- abMax - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
-
- abMax - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
-
- AbstractFile - Class in umich.ms.util.file
-
Author: Dmitry Avtonomov (dmitriya)
- AbstractFile(String) - Constructor for class umich.ms.util.file.AbstractFile
-
- AbstractLCMSDataSource<T extends Index<?>> - Class in umich.ms.fileio.filetypes
-
Provides some basic defaults for simple LCMSFile interface methods.
- AbstractLCMSDataSource(String) - Constructor for class umich.ms.fileio.filetypes.AbstractLCMSDataSource
-
Create a new source with autoload of spectra disabled.
- AbstractScan - Class in umich.ms.datatypes.scan
-
The most general representation of a Scan.
- AbstractScan(int) - Constructor for class umich.ms.datatypes.scan.AbstractScan
-
Creates a scan with STRONG storage strategy.
- AbstractSpectrum - Class in umich.ms.datatypes.spectrum
-
Author: Dmitry Avtonomov (dmitriya)
- AbstractSpectrum() - Constructor for class umich.ms.datatypes.spectrum.AbstractSpectrum
-
- AbstractXMLBasedDataSource<E extends XMLBasedIndexElement,I extends Index<E>> - Class in umich.ms.fileio.filetypes.xmlbased
-
- AbstractXMLBasedDataSource(String) - Constructor for class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
-
- AbstractXMLBasedIndexElement - Class in umich.ms.fileio.filetypes.xmlbased
-
- AbstractXMLBasedIndexElement(int, int, OffsetLength) - Constructor for class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedIndexElement
-
- abTot - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
-
- abTot - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
-
- ACC_NUMPRESS_LINEAR - Static variable in class umich.ms.external.msnumpress.MSNumpress
-
- ACC_NUMPRESS_PIC - Static variable in class umich.ms.external.msnumpress.MSNumpress
-
- ACC_NUMPRESS_SLOF - Static variable in class umich.ms.external.msnumpress.MSNumpress
-
- accepts(Path) - Method in interface umich.ms.fileio.filetypes.LCMSDataSourceDetector
-
- accession - Variable in class umich.ms.fileio.filetypes.mzml.util.CVTerm
-
- accession - Variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
- accession - Variable in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
-
- activateObject(PooledObject<ByteArrayHolder>) - Method in class umich.ms.util.ByteArrayHolderFactory
-
- ActivationCVTerm - Class in umich.ms.fileio.filetypes.mzml.util
-
- ActivationCVTerm(String, String, String, String) - Constructor for class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
-
- ActivationCVTerm(String, String, String) - Constructor for class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
-
- ActivationInfo - Class in umich.ms.datatypes.scan.props
-
- ActivationInfo() - Constructor for class umich.ms.datatypes.scan.props.ActivationInfo
-
- activationMethodFromAccession(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
Returns the possible shortest abbreviation for a given activation method.
- activationMethodFromAccession(CharArray) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
Returns the possible shortest abbreviation for a given activation method.
- add(T) - Method in class umich.ms.datatypes.index.impl.IndexDefault
-
- add(T) - Method in interface umich.ms.datatypes.index.Index
-
Add a new index element to this index.
- add(LCMSRange) - Method in class umich.ms.datatypes.LCMSRangeSet
-
This add method gradually removes scan-ranges from the input range as it
descends down the hierarchy.
- add(IScan) - Method in class umich.ms.datatypes.scancollection.ScanIndex
-
Adds a scan to the index.
- add(IScan) - Method in class umich.ms.datatypes.scancollection.ScanIndexRoot
-
- add(AgilentMSPeak) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
-
- add(AgilentCompound) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
-
- addAll(Collection<? extends AgilentMSPeak>) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
-
- addCloseTag(T) - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
-
- addCurScanAndFlushVars() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
-
- addIndexElement(T) - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
-
- addInstrument(Instrument, String) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
If only one instrument is added, it will be set as the default instrument, all the scans, that you add
to the ScanCollection will implicitly refer to this one instrument.
- addRefParamGroup(String, List<CVParamType>) - Method in class umich.ms.fileio.filetypes.mzml.MZMLRunInfo
-
- addScan(IScan) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
Adds a new scan to this collection, maintains all the proper inside mappings.
- addScan(IScan) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
Adds a new scan to this collection, maintains all the proper inside mappings.
- addStartTag(T) - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
-
- adduct - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- advanceReaderToNext(XMLStreamReader, String) - Static method in class umich.ms.util.xml.XmlUtils
-
Advances the Stream Reader to the next occurrence of a user-specified tag.
- AgilentCefFile - Class in umich.ms.fileio.filetypes.agilent.cef.example
-
Factory for features detected by Agilent MassHunter, stored as .cef files.
- AgilentCefFile(Path) - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
-
- AgilentCefTest - Class in umich.ms.fileio.filetypes.agilent.cef.example
-
Created by Dmitry Avtonomov on 2015-09-22.
- AgilentCefTest() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefTest
-
- AgilentCompound - Class in umich.ms.fileio.filetypes.agilent.cef.example
-
One entry in Agilent .cef file, created by Molecular Feature Extractor algorithm.
- AgilentCompound() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
-
- AgilentCompounds - Class in umich.ms.fileio.filetypes.agilent.cef.example
-
All compounds from an Agilent .cef file.
- AgilentCompounds() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
-
- AgilentCompounds(int) - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
-
- AgilentMSPeak - Class in umich.ms.fileio.filetypes.agilent.cef.example
-
- AgilentMSPeak() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
-
- amu2ppm(double, double) - Static method in class umich.ms.util.SpectrumUtils
-
Given an absolute m/z difference (amu parameter), find out how much ppm that is.
