementation of IScanCollection.
ScanCollectionDefault() - Constructor for class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
ScanCollectionDefault(boolean) - Constructor for class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
With this constructor you can pre-configure the scan collection to automatically load spectra if they were not parsed in the first place.
ScanCollectionHelper - Class in umich.ms.datatypes.scancollection
Helper utils for ScanCollections.
scanCount - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
ScanDefault - Class in umich.ms.datatypes.scan.impl
All the constructors produce Scans that have StorageStrategy set to StorageStrategy.STRONG, it's up to the client to reset this to anything else.
ScanDefault(int) - Constructor for class umich.ms.datatypes.scan.impl.ScanDefault
 
ScanDefault(IScanCollection, int) - Constructor for class umich.ms.datatypes.scan.impl.ScanDefault
 
ScanDefault(int, double, int, boolean) - Constructor for class umich.ms.datatypes.scan.impl.ScanDefault
 
ScanDefault(IScanCollection, int, double, int, boolean) - Constructor for class umich.ms.datatypes.scan.impl.ScanDefault
 
ScanIndex - Class in umich.ms.datatypes.scancollection
 
ScanIndex() - Constructor for class umich.ms.datatypes.scancollection.ScanIndex
 
ScanIndexRoot - Class in umich.ms.datatypes.scancollection
 
ScanIndexRoot() - Constructor for class umich.ms.datatypes.scancollection.ScanIndexRoot
 
scanList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
ScanListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List and descriptions of scans.
ScanListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ScanListType
 
scanMzWindowLower - Variable in class umich.ms.datatypes.scan.AbstractScan
Note that this number might not correspond to the lowest actual m/z in the spectrumRef.
scanMzWindowUpper - Variable in class umich.ms.datatypes.scan.AbstractScan
Note that this number might not correspond to the highest actual m/z in the spectrumRef.
scanNumFromRT(double, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method ScanNumFromRT
scanNumRaw - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.VarsHolder
 
scanOrigin - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
scans - Variable in class umich.ms.datatypes.LCMSData
 
scans - Variable in class umich.ms.datatypes.scan.AbstractScan
If this scan was added to a scan collection, this field should reference it
scanSettings - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsListType
 
scanSettingsList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
ScanSettingsListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List with the descriptions of the acquisition settings applied prior to the start of data acquisition.
ScanSettingsListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsListType
 
scanSettingsRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
 
ScanSettingsType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Description of the acquisition settings of the instrument prior to the start of the run.
ScanSettingsType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsType
 
scanType - Variable in class umich.ms.datatypes.scan.AbstractScan
Type of scan (Full, Zoom, SIM, etc.).
ScanType - Enum in umich.ms.datatypes.scan.props
The type of scanning used in MS.
scanType - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
 
ScanType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile.
ScanType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
 
scanType - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
scanWindow - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanWindowListType
 
scanWindowList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
 
ScanWindowListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Java class for ScanWindowListType complex type.
ScanWindowListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.ScanWindowListType
 
schedule(int) - Method in class umich.ms.fileio.chunk.ChunkedFile
 
search(Interval1D<K>) - Method in class umich.ms.util.IntervalST
Return an interval in data structure that intersects the given interval; Return null if no such interval exists.
Running time is proportional to log N
searchAll(Interval1D<K>) - Method in class umich.ms.util.IntervalST
Return ALL intervals in data structure that intersect the given interval.
Running time is proportional to R log N, where R is the number of intersections.
searchDatabase - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputsType
 
searchDatabase - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputsType
 
searchDatabase - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
SearchDatabase - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
SearchDatabase() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
 
searchDatabase - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
SearchDatabase - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
SearchDatabase() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
 
searchDatabase - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
searchDatabaseRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
 
searchDatabaseRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseRefType
 
searchDatabaseRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
 
searchDatabaseRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
 
searchDatabaseRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseRefType
 
searchDatabaseRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
 
SearchDatabaseRefType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
One of the search databases used.
SearchDatabaseRefType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseRefType
 
SearchDatabaseRefType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
One of the search databases used.
SearchDatabaseRefType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseRefType
 
SearchDatabaseType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A database for searching mass spectra.
SearchDatabaseType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
 
SearchDatabaseType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A database for searching mass spectra.
SearchDatabaseType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
 
searchEngine - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
searchEngine - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
searchEngine - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
searchEngine - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
searchEngine - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
searchEngine - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
searchEngineVersion - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
searchEngineVersion - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
searchEngineVersion - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
searchHit - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
 
SearchHit - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
SearchHit() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
searchHit - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchResult
 
SearchHit - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
SearchHit() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
searchHit - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchResult
 
searchId - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
searchId - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
 
searchId - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchResult
 
searchId - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
searchId - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchResult
 
searchId - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
searchModification - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationParamsType
 
searchModification - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationParamsType
 
SearchModificationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Specification of a search modification as parameter for a spectra search.
SearchModificationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
 
SearchModificationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Specification of a search modification as parameter for a spectra search.
SearchModificationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
 
searchResult - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
SearchResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
SearchResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchResult
 
searchResult - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
SearchResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
SearchResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchResult
 
searchResult - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
searchScore - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
searchScore - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
searchScore - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
searchScoreSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult
 
searchScoreSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
 
searchScoreSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetResult
 
searchScoreSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
 
SearchScoreSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
SearchScoreSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchScoreSummary
 
searchScoreSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetResult
 
searchScoreSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
 
SearchScoreSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
SearchScoreSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchScoreSummary
 
SearchScoreSummaryIProphet - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
SearchScoreSummaryIProphet() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchScoreSummaryIProphet
 
SearchScoreSummaryIProphet - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
SearchScoreSummaryIProphet() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchScoreSummaryIProphet
 
searchSpecification - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
searchSpecification - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
searchSpecification - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
searchSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
searchSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
SearchSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
SearchSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
searchSummary - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
SearchSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
SearchSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
searchType - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
searchType - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
secondSpotID - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern.Orientation
 
seek(long) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
seek(long) - Method in class umich.ms.external.BufferedRandomAccessFile
Moves the internal pointer to the passed (byte) position in the file.
selectedIon - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SelectedIonListType
 
selectedIonList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
 
SelectedIonListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
The list of selected precursor ions.
SelectedIonListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SelectedIonListType
 
semiSpecific - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
 
semiSpecific - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
 
sense - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
 
sense - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
 
sense - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
 
sensitivity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
 
sensitivity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
 
sensitivity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
 
sensitivity - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
 
sensitivity - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
 
separation - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
separationTechnique - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Separation
 
SeparationTechniqueType - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for separationTechniqueType complex type.
SeparationTechniqueType() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.SeparationTechniqueType
 
seq - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
seq - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
 
seq - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
 
sequence - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint
 
sequence - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SequenceSearchConstraint
 
sequence - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SequenceSearchConstraint
 
sequenceCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
sequenceCollection - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
SequenceCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The collection of sequences (DBSequence or Peptide) identified and their relationship between each other (PeptideEvidence) to be referenced elsewhere in the results.
SequenceCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SequenceCollectionType
 
SequenceCollectionType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The collection of sequences (DBSequence or Peptide) identified and their relationship between each other (PeptideEvidence) to be referenced elsewhere in the results.
SequenceCollectionType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SequenceCollectionType
 
sequenceSearchConstraint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
sequenceSearchConstraint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
SequenceSearchConstraint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
SequenceSearchConstraint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SequenceSearchConstraint
 
sequenceSearchConstraint - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
SequenceSearchConstraint - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
SequenceSearchConstraint() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SequenceSearchConstraint
 
SequentialScanReader - Interface in umich.ms.fileio.filetypes
A universal interface that can be used if you want to traverse all scans in a run and don't care about higher level stuff that IScanCollection provides.
serialNumber - Variable in class umich.ms.datatypes.scan.props.Instrument
 
setAbMax(int) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
setAbMax(double) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
setAbsolute(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
Sets the value of the absolute property.
setAbsolute(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
Sets the value of the absolute property.
setAbsolute(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
Sets the value of the absolute property.
setAbTot(int) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
setAbTot(double) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
setAccession(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CVParamType
Sets the value of the accession property.
setAccession(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
Sets the value of the accession property.
setAccession(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CVParamType
Sets the value of the accession property.
setAccession(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
Sets the value of the accession property.
setAccession(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Sets the value of the accession property.
setAccession(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the accession property.
setAct(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the act property.
setActivation(ParamGroupType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Sets the value of the activation property.
setActivationEnergyHi(Double) - Method in class umich.ms.datatypes.scan.props.ActivationInfo
Either the end of the collision energy ramp or just the collision energy.
setActivationEnergyLo(Double) - Method in class umich.ms.datatypes.scan.props.ActivationInfo
Either the beginning of the collision energy ramp or just the collision energy.
setActivationInfo(ActivationInfo) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
setActivationMethod(String) - Method in class umich.ms.datatypes.scan.props.ActivationInfo
 
setActivationMethod(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Sets the value of the activationMethod property.
setActivationMethod(ActivationMethodType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the activationMethod property.
setActivationMethod(ActivationMethodType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the activationMethod property.
setActivationMethod(ActivationMethodType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the activationMethod property.
setActivationTime(Double) - Method in class umich.ms.datatypes.scan.props.ActivationInfo
 
setActivityDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProtocolApplicationType
Sets the value of the activityDate property.
setActivityDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProtocolApplicationType
Sets the value of the activityDate property.
setAdditionalSearchParams(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Sets the value of the additionalSearchParams property.
setAdditionalSearchParams(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Sets the value of the additionalSearchParams property.
setAdduct(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
setAdjRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Sets the value of the adjRatioMean property.
setAdjRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Sets the value of the adjRatioMean property.
setAdjRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Sets the value of the adjRatioStandardDev property.
setAdjRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Sets the value of the adjRatioStandardDev property.
setAlgo(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Compound
Sets the value of the algo property.
setAllNttProb(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult
Sets the value of the allNttProb property.
setAllNttProb(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
Sets the value of the allNttProb property.
setAllNttProb(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetResult
Sets the value of the allNttProb property.
setAllNttProb(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
Sets the value of the allNttProb property.
setAllNttProb(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetResult
Sets the value of the allNttProb property.
setAllNttProb(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
Sets the value of the allNttProb property.
setAltPosToNegRatio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Sets the value of the altPosToNegRatio property.
setAltPosToNegRatio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Sets the value of the altPosToNegRatio property.
setAltPosToNegRatio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Sets the value of the altPosToNegRatio property.
setAltPosToNegRatio(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Sets the value of the altPosToNegRatio property.
setAltPosToNegRatio(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Sets the value of the altPosToNegRatio property.
setAltPosToNegRatio(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Sets the value of the altPosToNegRatio property.
setAminoacid(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Sets the value of the aminoacid property.
setAminoacid(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Sets the value of the aminoacid property.
setAminoacid(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Sets the value of the aminoacid property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisResult
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisResult
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisResult
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisResult
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
Sets the value of the analysis property.
setAnalysis(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
Sets the value of the analysis property.
setAnalysisCollection(AnalysisCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the analysisCollection property.
setAnalysisCollection(AnalysisCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the analysisCollection property.
setAnalysisData(AnalysisDataType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DataCollectionType
Sets the value of the analysisData property.
setAnalysisData(AnalysisDataType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DataCollectionType
Sets the value of the analysisData property.
setAnalysisDistributionFile(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Sets the value of the analysisDistributionFile property.
setAnalysisDistributionFile(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Sets the value of the analysisDistributionFile property.
setAnalysisParams(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionProtocolType
Sets the value of the analysisParams property.
setAnalysisParams(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionProtocolType
Sets the value of the analysisParams property.
setAnalysisProtocolCollection(AnalysisProtocolCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the analysisProtocolCollection property.
setAnalysisProtocolCollection(AnalysisProtocolCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the analysisProtocolCollection property.
setAnalysisSampleCollection(AnalysisSampleCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the analysisSampleCollection property.
setAnalysisSampleCollection(AnalysisSampleCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the analysisSampleCollection property.
setAnalysisSoftwareList(AnalysisSoftwareListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the analysisSoftwareList property.
setAnalysisSoftwareList(AnalysisSoftwareListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the analysisSoftwareList property.
setAnalysisSoftwareRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionProtocolType
Sets the value of the analysisSoftwareRef property.
setAnalysisSoftwareRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProviderType
Sets the value of the analysisSoftwareRef property.
setAnalysisSoftwareRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Sets the value of the analysisSoftwareRef property.
setAnalysisSoftwareRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionProtocolType
Sets the value of the analysisSoftwareRef property.
setAnalysisSoftwareRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProviderType
Sets the value of the analysisSoftwareRef property.
setAnalysisSoftwareRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Sets the value of the analysisSoftwareRef property.
setAnalyzer(String) - Method in class umich.ms.datatypes.scan.props.Instrument
 
setAnnotation(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Sets the value of the annotation property.
setAnnotation(ProteinAnnotation) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishableProtein
Sets the value of the annotation property.
setAnnotation(ProteinAnnotation) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishableProtein
Sets the value of the annotation property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
Sets the value of the any property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
Sets the value of the any property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
Sets the value of the any property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisResult
Sets the value of the any property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
Sets the value of the any property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisResult
Sets the value of the any property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
Sets the value of the any property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisResult
Sets the value of the any property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
Sets the value of the any property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisResult
Sets the value of the any property.
setAny(Object) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
Sets the value of the any property.
setArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Sets the value of the area property.
setArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Sets the value of the area property.
setArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Sets the value of the area property.
setArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Sets the value of the area property.
setArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Sets the value of the area property.
setArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Sets the value of the area property.
setAreaError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Sets the value of the areaError property.
setAreaError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Sets the value of the areaError property.
setAreaError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Sets the value of the areaError property.
setAreaError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Sets the value of the areaError property.
setAreaError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Sets the value of the areaError property.
setAreaError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Sets the value of the areaError property.
setAreaFlag(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Sets the value of the areaFlag property.
setAreaFlag(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Sets the value of the areaFlag property.
setAreaFlag(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Sets the value of the areaFlag property.
setAreaFlag(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Sets the value of the areaFlag property.
setAreaFlag(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Sets the value of the areaFlag property.
setAreaFlag(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Sets the value of the areaFlag property.
setArrayLength(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
Sets the value of the arrayLength property.
setAsapProtId(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Sets the value of the asapProtId property.
setAsapProtId(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Sets the value of the asapProtId property.
setAsapratioId(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Sets the value of the asapratioId property.
setAsapratioId(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Sets the value of the asapratioId property.
setAsapratioLcHeavypeak(AsapratioLcHeavypeak) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Sets the value of the asapratioLcHeavypeak property.
setAsapratioLcHeavypeak(AsapratioLcHeavypeak) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Sets the value of the asapratioLcHeavypeak property.
setAsapratioLcHeavypeak(AsapratioLcHeavypeak) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Sets the value of the asapratioLcHeavypeak property.
setAsapratioLcLightpeak(AsapratioLcLightpeak) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Sets the value of the asapratioLcLightpeak property.
setAsapratioLcLightpeak(AsapratioLcLightpeak) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Sets the value of the asapratioLcLightpeak property.
setAsapratioLcLightpeak(AsapratioLcLightpeak) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Sets the value of the asapratioLcLightpeak property.
setAsapratioPeptideData(AsapratioPeptideData) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
Sets the value of the asapratioPeptideData property.
setAsapratioPeptideData(AsapratioPeptideData) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
Sets the value of the asapratioPeptideData property.
setAsapratioPeptideData(AsapratioPeptideData) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
Sets the value of the asapratioPeptideData property.
setAssumedCharge(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the assumedCharge property.
setAssumedCharge(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the assumedCharge property.
setAssumedCharge(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the assumedCharge property.
setAt(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
Sets the value of the at property.
setAuditCollection(AuditCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the auditCollection property.
setAuditCollection(AuditCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the auditCollection property.
setAuthor(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Sets the value of the author property.
setAuthor(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Sets the value of the author property.
setAuthor(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Sets the value of the author property.
setAuthor(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Sets the value of the author property.
setAuthor(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Sets the value of the author property.
setAuthor(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Sets the value of the author property.
setAuthor(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Sets the value of the author property.
setAuthor(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Sets the value of the author property.
setAuthor(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Sets the value of the author property.
setAuthors(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Sets the value of the authors property.
setAuthors(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Sets the value of the authors property.
setAvgMassDelta(double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
Sets the value of the avgMassDelta property.
setAvgMassDelta(double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
Sets the value of the avgMassDelta property.
setAvgMassDelta(Double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
Sets the value of the avgMassDelta property.
setAvgMassDelta(Double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
Sets the value of the avgMassDelta property.
setBackground(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Sets the value of the background property.
setBackground(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Sets the value of the background property.
setBackground(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Sets the value of the background property.
setBackground(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Sets the value of the background property.
setBackground(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Sets the value of the background property.
setBackground(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Sets the value of the background property.
setBackgroundFittingError(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Sets the value of the backgroundFittingError property.
setBackgroundFittingError(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Sets the value of the backgroundFittingError property.
setBackgroundRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Sets the value of the backgroundRatioMean property.
setBackgroundRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Sets the value of the backgroundRatioMean property.
setBackgroundRatioStdev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Sets the value of the backgroundRatioStdev property.
setBackgroundRatioStdev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Sets the value of the backgroundRatioStdev property.
setBah(ByteArrayHolder) - Method in class umich.ms.fileio.chunk.FileChunk
 
setBah(ByteArrayHolder, ObjectPool<ByteArrayHolder>) - Method in class umich.ms.fileio.chunk.FileChunk
Sets the byte[] and indicates which pool this array is from.
setBaseName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Sets the value of the baseName property.
setBaseName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Sets the value of the baseName property.
setBaseName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Sets the value of the baseName property.
setBaseName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Sets the value of the baseName property.
setBaseName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Sets the value of the baseName property.
setBaseName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Sets the value of the baseName property.
setBasePeakIntensity(Double) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setBasePeakIntensity(Double) - Method in interface umich.ms.datatypes.scan.IScan
 
setBasePeakIntensity(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the basePeakIntensity property.
setBasePeakMz(Double) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setBasePeakMz(Double) - Method in interface umich.ms.datatypes.scan.IScan
 
setBasePeakMz(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the basePeakMz property.
setBinary(byte[]) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
Sets the value of the binary property.
setBinary(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Sets the value of the binary property.
setBinary(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Sets the value of the binary property.
setBinary(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Sets the value of the binary property.
setBinaryDataArrayList(BinaryDataArrayListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Sets the value of the binaryDataArrayList property.
setBinaryDataArrayList(BinaryDataArrayListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Sets the value of the binaryDataArrayList property.
setBinaryRefFiles(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Sets the value of the binaryRefFiles property.
setBinaryRefFiles(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Sets the value of the binaryRefFiles property.
setBinNo(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Sets the value of the binNo property.
setBinNo(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Sets the value of the binNo property.
setBinNo(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Sets the value of the binNo property.
setBinNo(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Sets the value of the binNo property.
setBinNo(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Sets the value of the binNo property.
setBinNo(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Sets the value of the binNo property.
setBIons(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the bIons property.
setBScore(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the bScore property.
setByteorder(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
Sets the value of the byteorder property.
setByteOrder(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Sets the value of the byteOrder property.
setCalcNeutralPepMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the calcNeutralPepMass property.
setCalcNeutralPepMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the calcNeutralPepMass property.
setCalcNeutralPepMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the calcNeutralPepMass property.
setCalcNeutralPepMass(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
Sets the value of the calcNeutralPepMass property.
setCalcNeutralPepMass(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
Sets the value of the calcNeutralPepMass property.
setCalcNeutralPepMass(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the calcNeutralPepMass property.
setCalcNeutralPepMass(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
Sets the value of the calcNeutralPepMass property.
setCalcNeutralPepMass(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
Sets the value of the calcNeutralPepMass property.
setCalcNeutralPepMass(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the calcNeutralPepMass property.
setCalcPI(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the calcPI property.
setCalcPI(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the calcPI property.
setCalcPI(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the calcPI property.
setCalculatedMassToCharge(double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Sets the value of the calculatedMassToCharge property.
setCalculatedMassToCharge(Double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Sets the value of the calculatedMassToCharge property.
setCalculatedPI(float) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Sets the value of the calculatedPI property.
setCalculatedPI(Float) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Sets the value of the calculatedPI property.
setCategory(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.OntologyEntryType
Sets the value of the category property.
setCentroided(Boolean) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
setCentroided(Boolean) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setCentroided(Boolean) - Method in interface umich.ms.datatypes.scan.IScan
 
