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A

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 a IndexElement to the index.
add(T) - Method in interface umich.ms.datatypes.index.Index
Add a new index element to this index.
add(LCMSRange) - Method in class umich.ms.datatypes.LCMSRangeSet
This add method gradually removes scan-ranges from the input range as it descends down the hierarchy.
add(IScan) - Method in class umich.ms.datatypes.scancollection.ScanIndex
Adds a scan to the index.
add(IScan) - Method in class umich.ms.datatypes.scancollection.ScanIndexRoot
 
add(AgilentMSPeak) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
add(AgilentCompound) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompounds
 
addAll(Collection<? extends AgilentMSPeak>) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
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.

B

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
 

C

call() - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexBuilder
 
call() - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
call() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexBuilder
 
call() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
charArray - Variable in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.ATTR
 
charArray - Variable in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.TAG
 
CHARGE_UNKNOWN - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
CHARGE_UNKNOWN - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
check() - Method in class umich.ms.util.IntervalST
Check integrity of subtree count fields.
childScans - Variable in class umich.ms.datatypes.scan.AbstractScan
A list of MS/MS scans, that originated from this one
ChunkedFile - Class in umich.ms.fileio.chunk
 
ChunkedFile(Path) - Constructor for class umich.ms.fileio.chunk.ChunkedFile
 
ChunkedFile(Path, int, int) - Constructor for class umich.ms.fileio.chunk.ChunkedFile
 
clear() - Method in class umich.ms.util.ByteArrayHolder
 
clear() - Method in class umich.ms.util.StrongReference
 
cloneWithoutPeaks() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
close() - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
close() - Method in class umich.ms.util.base64.Base64Context
should be called when context becomes useless
close() - Method in class umich.ms.util.base64.Base64ContextPooled
 
close() - Method in class umich.ms.util.ByteArrayHolder
Closing a ByteArrayOutputStream has no effect.
close() - Method in class umich.ms.util.file.AbstractFile
 
compareTo(AgilentMSPeak) - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
compareTo(Interval1D<V>) - Method in class umich.ms.util.Interval1D
 
configureJavaUtilLogging() - Static method in class umich.ms.logging.LogHelper
Configures JUL (java.util.logging) using the logging.properties file located in this package.
contains(LCMSDataSubset) - Method in class umich.ms.datatypes.LCMSDataSubset
Checks if data ranges described by this subset fully contain ranges specified in another set.
contains(V) - Method in class umich.ms.util.Interval1D
Does this interval contain a point?
contains(Interval1D<K>) - Method in class umich.ms.util.IntervalST
Check if the tree contains this exact interval.
containsAlphabetOrPad(byte[]) - Method in class umich.ms.util.base64.Base64
Tests a given byte array to see if it contains any characters within the alphabet or PAD.
convertJAXBObjectToDomain(Class<T>, Object) - Method in class umich.ms.fileio.filetypes.gpmdb.GPMDBFile
 
count - Variable in class umich.ms.util.ByteArrayHolder
The number of valid bytes in the buffer.
counter - Static variable in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
 
create() - Static method in class umich.ms.datatypes.LCMSRange
A range that will contain all the scans in an LCMS run, no filters applied.
create(Range<Integer>) - Static method in class umich.ms.datatypes.LCMSRange
A range that will contain all scans within the specified scan number range.
create(Range<Integer>, Integer) - Static method in class umich.ms.datatypes.LCMSRange
A range that will contain all scans with the scan number range, but only at a specific MS-Level.
create(Range<Integer>, Integer, DoubleRange) - Static method in class umich.ms.datatypes.LCMSRange
A range, containing all scans within the scan number range at a specific MS-Level and a specific precursor range.
create() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefFile
 
create(Path) - Static method in class umich.ms.fileio.filetypes.LCMSDataSourceFactory
Try and create a data source from a given file path.
create(CVParamType) - Static method in class umich.ms.fileio.filetypes.mzml.util.CvAttrs
 
create(InputStream) - Static method in class umich.ms.fileio.filetypes.pepxml.PepXmlStream
 
create() - Method in class umich.ms.fileio.filetypes.xmlbased.XMLStreamReaderFactory
 
create() - Method in class umich.ms.util.ByteArrayHolderFactory
 
createDummyInfo() - Static method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
Only use if you can't get real run info.
createEmpty() - Static method in class umich.ms.fileio.filetypes.mzml.MZMLPeaksDecoder.DecodedData
 
createEmpty() - Static method in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
createScanStub(int) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
createScanStub(int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Creates a scan stub, using the right StorageStrategy.
CvAttrs - Class in umich.ms.fileio.filetypes.mzml.util
 