- analyzer - Variable in class umich.ms.datatypes.scan.props.Instrument
-
- asString - Variable in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
-
- ATTR_OFFSET_ID - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
-
- ATTR_OFFSET_ID - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
-
- available() - Method in class umich.ms.util.base64.Base64Context
-
Returns the amount of buffered data available for reading.
- Base64 - Class in umich.ms.util.base64
-
Follows implementation from Apache Commons Codec (org.apache.commons.codec.binary.Base64).
- Base64() - Constructor for class umich.ms.util.base64.Base64
-
Creates a Base64 codec used for decoding (all modes) and encoding in
URL-unsafe mode.
- Base64(int) - Constructor for class umich.ms.util.base64.Base64
-
- Base64(int, byte[], boolean) - Constructor for class umich.ms.util.base64.Base64
-
Creates a Base64 codec used for decoding (all modes) and encoding in
URL-unsafe mode.
- base64Chars - Static variable in class umich.ms.util.base64.Base64Slow
-
Table of the sixty-four characters that are used as
the Base64 alphabet: [a-z0-9A-Z+/]
- Base64Context - Class in umich.ms.util.base64
-
- Base64Context() - Constructor for class umich.ms.util.base64.Base64Context
-
- Base64ContextPooled - Class in umich.ms.util.base64
-
- Base64ContextPooled() - Constructor for class umich.ms.util.base64.Base64ContextPooled
-
- Base64DecodingException - Exception in umich.ms.util.base64
-
Exception that is thrown when an unexpected character is encountered
during Base64 decoding.
- Base64DecodingException(String, char) - Constructor for exception umich.ms.util.base64.Base64DecodingException
-
Construct an new exception.
- Base64Slow - Class in umich.ms.util.base64
-
Implements Base64 encoding and decoding as defined by RFC 2045: "Multi-purpose Internet
Mail Extensions (MIME) Part One: Format of Internet Message Bodies" page 23.
- basePeakIntensity - Variable in class umich.ms.datatypes.scan.AbstractScan
-
Intensity of the most intense peak
- basePeakMz - Variable in class umich.ms.datatypes.scan.AbstractScan
-
m/z of the most intense peak
- buf - Variable in class umich.ms.util.ByteArrayHolder
-
The buffer where data is stored.
- BUF_SIZE - Static variable in class umich.ms.util.file.AbstractFile
-
- BufferedRandomAccessFile - Class in umich.ms.external.apache.cassandra.io
-
A BufferedRandomAccessFile is like a
RandomAccessFile, but it uses a private buffer so that most
operations do not require a disk access.
- BufferedRandomAccessFile(File, String) - Constructor for class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
-
Open a new BufferedRandomAccessFile on file
in mode mode, which should be "r" for reading only, or
"rw" for reading and writing.
- BufferedRandomAccessFile(File, String, int) - Constructor for class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
-
- BufferedRandomAccessFile(String, String) - Constructor for class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
-
Open a new BufferedRandomAccessFile on the file named
name in mode mode, which should be "r" for
reading only, or "rw" for reading and writing.
- BufferedRandomAccessFile(String, String, int) - Constructor for class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
-
- BufferedRandomAccessFile - Class in umich.ms.external
-
This is an optimized version of the BufferedRandomAccessFile class as described by
Nick Zhang on JavaWorld.com.
- BufferedRandomAccessFile(String, String, int) - Constructor for class umich.ms.external.BufferedRandomAccessFile
-
Creates a new instance of the BufferedRandomAccessFile.
- BufferedRandomAccessFile(File, String, int) - Constructor for class umich.ms.external.BufferedRandomAccessFile
-
- BuffSz_ - Static variable in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
-
- buildIndex(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexBuilder
-
For use with Executors, consider using instead of calling this method directly.
- buildIndex(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexBuilder
-
For use with Executors, consider using instead of calling this method directly.
- buildIndex(I) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
-
Be careful with this method, it will go over the whole file, building index from scans that it can find.
- buildIndex(IndexBuilder.Info) - Method in interface umich.ms.fileio.filetypes.xmlbased.IndexBuilder
-
- ByteArrayHolder - Class in umich.ms.util
-
Auto-growing array of bytes, with access to the underlying data.
- ByteArrayHolder(int) - Constructor for class umich.ms.util.ByteArrayHolder
-
Creates a new byte array output stream, with a buffer capacity of
the specified size, in bytes.
- ByteArrayHolder() - Constructor for class umich.ms.util.ByteArrayHolder
-
Creates a new byte array output stream.
- ByteArrayHolder(byte[]) - Constructor for class umich.ms.util.ByteArrayHolder
-
- ByteArrayHolderFactory - Class in umich.ms.util
-
- ByteArrayHolderFactory() - Constructor for class umich.ms.util.ByteArrayHolderFactory
-
- ByteArrayHolderFactory(int) - Constructor for class umich.ms.util.ByteArrayHolderFactory
-
- DATA_FACTORY - Static variable in class umich.ms.fileio.filetypes.xmlbased.MultiSpectraParser
-
- date - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- DEBUG - Static variable in class umich.ms.fileio.Opts
-
- decode(String, byte[], int) - Static method in class umich.ms.external.msnumpress.MSNumpress
-
Convenience function for decoding binary data encoded by MSNumpress.
- decode(byte[], int, Integer, int, EnumSet<PeaksCompression>) - Static method in class umich.ms.fileio.filetypes.mzml.MZMLPeaksDecoder
-
Converts a base64 encoded mz or intensity string used in mzML files to an array of doubles.
- decode(byte[], int, PeaksCompression) - Static method in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder
-
Convenience shortcut, which assumes the whole bytesIn array is useful data.
- decode(byte[], int, int, PeaksCompression) - Static method in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder
-
Converts a base64 encoded mz-intensity string from used in mzXML and mzML
files to an array of doubles.