setCentroided(Boolean) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Sets the value of the centroided property.
setCentroided(Boolean) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the centroided property.
setCentroidingPreference(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Sets the value of the centroidingPreference property.
setCentroidingPreference(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Sets the value of the centroidingPreference property.
setCentroidingPreference(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Sets the value of the centroidingPreference property.
setCentroidingPreference(int) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Sets the value of the centroidingPreference property.
setCentroidingPreference(int) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Sets the value of the centroidingPreference property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.FragmentMasses
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AffectedChannel
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ContributingChannel
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.FragmentMasses
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AffectedChannel
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ContributingChannel
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.FragmentMasses
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AffectedChannel
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ContributingChannel
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FragmentMasses
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AffectedChannel
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ContributingChannel
Sets the value of the channel property.
setChannel(long) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FragmentMasses
Sets the value of the channel property.
setChannelCode(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Sets the value of the channelCode property.
setChannelCode(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Sets the value of the channelCode property.
setChannelCode(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Sets the value of the channelCode property.
setChannelCode(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Sets the value of the channelCode property.
setChannelCode(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Sets the value of the channelCode property.
setCharge(Integer) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
setCharge(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IonTypeType
Sets the value of the charge property.
setCharge(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IonTypeType
Sets the value of the charge property.
setCharge(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Sets the value of the charge property.
setCharge(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
Sets the value of the charge property.
setCharge(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Sets the value of the charge property.
setCharge(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
Sets the value of the charge property.
setCharge(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Sets the value of the charge property.
setCharge(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
Sets the value of the charge property.
setCharge(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
Sets the value of the charge property.
setCharge(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
Sets the value of the charge property.
setCharge(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the charge property.
setCharge(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
Sets the value of the charge property.
setCharge(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
Sets the value of the charge property.
setCharge(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the charge property.
setChargeDeconvoluted(Boolean) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Sets the value of the chargeDeconvoluted property.
setChargeDeconvoluted(Boolean) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the chargeDeconvoluted property.
setChargeEstCorrect(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType
Sets the value of the chargeEstCorrect property.
setChargeEstCorrect(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocErrorDataType
Sets the value of the chargeEstCorrect property.
setChargeEstCorrect(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocErrorDataType
Sets the value of the chargeEstCorrect property.
setChargeState(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Sets the value of the chargeState property.
setChargeState(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Sets the value of the chargeState property.
setChildScans(List<Integer>) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setChildScans(List<Integer>) - Method in interface umich.ms.datatypes.scan.IScan
 
setChromatogramList(ChromatogramListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Sets the value of the chromatogramList property.
setChunkBufferSize(int) - Method in class umich.ms.fileio.chunk.ChunkedFile
 
setCidGasPressure(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the cidGasPressure property.
setCidIndex(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Sets the value of the cidIndex property.
setCidIndex(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Sets the value of the cidIndex property.
setCidIndex(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Sets the value of the cidIndex property.
setCode(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AmbiguousResidueType
Sets the value of the code property.
setCode(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ResidueType
Sets the value of the code property.
setCode(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AmbiguousResidueType
Sets the value of the code property.
setCode(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ResidueType
Sets the value of the code property.
setCollisionEnergy(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the collisionEnergy property.
setCollisionEnergy(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the collisionEnergy property.
setCollisionEnergy(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the collisionEnergy property.
setCollisionEnergy(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the collisionEnergy property.
setCollisionGas(Boolean) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Sets the value of the collisionGas property.
setComments(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Sets the value of the comments property.
setComments(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Sets the value of the comments property.
setComments(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Sets the value of the comments property.
setCompensationVoltage(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the compensationVoltage property.
setCompensationVoltage(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the compensationVoltage property.
setCompensationVoltage(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the compensationVoltage property.
setCompensationVoltage(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the compensationVoltage property.
setCompletionTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
Sets the value of the completionTime property.
setComponentList(ComponentListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
Sets the value of the componentList property.
setCompoundList(CompoundList) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.CEF
Sets the value of the compoundList property.
setCompressedLen(int) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Sets the value of the compressedLen property.
setCompressionType(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Sets the value of the compressionType property.
setConfidence(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the confidence property.
setConfidence(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the confidence property.
setContactRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ContactRoleType
Sets the value of the contactRef property.
setContactRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ContactRoleType
Sets the value of the contactRef property.
setContactRole(ContactRoleType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
Sets the value of the contactRole property.
setContactRole(ContactRoleType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProviderType
Sets the value of the contactRole property.
setContactRole(ContactRoleType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
Sets the value of the contactRole property.
setContactRole(ContactRoleType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProviderType
Sets the value of the contactRole property.
setContent(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Note
Sets the value of the content property.
setContent(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
Sets the value of the content property.
setContentType(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Sets the value of the contentType property.
setCorrection(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.IsotopicContributions.ContributingChannel.AffectedChannel
Sets the value of the correction property.
setCorrection(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AffectedChannel
Sets the value of the correction property.
setCorrection(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AffectedChannel
Sets the value of the correction property.
setCorrection(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AffectedChannel
Sets the value of the correction property.
setCorrection(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AffectedChannel
Sets the value of the correction property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ProductListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SampleListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsListType
Sets the value of the count property.
setCount(int) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanWindowListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SelectedIonListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileRefListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumListType
Sets the value of the count property.
setCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.TargetListType
Sets the value of the count property.
setCpdAlgo(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Sets the value of the cpdAlgo property.
setCreationDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the creationDate property.
setCreationDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the creationDate property.
setCTermGain(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Sets the value of the cTermGain property.
setCTermGain(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Sets the value of the cTermGain property.
setCurrentController(int, int) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method SetCurrentController
setCustomizations(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
Sets the value of the customizations property.
setCustomizations(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
Sets the value of the customizations property.
setCut(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
Sets the value of the cut property.
setCut(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
Sets the value of the cut property.
setCut(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
Sets the value of the cut property.
setCvList(CVListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the cvList property.
setCvList(CVListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the cvList property.
setCvList(CVListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the cvList property.
setCvParam(CVParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FileFormatType
Sets the value of the cvParam property.
setCvParam(CVParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParamType
Sets the value of the cvParam property.
setCvParam(CVParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.RoleType
Sets the value of the cvParam property.
setCvParam(CVParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIDFormatType
Sets the value of the cvParam property.
setCvParam(CVParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FileFormatType
Sets the value of the cvParam property.
setCvParam(CVParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParamType
Sets the value of the cvParam property.
setCvParam(CVParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.RoleType
Sets the value of the cvParam property.
setCvParam(CVParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIDFormatType
Sets the value of the cvParam property.
setCvRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CVParamType
Sets the value of the cvRef property.
setCvRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CVParamType
Sets the value of the cvRef property.
setCvRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Sets the value of the cvRef property.
setDatabase(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.DatabaseRefreshTimestamp
Sets the value of the database property.
setDatabase(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatabaseRefreshTimestamp
Sets the value of the database property.
setDatabase(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatabaseRefreshTimestamp
Sets the value of the database property.
setDatabaseFilters(DatabaseFiltersType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Sets the value of the databaseFilters property.
setDatabaseFilters(DatabaseFiltersType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Sets the value of the databaseFilters property.
setDatabaseName(ParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Sets the value of the databaseName property.
setDatabaseName(ParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Sets the value of the databaseName property.
setDatabaseName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Sets the value of the databaseName property.
setDatabaseName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Sets the value of the databaseName property.
setDatabaseName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Sets the value of the databaseName property.
setDatabaseReleaseDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Sets the value of the databaseReleaseDate property.
setDatabaseReleaseDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Sets the value of the databaseReleaseDate property.
setDatabaseReleaseDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Sets the value of the databaseReleaseDate property.
setDatabaseReleaseIdentifier(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Sets the value of the databaseReleaseIdentifier property.
setDatabaseReleaseIdentifier(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Sets the value of the databaseReleaseIdentifier property.
setDatabaseReleaseIdentifier(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Sets the value of the databaseReleaseIdentifier property.
setDatabaseTranslation(DatabaseTranslationType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Sets the value of the databaseTranslation property.
setDatabaseTranslation(DatabaseTranslationType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Sets the value of the databaseTranslation property.
setDataCollection(DataCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the dataCollection property.
setDataCollection(DataCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the dataCollection property.
setDatanum(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Sets the value of the datanum property.
setDatanum(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Sets the value of the datanum property.
setDatanum(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Sets the value of the datanum property.
setDatanum(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Sets the value of the datanum property.
setDataProcessingList(DataProcessingListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the dataProcessingList property.
setDataProcessingRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
Sets the value of the dataProcessingRef property.
setDataProcessingRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Sets the value of the dataProcessingRef property.
setDataProcessingRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Sets the value of the dataProcessingRef property.
setDatasetDerivation(MsmsPipelineAnalysis.DatasetDerivation) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
Sets the value of the datasetDerivation property.
setDatasetDerivation(DatasetDerivation) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
Sets the value of the datasetDerivation property.
setDatasetDerivation(DatasetDerivation) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
Sets the value of the datasetDerivation property.
setDatasetDerivation(DatasetDerivation) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
Sets the value of the datasetDerivation property.
setDatasetDerivation(DatasetDerivation) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
Sets the value of the datasetDerivation property.
setDataSource(LCMSDataSource<?>) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
setDataSource(LCMSDataSource<?>) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Set the data source from which the collection will be filled.
setDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
Sets the value of the date property.
setDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
Sets the value of the date property.
setDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
Sets the value of the date property.
setDBSequenceRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Sets the value of the dbSequenceRef property.
setDBSequenceRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
Sets the value of the dbSequenceRef property.
setDBSequenceRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Sets the value of the dbSequenceRef property.
setDBSequenceRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
Sets the value of the dbSequenceRef property.
setDeadVolume(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
Sets the value of the deadVolume property.
setDecimalPvalue(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Sets the value of the decimalPvalue property.
setDecimalPvalue(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Sets the value of the decimalPvalue property.
setDecimalRatio(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the decimalRatio property.
setDecimalRatio(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the decimalRatio property.
setDecimalRatio(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the decimalRatio property.
setDefaultArrayLength(int) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Sets the value of the defaultArrayLength property.
setDefaultArrayLength(int) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Sets the value of the defaultArrayLength property.
setDefaultDataProcessingRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramListType
Sets the value of the defaultDataProcessingRef property.
setDefaultDataProcessingRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumListType
Sets the value of the defaultDataProcessingRef property.
setDefaultInstrumentConfigurationRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Sets the value of the defaultInstrumentConfigurationRef property.
setDefaultInstrumentID(String) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
Call with null parameter to unset.
setDefaultSize(int) - Method in class umich.ms.util.ByteArrayHolderFactory
Sets the default size of byte buffers, produced by this factory.
setDefaultSizeMax(int) - Method in class umich.ms.util.ByteArrayHolderFactory
Updates the default byte buffer size, if the new value is larger, than the current default.
setDefaultSourceFileRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Sets the value of the defaultSourceFileRef property.
setDefaultStorageStrategy(StorageStrategy) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
setDefaultStorageStrategy(StorageStrategy) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
 
setDegenFlag(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Sets the value of the degenFlag property.
setDegenFlag(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Sets the value of the degenFlag property.
setDeisotoped(Boolean) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Sets the value of the deisotoped property.
setDeisotoped(Boolean) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the deisotoped property.
setDelta(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the delta property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Sets the value of the description property.
setDescription(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
Sets the value of the description property.
setDetector(String) - Method in class umich.ms.datatypes.scan.props.Instrument
 
setDevice(Device) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Sets the value of the device property.
setDirectory(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InteractSummary
Sets the value of the directory property.
setDirectory(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InputFileType
Sets the value of the directory property.
setDirectory(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InteractSummary
Sets the value of the directory property.
setDirectory(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InputFileType
Sets the value of the directory property.
setDirectory(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InteractSummary
Sets the value of the directory property.
setDoi(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Sets the value of the doi property.
setDoi(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Sets the value of the doi property.
setDomain(Domain) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Peptide
 
setDuration(Double) - Method in class umich.ms.datatypes.scan.props.InjectionInfo
 
setEditor(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Sets the value of the editor property.
setEditor(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Sets the value of the editor property.
setElution(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Sets the value of the elution property.
setElution(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Sets the value of the elution property.
setElution(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Sets the value of the elution property.
setEmail(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Sets the value of the email property.
setEncodedLength(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.BinaryDataArrayType
Sets the value of the encodedLength property.
setEnd(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the end property.
setEnd(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Peptide
Sets the value of the end property.
setEnd(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Sets the value of the end property.
setEnd(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Sets the value of the end property.
setEndMz(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the endMz property.
setEndScan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the endScan property.
setEndScan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the endScan property.
setEndScan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the endScan property.
setEndTime(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Sets the value of the endTime property.
setEnsemblName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Sets the value of the ensemblName property.
setEnsemblName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Sets the value of the ensemblName property.
setEnzymaticSearchConstraint(MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Sets the value of the enzymaticSearchConstraint property.
setEnzymaticSearchConstraint(EnzymaticSearchConstraint) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Sets the value of the enzymaticSearchConstraint property.
setEnzymaticSearchConstraint(EnzymaticSearchConstraint) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Sets the value of the enzymaticSearchConstraint property.
setEnzyme(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
Sets the value of the enzyme property.
setEnzyme(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EnzymaticSearchConstraint
Sets the value of the enzyme property.
setEnzyme(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.EnzymaticSearchConstraint
Sets the value of the enzyme property.
setEnzymeName(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Sets the value of the enzymeName property.
setEnzymeName(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Sets the value of the enzymeName property.
setEnzymes(EnzymesType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Sets the value of the enzymes property.
setEnzymes(EnzymesType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Sets the value of the enzymes property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Intensity
Sets the value of the error property.
setError(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Intensity
Sets the value of the error property.
setEstTotCorrect(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Sets the value of the estTotCorrect property.
setEstTotCorrect(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Sets the value of the estTotCorrect property.
setEstTotCorrect(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Sets the value of the estTotCorrect property.
setEstTotNumCorrect(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Sets the value of the estTotNumCorrect property.
setEstTotNumCorrect(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Sets the value of the estTotNumCorrect property.
setEstTotNumCorrect(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Sets the value of the estTotNumCorrect property.
setEstTotNumCorrectPep(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Sets the value of the estTotNumCorrectPep property.
setEstTotNumCorrectPep(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Sets the value of the estTotNumCorrectPep property.
setEstTotNumCorrectPsm(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Sets the value of the estTotNumCorrectPsm property.
setEstTotNumCorrectPsm(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Sets the value of the estTotNumCorrectPsm property.
setExclude(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FilterType
Sets the value of the exclude property.
setExclude(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FilterType
Sets the value of the exclude property.
setExcludeEmptyScans(boolean) - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
If true, empty scans will be discarded during parsing.
Need to be called prior to parsing.
setExcludeEmptyScans(boolean) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
If true, empty scans will be discarded during parsing.
Need to be called prior to parsing.
setExpect(double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the expect property.
setExpect(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the expect property.
setExpect(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Sets the value of the expect property.
setExperimentalMassToCharge(double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Sets the value of the experimentalMassToCharge property.
setExperimentalMassToCharge(double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Sets the value of the experimentalMassToCharge property.
setExpSiblingIonBin(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the expSiblingIonBin property.
setExpSiblingIonBin(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the expSiblingIonBin property.
setExpSiblingIonInstances(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the expSiblingIonInstances property.
setExpSiblingIonInstances(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the expSiblingIonInstances property.
setExpTotInstances(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the expTotInstances property.
setExpTotInstances(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the expTotInstances property.
setExternalFormatDocumentation(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ExternalDataType
Sets the value of the externalFormatDocumentation property.
setExternalFormatDocumentation(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ExternalDataType
Sets the value of the externalFormatDocumentation property.
setExternalSpectrumID(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Sets the value of the externalSpectrumID property.
setExternalSpectrumID(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
Sets the value of the externalSpectrumID property.
setFactory(ByteArrayHolderFactory) - Method in class umich.ms.util.PooledByteArrayHolders
You should be very careful about this one.
setFalsePositiveErrorRate(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
Sets the value of the falsePositiveErrorRate property.
setFalsePositiveErrorRate(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
Sets the value of the falsePositiveErrorRate property.
setFI(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the fi property.
setFidelity(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
Sets the value of the fidelity property.
setFidelity(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
Sets the value of the fidelity property.
setFidelity(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
Sets the value of the fidelity property.
setFile(File) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Sets the value of the file property.
setFileContent(ParamGroupType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.FileDescriptionType
Sets the value of the fileContent property.
setFileDescription(FileDescriptionType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the fileDescription property.
setFileFormat(FileFormatType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ExternalDataType
Sets the value of the fileFormat property.
setFileFormat(FileFormatType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ExternalDataType
Sets the value of the fileFormat property.
setFileName(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
Sets the value of the fileName property.
setFilename(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InteractSummary
Sets the value of the filename property.
setFilename(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InteractSummary
Sets the value of the filename property.
setFilename(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InteractSummary
Sets the value of the filename property.
setFilePointer(long) - Method in class umich.ms.fileio.util.ReverseLineInputStream
 
setFileSha1(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
Sets the value of the fileSha1 property.
setFileType(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
Sets the value of the fileType property.
setFilter(String) - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawIndexElement
 
setFilterLine(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the filterLine property.
setFilterType(ParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FilterType
Sets the value of the filterType property.
setFilterType(ParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FilterType
Sets the value of the filterType property.
setFinalPeptideWtIters(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Sets the value of the finalPeptideWtIters property.
setFinalPeptideWtIters(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Sets the value of the finalPeptideWtIters property.
setFirst(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Sets the value of the first property.
setFirstName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
Sets the value of the firstName property.
setFirstName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
Sets the value of the firstName property.
setFirstSpotID(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern.Orientation
Sets the value of the firstSpotID property.
setFixedMod(boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
Sets the value of the fixedMod property.
setFixedMod(boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
Sets the value of the fixedMod property.
setFlybase(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Sets the value of the flybase property.
setFlybase(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Sets the value of the flybase property.
setFollowLinks(boolean) - Method in class umich.ms.fileio.util.FileListing
 