CVTerm - Class in umich.ms.fileio.filetypes.mzml.util
Just the most generic representation of a CV term.
CVTerm(String, String) - Constructor for class umich.ms.fileio.filetypes.mzml.util.CVTerm
 

D

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
 

E

encode(String) - Static method in class umich.ms.util.base64.Base64Slow
Encode a String in Base64.
encode(String, String) - Static method in class umich.ms.util.base64.Base64Slow
Encode a String in Base64.
encode(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
Encode bytes in Base64.
encode(byte[], boolean) - Static method in class umich.ms.util.base64.Base64Slow
Encode bytes in Base64.
encode(InputStream, OutputStream) - Static method in class umich.ms.util.base64.Base64Slow
Encode data from the InputStream to the OutputStream in Base64.
encode(InputStream, OutputStream, boolean) - Static method in class umich.ms.util.base64.Base64Slow
Encode data from the InputStream to the OutputStream in Base64.
encodeFixedPoint(double, byte[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
 
encodeInt(long, byte[], int) - Static method in class umich.ms.external.msnumpress.MSNumpress
This encoding works on a 4 byte integer, by truncating initial zeros or ones.
encodeLinear(double[], int, byte[], double) - Static method in class umich.ms.external.msnumpress.MSNumpress
Encodes the doubles in data by first using a - lossy conversion to a 4 byte 5 decimal fixed point repressentation - storing the residuals from a linear prediction after first to values - encoding by encodeInt (see above)
encodePic(double[], int, byte[]) - Static method in class umich.ms.external.msnumpress.MSNumpress
Encodes ion counts by simply rounding to the nearest 4 byte integer, and compressing each integer with encodeInt.
encodeSlof(double[], int, byte[], double) - Static method in class umich.ms.external.msnumpress.MSNumpress
Encodes ion counts by taking the natural logarithm, and storing a fixed point representation of this.
encodeToString(byte[]) - Static method in class umich.ms.util.base64.Base64Slow
Encode bytes in Base64.
encodeToString(byte[], boolean) - Static method in class umich.ms.util.base64.Base64Slow
Encode bytes in Base64.
enqueue() - Method in class umich.ms.util.StrongReference
 
ensureBufferHasCapacityLeft(int) - Method in class umich.ms.util.base64.Base64Context
Ensure, that the output data buffer has enough space left for size mode bytes.
ensureBufferHasCapacityLeft(int) - Method in class umich.ms.util.base64.Base64ContextPooled
 
ensureCapacity(int) - Method in class umich.ms.util.ByteArrayHolder
Increases the capacity if necessary to ensure that it can hold at least the number of elements specified by the minimum capacity argument.
ensureCapacity(int, boolean) - Method in class umich.ms.util.ByteArrayHolder
 
ensureHasSpace(int) - Method in class umich.ms.util.ByteArrayHolder
Checks if there is enough space in the buffer to write N additional bytes.
equals(Object) - Method in class umich.ms.datatypes.LCMSDataSubset
 
equals(Object) - Method in class umich.ms.datatypes.scan.props.Instrument
 
equals(Object) - Method in class umich.ms.fileio.chunk.FileChunk
 
equals(Object) - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser.OffsetId
 
equals(Object) - Method in class umich.ms.util.Interval1D
 
Example - Class in umich.ms.fileio.filetypes.mzxml.example
 
Example() - Constructor for class umich.ms.fileio.filetypes.mzxml.example.Example
 
Example2 - Class in umich.ms.fileio.filetypes.mzxml.example
Created by Dmitry Avtonomov on 2016-04-18.
Example2() - Constructor for class umich.ms.fileio.filetypes.mzxml.example.Example2
 
Example3 - Class in umich.ms.fileio.filetypes.mzxml.example
Created by Dmitry Avtonomov on 2016-04-18.
Example3() - Constructor for class umich.ms.fileio.filetypes.mzxml.example.Example3
 
Example4 - Class in umich.ms.fileio.filetypes.mzxml.example
Created by Dmitry Avtonomov on 2016-04-18.
Example4() - Constructor for class umich.ms.fileio.filetypes.mzxml.example.Example4
 
excludeEmptyScans - Variable in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
When set to true, will discard scans with no m/z values.