- decode(byte[], Base64Context) - Method in class umich.ms.util.base64.Base64
-
Decodes a byte[] containing characters in the Base-N alphabet.
- decode(byte[], int, int, Base64Context) - Method in class umich.ms.util.base64.Base64
-
Decodes a byte[] containing characters in the Base-N alphabet.
- decode(char[], Base64Context) - Method in class umich.ms.util.base64.Base64
-
Decodes a char[] containing characters in the Base-N alphabet.
- decode(char[], int, int, Base64Context) - Method in class umich.ms.util.base64.Base64
-
Decodes a char[] containing characters in the Base-N alphabet.
- decode(String) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode a Base64 encoded String.
- decode(String, String) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode a Base64 encoded String.
- decode(String, String, String) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode a Base64 encoded String.
- decode(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded bytes.
- decode(byte[], OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded bytes to the an OutputStream.
- decode(InputStream, OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded data from the InputStream to the OutputStream.
- decode(InputStream, OutputStream, boolean) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded data from the InputStream to the OutputStream.
- DecodedData(double[], double, int, double, int, double, int, double) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLPeaksDecoder.DecodedData
-
- DecodedData(double[], double[], int, double, int, double, int, double, double) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
-
- decodeFixedPoint(byte[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
-
- decodeLinear(byte[], int, double[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
-
Decodes data encoded by encodeLinear.
- decodePic(byte[], int, double[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
-
Decodes data encoded by encodePic
- decodeSlof(byte[], int, double[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
-
Decodes data encoded by encodeSlof
- decodeToBytes(String) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode a Base64 encoded String.
- decodeToBytes(String, String) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode a Base64 encoded String.
- decodeToBytes(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded bytes.
- decodeToBytes(InputStream) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded data from the InputStream to a byte array.
- decodeToStream(String, OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode a Base64 encoded String to an OutputStream.
- decodeToStream(String, String, OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode a Base64 encoded String to an OutputStream.
- decodeToStream(byte[], OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded bytes to the an OutputStream.
- decodeToString(String) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode a Base64 encoded String.
- decodeToString(String, String) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode a Base64 encoded String.
- decodeToString(String, String, String) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode a Base64 encoded String.
- decodeToString(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded bytes.
- decodeToString(byte[], String) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded bytes.
- decodeToString(InputStream) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded data from the InputStream to a String.
- decodeToString(InputStream, String) - Static method in class umich.ms.util.base64.Base64Slow
-
Decode Base64 encoded data from the InputStream to a String.
- DEFAULT_BUFFER_RESIZE_FACTOR - Static variable in class umich.ms.util.base64.Base64
-
- DEFAULT_BUFFER_SIZE - Static variable in class umich.ms.util.base64.Base64
-
- DEFAULT_STORAGE_STRATEGY - Static variable in interface umich.ms.datatypes.scancollection.IScanCollection
-
The storage strategy, that should be used by default by all implementations
of this interface.
- defaultInstrumentID - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- defaultSize - Variable in class umich.ms.util.ByteArrayHolderFactory
-
- defaultSize - Variable in class umich.ms.util.PooledByteArrayHolders
-
- defaultStorageStrategy - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
- defaultStringRepresentation - Variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
- description - Variable in class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
-
- description - Variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
- detector - Variable in class umich.ms.datatypes.scan.props.Instrument
-
- distributeParseLoad(int, ArrayList<OffsetLength>) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
-
- doesNeedSpectrumParsing(IScan) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
-
- DoubleRange - Class in umich.ms.util
-
Represents a range of doubles, e.g.
- DoubleRange(Double, Double) - Constructor for class umich.ms.util.DoubleRange
-
- factory - Variable in class umich.ms.util.PooledByteArrayHolders
-
- fetchAttribute(Attributes, MZXMLMultiSpectraParser.ATTR) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
-
- fetchIndex() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
-
Returns the index, or parses it from the original file and caches for future reuse.
- fetchIndex() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
-
- fetchIndex() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
-
- fetchIndex() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
-
- fetchRunInfo() - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
-
- fetchRunInfo() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
-
Gets the run info, parsing it if it yet hasn't been, and caches for reuse.
- fetchRunInfo() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
-
- fetchSpectrum() - Method in class umich.ms.datatypes.scan.impl.ScanDefault
-
- fetchSpectrum() - Method in interface umich.ms.datatypes.scan.IScan
-
Get the spectrum, possibly preloading it from disk.
- fetchXrawfile() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
-
- FILE_TYPE_NAME - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
-
- FILE_TYPE_NAME - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
-
- FileChunk - Class in umich.ms.fileio.chunk
-
- FileChunk(int, long, int) - Constructor for class umich.ms.fileio.chunk.FileChunk
-
- FileChunkSource - Interface in umich.ms.fileio.chunk
-
Supplies chunks of raw bytes from a file.
- FileListing - Class in umich.ms.util.file
-
Created by Dmitry Avtonomov on 2015-10-21.
- FileListing(Path, String) - Constructor for class umich.ms.util.file.FileListing
-
- FileParsingException - Exception in umich.ms.fileio.exceptions
-
Is thrown when anything bad happens during parsing LC/MS files.
- FileParsingException() - Constructor for exception umich.ms.fileio.exceptions.FileParsingException
-
- FileParsingException(String) - Constructor for exception umich.ms.fileio.exceptions.FileParsingException
-
- FileParsingException(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.FileParsingException
-
- FileParsingException(Throwable) - Constructor for exception umich.ms.fileio.exceptions.FileParsingException
-
- filter - Variable in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawIndexElement
-
- finalizePrecursorWindows(IScanCollection) - Static method in class umich.ms.datatypes.scancollection.ScanCollectionHelper
-
Calling this method only makes sense if the whole LC/MS structure has been parsed.