setFormat(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
Sets the value of the format property.
setFpkmAdjustedProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the fpkmAdjustedProbability property.
setFpkmAdjustedProbability(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the fpkmAdjustedProbability property.
setFpkmBin(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the fpkmBin property.
setFpkmBin(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the fpkmBin property.
setFpkmFlag(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Sets the value of the fpkmFlag property.
setFpkmFlag(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Sets the value of the fpkmFlag property.
setFpkmLowerBoundExcl(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Sets the value of the fpkmLowerBoundExcl property.
setFpkmLowerBoundExcl(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Sets the value of the fpkmLowerBoundExcl property.
setFpkmLowerBoundIncl(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Sets the value of the fpkmLowerBoundIncl property.
setFpkmLowerBoundIncl(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Sets the value of the fpkmLowerBoundIncl property.
setFpkmUpperBoundExcl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Sets the value of the fpkmUpperBoundExcl property.
setFpkmUpperBoundExcl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Sets the value of the fpkmUpperBoundExcl property.
setFpkmUpperBoundIncl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Sets the value of the fpkmUpperBoundIncl property.
setFpkmUpperBoundIncl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Sets the value of the fpkmUpperBoundIncl property.
setFragmentation(FragmentationType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Sets the value of the fragmentation property.
setFragmentation(FragmentationType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Sets the value of the fragmentation property.
setFragmentationTable(FragmentationTableType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
Sets the value of the fragmentationTable property.
setFragmentationTable(FragmentationTableType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
Sets the value of the fragmentationTable property.
setFragmentMassType(MassType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Sets the value of the fragmentMassType property.
setFragmentMassType(MassType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Sets the value of the fragmentMassType property.
setFragmentMassType(MassType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Sets the value of the fragmentMassType property.
setFragmentTolerance(ToleranceType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Sets the value of the fragmentTolerance property.
setFragmentTolerance(ToleranceType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Sets the value of the fragmentTolerance property.
setFrame(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Sets the value of the frame property.
setFrame(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Sets the value of the frame property.
setFullAnalysisDistributionFile(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPvalueAnalysisSummary
Sets the value of the fullAnalysisDistributionFile property.
setFullAnalysisDistributionFile(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPvalueAnalysisSummary
Sets the value of the fullAnalysisDistributionFile property.
setFullName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
Sets the value of the fullName property.
setFullName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
Sets the value of the fullName property.
setFullName(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
Sets the value of the fullName property.
setFv(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
Sets the value of the fv property.
setFvalue(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the fvalue property.
setFvalue(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the fvalue property.
setFvalue(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the fvalue property.
setGenerationNo(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation
Sets the value of the generationNo property.
setGenerationNo(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatasetDerivation
Sets the value of the generationNo property.
setGenerationNo(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatasetDerivation
Sets the value of the generationNo property.
setGenerationNo(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DatasetDerivation
Sets the value of the generationNo property.
setGenerationNo(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DatasetDerivation
Sets the value of the generationNo property.
setGroup(Group) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the group property.
setGroupNumber(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
Sets the value of the groupNumber property.
setGroupNumber(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
Sets the value of the groupNumber property.
setGroupsFlag(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Sets the value of the groupsFlag property.
setGroupsFlag(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Sets the value of the groupsFlag property.
setGroupSiblingId(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the groupSiblingId property.
setGroupSiblingId(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the groupSiblingId property.
setHeavy2LightAdjRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Sets the value of the heavy2LightAdjRatioMean property.
setHeavy2LightAdjRatioMean(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Sets the value of the heavy2LightAdjRatioMean property.
setHeavy2LightAdjRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Sets the value of the heavy2LightAdjRatioStandardDev property.
setHeavy2LightAdjRatioStandardDev(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Sets the value of the heavy2LightAdjRatioStandardDev property.
setHeavy2LightError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
Sets the value of the heavy2LightError property.
setHeavy2LightError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
Sets the value of the heavy2LightError property.
setHeavy2LightError(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
Sets the value of the heavy2LightError property.
setHeavy2LightMean(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
Sets the value of the heavy2LightMean property.
setHeavy2LightMean(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
Sets the value of the heavy2LightMean property.
setHeavy2LightMean(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
Sets the value of the heavy2LightMean property.
setHeavy2LightRatio(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the heavy2LightRatio property.
setHeavy2LightRatio(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the heavy2LightRatio property.
setHeavy2LightRatio(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the heavy2LightRatio property.
setHeavy2LightRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Sets the value of the heavy2LightRatioMean property.
setHeavy2LightRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Sets the value of the heavy2LightRatioMean property.
setHeavy2LightRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Sets the value of the heavy2LightRatioMean property.
setHeavy2LightRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Sets the value of the heavy2LightRatioMean property.
setHeavy2LightRatioMean(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Sets the value of the heavy2LightRatioMean property.
setHeavy2LightRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Sets the value of the heavy2LightRatioMean property.
setHeavy2LightRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Sets the value of the heavy2LightRatioStandardDev property.
setHeavy2LightRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Sets the value of the heavy2LightRatioStandardDev property.
setHeavy2LightRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Sets the value of the heavy2LightRatioStandardDev property.
setHeavy2LightRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Sets the value of the heavy2LightRatioStandardDev property.
setHeavy2LightRatioStandardDev(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Sets the value of the heavy2LightRatioStandardDev property.
setHeavy2LightRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Sets the value of the heavy2LightRatioStandardDev property.
setHeavyArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the heavyArea property.
setHeavyArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the heavyArea property.
setHeavyArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the heavyArea property.
setHeavyFirstscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the heavyFirstscan property.
setHeavyFirstscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the heavyFirstscan property.
setHeavyFirstscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the heavyFirstscan property.
setHeavyLastscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the heavyLastscan property.
setHeavyLastscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the heavyLastscan property.
setHeavyLastscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the heavyLastscan property.
setHeavyMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Sets the value of the heavyMass property.
setHeavyMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the heavyMass property.
setHeavyMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Sets the value of the heavyMass property.
setHeavyMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the heavyMass property.
setHeavyMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Sets the value of the heavyMass property.
setHeavyMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the heavyMass property.
setHighMz(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the highMz property.
setHitRank(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the hitRank property.
setHitRank(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the hitRank property.
setHitRank(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the hitRank property.
setHyperscore(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the hyperscore property.
setId(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the id property.
setId(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the id property.
setId(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Sets the value of the id property.
setId(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IdentifiableType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IdentifiableType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.DataProcessingType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SampleType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileType
Sets the value of the id property.
setId(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Sets the value of the id property.
setId(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
Sets the value of the id property.
setId(Long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AnalysisResult
Sets the value of the id property.
setId(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisResult
Sets the value of the id property.
setId(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
Sets the value of the id property.
setId(Long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisResult
Sets the value of the id property.
setId(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
Sets the value of the id property.
setId(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisResult
Sets the value of the id property.
setId(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
Sets the value of the id property.
setId(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisResult
Sets the value of the id property.
setId(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
Sets the value of the id property.
setInclude(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FilterType
Sets the value of the include property.
setInclude(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FilterType
Sets the value of the include property.
setInclude(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPDta
Sets the value of the include property.
setInclude(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Sets the value of the include property.
setInclude(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Sets the value of the include property.
setInclude(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPDta
Sets the value of the include property.
setInclude(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Sets the value of the include property.
setInclude(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Sets the value of the include property.
setIncludeDirectories(boolean) - Method in class umich.ms.fileio.util.FileListing
 
setIncludeFiles(boolean) - Method in class umich.ms.fileio.util.FileListing
 
setIndependent(boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymesType
Sets the value of the independent property.
setIndependent(Boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymesType
Sets the value of the independent property.
setIndependent(Boolean) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
Sets the value of the independent property.
setIndependent(boolean) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
Sets the value of the independent property.
setIndependent(Boolean) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
Sets the value of the independent property.
setIndex(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Sets the value of the index property.
setIndex(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Sets the value of the index property.
setIndex(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the index property.
setIndex(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the index property.
setIndex(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the index property.
setInitialMinPeptideProb(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the initialMinPeptideProb property.
setInitialMinPeptideProb(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the initialMinPeptideProb property.
setInitialPeptideWtIters(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Sets the value of the initialPeptideWtIters property.
setInitialPeptideWtIters(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Sets the value of the initialPeptideWtIters property.
setInitialProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the initialProbability property.
setInitialProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the initialProbability property.
setInjectionInfo(InjectionInfo) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setInjectionInfo(InjectionInfo) - Method in interface umich.ms.datatypes.scan.IScan
 
setInputs(InputsType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DataCollectionType
Sets the value of the inputs property.
setInputs(InputsType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DataCollectionType
Sets the value of the inputs property.
setInstrument(Instrument) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setInstrument(Instrument) - Method in interface umich.ms.datatypes.scan.IScan
 
setInstrumentConfigurationList(InstrumentConfigurationListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the instrumentConfigurationList property.
setInstrumentConfigurationRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
Sets the value of the instrumentConfigurationRef property.
setIntensities(double[]) - Method in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
 
setIntensity(Double) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
setIntensity(int, double) - Method in interface umich.ms.datatypes.spectrum.IIndexedSpectrum
Deprecated.
 
setIntensityCutoff(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Sets the value of the intensityCutoff property.
setIonDescription(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
setIonId(IonId) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
setIonisation(String) - Method in class umich.ms.datatypes.scan.props.Instrument
 
setIonisationEnergy(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the ionisationEnergy property.
setIpiName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Sets the value of the ipiName property.
setIpiName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Sets the value of the ipiName property.
setIs(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
Sets the value of the is property.
setIsContributingEvidence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the isContributingEvidence property.
setIsContributingEvidence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the isContributingEvidence property.
setIsDecoy(boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Sets the value of the isDecoy property.
setIsDecoy(Boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Sets the value of the isDecoy property.
setIsHeavy(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Sets the value of the isHeavy property.
setIsHeavy(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Sets the value of the isHeavy property.
setIsHeavy(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Sets the value of the isHeavy property.
setIsHeavy(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Sets the value of the isHeavy property.
setIsHeavy(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Sets the value of the isHeavy property.
setIsHeavy(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Sets the value of the isHeavy property.
setIsNondegenerateEvidence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the isNondegenerateEvidence property.
setIsNondegenerateEvidence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the isNondegenerateEvidence property.
setIsolationWindow(ParamGroupType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Sets the value of the isolationWindow property.
setIsolationWindow(ParamGroupType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ProductType
Sets the value of the isolationWindow property.
setIsotopeNumber(int) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
setIsotopicContributions(LibraSummary.IsotopicContributions) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Sets the value of the isotopicContributions property.
setIsotopicContributions(IsotopicContributions) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Sets the value of the isotopicContributions property.
setIsotopicContributions(IsotopicContributions) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Sets the value of the isotopicContributions property.
setIsotopicContributions(IsotopicContributions) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Sets the value of the isotopicContributions property.
setIsotopicContributions(IsotopicContributions) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Sets the value of the isotopicContributions property.
setIsRejected(Boolean) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult
Sets the value of the isRejected property.
setIsRejected(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the isRejected property.
setIsRejected(boolean) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraResult
Sets the value of the isRejected property.
setIsRejected(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the isRejected property.
setIsRejected(Boolean) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraResult
Sets the value of the isRejected property.
setIsRejected(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the isRejected property.
setIssue(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Sets the value of the issue property.
setIssue(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Sets the value of the issue property.
setJavolutionLogLevel(Logger) - Static method in class umich.ms.logging.LogHelper
Set Javolution log level according to the provided logger.
setJavolutionLogLevel(LogContext.Level) - Static method in class umich.ms.logging.LogHelper
 
setJavolutionLogLevelFatal() - Static method in class umich.ms.logging.LogHelper
 
setLabel(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Bioml
Sets the value of the label property.
setLabel(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the label property.
setLabel(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Note
Sets the value of the label property.
setLabel(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Sets the value of the label property.
setLabel(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Sets the value of the label property.
setLabel(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Xdata
Sets the value of the label property.
setLabel(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Ydata
Sets the value of the label property.
setLabeledResidues(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Sets the value of the labeledResidues property.
setLabeledResidues(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Sets the value of the labeledResidues property.
setLabeledResidues(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Sets the value of the labeledResidues property.
setLabeledResidues(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Sets the value of the labeledResidues property.
setLabeledResidues(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Sets the value of the labeledResidues property.
setLabeledResidues(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Sets the value of the labeledResidues property.
setLaserFrequency(Duration) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Sets the value of the laserFrequency property.
setLaserIntensity(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Sets the value of the laserIntensity property.
setLaserShootCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Sets the value of the laserShootCount property.
setLast(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Sets the value of the last property.
setLastName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
Sets the value of the lastName property.
setLastName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
Sets the value of the lastName property.
setLeftValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Sets the value of the leftValley property.
setLeftValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Sets the value of the leftValley property.
setLeftValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Sets the value of the leftValley property.
setLeftValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Sets the value of the leftValley property.
setLeftValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Sets the value of the leftValley property.
setLeftValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Sets the value of the leftValley property.
setLength(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
Sets the value of the length property.
setLength(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
Sets the value of the length property.
setLightArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the lightArea property.
setLightArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the lightArea property.
setLightArea(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the lightArea property.
setLightFirstscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the lightFirstscan property.
setLightFirstscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the lightFirstscan property.
setLightFirstscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the lightFirstscan property.
setLightLastscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the lightLastscan property.
setLightLastscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the lightLastscan property.
setLightLastscan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the lightLastscan property.
setLightMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Sets the value of the lightMass property.
setLightMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the lightMass property.
setLightMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Sets the value of the lightMass property.
setLightMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the lightMass property.
setLightMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Sets the value of the lightMass property.
setLightMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the lightMass property.
setLightSequence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Sets the value of the lightSequence property.
setLightSequence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Sets the value of the lightSequence property.
setLocalPath(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Sets the value of the localPath property.
setLocalPath(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Sets the value of the localPath property.
setLocalPath(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Sets the value of the localPath property.
setLocation(Location) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Compound
Sets the value of the location property.
setLocation(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ExternalDataType
Sets the value of the location property.
setLocation(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
Sets the value of the location property.
setLocation(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
Sets the value of the location property.
setLocation(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ExternalDataType
Sets the value of the location property.
setLocation(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
Sets the value of the location property.
setLocation(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
Sets the value of the location property.
setLocation(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileType
Sets the value of the location property.
setLocusLinkName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Sets the value of the locusLinkName property.
setLocusLinkName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Sets the value of the locusLinkName property.
setLogratio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Point
Sets the value of the logratio property.
setLogratio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Point
Sets the value of the logratio property.
setLowMz(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the lowMz property.
setM(Double) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
Sets the value of the m property.
setMaldi(Scan.Maldi) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the maldi property.
setMaldiMatrix(OntologyEntryType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
Sets the value of the maldiMatrix property.
setManufacturer(String) - Method in class umich.ms.datatypes.scan.props.Instrument
 
setMass(double) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
setMass(float) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ResidueType
Sets the value of the mass property.
setMass(float) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ResidueType
Sets the value of the mass property.
setMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Sets the value of the mass property.
setMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Sets the value of the mass property.
setMass(double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
Sets the value of the mass property.
setMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Sets the value of the mass property.
setMass(double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModAminoacidMass
Sets the value of the mass property.
setMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Sets the value of the mass property.
setMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Sets the value of the mass property.
setMass(double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModAminoacidMass
Sets the value of the mass property.
setMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Sets the value of the mass property.
setMass(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModAminoacidMass
Sets the value of the mass property.
setMass(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModAminoacidMass
Sets the value of the mass property.
setMassDelta(float) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
Sets the value of the massDelta property.
setMassDelta(float) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
Sets the value of the massDelta property.
setMassdiff(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Sets the value of the massdiff property.
setMassdiff(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Sets the value of the massdiff property.
setMassdiff(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the massdiff property.
setMassdiff(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Sets the value of the massdiff property.
setMassdiff(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Sets the value of the massdiff property.
setMassdiff(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the massdiff property.
setMassdiff(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Sets the value of the massdiff property.
setMassdiff(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Sets the value of the massdiff property.
setMassdiff(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Sets the value of the massdiff property.
setMassdiff(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the massdiff property.
setMassdiff(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Sets the value of the massdiff property.
setMassdiff(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Sets the value of the massdiff property.
setMassTableRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Sets the value of the massTableRef property.
setMassTableRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Sets the value of the massTableRef property.
setMassTol(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the massTol property.
setMasstol(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Sets the value of the masstol property.
setMassTol(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the massTol property.
setMasstol(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Sets the value of the masstol property.
setMassTol(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the massTol property.
setMasstol(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Sets the value of the masstol property.
setMassTolerance(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Sets the value of the massTolerance property.
setMassTolerance(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Sets the value of the massTolerance property.
setMassTolerance(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Sets the value of the massTolerance property.
setMassTolerance(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Sets the value of the massTolerance property.
setMassTolerance(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Sets the value of the massTolerance property.
setMassTolerance(int, double, int) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile
method SetMassTolerance
setMax(Double) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRange
Sets the value of the max property.
setMaxFpkm(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the maxFpkm property.
setMaxFpkm(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the maxFpkm property.
setMaxI(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the maxI property.
setMaxInt(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
setMaxIntMz(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
setMaxMZ(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
setMaxNumInternalCleavages(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
Sets the value of the maxNumInternalCleavages property.
setMaxNumInternalCleavages(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EnzymaticSearchConstraint
Sets the value of the maxNumInternalCleavages property.
setMaxNumInternalCleavages(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.EnzymaticSearchConstraint
Sets the value of the maxNumInternalCleavages property.
setmCount(int) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
setMean(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioResult
Sets the value of the mean property.
setMean(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioResult
Sets the value of the mean property.
setMean(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioResult
Sets the value of the mean property.
setMeasureRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentArrayType
Sets the value of the measureRef property.
setMeasureRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentArrayType
Sets the value of the measureRef property.
setMh(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the mh property.
setMh(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the mh property.
setMidInitials(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PersonType
Sets the value of the midInitials property.
setMidInitials(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PersonType
Sets the value of the midInitials property.
setMin(Double) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRange
Sets the value of the min property.
setMinDistance(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Sets the value of the minDistance property.
setMinDistance(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Sets the value of the minDistance property.
setMinInt(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
setMinIntNonZero(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
setMinMZ(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
setMinNumberTermini(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.EnzymaticSearchConstraint
Sets the value of the minNumberTermini property.
setMinNumberTermini(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EnzymaticSearchConstraint
Sets the value of the minNumberTermini property.
setMinNumberTermini(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.EnzymaticSearchConstraint
Sets the value of the minNumberTermini property.
setMinNumChromatogramPoints(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Sets the value of the minNumChromatogramPoints property.
setMinNumChromatogramPoints(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Sets the value of the minNumChromatogramPoints property.
setMinNumEnzTerm(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.DatabaseRefreshTimestamp
Sets the value of the minNumEnzTerm property.
setMinNumEnzTerm(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DatabaseRefreshTimestamp
Sets the value of the minNumEnzTerm property.
setMinNumEnzTerm(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DatabaseRefreshTimestamp
Sets the value of the minNumEnzTerm property.
setMinNumIsotopePeaks(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Sets the value of the minNumIsotopePeaks property.
setMinNumIsotopePeaks(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Sets the value of the minNumIsotopePeaks property.
setMinPepProb(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Sets the value of the minPepProb property.
setMinPepProb(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Sets the value of the minPepProb property.
setMinPeptideProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Sets the value of the minPeptideProbability property.
setMinPeptideProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the minPeptideProbability property.
setMinPeptideProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
Sets the value of the minPeptideProbability property.
setMinPeptideProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Sets the value of the minPeptideProbability property.
setMinPeptideProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the minPeptideProbability property.
setMinPeptideProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
Sets the value of the minPeptideProbability property.
setMinPeptideWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Sets the value of the minPeptideWeight property.
setMinPeptideWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the minPeptideWeight property.
setMinPeptideWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
Sets the value of the minPeptideWeight property.
setMinPeptideWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Sets the value of the minPeptideWeight property.
setMinPeptideWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the minPeptideWeight property.
setMinPeptideWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
Sets the value of the minPeptideWeight property.
setMinPepWt(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Sets the value of the minPepWt property.
setMinPepWt(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Sets the value of the minPepWt property.
setMinProb(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Sets the value of the minProb property.
setMinProb(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
Sets the value of the minProb property.
setMinProb(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
Sets the value of the minProb property.
setMinProb(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
Sets the value of the minProb property.
setMinProb(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Sets the value of the minProb property.
setMinProb(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
Sets the value of the minProb property.
setMinProb(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
Sets the value of the minProb property.
setMinProb(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Sets the value of the minProb property.
setMinProb(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
Sets the value of the minProb property.
setMinProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
Sets the value of the minProbability property.
setMinProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
Sets the value of the minProbability property.
setMinProteinProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Sets the value of the minProteinProbability property.
setMinProteinProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
Sets the value of the minProteinProbability property.
setMinProteinProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Sets the value of the minProteinProbability property.
setMinProteinProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
Sets the value of the minProteinProbability property.
setMinProtProb(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Sets the value of the minProtProb property.
setMinProtProb(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Sets the value of the minProtProb property.
setMinSpacing(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
Sets the value of the minSpacing property.
setMinSpacing(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
Sets the value of the minSpacing property.
setMinSpacing(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
Sets the value of the minSpacing property.
setMissedCleavages(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the missedCleavages property.
setMissedCleavages(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Sets the value of the missedCleavages property.
setMissedCleavages(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Sets the value of the missedCleavages property.
setModCtermMass(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
Sets the value of the modCtermMass property.
setModCtermMass(double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
Sets the value of the modCtermMass property.
setModCtermMass(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
Sets the value of the modCtermMass property.
setModCtermMass(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
Sets the value of the modCtermMass property.
setModCtermMass(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
Sets the value of the modCtermMass property.
setModel(String) - Method in class umich.ms.datatypes.scan.props.Instrument
 