F

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
Reads the last several kB of the file, looking for MZMLIndexParser.TAG_INDEXOFFSET tag.
findIndexOffset(RandomAccessFile) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
Reads the last few kB of the file, looking for MZXMLIndexParser.TAG_INDEXOFFSET tag.
findMzIdxCeiling(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
findMzIdxCeiling(double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
Finds the idx of MZ that is equal or greater than the provided one.
findMzIdxFloor(double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
findMzIdxFloor(double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
Finds the idx of MZ that is equal or less than the provided one.
findMzIdxs(double, double) - Method in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
 
findMzIdxs(double, double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
Finds indexes of MZs that are within a tolerance window (inclusive)
findMzIdxsWithinPpm(double, double) - Method in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
findMzIdxsWithinPpm(double, double) - Method in interface umich.ms.datatypes.spectrum.ISpectrum
Finds indexes of MZs that are within a PPM tolerance window (inclusive)
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.

G

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
Convenience method, calls ScanCollectionDefault.getNextScanAtMsLevel(int, int) internally
getNextScanAtSameMsLevel(IScan) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Convenience method, calls IScanCollection.getNextScanAtMsLevel(int, int) internally
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
Deprecated.
This is just a side effect of encapsulating the old Maps into the new ScanIndex. Use ScanCollectionDefault.getMapNum2scan() instead.
getNum2scan() - Method in class umich.ms.datatypes.scancollection.ScanIndex
 
getNumber() - Method in class umich.ms.datatypes.index.impl.IndexElementDefault
 
getNumber() - Method in interface umich.ms.datatypes.index.IndexElement
Internal scan number, starting from 1, incrementing by one for each consecutive scan.
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
Convenience method, calls ScanCollectionDefault.getPrevScanAtMsLevel(int, int) internally
getPrevScanAtSameMsLevel(IScan) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Convenience method, calls IScanCollection.getPrevScanAtMsLevel(int, int) internally
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
Deprecated.
This is just a side effect of encapsulating the old Maps into the new ScanIndex. Use ScanCollectionDefault.getMapRt2scan() instead.
getRt2scan() - Method in class umich.ms.datatypes.scancollection.ScanIndex
 
getRtHi() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
getRtLo() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
getRtMax() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
RT of the last scan in this scan collection.
getRtMax() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
RT of the last scan in this scan collection.
getRtMin() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
RT of the first scan.
getRtMin() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
RT of the first scan.
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
Same as ScanCollectionDefault.getScansByRtSpan(double, double), but only searches at one MS Level.
getScansByRtSpanAtMsLevel(double, double, int) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Same as IScanCollection.getScansByRtSpan(double, double), but only searches at one MS Level
getScansByRtUpper(double) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
Scan List with the closest RT greater or equal to the provided one are returned.
getScansByRtUpper(double) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Scan List with the closest RT greater or equal to the provided one are returned.
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
 

H

Hash - Class in umich.ms.datatypes.lcmsrun
 
Hash(String, Hash.TYPE) - Constructor for class umich.ms.datatypes.lcmsrun.Hash
 
hash - Variable in class umich.ms.datatypes.lcmsrun.OriginalFile
 
Hash.TYPE - Enum in umich.ms.datatypes.lcmsrun
 
hashCode() - Method in class umich.ms.datatypes.LCMSDataSubset
 
hashCode() - Method in class umich.ms.datatypes.scan.props.Instrument
 
hashCode() - Method in class umich.ms.fileio.chunk.FileChunk
 
hashCode() - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser.OffsetId
 
hashCode() - Method in class umich.ms.util.Interval1D
 
height() - Method in class umich.ms.util.IntervalST
 
hi - Variable in class umich.ms.util.Interval1D
 

I

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
 

J

join(Iterable<?>, String) - Static method in class umich.ms.util.StringUtils
Join strings with a separator.
join(Iterator<?>, String) - Static method in class umich.ms.util.StringUtils
Join strings with a separator.