- finalizeReferent() - Method in class umich.ms.datatypes.LCMSData.User
-
- finalizeScanCollection(IScanCollection) - Static method in class umich.ms.datatypes.scancollection.ScanCollectionHelper
-
Sets relationships between parent/child scans based on scan numbering.
- findClosestMzIdx(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
-
- findClosestMzIdx(double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
-
- findFiles() - Method in class umich.ms.util.file.FileListing
-
- findIndexOffset(RandomAccessFile) - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
-
- findIndexOffset(RandomAccessFile) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
-
- findMzIdxCeiling(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
-
- findMzIdxCeiling(double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
-
Finds the idx of MZ that is equal or greater than the provided one.
- findMzIdxFloor(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
-
- findMzIdxFloor(double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
-
Finds the idx of MZ that is equal or less than the provided one.
- findMzIdxs(double, double) - Method in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
-
- findMzIdxs(double, double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
-
Finds indexes of MZs that are within a tolerance window (inclusive)
- findMzIdxsWithinPpm(double, double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
-
- findMzIdxsWithinPpm(double, double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
-
Finds indexes of MZs that are within a PPM tolerance window (inclusive)
- findPrevLine() - Method in class umich.ms.util.ReverseLineInputStream
-
- findScanLength(long) - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
-
Finds the length of a scan entry in the original file by reading it,
starting at the provided offset and looking for an "end of scan" tag.
- findScanLength(long) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
-
Finds the length of a scan entry in the original file by reading it,
starting at the provided offset and looking for an "end of scan" tag.
- findThisStreamFirstScanLen() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
-
Intended use: find the length of the last scan entry in the file.
- fixIndex(MZXMLIndex) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
-
- fixIndex(I) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
-
The index as it is built by index builder contains offsets of "scan" tags, and their lengths.
- flush() - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
-
Flush any bytes in the file's buffer that have not yet been written to
disk.
- flushBinDataDescription() - Method in class umich.ms.fileio.filetypes.mzml.MzmlVars
-
- flushVarsIfNoCurScan() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
-
If the current vars variable doesn't contain a scan, that we've started processing, then flushes all
the fields in vars and returns true, otherwise does nothing and returns false.
- FMT_DOUBLE_2_DIGITS_AFTER_DOT - Static variable in class umich.ms.datatypes.scan.AbstractScan
-
- fromAccession(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
- fromAccession(CharArray) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
- fromInterval1D(Interval1D<Double>) - Static method in class umich.ms.util.DoubleRange
-
- fromPSIMSOntology(String) - Static method in enum umich.ms.datatypes.scan.props.ScanType
-
Get enum value from PSI-MS ontology terms.
- fromString(String) - Static method in enum umich.ms.datatypes.scan.props.ScanType
-
Case-insensitive conversion from a string representation to values of this Enum.
- FRQ - Static variable in class umich.ms.datatypes.LCMSData
-
- FULL_SCAN_RANGE - Static variable in class umich.ms.datatypes.LCMSRange
-
Represents the whole range of scans by number in any LCMS run.
- 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
-
- getAbMax() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
-
- getAbMax() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
-
- getAbTot() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
-
- getAbTot() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
-
- 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
-
- 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.
- getAdduct() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- getAnalyzer() - Method in class umich.ms.datatypes.scan.props.Instrument
-
- getBah() - Method in class umich.ms.fileio.chunk.FileChunk
-
- getBasePeakIntensity() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- getBasePeakIntensity() - Method in interface umich.ms.datatypes.scan.IScan
-
- getBasePeakMz() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- getBasePeakMz() - Method in interface umich.ms.datatypes.scan.IScan
-
- getBufferedInputStream() - Method in class umich.ms.util.file.AbstractFile
-
- 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.
- getCapacity() - Method in class umich.ms.util.ByteArrayHolder
-
- getCapacityLeft() - Method in class umich.ms.util.ByteArrayHolder
-
- getCentroided() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- getChangelog() - Static method in class umich.ms.msfiletoolbox.MsftbxInfo
-
- 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.
- getChildScans() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- getChildScans() - Method in interface umich.ms.datatypes.scan.IScan
-
- 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
-
- getCloseTagLocs() - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
-
- getCompounds() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
-
- getCompressions() - Method in class umich.ms.fileio.filetypes.mzml.MzmlVars
-
- getDataSource() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
- getDataSource() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
- getDefaultBufferSize() - Method in class umich.ms.util.base64.Base64
-
Get the default buffer size.
- getDefaultInstrument() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- getDefaultInstrumentID() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- getDefaultSize() - Method in class umich.ms.util.ByteArrayHolderFactory
-
- getDefaultStorageStrategy() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
- getDefaultStorageStrategy() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
- getDetector() - Method in class umich.ms.datatypes.scan.props.Instrument
-
- 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.
- getDuration() - Method in class umich.ms.datatypes.scan.props.InjectionInfo
-
- 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
- getFactory() - Method in class umich.ms.fileio.chunk.ChunkedFile
-
- 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.
- 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]
- getHi() - Method in class umich.ms.util.Interval1D
-
- 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.mzml.MZMLIndexElement
-
- getId() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexElement
-
- 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.mzml.MZMLFile
-
- getIndex() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
-
- 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.mzxml.MZXMLFile
-
- getIndexBuilder(IndexBuilder.Info) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
-
- getIndexElements() - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
-
- getInfo() - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
-
- getInjectionInfo() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- getInjectionInfo() - Method in interface umich.ms.datatypes.scan.IScan
-
- getInstance() - Static method in class umich.ms.util.PooledByteArrayHolders
-
- 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
-
- getInstruments() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- 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.
- 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
-
- getIsotopeNumber() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- getLength() - Method in class umich.ms.fileio.chunk.FileChunk
-
- getLo() - Method in class umich.ms.util.Interval1D
-
- 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.