setModel1NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model1NegDistr property.
setModel1NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model1NegDistr property.
setModel1NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model1NegDistr property.
setModel1PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model1PosDistr property.
setModel1PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model1PosDistr property.
setModel1PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model1PosDistr property.
setModel2NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model2NegDistr property.
setModel2NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model2NegDistr property.
setModel2NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model2NegDistr property.
setModel2PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model2PosDistr property.
setModel2PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model2PosDistr property.
setModel2PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model2PosDistr property.
setModel3NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model3NegDistr property.
setModel3NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model3NegDistr property.
setModel3NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model3NegDistr property.
setModel3PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model3PosDistr property.
setModel3PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model3PosDistr property.
setModel3PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model3PosDistr property.
setModel4NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model4NegDistr property.
setModel4NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model4NegDistr property.
setModel4NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model4NegDistr property.
setModel4PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model4PosDistr property.
setModel4PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model4PosDistr property.
setModel4PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model4PosDistr property.
setModel5NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model5NegDistr property.
setModel5NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model5NegDistr property.
setModel5NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model5NegDistr property.
setModel5PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model5PosDistr property.
setModel5PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model5PosDistr property.
setModel5PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model5PosDistr property.
setModel6NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model6NegDistr property.
setModel6NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model6NegDistr property.
setModel6NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model6NegDistr property.
setModel6PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model6PosDistr property.
setModel6PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model6PosDistr property.
setModel6PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model6PosDistr property.
setModel7NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model7NegDistr property.
setModel7NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model7NegDistr property.
setModel7NegDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model7NegDistr property.
setModel7PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the model7PosDistr property.
setModel7PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the model7PosDistr property.
setModel7PosDistr(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the model7PosDistr property.
setModelDistr(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Point
Sets the value of the modelDistr property.
setModelDistr(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Point
Sets the value of the modelDistr property.
setModificationInfo(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the modificationInfo property.
setModificationInfo(ModificationInfo) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the modificationInfo property.
setModificationInfo(ModificationInfo) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the modificationInfo property.
setModificationParams(ModificationParamsType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Sets the value of the modificationParams property.
setModificationParams(ModificationParamsType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Sets the value of the modificationParams property.
setModified(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
Sets the value of the modified property.
setModifiedPeptide(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
Sets the value of the modifiedPeptide property.
setModifiedPeptide(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
Sets the value of the modifiedPeptide property.
setModifiedPeptide(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
Sets the value of the modifiedPeptide property.
setModifiedPeptide(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
Sets the value of the modifiedPeptide property.
setModifiedPeptide(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
Sets the value of the modifiedPeptide property.
setModNtermMass(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo
Sets the value of the modNtermMass property.
setModNtermMass(double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModificationInfo
Sets the value of the modNtermMass property.
setModNtermMass(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModificationInfo
Sets the value of the modNtermMass property.
setModNtermMass(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Mod
Sets the value of the modNtermMass property.
setModNtermMass(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Mod
Sets the value of the modNtermMass property.
setMolId(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
setMonoisotopicMassDelta(double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ModificationType
Sets the value of the monoisotopicMassDelta property.
setMonoisotopicMassDelta(double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
Sets the value of the monoisotopicMassDelta property.
setMonoisotopicMassDelta(Double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ModificationType
Sets the value of the monoisotopicMassDelta property.
setMonoisotopicMassDelta(Double) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
Sets the value of the monoisotopicMassDelta property.
setMSDetails(MSDetails) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Sets the value of the msDetails property.
setMsDetector(OntologyEntryType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Sets the value of the msDetector property.
setMsDetector(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Sets the value of the msDetector property.
setMsDetector(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Sets the value of the msDetector property.
setMsDetector(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Sets the value of the msDetector property.
setMsInstrumentID(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Sets the value of the msInstrumentID property.
setMsInstrumentID(Integer) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the msInstrumentID property.
setMsIonisation(OntologyEntryType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Sets the value of the msIonisation property.
setMsIonization(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Sets the value of the msIonization property.
setMsIonization(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Sets the value of the msIonization property.
setMsIonization(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Sets the value of the msIonization property.
setMsLevel(Integer) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setMsLevel(Integer) - Method in interface umich.ms.datatypes.scan.IScan
 
setMsLevel(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the msLevel property.
setMsLvls(Set<Integer>) - Method in class umich.ms.datatypes.LCMSDataSubset
 
setMsManufacturer(MsRun.MsInstrument.MsManufacturer) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Sets the value of the msManufacturer property.
setMsManufacturer(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Sets the value of the msManufacturer property.
setMsManufacturer(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Sets the value of the msManufacturer property.
setMsManufacturer(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Sets the value of the msManufacturer property.
setMsMassAnalyzer(MsRun.MsInstrument.MsMassAnalyzer) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Sets the value of the msMassAnalyzer property.
setMsMassAnalyzer(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Sets the value of the msMassAnalyzer property.
setMsMassAnalyzer(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Sets the value of the msMassAnalyzer property.
setMsMassAnalyzer(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Sets the value of the msMassAnalyzer property.
setMsModel(OntologyEntryType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Sets the value of the msModel property.
setMsModel(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Sets the value of the msModel property.
setMsModel(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Sets the value of the msModel property.
setMsModel(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Sets the value of the msModel property.
setMSPeaks(MSPeaks) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Sets the value of the msPeaks property.
setMsResolution(OntologyEntryType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Sets the value of the msResolution property.
setMz(int, double) - Method in interface umich.ms.datatypes.spectrum.IIndexedSpectrum
Deprecated.
 
setMz(double) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
setMz(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.FragmentMasses
Sets the value of the mz property.
setMz(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.FragmentMasses
Sets the value of the mz property.
setMz(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.FragmentMasses
Sets the value of the mz property.
setMz(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FragmentMasses
Sets the value of the mz property.
setMz(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Intensity
Sets the value of the mz property.
setMz(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FragmentMasses
Sets the value of the mz property.
setMz(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Intensity
Sets the value of the mz property.
setMzIntPair(int, double, double) - Method in interface umich.ms.datatypes.spectrum.IIndexedSpectrum
Deprecated.
 
setMzRangeEnd(Double) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
setMzRanges(List<DoubleRange>) - Method in class umich.ms.datatypes.LCMSDataSubset
 
setMzRangeStart(Double) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
setMzs(double[]) - Method in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
 
setMzTarget(Double) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
setName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.IdentifiableType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.IdentifiableType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SampleType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InputFileType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InputFileType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixturemodelDistribution
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InputFileType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixturemodelDistribution
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
Sets the value of the name property.
setName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
Sets the value of the name property.
setNegBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
Sets the value of the negBandwidth property.
setNegBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
Sets the value of the negBandwidth property.
setNegBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
Sets the value of the negBandwidth property.
setNegBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
Sets the value of the negBandwidth property.
setNegBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
Sets the value of the negBandwidth property.
setNegBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
Sets the value of the negBandwidth property.
setNegDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
Sets the value of the negDens property.
setNegDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel.Point
Sets the value of the negDens property.
setNegDens(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
Sets the value of the negDens property.
setNegDens(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Point
Sets the value of the negDens property.
setNegDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
Sets the value of the negDens property.
setNegDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Point
Sets the value of the negDens property.
setNegFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Sets the value of the negFreq property.
setNegFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Sets the value of the negFreq property.
setNegFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Sets the value of the negFreq property.
setNegFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Sets the value of the negFreq property.
setNegFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Sets the value of the negFreq property.
setNegFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Sets the value of the negFreq property.
setNegmodelDistribution(PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.NegmodelDistribution) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution
Sets the value of the negmodelDistribution property.
setNegmodelDistribution(NegmodelDistribution) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixturemodelDistribution
Sets the value of the negmodelDistribution property.
setNegmodelDistribution(NegmodelDistribution) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixturemodelDistribution
Sets the value of the negmodelDistribution property.
setNegObsDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
Sets the value of the negObsDens property.
setNegObsDens(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
Sets the value of the negObsDens property.
setNegObsDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
Sets the value of the negObsDens property.
setNeighboringBinSmoothing(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmInformation
Sets the value of the neighboringBinSmoothing property.
setNeighboringBinSmoothing(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspInformation
Sets the value of the neighboringBinSmoothing property.
setNeighboringBinSmoothing(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmInformation
Sets the value of the neighboringBinSmoothing property.
setNeighboringBinSmoothing(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspInformation
Sets the value of the neighboringBinSmoothing property.
setNEnzymaticTermini(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the nEnzymaticTermini property.
setNEnzymaticTermini(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the nEnzymaticTermini property.
setNextscore(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the nextscore property.
setNiAdjustedProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the niAdjustedProbability property.
setNiAdjustedProbability(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the niAdjustedProbability property.
setNiLowerBoundExcl(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Sets the value of the niLowerBoundExcl property.
setNiLowerBoundExcl(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Sets the value of the niLowerBoundExcl property.
setNiLowerBoundIncl(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Sets the value of the niLowerBoundIncl property.
setNiLowerBoundIncl(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Sets the value of the niLowerBoundIncl property.
setNIndistinguishableProteins(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the nIndistinguishableProteins property.
setNIndistinguishableProteins(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the nIndistinguishableProteins property.
setNInstances(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the nInstances property.
setNInstances(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the nInstances property.
setNiUpperBoundExcl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Sets the value of the niUpperBoundExcl property.
setNiUpperBoundExcl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Sets the value of the niUpperBoundExcl property.
setNiUpperBoundIncl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Sets the value of the niUpperBoundIncl property.
setNiUpperBoundIncl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Sets the value of the niUpperBoundIncl property.
setNoCut(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
Sets the value of the noCut property.
setNoCut(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
Sets the value of the noCut property.
setNoCut(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
Sets the value of the noCut property.
setNormalization(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Sets the value of the normalization property.
setNormalization(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Sets the value of the normalization property.
setNormalization(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Sets the value of the normalization property.
setNormalization(int) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Sets the value of the normalization property.
setNormalization(int) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Sets the value of the normalization property.
setNormalized(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
Sets the value of the normalized property.
setNormalized(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
Sets the value of the normalized property.
setNormalized(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
Sets the value of the normalized property.
setNote(Note) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Sets the value of the note property.
setNSiblingPeptides(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the nSiblingPeptides property.
setNSiblingPeptides(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the nSiblingPeptides property.
setNSiblingPeptidesBin(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the nSiblingPeptidesBin property.
setNSiblingPeptidesBin(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the nSiblingPeptidesBin property.
setNspAdjustedProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the nspAdjustedProbability property.
setNspAdjustedProbability(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the nspAdjustedProbability property.
setNspDistributionIters(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Sets the value of the nspDistributionIters property.
setNspDistributionIters(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Sets the value of the nspDistributionIters property.
setNspFlag(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Sets the value of the nspFlag property.
setNspFlag(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Sets the value of the nspFlag property.
setNspInformation(NspInformation) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Sets the value of the nspInformation property.
setNspInformation(NspInformation) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Sets the value of the nspInformation property.
setNspLowerBoundExcl(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Sets the value of the nspLowerBoundExcl property.
setNspLowerBoundExcl(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Sets the value of the nspLowerBoundExcl property.
setNspLowerBoundIncl(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Sets the value of the nspLowerBoundIncl property.
setNspLowerBoundIncl(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Sets the value of the nspLowerBoundIncl property.
setNspUpperBoundExcl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Sets the value of the nspUpperBoundExcl property.
setNspUpperBoundExcl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Sets the value of the nspUpperBoundExcl property.
setNspUpperBoundIncl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Sets the value of the nspUpperBoundIncl property.
setNspUpperBoundIncl(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Sets the value of the nspUpperBoundIncl property.
setNTermGain(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Sets the value of the nTermGain property.
setNTermGain(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Sets the value of the nTermGain property.
setNum(Integer) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Device
Sets the value of the num property.
setNum(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.ScanOrigin
Sets the value of the num property.
setNum(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the num property.
setNumber(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
Sets the value of the number property.
setNumber(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
Sets the value of the number property.
setNumber(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
Sets the value of the number property.
setNumber(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
Sets the value of the number property.
setNumber(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraResult
Sets the value of the number property.
setNumber(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
Sets the value of the number property.
setNumber(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraResult
Sets the value of the number property.
setNumCorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
Sets the value of the numCorr property.
setNumCorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
Sets the value of the numCorr property.
setNumCorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
Sets the value of the numCorr property.
setNumCorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
Sets the value of the numCorr property.
setNumCorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
Sets the value of the numCorr property.
setNumCorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
Sets the value of the numCorr property.
setNumDatabaseSequences(long) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Sets the value of the numDatabaseSequences property.
setNumDatabaseSequences(Long) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Sets the value of the numDatabaseSequences property.
setNumIncorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.ErrorPoint
Sets the value of the numIncorr property.
setNumIncorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
Sets the value of the numIncorr property.
setNumIncorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ErrorPoint
Sets the value of the numIncorr property.
setNumIncorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
Sets the value of the numIncorr property.
setNumIncorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ErrorPoint
Sets the value of the numIncorr property.
setNumIncorr(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
Sets the value of the numIncorr property.
setNumInput1Spectra(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the numInput1Spectra property.
setNumInput1Spectra(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the numInput1Spectra property.
setNumInput2Spectra(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the numInput2Spectra property.
setNumInput2Spectra(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the numInput2Spectra property.
setNumInput3Spectra(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the numInput3Spectra property.
setNumInput3Spectra(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the numInput3Spectra property.
setNumInput4Spectra(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the numInput4Spectra property.
setNumInput4Spectra(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the numInput4Spectra property.
setNumInput5Spectra(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the numInput5Spectra property.
setNumInput5Spectra(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the numInput5Spectra property.
setNumIterations(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Sets the value of the numIterations property.
setNumIterations(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Sets the value of the numIterations property.
setNumIterations(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Sets the value of the numIterations property.
setNumMatchedIons(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the numMatchedIons property.
setNumMatchedIons(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the numMatchedIons property.
setNumMatchedIons(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the numMatchedIons property.
setNumMatchedPeptides(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the numMatchedPeptides property.
setNumMatchedPeptides(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the numMatchedPeptides property.
setNumMatchedPeptides(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the numMatchedPeptides property.
setNumMissedCleavages(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the numMissedCleavages property.
setNumMissedCleavages(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the numMissedCleavages property.
setNumMissedCleavages(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the numMissedCleavages property.
setNumPredictedCorrectProts(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the numPredictedCorrectProts property.
setNumPredictedCorrectProts(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the numPredictedCorrectProts property.
setNumResidues(long) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Sets the value of the numResidues property.
setNumResidues(Long) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Sets the value of the numResidues property.
setNumScansToProcess(Integer) - Method in class umich.ms.fileio.filetypes.util.MultiSpectraParser
 
setNumSequencesSearched(long) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
Sets the value of the numSequencesSearched property.
setNumSequencesSearched(Long) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
Sets the value of the numSequencesSearched property.
setNumThreadsForParsing(Integer) - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
How many batches of scans will be processed in parallel.
setNumThreadsForParsing(Integer) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
How many batches of scans will be processed in parallel.
setNumTolTerm(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Sets the value of the numTolTerm property.
setNumTolTerm(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the numTolTerm property.
setNumTolTerm(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Sets the value of the numTolTerm property.
setNumTolTerm(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the numTolTerm property.
setNumTolTerm(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Sets the value of the numTolTerm property.
setNumTolTerm(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the numTolTerm property.
setNumTotProteins(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the numTotProteins property.
setNumTotProteins(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the numTotProteins property.
setNumTotProteins(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the numTotProteins property.
setNumvalues(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
Sets the value of the numvalues property.
setObs1Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the obs1Distr property.
setObs1Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the obs1Distr property.
setObs1Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the obs1Distr property.
setObs2Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the obs2Distr property.
setObs2Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the obs2Distr property.
setObs2Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the obs2Distr property.
setObs3Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the obs3Distr property.
setObs3Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the obs3Distr property.
setObs3Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the obs3Distr property.
setObs4Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the obs4Distr property.
setObs4Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the obs4Distr property.
setObs4Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the obs4Distr property.
setObs5Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the obs5Distr property.
setObs5Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the obs5Distr property.
setObs5Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the obs5Distr property.
setObs6Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the obs6Distr property.
setObs6Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the obs6Distr property.
setObs6Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the obs6Distr property.
setObs7Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.DistributionPoint
Sets the value of the obs7Distr property.
setObs7Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DistributionPoint
Sets the value of the obs7Distr property.
setObs7Distr(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DistributionPoint
Sets the value of the obs7Distr property.
setObsDistr(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Point
Sets the value of the obsDistr property.
setObsDistr(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Point
Sets the value of the obsDistr property.
setOccamFlag(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Sets the value of the occamFlag property.
setOccamFlag(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Sets the value of the occamFlag property.
setOffset(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary.FragmentMasses
Sets the value of the offset property.
setOffset(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.FragmentMasses
Sets the value of the offset property.
setOffset(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.FragmentMasses
Sets the value of the offset property.
setOffsetLength(OffsetLength) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedIndexElement
Use carefully, the only intended use for this mutator is to extend the already existing offset-length pairs if the original length was not extending all the way up to the next "scan" tag.
setOffsetLength(OffsetLength) - Method in interface umich.ms.fileio.filetypes.xmlbased.XMLBasedIndexElement
This mutator is needed to facilitate "fixing" of index after it was created.
setOperator(Operator) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Sets the value of the operator property.
setOptions(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
Sets the value of the options property.
setOptions(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Sets the value of the options property.
setOptions(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Sets the value of the options property.
setOptions(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Sets the value of the options property.
setOptions(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Sets the value of the options property.
setOptions(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Sets the value of the options property.
setOrder(int) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentType
Sets the value of the order property.
setOrder(BigInteger) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ProcessingMethodType
Sets the value of the order property.
setOrganism(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the organism property.
setOrganism(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the organism property.
setOrganizationRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AffiliationType
Sets the value of the organizationRef property.
setOrganizationRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParentOrganizationType
Sets the value of the organizationRef property.
setOrganizationRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AffiliationType
Sets the value of the organizationRef property.
setOrganizationRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParentOrganizationType
Sets the value of the organizationRef property.
setOrientation(MsRun.Spotting.Plate.Pattern.Orientation) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern
Sets the value of the orientation property.
setOrigDatabaseUrl(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Sets the value of the origDatabaseUrl property.
setOrigDatabaseUrl(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Sets the value of the origDatabaseUrl property.
setOrigDatabaseUrl(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Sets the value of the origDatabaseUrl property.
setOriginalResidue(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
Sets the value of the originalResidue property.
setOriginalResidue(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
Sets the value of the originalResidue property.
setOutData(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Sets the value of the outData property.
setOutData(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Sets the value of the outData property.
setOutData(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Sets the value of the outData property.
setOutDataType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Sets the value of the outDataType property.
setOutDataType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Sets the value of the outDataType property.
setOutDataType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Sets the value of the outDataType property.
setOutputType(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraSummary
Sets the value of the outputType property.
setOutputType(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.LibraSummary
Sets the value of the outputType property.
setOutputType(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.LibraSummary
Sets the value of the outputType property.
setOutputType(int) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.LibraSummary
Sets the value of the outputType property.
setOutputType(int) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.LibraSummary
Sets the value of the outputType property.
setP(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
Sets the value of the p property.
setPages(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Sets the value of the pages property.
setPages(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Sets the value of the pages property.
setParent(ParentOrganizationType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.OrganizationType
Sets the value of the parent property.
setParent(ParentOrganizationType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.OrganizationType
Sets the value of the parent property.
setParentFile(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
Sets the value of the parentFile property.
setParentFile(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
Sets the value of the parentFile property.
setParentFile(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
Sets the value of the parentFile property.
setParentFile(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
Sets the value of the parentFile property.
setParentFile(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
Sets the value of the parentFile property.
setParentFileID(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.ScanOrigin
Sets the value of the parentFileID property.
setParentScanNum(Integer) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
setParentScanRefRaw(String) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
 
setParentTolerance(ToleranceType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Sets the value of the parentTolerance property.
setParentTolerance(ToleranceType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Sets the value of the parentTolerance property.
setParsingTimeout(long) - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
Timeout (in seconds) that worker threads are allowed for parsing one batch of spectra.
setParsingTimeout(long) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Timeout (in seconds) that worker threads are allowed for parsing one batch of spectra.
setPassThreshold(boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionHypothesisType
Sets the value of the passThreshold property.
setPassThreshold(boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Sets the value of the passThreshold property.
setPassThreshold(boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionHypothesisType
Sets the value of the passThreshold property.
setPassThreshold(boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Sets the value of the passThreshold property.
setPath(Path) - Method in class umich.ms.fileio.util.FileListing
 
setPattern(MsRun.Spotting.Plate.Pattern) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Sets the value of the pattern property.
setPattern(Pattern) - Method in class umich.ms.fileio.util.FileListing
 