L

LCMSData - Class in umich.ms.datatypes
A wrapper uniting a data source and a scan collection.
LCMSData(LCMSDataSource<?>) - Constructor for class umich.ms.datatypes.LCMSData
Will create LCMSData backed up by ScanCollectionDefault with spectra auto-loading turned off.
LCMSData(LCMSDataSource<?>, IScanCollection) - Constructor for class umich.ms.datatypes.LCMSData
You can pass you IScanCollection implementation, but you likely won't want to do that.
LCMSData.User - Class in umich.ms.datatypes
This is a PhantomRef for the object, that requests loading of data, so we could track it being garbage collected.
LCMSDataSource<T extends Index<?>> - Interface in umich.ms.fileio.filetypes
Wrapper interface for working with all LC/MS files.
LCMSDataSourceDetector - Interface in umich.ms.fileio.filetypes
Implementations of this interface should be marked as Service Providers using @ProviderFor annotation.
LCMSDataSourceFactory - Class in umich.ms.fileio.filetypes
Factory for automatic detection of supported filetypes and creating corresponding LCMSDataSources.
LCMSDataSubset - Class in umich.ms.datatypes
Represents a subset of a ScanCollection.
LCMSDataSubset() - Constructor for class umich.ms.datatypes.LCMSDataSubset
 
LCMSDataSubset(Integer, Integer, Set<Integer>, List<DoubleRange>) - Constructor for class umich.ms.datatypes.LCMSDataSubset
 
LCMSRange - Class in umich.ms.datatypes
NOT IN USE YET, SUPPOSED TO REPLACE LCMSDataSubset Represents a subset of data in an LCMS run.
LCMSRange() - Constructor for class umich.ms.datatypes.LCMSRange
Creates a range, that includes the whole run.
LCMSRange(Range<Integer>, Integer, DoubleRange) - Constructor for class umich.ms.datatypes.LCMSRange
 
LCMSRangeSet - Class in umich.ms.datatypes
NOT IN USE YET, SUPPOSED TO REPLACE LCMSDataSubset A union of several LCMSRange objects.
LCMSRangeSet() - Constructor for class umich.ms.datatypes.LCMSRangeSet
 
LCMSRangeSet.MsLevelRangeSet - Class in umich.ms.datatypes
 
LCMSRunInfo - Class in umich.ms.datatypes.lcmsrun
Temporarily stores processed LC/MS file run header.
LCMSRunInfo() - Constructor for class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
length() - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
length - Variable in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
 
length() - Method in class umich.ms.util.DoubleRange
 
length - Variable in class umich.ms.util.OffsetLength
Length
lineLength - Variable in class umich.ms.util.base64.Base64
Chunksize for encoding.
lo - Variable in class umich.ms.util.Interval1D
 
load(LCMSDataSubset) - Method in class umich.ms.datatypes.LCMSData
Will load scan meta-info and spectra for the specified subset.
load(LCMSDataSubset, Object) - Method in class umich.ms.datatypes.LCMSData
Will load scan meta-info and spectra for the specified subset.
loadData(LCMSDataSubset) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
loadData(LCMSDataSubset, StorageStrategy) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
loadData(LCMSDataSubset, StorageStrategy) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
IMPLEMENTATIONS MUST BE SYNCHRONIZED Loads spectra for a subset of scans, or all of them, depending on the configuration.
loadData(LCMSDataSubset) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
IMPLEMENTATIONS MUST BE SYNCHRONIZED Loads spectra for a subset of scans, or all of them, depending on the configuration.
locate(List<byte[]>, List<POSITION>, InputStream, long) - Static method in class umich.ms.util.xml.XmlUtils
Locates specific sequences of bytes in the input stream.
locate(String, TAG_TYPE, POSITION, String, TAG_TYPE, POSITION, long, InputStream) - Static method in class umich.ms.util.xml.XmlUtils
Deprecated.
Try using XmlUtils.locate(List, List, InputStream, long). This method uses an XML parser internally, so it's 1) slower than the other method 2) it's reporting of locations is in Characters, not Bytes!
location - Variable in class umich.ms.datatypes.lcmsrun.OriginalFile
 