- getMapMsLevel2rangeGroups() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
Get a map, holding spectra groupped by precursor m/z isolation window.
- 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
-
- getMaxInt() - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
-
- getMaxInt() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
-
The highest intensity in the spectrumRef.
- 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.
- getmCount() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- 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.
- 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.
- getModel() - Method in class umich.ms.datatypes.scan.props.Instrument
-
- getMolId() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- 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
-
- getMsLvl2index() - Method in class umich.ms.datatypes.scancollection.ScanIndexRoot
-
- getMsLvls() - Method in class umich.ms.datatypes.LCMSDataSubset
-
- getMz(int) - Method in interface umich.ms.datatypes.spectrum.IIndexedSpectrum
-
Deprecated.
- getMz() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
-
- 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.
- getMzTarget() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
-
In case of DDA runs, the m/z value for the actual peak that triggered fragmentation.
- getMzTargetMono() - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
-
The assumed monoisotopic m/z of the selected ion.
- 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.thermo.raw.ThermoRawFile
-
- getName() - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
-
- getNextLine() - Method in class umich.ms.external.BufferedRandomAccessFile
-
Returns the next line from the file.
- 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
-
- 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.
- 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.
- getNumScansToProcess() - Method in class umich.ms.fileio.filetypes.xmlbased.MultiSpectraParser
-
- 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.
- getOffset() - Method in class umich.ms.fileio.chunk.FileChunk
-
- getOffsetLength() - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedIndexElement
-
- getOffsetLength() - Method in interface umich.ms.fileio.filetypes.xmlbased.XMLBasedIndexElement
-
- getOriginalFiles() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- 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
-
- getParsedInfo() - Method in class umich.ms.fileio.filetypes.mzml.MZMLRunInfo
-
- 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.util.file.AbstractFile
-
Absolute normalized path to the file.
- getPath() - Method in class umich.ms.util.file.FileListing
-
- getPattern() - Method in class umich.ms.util.file.FileListing
-
- getPeaks() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
-
- getPolarity() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- getPolarity() - Method in interface umich.ms.datatypes.scan.IScan
-
- getPool() - Method in class umich.ms.fileio.chunk.ChunkedFile
-
- getPool() - Method in class umich.ms.fileio.chunk.FileChunk
-
- getPool() - Method in class umich.ms.util.PooledByteArrayHolders
-
- getPool() - Static method in class umich.ms.util.ZlibInflater
-
The ByteArrayHolder pool, that this decoder is using.
- getPosition() - Method in class umich.ms.util.ByteArrayHolder
-
This is the position of the next write to the underlying buffer.
- getPrecursor() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- getPrecursor() - Method in interface umich.ms.datatypes.scan.IScan
-
- 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
-
- getRandomAccessFile() - Method in class umich.ms.util.file.AbstractFile
-
- 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
-
- getRefParamGroups() - Method in class umich.ms.fileio.filetypes.mzml.MZMLRunInfo
-
- getRefParamGroupsAttrs() - Method in class umich.ms.fileio.filetypes.mzml.MZMLRunInfo
-
- 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
-
- 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.
- 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.
- getRunStartTime() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- 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.
- 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
- 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
-
- 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.
- getScanType() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- getScanType() - Method in interface umich.ms.datatypes.scan.IScan
-
- getSerialNumber() - Method in class umich.ms.datatypes.scan.props.Instrument
-
- getShortName() - Method in class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
-
- getSign() - Method in enum umich.ms.datatypes.scan.props.Polarity
-
- getSoftware() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- getSource() - Method in class umich.ms.datatypes.LCMSData
-
- 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.xmlbased.MultiSpectraParser
-
- 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.
- getSpectrumRef() - Method in class umich.ms.datatypes.scan.impl.ScanDefault
-
- getStartTagLocs() - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
-
- getStorageStrategy() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- getStorageStrategy() - Method in interface umich.ms.datatypes.scan.IScan
-
- getSumInt() - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
-
- getSumInt() - Method in interface umich.ms.datatypes.spectrum.ISpectrum
-
The sum of all intensities.
- 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.
- getTic() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- getTic() - Method in interface umich.ms.datatypes.scan.IScan
-
- getUnderlyingBytes() - Method in class umich.ms.util.ByteArrayHolder
-
- getValue() - Method in class umich.ms.util.IntervalST.Node
-
- getVersion() - Static method in class umich.ms.msfiletoolbox.MsftbxInfo
-
- getZ() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
-
- getZ() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- 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.
- 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.
- 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
-
- id - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexElement
-
- id - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser.OffsetId
-
- ID_UNKNOWN - Static variable in class umich.ms.datatypes.scan.props.Instrument
-
- IIndexedSpectrum - Interface in umich.ms.datatypes.spectrum
-
Deprecated.
- Index<T extends IndexElement> - Interface in umich.ms.datatypes.index
-
- index - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
- index - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
-
- index - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
-
- index - Variable in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
-
- index - Variable in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
-
- INDEX_NAME - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
-
- INDEX_NAME - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
-
- INDEX_OFFSET_MIN_VALUE - Static variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
-
- INDEX_OFFSET_MIN_VALUE - Static variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
-
- IndexBrokenException - Exception in umich.ms.fileio.exceptions
-
- IndexBrokenException() - Constructor for exception umich.ms.fileio.exceptions.IndexBrokenException
-
- IndexBrokenException(String) - Constructor for exception umich.ms.fileio.exceptions.IndexBrokenException
-
- IndexBrokenException(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.IndexBrokenException
-
- IndexBrokenException(Throwable) - Constructor for exception umich.ms.fileio.exceptions.IndexBrokenException
-
- IndexBrokenException(String, Throwable, boolean, boolean) - Constructor for exception umich.ms.fileio.exceptions.IndexBrokenException
-
- IndexBuilder<T extends XMLBasedIndexElement> - Interface in umich.ms.fileio.filetypes.xmlbased
-
- IndexBuilder.Info - Class in umich.ms.fileio.filetypes.xmlbased
-
- IndexBuilder.Result<T extends XMLBasedIndexElement> - Class in umich.ms.fileio.filetypes.xmlbased
-
- IndexDefault<T extends IndexElement> - Class in umich.ms.datatypes.index.impl
-
Raw and ID maps are lazily created on the first request for a search.