setPctSpectrumIds(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the pctSpectrumIds property.
setPctSpectrumIds(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the pctSpectrumIds property.
setPeaksCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the peaksCount property.
setPeptide(Peptide) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Sets the value of the peptide property.
setPeptide(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the peptide property.
setPeptide(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the peptide property.
setPeptide(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the peptide property.
setPeptideBinaryInd(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Sets the value of the peptideBinaryInd property.
setPeptideBinaryInd(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Sets the value of the peptideBinaryInd property.
setPeptideEvidenceRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceRefType
Sets the value of the peptideEvidenceRef property.
setPeptideEvidenceRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideHypothesisType
Sets the value of the peptideEvidenceRef property.
setPeptideEvidenceRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceRefType
Sets the value of the peptideEvidenceRef property.
setPeptideEvidenceRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideHypothesisType
Sets the value of the peptideEvidenceRef property.
setPeptideGroupDesignator(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the peptideGroupDesignator property.
setPeptideGroupDesignator(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the peptideGroupDesignator property.
setPeptideIndex(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPDta
Sets the value of the peptideIndex property.
setPeptideIndex(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPDta
Sets the value of the peptideIndex property.
setPeptideInds(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Sets the value of the peptideInds property.
setPeptideInds(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Sets the value of the peptideInds property.
setPeptideNextAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Sets the value of the peptideNextAa property.
setPeptideNextAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the peptideNextAa property.
setPeptideNextAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Sets the value of the peptideNextAa property.
setPeptideNextAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the peptideNextAa property.
setPeptideNextAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Sets the value of the peptideNextAa property.
setPeptideNextAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the peptideNextAa property.
setPeptidePrevAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Sets the value of the peptidePrevAa property.
setPeptidePrevAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the peptidePrevAa property.
setPeptidePrevAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Sets the value of the peptidePrevAa property.
setPeptidePrevAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the peptidePrevAa property.
setPeptidePrevAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Sets the value of the peptidePrevAa property.
setPeptidePrevAa(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the peptidePrevAa property.
setPeptideRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Sets the value of the peptideRef property.
setPeptideRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Sets the value of the peptideRef property.
setPeptideRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Sets the value of the peptideRef property.
setPeptideRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Sets the value of the peptideRef property.
setPeptideSequence(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideType
Sets the value of the peptideSequence property.
setPeptideSequence(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideType
Sets the value of the peptideSequence property.
setPeptideSequence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishablePeptide
Sets the value of the peptideSequence property.
setPeptideSequence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModificationInfo
Sets the value of the peptideSequence property.
setPeptideSequence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the peptideSequence property.
setPeptideSequence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishablePeptide
Sets the value of the peptideSequence property.
setPeptideSequence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModificationInfo
Sets the value of the peptideSequence property.
setPeptideSequence(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the peptideSequence property.
setPeptideTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Sets the value of the peptideTerminus property.
setPeptideTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Sets the value of the peptideTerminus property.
setPeptideTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Sets the value of the peptideTerminus property.
setPercentCoverage(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the percentCoverage property.
setPercentCoverage(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the percentCoverage property.
setPhone(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Sets the value of the phone property.
setPlateID(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Sets the value of the plateID property.
setPlateID(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Sets the value of the plateID property.
setPlateManufacturer(OntologyEntryType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Sets the value of the plateManufacturer property.
setPlateModel(OntologyEntryType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Sets the value of the plateModel property.
setPm(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
Sets the value of the pm property.
setPolarity(Polarity) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setPolarity(Polarity) - Method in interface umich.ms.datatypes.scan.IScan
 
setPolarity(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the polarity property.
setPool(ObjectPool<ByteArrayHolder>) - Method in class umich.ms.fileio.chunk.FileChunk
 
setPosBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType
Sets the value of the posBandwidth property.
setPosBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel
Sets the value of the posBandwidth property.
setPosBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Mixturemodel
Sets the value of the posBandwidth property.
setPosBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelType
Sets the value of the posBandwidth property.
setPosBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Mixturemodel
Sets the value of the posBandwidth property.
setPosBandwidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelType
Sets the value of the posBandwidth property.
setPosDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
Sets the value of the posDens property.
setPosDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel.Point
Sets the value of the posDens property.
setPosDens(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
Sets the value of the posDens property.
setPosDens(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Point
Sets the value of the posDens property.
setPosDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
Sets the value of the posDens property.
setPosDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Point
Sets the value of the posDens property.
setPosFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Sets the value of the posFreq property.
setPosFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Sets the value of the posFreq property.
setPosFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Sets the value of the posFreq property.
setPosFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Sets the value of the posFreq property.
setPosFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Sets the value of the posFreq property.
setPosFreq(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Sets the value of the posFreq property.
setPosition(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo.ModAminoacidMass
Sets the value of the position property.
setPosition(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModAminoacidMass
Sets the value of the position property.
setPosition(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModAminoacidMass
Sets the value of the position property.
setPosition(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ModAminoacidMass
Sets the value of the position property.
setPosition(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ModAminoacidMass
Sets the value of the position property.
setPosition(int) - Method in class umich.ms.util.ByteArrayHolder
This is a dangerous method, be sure you know what you're doing.
setPosmodelDistribution(PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.PosmodelDistribution) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution
Sets the value of the posmodelDistribution property.
setPosmodelDistribution(PosmodelDistribution) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixturemodelDistribution
Sets the value of the posmodelDistribution property.
setPosmodelDistribution(PosmodelDistribution) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixturemodelDistribution
Sets the value of the posmodelDistribution property.
setPosObsDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
Sets the value of the posObsDens property.
setPosObsDens(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
Sets the value of the posObsDens property.
setPosObsDens(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
Sets the value of the posObsDens property.
setPossibleCharges(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Sets the value of the possibleCharges property.
setPost(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the post property.
setPost(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Sets the value of the post property.
setPost(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Sets the value of the post property.
setPosToNegRatio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.FpkmDistribution
Sets the value of the posToNegRatio property.
setPosToNegRatio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NiDistribution
Sets the value of the posToNegRatio property.
setPosToNegRatio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NspDistribution
Sets the value of the posToNegRatio property.
setPosToNegRatio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.FpkmDistribution
Sets the value of the posToNegRatio property.
setPosToNegRatio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NiDistribution
Sets the value of the posToNegRatio property.
setPosToNegRatio(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NspDistribution
Sets the value of the posToNegRatio property.
setPpmtol(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Sets the value of the ppmtol property.
setPpmtol(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Sets the value of the ppmtol property.
setPpmtol(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Sets the value of the ppmtol property.
setPre(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the pre property.
setPre(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Sets the value of the pre property.
setPre(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Sets the value of the pre property.
setPrecision(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Sets the value of the precision property.
setPrecursor(PrecursorInfo) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setPrecursor(PrecursorInfo) - Method in interface umich.ms.datatypes.scan.IScan
 
setPrecursor(PrecursorType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Sets the value of the precursor property.
setPrecursorCharge(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Sets the value of the precursorCharge property.
setPrecursorIntensity(float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Sets the value of the precursorIntensity property.
setPrecursorIntensity(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the precursorIntensity property.
setPrecursorIntensity(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the precursorIntensity property.
setPrecursorIntensity(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the precursorIntensity property.
setPrecursorIonCharge(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Sets the value of the precursorIonCharge property.
setPrecursorIonCharge(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Sets the value of the precursorIonCharge property.
setPrecursorIonCharge(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Sets the value of the precursorIonCharge property.
setPrecursorList(PrecursorListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Sets the value of the precursorList property.
setPrecursorMassType(MassType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Sets the value of the precursorMassType property.
setPrecursorMassType(MassType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Sets the value of the precursorMassType property.
setPrecursorMassType(MassType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Sets the value of the precursorMassType property.
setPrecursorNeutralMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the precursorNeutralMass property.
setPrecursorNeutralMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the precursorNeutralMass property.
setPrecursorNeutralMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the precursorNeutralMass property.
setPrecursorScanNum(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Sets the value of the precursorScanNum property.
setPredictedNumCorrect(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
Sets the value of the predictedNumCorrect property.
setPredictedNumCorrect(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
Sets the value of the predictedNumCorrect property.
setPredictedNumIncorrect(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
Sets the value of the predictedNumIncorrect property.
setPredictedNumIncorrect(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
Sets the value of the predictedNumIncorrect property.
setPriorProbability(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Sets the value of the priorProbability property.
setPriorProbability(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Sets the value of the priorProbability property.
setPriorProbability(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Sets the value of the priorProbability property.
setProbability(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult
Sets the value of the probability property.
setProbability(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
Sets the value of the probability property.
setProbability(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetResult
Sets the value of the probability property.
setProbability(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
Sets the value of the probability property.
setProbability(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetResult
Sets the value of the probability property.
setProbability(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
Sets the value of the probability property.
setProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the probability property.
setProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
Sets the value of the probability property.
setProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the probability property.
setProbability(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
Sets the value of the probability property.
setProduct(ProductType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ChromatogramType
Sets the value of the product property.
setProductList(ProductListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Sets the value of the productList property.
setProgramDetails(ProgramDetails) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the programDetails property.
setProgramDetails(ProgramDetails) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the programDetails property.
setProtein(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Sets the value of the protein property.
setProtein(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the protein property.
setProtein(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Sets the value of the protein property.
setProtein(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the protein property.
setProtein(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Sets the value of the protein property.
setProtein(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the protein property.
setProteinAnnotation(ProteinAnnotation) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the proteinAnnotation property.
setProteinAnnotation(ProteinAnnotation) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the proteinAnnotation property.
setProteinDescr(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Sets the value of the proteinDescr property.
setProteinDescr(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the proteinDescr property.
setProteinDescr(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Sets the value of the proteinDescr property.
setProteinDescr(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the proteinDescr property.
setProteinDescr(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Sets the value of the proteinDescr property.
setProteinDescr(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the proteinDescr property.
setProteinDescription(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Sets the value of the proteinDescription property.
setProteinDescription(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Sets the value of the proteinDescription property.
setProteinDetection(ProteinDetectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisCollectionType
Sets the value of the proteinDetection property.
setProteinDetection(ProteinDetectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisCollectionType
Sets the value of the proteinDetection property.
setProteinDetectionList(ProteinDetectionListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisDataType
Sets the value of the proteinDetectionList property.
setProteinDetectionList(ProteinDetectionListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisDataType
Sets the value of the proteinDetectionList property.
setProteinDetectionListRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionType
Sets the value of the proteinDetectionListRef property.
setProteinDetectionListRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionType
Sets the value of the proteinDetectionListRef property.
setProteinDetectionProtocol(ProteinDetectionProtocolType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisProtocolCollectionType
Sets the value of the proteinDetectionProtocol property.
setProteinDetectionProtocol(ProteinDetectionProtocolType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisProtocolCollectionType
Sets the value of the proteinDetectionProtocol property.
setProteinDetectionProtocolRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionType
Sets the value of the proteinDetectionProtocolRef property.
setProteinDetectionProtocolRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionType
Sets the value of the proteinDetectionProtocolRef property.
setProteinMw(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein
Sets the value of the proteinMw property.
setProteinMw(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the proteinMw property.
setProteinMw(double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AlternativeProtein
Sets the value of the proteinMw property.
setProteinMw(double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the proteinMw property.
setProteinMw(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AlternativeProtein
Sets the value of the proteinMw property.
setProteinMw(Double) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the proteinMw property.
setProteinName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.IndistinguishableProtein
Sets the value of the proteinName property.
setProteinName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.PeptideParentProtein
Sets the value of the proteinName property.
setProteinName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the proteinName property.
setProteinName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.IndistinguishableProtein
Sets the value of the proteinName property.
setProteinName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.PeptideParentProtein
Sets the value of the proteinName property.
setProteinName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the proteinName property.
setProteinSummaryHeader(ProteinSummaryHeader) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
Sets the value of the proteinSummaryHeader property.
setProteinSummaryHeader(ProteinSummaryHeader) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
Sets the value of the proteinSummaryHeader property.
setProteinTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Sets the value of the proteinTerminus property.
setProteinTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Sets the value of the proteinTerminus property.
setProteinTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Sets the value of the proteinTerminus property.
setProteinTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Sets the value of the proteinTerminus property.
setProteinTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Sets the value of the proteinTerminus property.
setProvider(ProviderType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the provider property.
setProvider(ProviderType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the provider property.
setPseudoName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinGroup
Sets the value of the pseudoName property.
setPseudoName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinGroup
Sets the value of the pseudoName property.
setPublication(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Sets the value of the publication property.
setPublication(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Sets the value of the publication property.
setPublisher(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Sets the value of the publisher property.
setPublisher(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Sets the value of the publisher property.
setPvalue(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatioPvalue
Sets the value of the pvalue property.
setPvalue(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatioPvalue
Sets the value of the pvalue property.
setQuantLabelMasses(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioTimestamp
Sets the value of the quantLabelMasses property.
setQuantLabelMasses(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioTimestamp
Sets the value of the quantLabelMasses property.
setQuantLabelMasses(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioTimestamp
Sets the value of the quantLabelMasses property.
setRank(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Sets the value of the rank property.
setRank(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Sets the value of the rank property.
setRatio(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Sets the value of the ratio property.
setRatio(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
Sets the value of the ratio property.
setRatio(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Sets the value of the ratio property.
setRatio(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
Sets the value of the ratio property.
setRatio(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Sets the value of the ratio property.
setRatio(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
Sets the value of the ratio property.
setRatio(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Intensity
Sets the value of the ratio property.
setRatio(float) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Intensity
Sets the value of the ratio property.
setRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Sets the value of the ratioMean property.
setRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Sets the value of the ratioMean property.
setRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Sets the value of the ratioMean property.
setRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Sets the value of the ratioMean property.
setRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Sets the value of the ratioMean property.
setRatioMean(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Sets the value of the ratioMean property.
setRatioNumberPeptides(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Sets the value of the ratioNumberPeptides property.
setRatioNumberPeptides(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Sets the value of the ratioNumberPeptides property.
setRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Sets the value of the ratioStandardDev property.
setRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Sets the value of the ratioStandardDev property.
setRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Sets the value of the ratioStandardDev property.
setRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Sets the value of the ratioStandardDev property.
setRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Sets the value of the ratioStandardDev property.
setRatioStandardDev(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Sets the value of the ratioStandardDev property.
setRawData(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Sets the value of the rawData property.
setRawData(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Sets the value of the rawData property.
setRawData(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Sets the value of the rawData property.
setRawDataType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Sets the value of the rawDataType property.
setRawDataType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Sets the value of the rawDataType property.
setRawDataType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Sets the value of the rawDataType property.
setReaderPool(ObjectPool<XMLStreamReaderImpl>) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
setReaderPool(ObjectPool<XMLStreamReaderImpl>) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
Set the pool of readers.
setRecursive(boolean) - Method in class umich.ms.fileio.util.FileListing
 
setRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupRefType
Sets the value of the ref property.
setRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareRefType
Sets the value of the ref property.
setRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileRefType
Sets the value of the ref property.
setReferenceableParamGroupList(ReferenceableParamGroupListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the referenceableParamGroupList property.
setReferenceDatabase(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the referenceDatabase property.
setReferenceDatabase(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the referenceDatabase property.
setReferenceIsotope(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Sets the value of the referenceIsotope property.
setReferenceIsotope(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
Sets the value of the referenceIsotope property.
setReferenceIsotope(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Sets the value of the referenceIsotope property.
setReferenceIsotope(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
Sets the value of the referenceIsotope property.
setRefseqName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Sets the value of the refseqName property.
setRefseqName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Sets the value of the refseqName property.
setReject(Boolean) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
Sets the value of the reject property.
setReject(boolean) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
Sets the value of the reject property.
setReject(Boolean) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
Sets the value of the reject property.
setReleaseDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Sets the value of the releaseDate property.
setReleaseDate(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Sets the value of the releaseDate property.
setReplacementResidue(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
Sets the value of the replacementResidue property.
setReplacementResidue(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
Sets the value of the replacementResidue property.
setResidueSubstitutionList(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the residueSubstitutionList property.
setResidueSubstitutionList(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the residueSubstitutionList property.
setRetentionTime(Duration) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the retentionTime property.
setRetentionTimeSec(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the retentionTimeSec property.
setRetentionTimeSec(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the retentionTimeSec property.
setRetentionTimeSec(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the retentionTimeSec property.
setRightValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Sets the value of the rightValley property.
setRightValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Sets the value of the rightValley property.
setRightValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Sets the value of the rightValley property.
setRightValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Sets the value of the rightValley property.
setRightValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Sets the value of the rightValley property.
setRightValley(int) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Sets the value of the rightValley property.
setRobot(MsRun.Spotting.Robot) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting
Sets the value of the robot property.
setRobotManufacturer(OntologyEntryType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
Sets the value of the robotManufacturer property.
setRobotModel(OntologyEntryType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
Sets the value of the robotModel property.
setRole(RoleType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ContactRoleType
Sets the value of the role property.
setRole(RoleType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ContactRoleType
Sets the value of the role property.
setRt(Double) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setRt(Double) - Method in interface umich.ms.datatypes.scan.IScan
 
setRt(double) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
setRt(double) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
setRt(Double) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
Sets the value of the rt property.
setRt(Double) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Sets the value of the rt property.
setRt(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the rt property.
setRtHi(double) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
setRtLo(double) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
setRTRange(RTRange) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.RTRanges
Sets the value of the rtRange property.
setRTRanges(RTRanges) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Sets the value of the rtRanges property.
setRun(RunType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the run property.
setRunInfo(LCMSRunInfo) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
setRunInfo(LCMSRunInfo) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
 
setRunOptions(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinprophetDetails
Sets the value of the runOptions property.
setRunOptions(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinprophetDetails
Sets the value of the runOptions property.
setRunStartTime(Date) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
setS(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Sets the value of the s property.
setSameScanRange(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Sets the value of the sameScanRange property.
setSameScanRange(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Sets the value of the sameScanRange property.
setSameScanRange(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Sets the value of the sameScanRange property.
setSampleEnzyme(MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Sets the value of the sampleEnzyme property.
setSampleEnzyme(SampleEnzyme) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Sets the value of the sampleEnzyme property.
setSampleEnzyme(SampleEnzyme) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Sets the value of the sampleEnzyme property.
setSampleEnzyme(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the sampleEnzyme property.
setSampleEnzyme(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the sampleEnzyme property.
setSampleList(SampleListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the sampleList property.
setSampleRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
Sets the value of the sampleRef property.
setSampleRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubSampleType
Sets the value of the sampleRef property.
setSampleRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
Sets the value of the sampleRef property.
setSampleRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubSampleType
Sets the value of the sampleRef property.
setSampleRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Sets the value of the sampleRef property.
setSat(Boolean) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Sets the value of the sat property.
setSatLimit(Integer) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Sets the value of the satLimit property.
setScanCollection(IScanCollection) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setScanCollection(IScanCollection) - Method in interface umich.ms.datatypes.scan.IScan
 
setScanCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Sets the value of the scanCount property.
setScanList(ScanListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Sets the value of the scanList property.
setScanMzWindowLower(Double) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setScanMzWindowLower(Double) - Method in interface umich.ms.datatypes.scan.IScan
 
setScanMzWindowUpper(Double) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setScanMzWindowUpper(Double) - Method in interface umich.ms.datatypes.scan.IScan
 
setScanNumHi(Integer) - Method in class umich.ms.datatypes.LCMSDataSubset
 
setScanNumLo(Integer) - Method in class umich.ms.datatypes.LCMSDataSubset
 
setScans(IScanCollection) - Method in class umich.ms.datatypes.scan.impl.ScanDefault
 
setScanSettingsList(ScanSettingsListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the scanSettingsList property.
setScanSettingsRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
Sets the value of the scanSettingsRef property.
setScanType(ScanType) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setScanType(ScanType) - Method in interface umich.ms.datatypes.scan.IScan
 
