- 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
-
- getNextScanAtSameMsLevel(IScan) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
- 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
-
- 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
-
- getPrevScanAtSameMsLevel(IScan) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
- 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
-
- 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
-
- getScansByRtSpanAtMsLevel(double, double, int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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.