- IndexDefault() - Constructor for class umich.ms.datatypes.index.impl.IndexDefault
-
- IndexElement - Interface in umich.ms.datatypes.index
-
A mapping from internal scan numbers (which start at one) to scan numbering in the original files.
- IndexElementDefault - Class in umich.ms.datatypes.index.impl
-
- IndexElementDefault(int, int) - Constructor for class umich.ms.datatypes.index.impl.IndexElementDefault
-
- IndexNotFoundException - Exception in umich.ms.fileio.exceptions
-
Thrown when mzML/mzXML has no index.
- IndexNotFoundException() - Constructor for exception umich.ms.fileio.exceptions.IndexNotFoundException
-
- IndexNotFoundException(String) - Constructor for exception umich.ms.fileio.exceptions.IndexNotFoundException
-
- IndexNotFoundException(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.IndexNotFoundException
-
- IndexNotFoundException(Throwable) - Constructor for exception umich.ms.fileio.exceptions.IndexNotFoundException
-
- IndexNotFoundException(String, Throwable, boolean, boolean) - Constructor for exception umich.ms.fileio.exceptions.IndexNotFoundException
-
- Info(long, int, InputStream, String) - Constructor for class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
-
- init() - Method in class umich.ms.fileio.chunk.ChunkedFile
-
Check if the file is still valid.
- injectionInfo - Variable in class umich.ms.datatypes.scan.AbstractScan
-
If a file contains injection information, it should be put here, otherwise this field might be null.
- InjectionInfo - Class in umich.ms.datatypes.scan.props
-
Info about ion injection into the mass spectrometer.
- InjectionInfo() - Constructor for class umich.ms.datatypes.scan.props.InjectionInfo
-
- inMinutes(String, String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
-
Converts mzML representation of time into minutes.
- instrument - Variable in class umich.ms.datatypes.scan.AbstractScan
-
Should be a reference to one of the instruments listed in the ScanCollection
- Instrument - Class in umich.ms.datatypes.scan.props
-
Author: Dmitry Avtonomov
- Instrument() - Constructor for class umich.ms.datatypes.scan.props.Instrument
-
- Instrument(String, String, String) - Constructor for class umich.ms.datatypes.scan.props.Instrument
-
- Instrument(String, String, String, String, String) - Constructor for class umich.ms.datatypes.scan.props.Instrument
-
- instrumentFromAccession(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
- InstrumentModelCVTerm - Class in umich.ms.fileio.filetypes.mzml.util
-
- InstrumentModelCVTerm(String, String, String, String) - Constructor for class umich.ms.fileio.filetypes.mzml.util.InstrumentModelCVTerm
-
- instruments - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- intensities - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
-
- intensity - Variable in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
-
- intensitySum - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
-
- intersects(Interval1D<V>) - Method in class umich.ms.util.Interval1D
-
Does this interval intersect that one?
- Interval1D<V extends Comparable<V>> - Class in umich.ms.util
-
A generic 1D line segment (interval).
- Interval1D(V, V) - Constructor for class umich.ms.util.Interval1D
-
Precondition: left <= right
- IntervalST<K extends Comparable<K>,V> - Class in umich.ms.util
-
A generic Interval Search Tree.
- IntervalST() - Constructor for class umich.ms.util.IntervalST
-
- IntervalST.Node<U extends Comparable<U>,W> - Class in umich.ms.util
-
BST helper node data type.
- ionDescription - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
-
- IonId - Class in umich.ms.fileio.filetypes.agilent.cef.example
-
- IonId() - Constructor for class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- ionisation - Variable in class umich.ms.datatypes.scan.props.Instrument
-
- is - Variable in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
-
- is - Variable in class umich.ms.fileio.filetypes.xmlbased.MultiSpectraParser
-
- isAutoloadSpectra - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
- isAutoloadSpectra() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
- isAutoloadSpectra(boolean) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
- isAutoloadSpectra() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
Decides if spectra should be automatically loaded, when a spectrumRef is requested from a Scan, but there is no
spectrumRef present.
- isAutoloadSpectra(boolean) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
Sets the new configuration for spectra autoloading.
- isBase64(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
-
Determines if the byte array is in base64 format.
- isBase64(String) - Static method in class umich.ms.util.base64.Base64Slow
-
Determines if the String is in base64 format.
- isBase64(String, String) - Static method in class umich.ms.util.base64.Base64Slow
-
Determines if the String is in base64 format.
- isBase64(File) - Static method in class umich.ms.util.base64.Base64Slow
-
Determines if the File is in base64 format.
- isBase64(InputStream) - Static method in class umich.ms.util.base64.Base64Slow
-
Reads data from the stream and determines if it is
in base64 format.
- IScan - Interface in umich.ms.datatypes.scan
-
If you are ever writing a wrapper for 3rd party Scan implementations
you must implement this interface
Author: Dmitry Avtonomov (dmitriya)
Email: dmitriy.avtonomov@gmail.com
- IScanCollection - Interface in umich.ms.datatypes.scancollection
-
Manages scan meta-info and spectral data loading.
- isCentroided - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- isCentroided() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
If any of data-processing entries in mzXML or a similar file has mentioned, that the files has been centroided.