setScanType(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.MSDetails
Sets the value of the scanType property.
setScanType(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the scanType property.
setScanWindowList(ScanWindowListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
Sets the value of the scanWindowList property.
setSearchDatabase(MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Sets the value of the searchDatabase property.
setSearchDatabase(SearchDatabase) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Sets the value of the searchDatabase property.
setSearchDatabase(SearchDatabase) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Sets the value of the searchDatabase property.
setSearchDatabaseRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
Sets the value of the searchDatabaseRef property.
setSearchDatabaseRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseRefType
Sets the value of the searchDatabaseRef property.
setSearchDatabaseRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
Sets the value of the searchDatabaseRef property.
setSearchDatabaseRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseRefType
Sets the value of the searchDatabaseRef property.
setSearchEngine(EngineType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Sets the value of the searchEngine property.
setSearchEngine(EngineType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
Sets the value of the searchEngine property.
setSearchEngine(EngineType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
Sets the value of the searchEngine property.
setSearchEngine(EngineType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Sets the value of the searchEngine property.
setSearchEngine(EngineType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
Sets the value of the searchEngine property.
setSearchEngine(EngineType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Sets the value of the searchEngine property.
setSearchEngineVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Sets the value of the searchEngineVersion property.
setSearchEngineVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Sets the value of the searchEngineVersion property.
setSearchEngineVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Sets the value of the searchEngineVersion property.
setSearchId(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
Sets the value of the searchId property.
setSearchId(Long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult
Sets the value of the searchId property.
setSearchId(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchResult
Sets the value of the searchId property.
setSearchId(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
Sets the value of the searchId property.
setSearchId(Long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchResult
Sets the value of the searchId property.
setSearchId(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
Sets the value of the searchId property.
setSearchScoreSummary(InterprophetResult.SearchScoreSummaryIProphet) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetResult
Sets the value of the searchScoreSummary property.
setSearchScoreSummary(PeptideprophetResult.SearchScoreSummary) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetResult
Sets the value of the searchScoreSummary property.
setSearchScoreSummary(SearchScoreSummaryIProphet) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetResult
Sets the value of the searchScoreSummary property.
setSearchScoreSummary(SearchScoreSummary) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetResult
Sets the value of the searchScoreSummary property.
setSearchScoreSummary(SearchScoreSummaryIProphet) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetResult
Sets the value of the searchScoreSummary property.
setSearchScoreSummary(SearchScoreSummary) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetResult
Sets the value of the searchScoreSummary property.
setSearchSpecification(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the searchSpecification property.
setSearchSpecification(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the searchSpecification property.
setSearchSpecification(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the searchSpecification property.
setSearchType(ParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Sets the value of the searchType property.
setSearchType(ParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Sets the value of the searchType property.
setSecondSpotID(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern.Orientation
Sets the value of the secondSpotID property.
setSelectedIonList(SelectedIonListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Sets the value of the selectedIonList property.
setSemiSpecific(boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Sets the value of the semiSpecific property.
setSemiSpecific(Boolean) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Sets the value of the semiSpecific property.
setSense(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme.Specificity
Sets the value of the sense property.
setSense(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
Sets the value of the sense property.
setSense(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
Sets the value of the sense property.
setSensitivity(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.RocErrorDataType.RocDataPoint
Sets the value of the sensitivity property.
setSensitivity(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.RocDataPoint
Sets the value of the sensitivity property.
setSensitivity(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.RocDataPoint
Sets the value of the sensitivity property.
setSensitivity(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryDataFilter
Sets the value of the sensitivity property.
setSensitivity(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryDataFilter
Sets the value of the sensitivity property.
setSeparation(MsRun.Separation) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Sets the value of the separation property.
setSeq(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the seq property.
setSeq(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DBSequenceType
Sets the value of the seq property.
setSeq(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DBSequenceType
Sets the value of the seq property.
setSequence(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SequenceSearchConstraint
Sets the value of the sequence property.
setSequence(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SequenceSearchConstraint
Sets the value of the sequence property.
setSequence(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SequenceSearchConstraint
Sets the value of the sequence property.
setSequenceCollection(SequenceCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the sequenceCollection property.
setSequenceCollection(SequenceCollectionType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the sequenceCollection property.
setSerialNumber(String) - Method in class umich.ms.datatypes.scan.props.Instrument
 
setSha1(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Sets the value of the sha1 property.
setSiteRegexp(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
Sets the value of the siteRegexp property.
setSiteRegexp(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
Sets the value of the siteRegexp property.
setSizeInDbEntries(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Sets the value of the sizeInDbEntries property.
setSizeInDbEntries(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Sets the value of the sizeInDbEntries property.
setSizeInDbEntries(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Sets the value of the sizeInDbEntries property.
setSizeOfResidues(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Sets the value of the sizeOfResidues property.
setSizeOfResidues(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Sets the value of the sizeOfResidues property.
setSizeOfResidues(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Sets the value of the sizeOfResidues property.
setSoftware(Software) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Sets the value of the software property.
setSoftware(Software) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
Sets the value of the software property.
setSoftwareList(SoftwareListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the softwareList property.
setSoftwareName(ParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
Sets the value of the softwareName property.
setSoftwareName(ParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
Sets the value of the softwareName property.
setSoftwareRef(SoftwareRefType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
Sets the value of the softwareRef property.
setSoftwareRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ProcessingMethodType
Sets the value of the softwareRef property.
setSourceFileList(SourceFileListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.FileDescriptionType
Sets the value of the sourceFileList property.
setSourceFileRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Sets the value of the sourceFileRef property.
setSourceFileRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
Sets the value of the sourceFileRef property.
setSourceFileRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Sets the value of the sourceFileRef property.
setSourceFileRefList(SourceFileRefListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsType
Sets the value of the sourceFileRefList property.
setSourceFiles(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the sourceFiles property.
setSourceFiles(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the sourceFiles property.
setSourceFilesAlt(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the sourceFilesAlt property.
setSourceFilesAlt(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the sourceFilesAlt property.
setSourceFileXtn(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the sourceFileXtn property.
setSourceFileXtn(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the sourceFileXtn property.
setSpecifiedResidueMasses(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Sets the value of the specifiedResidueMasses property.
setSpecifiedResidueMasses(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Sets the value of the specifiedResidueMasses property.
setSpectraDataRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputSpectraType
Sets the value of the spectraDataRef property.
setSpectraDataRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
Sets the value of the spectraDataRef property.
setSpectraDataRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputSpectraType
Sets the value of the spectraDataRef property.
setSpectraDataRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
Sets the value of the spectraDataRef property.
setSpectrum(ISpectrum, boolean) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setSpectrum(ISpectrum) - Method in class umich.ms.datatypes.scan.AbstractScan
Method was added for backwards compatibility, consider using the full signature version AbstractScan.setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean).
setSpectrum(ISpectrum, boolean) - Method in interface umich.ms.datatypes.scan.IScan
Set the spectrumRef for this scan.
setSpectrum(Spectrum) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Compound
Sets the value of the spectrum property.
setSpectrum(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the spectrum property.
setSpectrum(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the spectrum property.
setSpectrum(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the spectrum property.
setSpectrumID(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
Sets the value of the spectrumID property.
setSpectrumID(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
Sets the value of the spectrumID property.
setSpectrumIdentificationItemRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemRefType
Sets the value of the spectrumIdentificationItemRef property.
setSpectrumIdentificationItemRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemRefType
Sets the value of the spectrumIdentificationItemRef property.
setSpectrumIdentificationListRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputSpectrumIdentificationsType
Sets the value of the spectrumIdentificationListRef property.
setSpectrumIdentificationListRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
Sets the value of the spectrumIdentificationListRef property.
setSpectrumIdentificationListRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputSpectrumIdentificationsType
Sets the value of the spectrumIdentificationListRef property.
setSpectrumIdentificationListRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
Sets the value of the spectrumIdentificationListRef property.
setSpectrumIdentificationProtocolRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
Sets the value of the spectrumIdentificationProtocolRef property.
setSpectrumIdentificationProtocolRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
Sets the value of the spectrumIdentificationProtocolRef property.
setSpectrumIDFormat(SpectrumIDFormatType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectraDataType
Sets the value of the spectrumIDFormat property.
setSpectrumIDFormat(SpectrumIDFormatType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectraDataType
Sets the value of the spectrumIDFormat property.
setSpectrumImpl(ISpectrum) - Method in class umich.ms.datatypes.scan.AbstractScan
The implementation of IScan.setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean) in this base class will set all the Scan-level variables for you according to the spectrumRef provided, but you need to define how to store the spectrumRef itself.
setSpectrumImpl(ISpectrum) - Method in class umich.ms.datatypes.scan.impl.ScanDefault
 
setSpectrumList(SpectrumListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Sets the value of the spectrumList property.
setSpectrumNativeID(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the spectrumNativeID property.
setSpectrumNativeID(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the spectrumNativeID property.
setSpectrumRef(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
Sets the value of the spectrumRef property.
setSpectrumRef(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
Sets the value of the spectrumRef property.
setSpotDiameter(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
Sets the value of the spotDiameter property.
setSpotID(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
Sets the value of the spotID property.
setSpotID(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
Sets the value of the spotID property.
setSpotID(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
Sets the value of the spotID property.
setSpotIntegration(Boolean) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
Sets the value of the spotIntegration property.
setSpotting(MsRun.Spotting) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Sets the value of the spotting property.
setSpottingPattern(OntologyEntryType) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern
Sets the value of the spottingPattern property.
setSpotXCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Sets the value of the spotXCount property.
setSpotXPosition(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
Sets the value of the spotXPosition property.
setSpotYCount(BigInteger) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
Sets the value of the spotYCount property.
setSpotYPosition(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
Sets the value of the spotYPosition property.
setStart(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the start property.
setStart(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Peptide
Sets the value of the start property.
setStart(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Sets the value of the start property.
setStart(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Sets the value of the start property.
setStartMz(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the startMz property.
setStartScan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
Sets the value of the startScan property.
setStartScan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
Sets the value of the startScan property.
setStartScan(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
Sets the value of the startScan property.
setStartTime(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
Sets the value of the startTime property.
setStartTimeStamp(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
Sets the value of the startTimeStamp property.
setStaticQuant(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Sets the value of the staticQuant property.
setStaticQuant(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Sets the value of the staticQuant property.
setStaticQuant(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Sets the value of the staticQuant property.
setStaticQuantLabel(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioTimestamp
Sets the value of the staticQuantLabel property.
setStaticQuantLabel(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioTimestamp
Sets the value of the staticQuantLabel property.
setStaticQuantLabel(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioTimestamp
Sets the value of the staticQuantLabel property.
setStatus(byte) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Sets the value of the status property.
setStatus(byte) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Sets the value of the status property.
setStatus(byte) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
Sets the value of the status property.
setStatus(byte) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Sets the value of the status property.
setStatus(byte) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Sets the value of the status property.
setStatus(byte) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
Sets the value of the status property.
setStatus(byte) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Sets the value of the status property.
setStatus(byte) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Sets the value of the status property.
setStatus(byte) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
Sets the value of the status property.
setStatus(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Sets the value of the status property.
setStatus(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
Sets the value of the status property.
setStatus(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Sets the value of the status property.
setStatus(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Sets the value of the status property.
setStatus(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
Sets the value of the status property.
setStatus(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Sets the value of the status property.
setStatusLogHeaderField(int, String, MS_DataTypes, int) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method SetStatusLogHeaderField
setStatusLogHeaderNumFields(int) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method SetStatusLogHeaderNumFields
setStorageStrategy(StorageStrategy) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setStorageStrategy(StorageStrategy) - Method in interface umich.ms.datatypes.scan.IScan
Implementors of IScan interface must respect the value of reftype in constructors and IScan.setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean) implementations in order for memory management to work.
setStorageStrategy(LCMSDataSubset, StorageStrategy) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
setStorageStrategy(LCMSDataSubset, StorageStrategy, StorageStrategy) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
setStorageStrategy(LCMSDataSubset, StorageStrategy) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
 
setStorageStrategy(LCMSDataSubset, StorageStrategy, StorageStrategy) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
 
setStringInstrumentID(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
setSubsumingProteinEntry(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the subsumingProteinEntry property.
setSubsumingProteinEntry(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the subsumingProteinEntry property.
setSumI(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the sumI property.
setSumI(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Sets the value of the sumI property.
setSumInt(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
setSummaryXml(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
Sets the value of the summaryXml property.
setSummaryXml(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
Sets the value of the summaryXml property.
setSummaryXml(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
Sets the value of the summaryXml property.
setSummaryXml(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
Sets the value of the summaryXml property.
setSummaryXml(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
Sets the value of the summaryXml property.
setSwissprotName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Sets the value of the swissprotName property.
setSwissprotName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Sets the value of the swissprotName property.
setSymbol(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Sets the value of the symbol property.
setSymbol(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Sets the value of the symbol property.
setSymbol(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Sets the value of the symbol property.
setSymbol(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Sets the value of the symbol property.
setSymbol(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Sets the value of the symbol property.
setSymbol(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Sets the value of the symbol property.
setTargetList(TargetListType) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsType
Sets the value of the targetList property.
setTargetMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
Sets the value of the targetMass property.
setTargetMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
Sets the value of the targetMass property.
setTargetMass(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
Sets the value of the targetMass property.
setTasksPerCpuPerBatch(int) - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
How many spectra each CPU will be given in one batch.
setTasksPerCpuPerBatch(int) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
How many spectra each CPU will be given in one batch.
setTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Sets the value of the terminus property.
setTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Sets the value of the terminus property.
setTerminus(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Sets the value of the terminus property.
setThreshold(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionProtocolType
Sets the value of the threshold property.
setThreshold(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
Sets the value of the threshold property.
setThreshold(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionProtocolType
Sets the value of the threshold property.
setThreshold(ParamListType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
Sets the value of the threshold property.
setTic(Double) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setTic(Double) - Method in interface umich.ms.datatypes.scan.IScan
 
setTime(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Sets the value of the time property.
setTime(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Sets the value of the time property.
setTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
Sets the value of the time property.
setTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
Sets the value of the time property.
setTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
Sets the value of the time property.
setTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
Sets the value of the time property.
setTime(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Sets the value of the time property.
setTime(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Sets the value of the time property.
setTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
Sets the value of the time property.
setTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
Sets the value of the time property.
setTime(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Sets the value of the time property.
setTime(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Sets the value of the time property.
setTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
Sets the value of the time property.
setTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
Sets the value of the time property.
setTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
Sets the value of the time property.
setTime(XMLGregorianCalendar) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
Sets the value of the time property.
setTimePerSpot(Duration) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
Sets the value of the timePerSpot property.
setTimeWidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
Sets the value of the timeWidth property.
setTimeWidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
Sets the value of the timeWidth property.
setTimeWidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
Sets the value of the timeWidth property.
setTimeWidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
Sets the value of the timeWidth property.
setTimeWidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
Sets the value of the timeWidth property.
setTimeWidth(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
Sets the value of the timeWidth property.
setTitle(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Sets the value of the title property.
setTitle(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Sets the value of the title property.
setTotalNoSpectrumIds(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the totalNoSpectrumIds property.
setTotalNoSpectrumIds(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the totalNoSpectrumIds property.
setTotalNumberDistinctPeptides(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the totalNumberDistinctPeptides property.
setTotalNumberDistinctPeptides(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the totalNumberDistinctPeptides property.
setTotalNumberPeptides(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the totalNumberPeptides property.
setTotalNumberPeptides(Integer) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the totalNumberPeptides property.
setTotIonCurrent(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
Sets the value of the totIonCurrent property.
setTotNumIons(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
Sets the value of the totNumIons property.
setTotNumIons(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
Sets the value of the totNumIons property.
setTotNumIons(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
Sets the value of the totNumIons property.
setTotNumSpectra(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
Sets the value of the totNumSpectra property.
setTotNumSpectra(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
Sets the value of the totNumSpectra property.
setTotNumSpectra(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
Sets the value of the totNumSpectra property.
setTrailerHeaderField(int, String, MS_DataTypes, int) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method SetTrailerHeaderField
setTrailerHeaderNumFields(int) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method SetTrailerHeaderNumFields
setTranslationTableRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
Sets the value of the translationTableRef property.
setTranslationTableRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
Sets the value of the translationTableRef property.
setTremblName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
Sets the value of the tremblName property.
setTremblName(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
Sets the value of the tremblName property.
setTuneDataHeaderField(int, String, MS_DataTypes, int) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method SetTuneDataHeaderField
setTuneDataHeaderNumFields(int) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method SetTuneDataHeaderNumFields
setType(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Device
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Attribute
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.File
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Note
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.UserParamType
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.UserParamType
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
Sets the value of the type property.
setType(ModelDisType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.NegmodelDistribution
Sets the value of the type property.
setType(ModelDisType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.PosmodelDistribution
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
Sets the value of the type property.
setType(ModelDisType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NegmodelDistribution
Sets the value of the type property.
setType(ModelDisType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PosmodelDistribution
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
Sets the value of the type property.
setType(ModelDisType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NegmodelDistribution
Sets the value of the type property.
setType(ModelDisType) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PosmodelDistribution
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
Sets the value of the type property.
setType(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
Sets the value of the type property.
setUid(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
Sets the value of the uid property.
setUniqueStrippedPeptides(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
Sets the value of the uniqueStrippedPeptides property.
setUniqueStrippedPeptides(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
Sets the value of the uniqueStrippedPeptides property.
setUnitAccession(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
Sets the value of the unitAccession property.
setUnitAccession(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
Sets the value of the unitAccession property.
setUnitAccession(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Sets the value of the unitAccession property.
setUnitAccession(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Sets the value of the unitAccession property.
setUnitCvRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
Sets the value of the unitCvRef property.
setUnitCvRef(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
Sets the value of the unitCvRef property.
setUnitCvRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Sets the value of the unitCvRef property.
setUnitCvRef(Object) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Sets the value of the unitCvRef property.
setUnitName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
Sets the value of the unitName property.
setUnitName(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
Sets the value of the unitName property.
setUnitName(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Sets the value of the unitName property.
setUnitName(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Sets the value of the unitName property.
setUnits(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Xdata
Sets the value of the units property.
setUnits(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Ydata
Sets the value of the units property.
setUri(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
Sets the value of the uri property.
setUri(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
Sets the value of the uri property.
setUri(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
Sets the value of the uri property.
setUri(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
Sets the value of the uri property.
setURI(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
Sets the value of the uri property.
setURI(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Sets the value of the uri property.
setURL(String) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.File
Sets the value of the url property.
setURL(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
Sets the value of the url property.
setURL(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
Sets the value of the url property.
setURL(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
Sets the value of the url property.
setUse(short) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
Sets the value of the use property.
setUse(short) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
Sets the value of the use property.
setUse(short) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
Sets the value of the use property.
setUserParam(UserParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParamType
Sets the value of the userParam property.
setUserParam(UserParamType) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParamType
Sets the value of the userParam property.
setV(Integer) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
Sets the value of the v property.
setV(Integer) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Sets the value of the v property.
setValue(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Attribute
Sets the value of the value property.
setValue(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
Sets the value of the value property.
setValue(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
Sets the value of the value property.
setValue(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
Sets the value of the value property.
setValue(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
Sets the value of the value property.
setValue(Object) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
Sets the value of the value property.
setValue(Object) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
Sets the value of the value property.
setValue(Object) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
Sets the value of the value property.
setValue(byte[]) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
Sets the value of the value property.
setValue(float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Sets the value of the value property.
setValue(Object) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
Sets the value of the value property.
setValue(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InputFileType
Sets the value of the value property.
setValue(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
Sets the value of the value property.
setValue(Object) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
Sets the value of the value property.
setValue(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel.Point
Sets the value of the value property.
setValue(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InputFileType
Sets the value of the value property.
setValue(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
Sets the value of the value property.
setValue(Object) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
Sets the value of the value property.
setValue(float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Point
Sets the value of the value property.
setValue(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InputFileType
Sets the value of the value property.
setValue(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
Sets the value of the value property.
setValue(Object) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
Sets the value of the value property.
setValue(Float) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Point
Sets the value of the value property.
setValue(Object) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
Sets the value of the value property.
setValue(Object) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
Sets the value of the value property.
setValue(W) - Method in class umich.ms.util.IntervalST.Node
Use with caution.
setValueNamevalueType(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
Sets the value of the valueNamevalueType property.
setValueOntologyEntryType(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.OntologyEntryType
Sets the value of the valueOntologyEntryType property.
setValues(Values) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.GAMLValues
Sets the value of the values property.
setValueStr(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
Sets the value of the valueStr property.
setValueStr(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
Sets the value of the valueStr property.
setValueStr(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
Sets the value of the valueStr property.
setValueStr(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
Sets the value of the valueStr property.
setValueStr(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
Sets the value of the valueStr property.
setVariable(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
Sets the value of the variable property.
setVariable(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
Sets the value of the variable property.
setVariable(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
Sets the value of the variable property.
setVariable(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
Sets the value of the variable property.
setVariable(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
Sets the value of the variable property.
setVariable(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
Sets the value of the variable property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.CEF
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareType
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
Sets the value of the version property.
setVersion(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
Sets the value of the version property.
setVolume(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Sets the value of the volume property.
setVolume(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Sets the value of the volume property.
setWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
Sets the value of the weight property.
setWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
Sets the value of the weight property.
setWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
Sets the value of the weight property.
setWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
Sets the value of the weight property.
setWeight(double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
Sets the value of the weight property.
setWeight(Double) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
Sets the value of the weight property.
setWinCygReferenceDatabase(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the winCygReferenceDatabase property.
setWinCygReferenceDatabase(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the winCygReferenceDatabase property.
setWinCygSourceFiles(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
Sets the value of the winCygSourceFiles property.
setWinCygSourceFiles(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
Sets the value of the winCygSourceFiles property.
setWindowsParent(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
Sets the value of the windowsParent property.
setWindowsParent(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
Sets the value of the windowsParent property.
setWindowsParent(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
Sets the value of the windowsParent property.
setWindowsParent(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
Sets the value of the windowsParent property.
setWindowsParent(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
Sets the value of the windowsParent property.
setWindowWideness(Float) - Method in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
Sets the value of the windowWideness property.
setX(Double) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Sets the value of the x property.
setXdata(Xdata) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Sets the value of the xdata property.
setXpressLight(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
Sets the value of the xpressLight property.
setXpressLight(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioTimestamp
Sets the value of the xpressLight property.
setXpressLight(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
Sets the value of the xpressLight property.
setXpressLight(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioTimestamp
Sets the value of the xpressLight property.
setXpressLight(long) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
Sets the value of the xpressLight property.
setXpressLight(Integer) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioTimestamp
Sets the value of the xpressLight property.
setY(Integer) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
Sets the value of the y property.
setY(Double) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Sets the value of the y property.
setYdata(Ydata) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
Sets the value of the ydata property.
setYear(int) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
Sets the value of the year property.
setYear(Integer) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
Sets the value of the year property.
setYIons(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the yIons property.
setYScore(Double) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
Sets the value of the yScore property.
setZ(int) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
setZ(int) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
setZ(Integer) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
Sets the value of the z property.
setZ(Integer) - Method in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
Sets the value of the z property.
setzCarrier(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
sha1 - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
shortName - Variable in class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
 
siteRegexp - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.EnzymeType
 
siteRegexp - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.EnzymeType
 
size() - Method in class umich.ms.datatypes.index.impl.IndexDefault
 
size() - Method in interface umich.ms.datatypes.index.Index
Current size of the index.
size() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
size() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
 
size() - Method in class umich.ms.util.ByteArrayHolder
Returns the current size of the buffer.
size() - Method in class umich.ms.util.IntervalST
Return number of nodes in tree.
sizeInDbEntries - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
sizeInDbEntries - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
 
sizeInDbEntries - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
 
sizeOfResidues - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
sizeOfResidues - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
 
sizeOfResidues - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
 
software - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
software - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareListType
 
software - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
 
software - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
 
Software - Class in umich.ms.fileio.filetypes.mzxml.jaxb
Java class for anonymous complex type.
Software() - Constructor for class umich.ms.fileio.filetypes.mzxml.jaxb.Software
 
softwareList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
SoftwareListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List and descriptions of software used to acquire and/or process the data in this mzML file.
SoftwareListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareListType
 
softwareName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
 
softwareName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
 
softwareRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.InstrumentConfigurationType
 
softwareRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ProcessingMethodType
 