- isCentroided - Variable in class umich.ms.datatypes.scan.AbstractScan
-
Data might come already centroided out of the instrument or post-processing algorithms
- isCentroided() - Method in class umich.ms.datatypes.scan.AbstractScan
-
- isCentroided() - Method in interface umich.ms.datatypes.scan.IScan
-
- isDefaultExplicitlySet - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- isEmpty() - Method in class umich.ms.datatypes.LCMSRangeSet
-
- isEmpty() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
- isEmpty() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
Tells if the collection has at least one scan in it.
- isEmpty() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
-
- isEmpty() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
-
- isEnqueued() - Method in class umich.ms.util.StrongReference
-
- isExcludeEmptyScans() - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
-
Some ABSciex data has "peaks" tag empty and no "precursor" specified in such cases for MS2 - these are useless.
- isExcludeEmptyScans() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
-
- isFollowLinks() - Method in class umich.ms.util.file.FileListing
-
- isInAlphabet(byte[], boolean) - Method in class umich.ms.util.base64.Base64
-
Tests a given byte array to see if it contains only valid characters
within the alphabet.
- isInAlphabet(byte) - Method in class umich.ms.util.base64.Base64
-
Returns whether or not the octet is in the Base64 alphabet.
- isInAlphabet(String) - Method in class umich.ms.util.base64.Base64
-
Tests a given String to see if it contains only valid characters within
the alphabet.
- isIncludeDirectories() - Method in class umich.ms.util.file.FileListing
-
- isIncludeFiles() - Method in class umich.ms.util.file.FileListing
-
- isInSubset(IScan) - Method in class umich.ms.datatypes.LCMSDataSubset
-
In some cases we don't have the lower/upper mz window (for MS1 this
requires either this data to be in scan meta info, or the
spectrumRef to be parsed).
- isLoaded(LCMSDataSubset) - Method in class umich.ms.datatypes.LCMSData
-
Checks among the loaded by all users if this particular subset has already
been loaded by someone else.
- isNullOrBlank(CharSequence) - Static method in class umich.ms.util.StringUtils
-
- isNullOrEmpty(CharSequence) - Static method in class umich.ms.util.StringUtils
-
- isNullOrWhitespace(CharSequence) - Static method in class umich.ms.util.StringUtils
-
- isPeakPickingTerm(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
Checks if this accession maps to a known descendant of ["MS:1000035", "peak picking"] term.
- ISpectrum - Interface in umich.ms.datatypes.spectrum
-
Author: Dmitry Avtonomov (dmitriya)
- isPlatformSupported() - Static method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
-
Just checks if the OS is some flavor of windows.
- isRecursive() - Method in class umich.ms.util.file.FileListing
-
- isReleasingMemory - Variable in class umich.ms.datatypes.LCMSData
-
- isRequired - Variable in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.ATTR
-
- isRequired - Variable in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.ATTR
-
- isThermoLibInstalled() - Static method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
-
Checks if the MSFileReader Type Library from Thermo is installed as a COM object.
- isThermoSupportedHere() - Static method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
-
Checks if the particular machine the code runs on can read Thermo RAW files.
- isUrlSafe() - Method in class umich.ms.util.base64.Base64
-
Returns our current encode mode.
- isWhiteSpace(byte) - Static method in class umich.ms.util.base64.Base64
-
Checks if a byte value is whitespace or not.
- isWithinPpm(double, double, double) - Static method in class umich.ms.util.SpectrumUtils
-
Check if the 2nd m/z value is within some PPM distance from the 1st one.
- iterator() - Method in class umich.ms.fileio.filetypes.pepxml.PepXmlStream
-
- iterator() - Method in class umich.ms.util.IntervalST
-
- 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.
- 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
-
- 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.
- 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
- 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.
- 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.
- searchAll(Interval1D<K>) - Method in class umich.ms.util.IntervalST
-
Return ALL intervals in data structure that intersect the given interval.
- 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.
- 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
-
- 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
-
- 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
-
- setActivationTime(Double) - Method in class umich.ms.datatypes.scan.props.ActivationInfo
-
- setAdduct(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- setAnalyzer(String) - Method in class umich.ms.datatypes.scan.props.Instrument
-
- 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.
- setBasePeakIntensity(Double) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setBasePeakIntensity(Double) - Method in interface umich.ms.datatypes.scan.IScan
-
- setBasePeakMz(Double) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setBasePeakMz(Double) - Method in interface umich.ms.datatypes.scan.IScan
-
- 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
-
- setCharge(Integer) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
-
- setChildScans(List<Integer>) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setChildScans(List<Integer>) - Method in interface umich.ms.datatypes.scan.IScan
-
- setChunkBufferSize(int) - Method in class umich.ms.fileio.chunk.ChunkedFile
-
- 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.
- 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.
- setDefaultStorageStrategy(StorageStrategy) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
- setDefaultStorageStrategy(StorageStrategy) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
- setDetector(String) - Method in class umich.ms.datatypes.scan.props.Instrument
-
- setDuration(Double) - Method in class umich.ms.datatypes.scan.props.InjectionInfo
-
- setExcludeEmptyScans(boolean) - Method in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
-
If true, empty scans will be discarded during parsing.
- setExcludeEmptyScans(boolean) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
-
If true, empty scans will be discarded during parsing.
- setFactory(ByteArrayHolderFactory) - Method in class umich.ms.util.PooledByteArrayHolders
-
You should be very careful about this one.
- setFilePointer(long) - Method in class umich.ms.util.ReverseLineInputStream
-
- setFilter(String) - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawIndexElement
-
- setFollowLinks(boolean) - Method in class umich.ms.util.file.FileListing
-
- setIncludeDirectories(boolean) - Method in class umich.ms.util.file.FileListing
-
- setIncludeFiles(boolean) - Method in class umich.ms.util.file.FileListing
-
- setInjectionInfo(InjectionInfo) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setInjectionInfo(InjectionInfo) - Method in interface umich.ms.datatypes.scan.IScan
-
- setInstrument(Instrument) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setInstrument(Instrument) - Method in interface umich.ms.datatypes.scan.IScan
-
- 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.