SoftwareRefType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Reference to a previously defined software element
SoftwareRefType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareRefType
 
SoftwareType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Software information.
SoftwareType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareType
 
source - Variable in class umich.ms.datatypes.LCMSData
 
source - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
source - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ComponentListType
 
source - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
source - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
source - Variable in class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
source - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
source - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
source - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser
 
SourceComponentType - Class in umich.ms.fileio.filetypes.mzml.jaxb
This element must be used to describe a Source Component Type.
SourceComponentType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SourceComponentType
 
sourceFile - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputsType
 
sourceFile - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputsType
 
sourceFile - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileListType
 
sourceFileList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.FileDescriptionType
 
SourceFileListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List and descriptions of the source files this mzML document was generated or derived from
SourceFileListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileListType
 
sourceFileRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
 
sourceFileRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
 
sourceFileRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileRefListType
 
sourceFileRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
sourceFileRefList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsType
 
SourceFileRefListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Java class for SourceFileRefListType complex type.
SourceFileRefListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileRefListType
 
SourceFileRefType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Java class for SourceFileRefType complex type.
SourceFileRefType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileRefType
 
sourceFiles - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
sourceFiles - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
sourceFilesAlt - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
sourceFilesAlt - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
SourceFileType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A file from which this mzIdentML instance was created.
SourceFileType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SourceFileType
 
SourceFileType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A file from which this mzIdentML instance was created.
SourceFileType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SourceFileType
 
SourceFileType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Description of the source file, including location and type.
SourceFileType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SourceFileType
 
sourceFileXtn - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
sourceFileXtn - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
specificity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SampleEnzyme
 
specificity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SampleEnzyme
 
Specificity - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
Specificity() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Specificity
 
specificity - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SampleEnzyme
 
Specificity - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
Specificity() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Specificity
 
specificityRules - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchModificationType
 
specificityRules - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchModificationType
 
SpecificityRulesType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The specificity rules of the searched modification including for example the probability of a modification's presence or peptide or protein termini.
SpecificityRulesType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpecificityRulesType
 
SpecificityRulesType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The specificity rules of the searched modification including for example the probability of a modification's presence or peptide or protein termini.
SpecificityRulesType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpecificityRulesType
 
specifiedResidueMasses - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
 
specifiedResidueMasses - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
 
spectraData - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputsType
 
spectraData - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputsType
 
spectraDataRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputSpectraType
 
spectraDataRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
 
spectraDataRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputSpectraType
 
spectraDataRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
 
SpectraDataType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A data set containing spectra data (consisting of one or more spectra).
SpectraDataType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectraDataType
 
SpectraDataType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A data set containing spectra data (consisting of one or more spectra).
SpectraDataType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectraDataType
 
spectrum - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Compound
 
Spectrum - Class in umich.ms.fileio.filetypes.agilent.cef.jaxb
Java class for anonymous complex type.
Spectrum() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
 
spectrum - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumListType
 
spectrum - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
spectrum - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
spectrum - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
SpectrumDefault - Class in umich.ms.datatypes.spectrum.impl
Author: Dmitry Avtonomov (dmitriya) Email: dmitriy.avtonomov@gmail.com This is a straightforward implementation of AbstractSpectrum using Java arrays
SpectrumDefault(double[], double[], double, double, double, double, double) - Constructor for class umich.ms.datatypes.spectrum.impl.SpectrumDefault
The provided mz and intensity arrays must be sorted properly
SpectrumDefault(double[], double[]) - Constructor for class umich.ms.datatypes.spectrum.impl.SpectrumDefault
 
spectrumID - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
 
spectrumID - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
 
spectrumIdentification - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisCollectionType
 
spectrumIdentification - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisCollectionType
 
spectrumIdentificationItem - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
 
spectrumIdentificationItem - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
 
spectrumIdentificationItemRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideHypothesisType
 
spectrumIdentificationItemRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemRefType
 
spectrumIdentificationItemRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideHypothesisType
 
spectrumIdentificationItemRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemRefType
 
SpectrumIdentificationItemRefType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Reference(s) to the SpectrumIdentificationItem element(s) that support the given PeptideEvidence element.
SpectrumIdentificationItemRefType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemRefType
 
SpectrumIdentificationItemRefType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Reference(s) to the SpectrumIdentificationItem element(s) that support the given PeptideEvidence element.
SpectrumIdentificationItemRefType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemRefType
 
SpectrumIdentificationItemType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification.
SpectrumIdentificationItemType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationItemType
 
SpectrumIdentificationItemType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
An identification of a single (poly)peptide, resulting from querying an input spectra, along with the set of confidence values for that identification.
SpectrumIdentificationItemType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationItemType
 
spectrumIdentificationList - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisDataType
 
spectrumIdentificationList - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisDataType
 
spectrumIdentificationListRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.InputSpectrumIdentificationsType
 
spectrumIdentificationListRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
 
spectrumIdentificationListRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.InputSpectrumIdentificationsType
 
spectrumIdentificationListRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
 
SpectrumIdentificationListType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
Represents the set of all search results from SpectrumIdentification.
SpectrumIdentificationListType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
 
SpectrumIdentificationListType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
Represents the set of all search results from SpectrumIdentification.
SpectrumIdentificationListType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
 
spectrumIdentificationProtocol - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisProtocolCollectionType
 
spectrumIdentificationProtocol - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisProtocolCollectionType
 
spectrumIdentificationProtocolRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
 
spectrumIdentificationProtocolRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
 
SpectrumIdentificationProtocolType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The parameters and settings of a SpectrumIdentification analysis.
SpectrumIdentificationProtocolType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
SpectrumIdentificationProtocolType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The parameters and settings of a SpectrumIdentification analysis.
SpectrumIdentificationProtocolType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
spectrumIdentificationResult - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationListType
 
spectrumIdentificationResult - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationListType
 
SpectrumIdentificationResultType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
All identifications made from searching one spectrum.
SpectrumIdentificationResultType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationResultType
 
SpectrumIdentificationResultType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
All identifications made from searching one spectrum.
SpectrumIdentificationResultType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationResultType
 
SpectrumIdentificationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
An Analysis which tries to identify peptides in input spectra, referencing the database searched, the input spectra, the output results and the protocol that is run.
SpectrumIdentificationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationType
 
SpectrumIdentificationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
An Analysis which tries to identify peptides in input spectra, referencing the database searched, the input spectra, the output results and the protocol that is run.
SpectrumIdentificationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationType
 
spectrumIDFormat - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectraDataType
 
spectrumIDFormat - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectraDataType
 
SpectrumIDFormatType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The format of the spectrum identifier within the source file
SpectrumIDFormatType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIDFormatType
 
SpectrumIDFormatType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The format of the spectrum identifier within the source file
SpectrumIDFormatType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIDFormatType
 
spectrumList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
 
SpectrumListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
List and descriptions of spectra.
SpectrumListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumListType
 
spectrumNativeID - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
spectrumNativeID - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
spectrumQuery - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary
 
spectrumQuery - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsRunSummary
 
SpectrumQuery - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
SpectrumQuery() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
spectrumQuery - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsRunSummary
 
SpectrumQuery - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
SpectrumQuery() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
spectrumRef - Variable in class umich.ms.datatypes.scan.impl.ScanDefault
 
spectrumRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.PrecursorType
 
spectrumRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanType
 
SpectrumType - Class in umich.ms.fileio.filetypes.mzml.jaxb
The structure that captures the generation of a peak list (including the underlying acquisitions).
SpectrumType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
SpectrumUtils - Class in umich.ms.util
Utilities for working with ISpectrum objects.
splitCompoundsByAdduct() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
 
spot - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
 
spotDiameter - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
 
spotID - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SpectrumType
 
spotID - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
 
spotID - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Maldi
 
spotIntegration - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.DataProcessing
 
spotting - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
spottingPattern - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Pattern
 
spotXCount - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
 
spotXPosition - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
 
spotYCount - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate
 
spotYPosition - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Plate.Spot
 
start - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
start - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Peptide
 
start - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
start - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
startDocument() - Method in class umich.ms.fileio.util.jaxb.NamespaceFilter
 
startElement(String, String, String, Attributes) - Method in class umich.ms.fileio.util.jaxb.NamespaceFilter
 
startMz - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
startPrefixMapping(String, String) - Method in class umich.ms.fileio.util.jaxb.NamespaceFilter
 
startScan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery
 
startScan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SpectrumQuery
 
startScan - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SpectrumQuery
 
startTime - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun
 
startTimeStamp - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.RunType
 
staticQuant - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
 
staticQuant - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
 
staticQuant - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
 
staticQuantLabel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioTimestamp
 
staticQuantLabel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioTimestamp
 
staticQuantLabel - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioTimestamp
 
status - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
 
status - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
 
status - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioPeptideData
 
status - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
 
status - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
 
status - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioPeptideData
 
status - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
 
status - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
 
status - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioPeptideData
 
status - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
status - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPRatio
 
status - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
status - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
status - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPRatio
 
status - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
storageStrategy - Variable in class umich.ms.datatypes.scan.AbstractScan
 
StorageStrategy - Enum in umich.ms.datatypes.scan
Enum holding spectrumRef reference types.
stringInstrumentID - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.MsInstrument
This is not in mzXML 3.2 standard, but ProteoWizard version="2.2.3052" uses this attribute instead of msInstrumentID
StringUtils - Class in umich.ms.util
String utilities.
StrongReference<T> - Class in umich.ms.util
Use when you need to be able to switch between Weak and Strong referencing.
StrongReference(T) - Constructor for class umich.ms.util.StrongReference
 
STRUCTURE_ONLY - Static variable in class umich.ms.datatypes.LCMSDataSubset
Sets up the parsing parameters to parse only scans for the whole run, no spectra.
submitParseTasks(LCMSDataSubset, LCMSRunInfo, int, ExecutorService, byte[], ArrayList<OffsetLength>, int[], boolean) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
subSample - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SampleType
 
subSample - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SampleType
 
SubSampleType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
References to the individual component samples within a mixed parent sample.
SubSampleType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubSampleType
 
SubSampleType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
References to the individual component samples within a mixed parent sample.
SubSampleType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubSampleType
 
subset - Variable in class umich.ms.fileio.filetypes.util.MultiSpectraParser
 
substitutionModification - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideType
 
substitutionModification - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideType
 
SubstitutionModificationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A modification where one residue is substituted by another (amino acid change).
SubstitutionModificationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SubstitutionModificationType
 
SubstitutionModificationType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A modification where one residue is substituted by another (amino acid change).
SubstitutionModificationType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SubstitutionModificationType
 
subsumingProteinEntry - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
subsumingProteinEntry - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
subtract(LCMSRangeSet) - Method in class umich.ms.datatypes.LCMSRangeSet
Will modify the set.
sumI - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
sumI - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
 
sumInt - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
summaryXml - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis
 
summaryXml - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MsmsPipelineAnalysis
 
summaryXml - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MsmsPipelineAnalysis
 
summaryXml - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummary
 
summaryXml - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummary
 
swissprotName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
 
swissprotName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
 
symbol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
symbol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
symbol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
 
symbol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
 
symbol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
 
symbol - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
 
syncBufferPos() - Method in class umich.ms.util.base64.Base64Context
If your underlying buffer has navigation capabilities, you can use this method to sync positions of the reader with your structure.

T

TAG_END_OF_RUN - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
TAG_END_OF_RUN - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
TAG_INDEX - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
TAG_INDEX - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
TAG_INDEXOFFSET - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
TAG_INDEXOFFSET - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
TAG_MSRUN - Static variable in class umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser
 
TAG_MZML - Static variable in class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
TAG_OFFSET - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
TAG_OFFSET - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
TAG_RUN - Static variable in class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
TAG_SCAN - Static variable in class umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser
 
TAG_SPECTRUMLIST - Static variable in class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
tagPeaksStart(XMLStreamReaderImpl, int) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
tagPrecursorStart(XMLStreamReaderImpl) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
tagScanStart(XMLStreamReaderImpl) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
target - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.TargetListType
 
targetList - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ScanSettingsType
 
TargetListType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Target list (or 'inclusion list') configured prior to the run.
TargetListType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.TargetListType
 
targetMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.LibraResult.Intensity
 
targetMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Intensity
 
targetMass - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Intensity
 
tasksPerCpuPerBatch - Variable in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
How many spectra each CPU will be given in one batch.
terminalModification - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary
 
terminalModification - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchSummary
 
TerminalModification - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
TerminalModification() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
 
terminalModification - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchSummary
 
TerminalModification - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
TerminalModification() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
 
terminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
terminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
 
terminus - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
 
ThermoRawFile - Class in umich.ms.fileio.filetypes.thermo.raw
LC/MS data source for Thermo RAW files.
ThermoRawFile(String) - Constructor for class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
Create a new source with autoload of spectra disabled.
ThermoRawIndex - Class in umich.ms.fileio.filetypes.thermo.raw
There's nothing really special about Thermo index, we're using our default implementation.
ThermoRawIndex() - Constructor for class umich.ms.fileio.filetypes.thermo.raw.ThermoRawIndex
 
ThermoRawIndexElement - Class in umich.ms.fileio.filetypes.thermo.raw
Created by Dmitry Avtonomov on 2016-04-25.
ThermoRawIndexElement(int, int) - Constructor for class umich.ms.fileio.filetypes.thermo.raw.ThermoRawIndexElement
 
ThermoTest - Class in umich.ms.fileio.filetypes.thermo.raw.test
 
ThermoTest() - Constructor for class umich.ms.fileio.filetypes.thermo.raw.test.ThermoTest
 
threshold - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ProteinDetectionProtocolType
 
threshold - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SpectrumIdentificationProtocolType
 
threshold - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ProteinDetectionProtocolType
 
threshold - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SpectrumIdentificationProtocolType
 
tic - Variable in class umich.ms.datatypes.scan.AbstractScan
Total ion current
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.AnalysisTimestamp
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisTimestamp
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisTimestamp
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
 
time - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
 
time - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.AnalysisSummary
 
time - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
 
time - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.AnalysisSummary
 
time - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
 
time_reading - Variable in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
timePerSpot - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.Spotting.Robot
 
timeUnit - Variable in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
 
timeWidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcHeavypeak
 
timeWidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioLcLightpeak
 
timeWidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcHeavypeak
 
timeWidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioLcLightpeak
 
timeWidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcHeavypeak
 
timeWidth - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioLcLightpeak
 
title - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
title - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 
toByteArray() - Method in class umich.ms.util.ByteArrayHolder
Creates a newly allocated byte array.
toByteBuffer() - Method in class umich.ms.util.ByteArrayHolder
 
toDecodedData(double[]) - Static method in class umich.ms.fileio.filetypes.mzml.MZMLPeaksDecoder
 
ToleranceType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The tolerance of the search given as a plus and minus value with units.
ToleranceType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ToleranceType
 
ToleranceType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The tolerance of the search given as a plus and minus value with units.
ToleranceType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ToleranceType
 
toString() - Method in class umich.ms.datatypes.index.impl.IndexElementDefault
 
toString() - Method in class umich.ms.datatypes.LCMSDataSubset
 
toString() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
toString() - Method in class umich.ms.datatypes.scan.AbstractScan
 
toString() - Method in class umich.ms.datatypes.scan.props.ActivationInfo
 
toString() - Method in class umich.ms.datatypes.scan.props.Instrument
 
toString() - Method in enum umich.ms.datatypes.scan.props.Polarity
 
toString() - Method in class umich.ms.fileio.filetypes.mzml.util.CVTerm
 
toString() - Method in class umich.ms.fileio.filetypes.mzml.util.InstrumentModelCVTerm
 
toString() - Method in class umich.ms.fileio.filetypes.xmlbased.OffsetLength
 
toString() - Method in class umich.ms.util.base64.Base64Context
Returns a String useful for debugging (especially within a debugger.)
toString() - Method in class umich.ms.util.ByteArrayHolder
Converts the buffer's contents into a string decoding bytes using the platform's default character set.
toString(String) - Method in class umich.ms.util.ByteArrayHolder
Converts the buffer's contents into a string by decoding the bytes using the specified charsetName.
toString(int) - Method in class umich.ms.util.ByteArrayHolder
Deprecated.
This method does not properly convert bytes into characters. As of JDK 1.1, the preferred way to do this is via the toString(String enc) method, which takes an encoding-name argument, or the toString() method, which uses the platform's default character encoding.
toString() - Method in class umich.ms.util.Interval1D
 
toString() - Method in class umich.ms.util.IntervalST.Node
 
totalNoSpectrumIds - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
totalNoSpectrumIds - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
totalNumberDistinctPeptides - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
totalNumberDistinctPeptides - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
totalNumberPeptides - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
totalNumberPeptides - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
totIonCurrent - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan
 
totNumIons - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit
 
totNumIons - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchHit
 
totNumIons - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchHit
 
totNumSpectra - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling
 
totNumSpectra - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelling
 
totNumSpectra - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelling
 
trace - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
Trace - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Trace() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
 
translationTable - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.DatabaseTranslationType
 
translationTable - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.DatabaseTranslationType
 
translationTableRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.PeptideEvidenceType
 
translationTableRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.PeptideEvidenceType
 
TranslationTableType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
The table used to translate codons into nucleic acids e.g.
TranslationTableType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.TranslationTableType
 