- 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
-
- setIsotopeNumber(int) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- 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
-
- setManufacturer(String) - Method in class umich.ms.datatypes.scan.props.Instrument
-
- setMass(double) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
-
- 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
-
- setmCount(int) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- 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
-
- setModel(String) - Method in class umich.ms.datatypes.scan.props.Instrument
-
- setMolId(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- setMsLevel(Integer) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setMsLevel(Integer) - Method in interface umich.ms.datatypes.scan.IScan
-
- setMsLvls(Set<Integer>) - Method in class umich.ms.datatypes.LCMSDataSubset
-
- 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
-
- 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
-
- setMzTargetMono(Double) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
-
- setNumScansToProcess(Integer) - Method in class umich.ms.fileio.filetypes.xmlbased.MultiSpectraParser
-
- 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.
- 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.
- setParentScanNum(Integer) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
-
- setParentScanRefRaw(String) - Method in class umich.ms.datatypes.scan.props.PrecursorInfo
-
- 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.
- setPath(Path) - Method in class umich.ms.util.file.FileListing
-
- setPattern(Pattern) - Method in class umich.ms.util.file.FileListing
-
- setPolarity(Polarity) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setPolarity(Polarity) - Method in interface umich.ms.datatypes.scan.IScan
-
- setPool(ObjectPool<ByteArrayHolder>) - Method in class umich.ms.fileio.chunk.FileChunk
-
- setPosition(int) - Method in class umich.ms.util.ByteArrayHolder
-
This is a dangerous method, be sure you know what you're doing.
- setPrecursor(PrecursorInfo) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setPrecursor(PrecursorInfo) - Method in interface umich.ms.datatypes.scan.IScan
-
- setReaderPool(ObjectPool<XMLStreamReaderImpl>) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
-
- setRecursive(boolean) - Method in class umich.ms.util.file.FileListing
-
- 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
-
- 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
-
- setRunInfo(LCMSRunInfo) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
-
- setRunInfo(LCMSRunInfo) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
-
- setRunStartTime(Date) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- setScanCollection(IScanCollection) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setScanCollection(IScanCollection) - Method in interface umich.ms.datatypes.scan.IScan
-
- 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
-
- setScanType(ScanType) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setScanType(ScanType) - Method in interface umich.ms.datatypes.scan.IScan
-
- setSerialNumber(String) - Method in class umich.ms.datatypes.scan.props.Instrument
-
- 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.
- setSpectrumImpl(ISpectrum) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setSpectrumImpl(ISpectrum) - Method in class umich.ms.datatypes.scan.impl.ScanDefault
-
- 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
-
- setSumInt(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
-
- 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.
- setTic(Double) - Method in class umich.ms.datatypes.scan.AbstractScan
-
- setTic(Double) - Method in interface umich.ms.datatypes.scan.IScan
-
- setValue(W) - Method in class umich.ms.util.IntervalST.Node
-
Use with caution.
- 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
-
- setzCarrier(String) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
-
- shortName - Variable in class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
-
- 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.
- software - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
-
- 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.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
-
- SpectrumDefault - Class in umich.ms.datatypes.spectrum.impl
-
This is a straightforward implementation of AbstractSpectrum using Java arrays
Author: Dmitry Avtonomov (dmitriya)
- 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
-
- spectrumRef - Variable in class umich.ms.datatypes.scan.impl.ScanDefault
-
- SpectrumUtils - Class in umich.ms.util
-
Utilities for working with
ISpectrum objects.
- splitCompoundsByAdduct() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
-
- storageStrategy - Variable in class umich.ms.datatypes.scan.AbstractScan
-
- StorageStrategy - Enum in umich.ms.datatypes.scan
-
Enum holding spectrumRef reference types.
- 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
-
- subset - Variable in class umich.ms.fileio.filetypes.xmlbased.MultiSpectraParser
-
- subtract(LCMSRangeSet) - Method in class umich.ms.datatypes.LCMSRangeSet
-
Will modify the set.
- sumInt - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
-
- 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.
- value - Variable in class umich.ms.datatypes.lcmsrun.Hash
-
- valueOf(String) - Static method in enum umich.ms.datatypes.lcmsrun.Hash.TYPE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.datatypes.scan.PeaksCompression
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.datatypes.scan.props.Polarity
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.datatypes.scan.props.ScanType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.datatypes.scan.StorageStrategy
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.ATTR
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.TAG
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzml.MzmlVars.BIN_DATA_TYPE
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.ATTR
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.TAG
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.util.xml.POSITION
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum umich.ms.util.xml.TAG_TYPE
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum umich.ms.datatypes.lcmsrun.Hash.TYPE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.datatypes.scan.PeaksCompression
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.datatypes.scan.props.Polarity
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.datatypes.scan.props.ScanType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.datatypes.scan.StorageStrategy
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.ATTR
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.TAG
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.fileio.filetypes.mzml.MzmlVars.BIN_DATA_TYPE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.ATTR
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.TAG
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.util.xml.POSITION
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum umich.ms.util.xml.TAG_TYPE
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- vars - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
-
- vendor - Variable in class umich.ms.fileio.filetypes.mzml.util.InstrumentModelCVTerm
-
- version - Variable in class umich.ms.datatypes.lcmsrun.MsSoftware
-
- version - Static variable in class umich.ms.msfiletoolbox.MsftbxInfo
-
- version - Static variable in class umich.ms.util.base64.Base64Slow
-
Version number of this program