TranslationTableType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
The table used to translate codons into nucleic acids e.g.
TranslationTableType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.TranslationTableType
 
tremblName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinAnnotation
 
tremblName - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinAnnotation
 
type - Variable in class umich.ms.datatypes.lcmsrun.Hash
 
type - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Device
 
type - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Spectrum
 
type - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Aa
 
type - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Attribute
 
type - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.File
 
type - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
type - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Note
 
type - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
 
type - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.UserParamType
 
type - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.UserParamType
 
type - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
 
type - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
 
type - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.NegmodelDistribution
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.MixturemodelDistribution.PosmodelDistribution
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NegmodelDistribution
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PosmodelDistribution
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NegmodelDistribution
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PosmodelDistribution
 
type - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
 
type - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
 
type - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
 

U

uid - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Protein
 
umich.ms.datatypes - package umich.ms.datatypes
 
umich.ms.datatypes.index - package umich.ms.datatypes.index
 
umich.ms.datatypes.index.impl - package umich.ms.datatypes.index.impl
 
umich.ms.datatypes.lcmsrun - package umich.ms.datatypes.lcmsrun
 
umich.ms.datatypes.scan - package umich.ms.datatypes.scan
 
umich.ms.datatypes.scan.impl - package umich.ms.datatypes.scan.impl
 
umich.ms.datatypes.scan.props - package umich.ms.datatypes.scan.props
 
umich.ms.datatypes.scancollection - package umich.ms.datatypes.scancollection
 
umich.ms.datatypes.scancollection.impl - package umich.ms.datatypes.scancollection.impl
 
umich.ms.datatypes.spectrum - package umich.ms.datatypes.spectrum
 
umich.ms.datatypes.spectrum.impl - package umich.ms.datatypes.spectrum.impl
 
umich.ms.external - package umich.ms.external
 
umich.ms.external.apache.cassandra.io - package umich.ms.external.apache.cassandra.io
 
umich.ms.external.msnumpress - package umich.ms.external.msnumpress
 
umich.ms.fileio - package umich.ms.fileio
 
umich.ms.fileio.chunk - package umich.ms.fileio.chunk
 
umich.ms.fileio.exceptions - package umich.ms.fileio.exceptions
 
umich.ms.fileio.filetypes - package umich.ms.fileio.filetypes
 
umich.ms.fileio.filetypes.agilent.cef - package umich.ms.fileio.filetypes.agilent.cef
 
umich.ms.fileio.filetypes.agilent.cef.example - package umich.ms.fileio.filetypes.agilent.cef.example
 
umich.ms.fileio.filetypes.agilent.cef.jaxb - package umich.ms.fileio.filetypes.agilent.cef.jaxb
 
umich.ms.fileio.filetypes.gpmdb - package umich.ms.fileio.filetypes.gpmdb
 
umich.ms.fileio.filetypes.gpmdb.jaxb - package umich.ms.fileio.filetypes.gpmdb.jaxb
 
umich.ms.fileio.filetypes.mzidentml - package umich.ms.fileio.filetypes.mzidentml
 
umich.ms.fileio.filetypes.mzidentml.example - package umich.ms.fileio.filetypes.mzidentml.example
 
umich.ms.fileio.filetypes.mzidentml.jaxb.primitive - package umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
 
umich.ms.fileio.filetypes.mzidentml.jaxb.standard - package umich.ms.fileio.filetypes.mzidentml.jaxb.standard
 
umich.ms.fileio.filetypes.mzml - package umich.ms.fileio.filetypes.mzml
 
umich.ms.fileio.filetypes.mzml.jaxb - package umich.ms.fileio.filetypes.mzml.jaxb
 
umich.ms.fileio.filetypes.mzml.util - package umich.ms.fileio.filetypes.mzml.util
 
umich.ms.fileio.filetypes.mzxml - package umich.ms.fileio.filetypes.mzxml
 
umich.ms.fileio.filetypes.mzxml.deprecated - package umich.ms.fileio.filetypes.mzxml.deprecated
 
umich.ms.fileio.filetypes.mzxml.example - package umich.ms.fileio.filetypes.mzxml.example
 
umich.ms.fileio.filetypes.mzxml.jaxb - package umich.ms.fileio.filetypes.mzxml.jaxb
 
umich.ms.fileio.filetypes.pepxml - package umich.ms.fileio.filetypes.pepxml
 
umich.ms.fileio.filetypes.pepxml.example - package umich.ms.fileio.filetypes.pepxml.example
 
umich.ms.fileio.filetypes.pepxml.jaxb.nested - package umich.ms.fileio.filetypes.pepxml.jaxb.nested
 
umich.ms.fileio.filetypes.pepxml.jaxb.primitive - package umich.ms.fileio.filetypes.pepxml.jaxb.primitive
 
umich.ms.fileio.filetypes.pepxml.jaxb.standard - package umich.ms.fileio.filetypes.pepxml.jaxb.standard
 
umich.ms.fileio.filetypes.protxml - package umich.ms.fileio.filetypes.protxml
 
umich.ms.fileio.filetypes.protxml.example - package umich.ms.fileio.filetypes.protxml.example
 
umich.ms.fileio.filetypes.protxml.jaxb.primitive - package umich.ms.fileio.filetypes.protxml.jaxb.primitive
 
umich.ms.fileio.filetypes.protxml.jaxb.standard - package umich.ms.fileio.filetypes.protxml.jaxb.standard
 
umich.ms.fileio.filetypes.thermo.raw - package umich.ms.fileio.filetypes.thermo.raw
 
umich.ms.fileio.filetypes.thermo.raw.com4j - package umich.ms.fileio.filetypes.thermo.raw.com4j
MSFileReaderLib
umich.ms.fileio.filetypes.thermo.raw.test - package umich.ms.fileio.filetypes.thermo.raw.test
 
umich.ms.fileio.filetypes.util - package umich.ms.fileio.filetypes.util
 
umich.ms.fileio.filetypes.xmlbased - package umich.ms.fileio.filetypes.xmlbased
 
umich.ms.fileio.util - package umich.ms.fileio.util
 
umich.ms.fileio.util.jaxb - package umich.ms.fileio.util.jaxb
 
umich.ms.logging - package umich.ms.logging
 
umich.ms.msfiletoolbox - package umich.ms.msfiletoolbox
 
umich.ms.util - package umich.ms.util
 
umich.ms.util.base64 - package umich.ms.util.base64
 
uniqueStrippedPeptides - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Protein
 
uniqueStrippedPeptides - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Protein
 
unitAccession - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
 
unitAccession - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
 
unitAccession - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
 
unitAccession - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
 
unitCvRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
 
unitCvRef - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
 
unitCvRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
 
unitCvRef - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
 
unitName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
 
unitName - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
 
unitName - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
 
unitName - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
 
units - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Xdata
 
units - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Ydata
 
UnitsCV - Enum in umich.ms.fileio.filetypes.mzml.util
Used to convert retention times in mzML files.
UNKNOWN_ANALYZER - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
UNKNOWN_DETECTOR - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
UNKNOWN_IONISATION - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
UNKNOWN_MANUFACTURER - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
UNKNOWN_METHOD - Static variable in class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
 
UNKNOWN_MODEL - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
UNKNOWN_SERIAL_NUMBER - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
unload(LCMSDataSubset) - Method in class umich.ms.datatypes.LCMSData
Unloads spectra matched by this subset.
unload(LCMSDataSubset, Object, Set<LCMSDataSubset>) - Method in class umich.ms.datatypes.LCMSData
Unloads spectra matched by this subset.
unloadData(LCMSDataSubset) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
unloadData(LCMSDataSubset, Set<LCMSDataSubset>) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
unloadData(LCMSDataSubset) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
IMPLEMENTATIONS MUST BE SYNCHRONIZED
Unloads SPECTRA from the underlying ScanCollection.
unloadData(LCMSDataSubset, Set<LCMSDataSubset>) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
IMPLEMENTATIONS MUST BE SYNCHRONIZED
Unloads SPECTRA from the underlying ScanCollection.
unmarshal(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Adapter1
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Adapter2
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.Adapter1
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.Adapter2
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.Adapter1
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.Adapter2
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.Adapter1
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.Adapter2
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Adapter1
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Adapter2
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Adapter1
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Adapter2
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Adapter1
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Adapter2
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Adapter1
 
unmarshal(String) - Method in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Adapter2
 
unmarshal(Class<T>, String) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert a string to an object of a given class.
unmarshal(Class<T>, File) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert the contents of a file to an object of a given class.
unmarshal(Class<T>, Reader) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert the contents of a Reader to an object of a given class.
unmarshal(Class<T>, InputStream) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert the contents of an InputStream to an object of a given class.
unmarshal(Class<T>, Source) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Convert the contents of a Source to an object of a given class.
unmarshalCollection(Class<T>, String) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Converts the contents of the string to a List with objects of the given class.
unmarshalCollection(Class<T>, Reader) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Converts the contents of the Reader to a List with objects of the given class.
unmarshalCollection(Class<T>, InputStream) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Converts the contents of the InputStream to a List with objects of the given class.
unmarshalCollection(Class<T>, Source) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
Converts the contents of the Source to a List with objects of the given class.
unmarshall(Class<T>, XMLStreamReader) - Static method in class umich.ms.fileio.util.jaxb.JaxbUtils
 
uri - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
 
uri - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
 
uri - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
 
uri - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
 
uri - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
 
uri - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
 
url - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.File
 
url - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.SearchDatabase
 
url - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.SearchDatabase
 
url - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.SearchDatabase
 
use - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioContribution
 
use - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioContribution
 
use - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioContribution
 
userParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.ParamType
 
userParam - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.ParamType
 
userParam - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ParamGroupType
 
userParam - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.ReferenceableParamGroupType
 
UserParamType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.primitive
A single user-defined parameter.
UserParamType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.UserParamType
 
UserParamType - Class in umich.ms.fileio.filetypes.mzidentml.jaxb.standard
A single user-defined parameter.
UserParamType() - Constructor for class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.UserParamType
 
UserParamType - Class in umich.ms.fileio.filetypes.mzml.jaxb
Uncontrolled user parameters (essentially allowing free text).
UserParamType() - Constructor for class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
 

V

v - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
 
v - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
 
value - Variable in class umich.ms.datatypes.lcmsrun.Hash
 
value - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Attribute
 
value - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AbstractParamType
 
value - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AbstractParamType
 
value - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVParamType
 
value - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.UserParamType
 
value - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.MsRun.ParentFile
 
value - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
 
value - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Operator
 
value - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.Peaks
 
value - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
 
value - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.ActivationMethodType
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.EngineType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InputFileType
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.MassType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MixtureModelType.MixtureModelPoint
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.ModelDisType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary.MixtureModelling.Mixturemodel.Point
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ActivationMethodType
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EngineType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InputFileType
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MassType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MixtureModelPoint
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModelDisType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.Point
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.ActivationMethodType
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.EngineType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InputFileType
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.MassType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.MixtureModelPoint
 
value() - Method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModelDisType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
 
value - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.Point
 
value - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
 
value - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
 
valueNamevalueType - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.NamevalueType
 
valueOf(String) - Static method in enum umich.ms.datatypes.lcmsrun.Hash.TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.datatypes.scan.PeaksCompression
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.datatypes.scan.props.Polarity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.datatypes.scan.props.ScanType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.datatypes.scan.StorageStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.ATTR
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.TAG
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.ATTR
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.TAG
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.ActivationMethodType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.EngineType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.MassType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.ModelDisType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ActivationMethodType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EngineType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MassType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModelDisType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.ActivationMethodType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.EngineType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.MassType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModelDisType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0001
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0002
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0003
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0004
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Activations
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Corona
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_DataTypes
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Dep
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Detector
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_IonizationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_MSOrder
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Multiplex
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_PacketTypes
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_A
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_B
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_F
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_K
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_R
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_V
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Polarity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_PrecursorEnergy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_ScanData
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_ScanType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_SourceCID
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_SourceCIDType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_TurboScan
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Wideband
Returns the enum constant of this type with the specified name.
valueOntologyEntryType - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.OntologyEntryType
 
values() - Static method in enum umich.ms.datatypes.lcmsrun.Hash.TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.datatypes.scan.PeaksCompression
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.datatypes.scan.props.Polarity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.datatypes.scan.props.ScanType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.datatypes.scan.StorageStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.GAMLValues
 
Values - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Values() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Values
 
values - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.FragmentArrayType
 
values - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.FragmentArrayType
 
values() - Static method in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.ATTR
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.TAG
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.ATTR
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.TAG
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.ActivationMethodType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.EngineType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.MassType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.nested.ModelDisType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ActivationMethodType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.EngineType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.MassType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.primitive.ModelDisType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.ActivationMethodType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.EngineType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.MassType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.pepxml.jaxb.standard.ModelDisType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0001
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0002
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0003
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.__MIDL___MIDL_itf_XRawfile2_0000_0000_0004
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Activations
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Corona
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_DataTypes
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Dep
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Detector
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_IonizationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_MSOrder
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Multiplex
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_PacketTypes
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_A
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_B
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_F
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_K
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_R
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Param_V
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Polarity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_PrecursorEnergy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_ScanData
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_ScanType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_SourceCID
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_SourceCIDType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_TurboScan
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum umich.ms.fileio.filetypes.thermo.raw.com4j.MS_Wideband
Returns an array containing the constants of this enum type, in the order they are declared.
valueStr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.NameValueType
 
valueStr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.NameValueType
 
valueStr - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.NameValueType
 
valueStr - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.NameValueType
 
valueStr - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.NameValueType
 
variable - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.AminoacidModification
 
variable - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary.TerminalModification
 
variable - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AminoacidModification
 
variable - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.TerminalModification
 
variable - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AminoacidModification
 
variable - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.TerminalModification
 
vars - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
vars - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
vendor - Variable in class umich.ms.fileio.filetypes.mzml.util.InstrumentModelCVTerm
 
version - Variable in class umich.ms.datatypes.lcmsrun.MsSoftware
 
version - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.CEF
 
version - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.AnalysisSoftwareType
 
version - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.CvType
 
version - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.MzIdentMLType
 
version - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.SearchDatabaseType
 
version - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.AnalysisSoftwareType
 
version - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.CvType
 
version - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.MzIdentMLType
 
version - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.SearchDatabaseType
 
version - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.CVType
 
version - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.MzMLType
 
version - Variable in class umich.ms.fileio.filetypes.mzml.jaxb.SoftwareType
 
version - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Software
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.AsapratioSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.InterprophetSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.AnalysisSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.PeptideprophetSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AnalysisSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.AsapratioSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.InterprophetSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.PeptideprophetSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AnalysisSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.AsapratioSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.InterprophetSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.PeptideprophetSummary
 
version - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
version - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPProtAnalysisSummary
 
version - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProgramDetails
 
version - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPProtAnalysisSummary
 
version - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProgramDetails
 
version(Holder<Integer>, Holder<Integer>, Holder<Integer>, Holder<Integer>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXRawfile4
method Version
version - Static variable in class umich.ms.msfiletoolbox.MsftbxInfo
 
version - Static variable in class umich.ms.util.base64.Base64Slow
Version number of this program
volume - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
volume - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 

W

weight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPPeak
 
weight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ASAPSeq
 
weight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.Peptide
 
weight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPPeak
 
weight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ASAPSeq
 
weight - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.Peptide
 
WHOLE_RUN - Static variable in class umich.ms.datatypes.LCMSDataSubset
Sets up the parsing parameters to parse all the scans and spectra in a run.
WHOLE_RUN - Static variable in class umich.ms.datatypes.LCMSRange
 
WHOLE_RUN_MS1 - Static variable in class umich.ms.datatypes.LCMSRange
 
WHOLE_RUN_MS2 - Static variable in class umich.ms.datatypes.LCMSRange
 
WHOLE_RUN_STRUCTURE - Static variable in class umich.ms.datatypes.LCMSRange
 
winCygReferenceDatabase - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
winCygReferenceDatabase - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
winCygSourceFiles - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.ProteinSummaryHeader
 
winCygSourceFiles - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.ProteinSummaryHeader
 
windowsParent - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.MsmsPipelineAnalysis.DatasetDerivation.DataFilter
 
windowsParent - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.DataFilter
 
windowsParent - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.DataFilter
 
windowsParent - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.primitive.DataFilter
 
windowsParent - Variable in class umich.ms.fileio.filetypes.protxml.jaxb.standard.DataFilter
 
windowWideness - Variable in class umich.ms.fileio.filetypes.mzxml.jaxb.Scan.PrecursorMz
 
wrap(XMLStreamReaderImpl) - Method in class umich.ms.fileio.filetypes.xmlbased.XMLStreamReaderFactory
 
wrap(ByteArrayHolder) - Method in class umich.ms.util.ByteArrayHolderFactory
 
write(int) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
write(byte[]) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
write(byte[], int, int) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
write(int) - Method in class umich.ms.util.ByteArrayHolder
Writes the specified byte to this byte array output stream.
write(byte[], int, int) - Method in class umich.ms.util.ByteArrayHolder
Writes len bytes from the specified byte array starting at offset off to this byte array output stream.
writeErrorLog(float, String) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirUV
method WriteErrorLog
writeInstData(Holder<Byte>, int, MS_PacketTypes) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method WriteInstData
writeInstData(Holder<Byte>, int, MS_PacketTypes, int) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirUV
method WriteInstData
writeInstID(String, String, String, String, String) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method WriteInstID
writeInstID(String, String, String, String, String, String, String, String) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirUV
method WriteInstID
writeMethodScanEvents() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method WriteMethodScanEvents
writeRunHeaderInfo(double, double, String, String) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method WriteRunHeaderInfo
writeRunHeaderInfo(double) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirUV
method WriteRunHeaderInfo
writeStatusLog(float, Holder<Byte>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method WriteStatusLog
writeStatusLogHeader() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method WriteStatusLogHeader
writeTo(OutputStream) - Method in class umich.ms.util.ByteArrayHolder
Writes the complete contents of this byte array output stream to the specified output stream argument, as if by calling the output stream's write method using out.write(buf, 0, count).
writeTrailer(Holder<Byte>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method WriteTrailer
writeTrailerHeader() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method WriteTrailerHeader
writeTuneData(Holder<Byte>) - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method WriteTuneData
writeTuneDataHeader() - Method in interface umich.ms.fileio.filetypes.thermo.raw.com4j.IXVirMS
method WriteTuneDataHeader

X

x - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
 
xdata - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
 
Xdata - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Xdata() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Xdata
 
XMLBasedIndexElement - Interface in umich.ms.fileio.filetypes.xmlbased
 
XmlBasedRunHeaderParser - Class in umich.ms.fileio.filetypes.mzxml
For example look at source of MZXMLRunHeaderParser and MZMLRunHeaderParser.
XmlBasedRunHeaderParser() - Constructor for class umich.ms.fileio.filetypes.mzxml.XmlBasedRunHeaderParser
 
XMLStreamReaderFactory - Class in umich.ms.fileio.filetypes.xmlbased
Produces XMLStreamReaderImpl objects for reuse in XML parser-workers.
XMLStreamReaderFactory() - Constructor for class umich.ms.fileio.filetypes.xmlbased.XMLStreamReaderFactory
 
XPressAnalysisSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.primitive
Java class for anonymous complex type.
XPressAnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.primitive.XPressAnalysisSummary
 
XPressAnalysisSummary - Class in umich.ms.fileio.filetypes.protxml.jaxb.standard
Java class for anonymous complex type.
XPressAnalysisSummary() - Constructor for class umich.ms.fileio.filetypes.protxml.jaxb.standard.XPressAnalysisSummary
 
xpressLight - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
 
xpressLight - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioTimestamp
 
xpressLight - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
xpressLight - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioTimestamp
 
xpressLight - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
xpressLight - Variable in class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioTimestamp
 
XpressratioResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
XpressratioResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioResult
 
XpressratioResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
XpressratioResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioResult
 
XpressratioResult - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
XpressratioResult() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioResult
 
XpressratioSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
XpressratioSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioSummary
 
XpressratioSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
XpressratioSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioSummary
 
XpressratioSummary - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
XpressratioSummary() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioSummary
 
XpressratioTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.nested
Java class for anonymous complex type.
XpressratioTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.nested.XpressratioTimestamp
 
XpressratioTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.primitive
Java class for anonymous complex type.
XpressratioTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.primitive.XpressratioTimestamp
 
XpressratioTimestamp - Class in umich.ms.fileio.filetypes.pepxml.jaxb.standard
Java class for anonymous complex type.
XpressratioTimestamp() - Constructor for class umich.ms.fileio.filetypes.pepxml.jaxb.standard.XpressratioTimestamp
 
xRawfile5 - Variable in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 

Y

y - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.Location
 
y - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
 
ydata - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Trace
 
Ydata - Class in umich.ms.fileio.filetypes.gpmdb.jaxb
Java class for anonymous complex type.
Ydata() - Constructor for class umich.ms.fileio.filetypes.gpmdb.jaxb.Ydata
 
year - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.primitive.BibliographicReferenceType
 
year - Variable in class umich.ms.fileio.filetypes.mzidentml.jaxb.standard.BibliographicReferenceType
 
yIons - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 
yScore - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Domain
 

Z

z - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
z - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
z - Variable in class umich.ms.fileio.filetypes.agilent.cef.jaxb.P
 
z - Variable in class umich.ms.fileio.filetypes.gpmdb.jaxb.Group
 
zCarrier - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
ZlibInflater - Class in umich.ms.fileio.filetypes.util
Utility methods to inflate zlib compressed spectra (byte arrays).
zlibUncompressBuffer(byte[], Integer) - Static method in class umich.ms.fileio.filetypes.util.ZlibInflater
Convenience method for ZlibInflater.zlibUncompressBuffer(byte[], int, Integer).
Inflates zLib compressed byte[].
zlibUncompressBuffer(byte[], int, Integer) - Static method in class umich.ms.fileio.filetypes.util.ZlibInflater
Inflates zLib compressed byte[].

_

__MIDL___MIDL_itf_XRawfile2_0000_0000_0001 - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
__MIDL___MIDL_itf_XRawfile2_0000_0000_0002 - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
__MIDL___MIDL_itf_XRawfile2_0000_0000_0003 - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
__MIDL___MIDL_itf_XRawfile2_0000_0000_0004 - Enum in umich.ms.fileio.filetypes.thermo.raw.com4j
 
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