LogHelper - Class in umich.ms.logging
 

M

main(String[]) - Static method in class umich.ms.fileio.chunk.ChunkedFile
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCefTest
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzidentml.example.MzIdentMlExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzidentml.example.MzIdentMlReadWriteExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzxml.example.Example
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzxml.example.Example2
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzxml.example.Example3
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.mzxml.example.Example4
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.pepxml.example.PepXmlAnalysisSummaryExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.pepxml.example.PepXmlExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.pepxml.example.PepXmlSimpleExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.pepxml.example.PepXmlWriteExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.protxml.example.ProtXmlJaxbExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.protxml.example.ProtXmlSimpleExample
 
main(String[]) - Static method in class umich.ms.fileio.filetypes.thermo.raw.test.ThermoTest
 
main(String[]) - Static method in class umich.ms.util.Interval1D
 
main(String[]) - Static method in class umich.ms.util.IntervalST
test client
manufacturer - Variable in class umich.ms.datatypes.scan.props.Instrument
 
MAP_ANALYZER_TYPE - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MAP_INSTRUMENT_MODEL - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MAP_IONIZATION_TYPE - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MAP_MASS_SPECTRUM - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MAP_NOT_MASS_SPECTRUM - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MAP_NOT_MASS_SPECTRUM_CHAR - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MAP_PEAK_PICKING - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MAP_SPECTRUM_TYPE - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
mapById - Variable in class umich.ms.datatypes.index.impl.IndexDefault
 
mapByNum - Variable in class umich.ms.datatypes.index.impl.IndexDefault
 
mapByRawNum - Variable in class umich.ms.datatypes.index.impl.IndexDefault
 
mapCharArr2ActivationCVTerm - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
mapCharArr2PSIMSCV - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
mapIdRefToInternalScanNum(CharArray) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
Given a scan ID goes to the index and tries to find a mapping.
mapRawNumToInternalScanNum(int) - Method in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
Given a scan internal number (spectrum index) goes to the index and tries to find a mapping.
mapString2ActivationCVTerm - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
mapString2PSIMSCV - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
MASK_8BITS - Static variable in class umich.ms.util.base64.Base64
Mask used to extract 8 bits, used in decoding bytes
mass - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
MathHelper - Class in umich.ms.util
Math functions.
MAX_BYTES_FROM_END_TO_SEARCH_FOR_INDEX - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
MAX_BYTES_FROM_END_TO_SEARCH_FOR_INDEX - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
MAX_PRECURSOR_GROUP_SIZE_DIFF - Static variable in class umich.ms.datatypes.scancollection.ScanCollectionHelper
Defines the ratio of numbers of scans in the larges "precursor group" to the smallest "precursor group".
maxInt - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
maxIntensity - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
maxIntensityMz - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
maxIntensityPos - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
maxIntMz - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
maxMZ - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
mCount - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
merge(LCMSDataSubset) - Method in class umich.ms.datatypes.LCMSDataSubset
Doesn't modify original values, always returns a new one.
MIME_CHUNK_SIZE - Static variable in class umich.ms.util.base64.Base64
 
min(double...) - Static method in class umich.ms.util.MathHelper
Find the minimum in an array of numbers.
MIN_GROUP_OVERLAP - Static variable in interface umich.ms.datatypes.scancollection.IScanCollection
The minimum relative overlap between two spectra's MS1 ranges or MS2 isolation windows, for spectra to be considered as belonging to the same group.
minInt - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
minIntensity - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
minIntensityNonZero - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
minIntensityNonZeroPos - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
minIntensityPos - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
minIntNonZero - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
minMZ - Variable in class umich.ms.datatypes.spectrum.AbstractSpectrum
 
model - Variable in class umich.ms.datatypes.scan.props.Instrument
 
model - Variable in class umich.ms.fileio.filetypes.mzml.util.InstrumentModelCVTerm
 
molId - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.IonId
 
MS1_WITH_SPECTRA - Static variable in class umich.ms.datatypes.LCMSDataSubset
Sets up the parsing parameters to parse all scans, but spectra only for MS1 scans.
MS2_WITH_SPECTRA - Static variable in class umich.ms.datatypes.LCMSDataSubset
Sets up the parsing parameters to parse all scans, but spectra only for MS2 scans.
MsftbxInfo - Class in umich.ms.msfiletoolbox
 
MsftbxInfo() - Constructor for class umich.ms.msfiletoolbox.MsftbxInfo
 
msLevel - Variable in class umich.ms.datatypes.scan.AbstractScan
 
msLevel2rangeGroups - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
MsLevelRangeSet() - Constructor for class umich.ms.datatypes.LCMSRangeSet.MsLevelRangeSet
 
msLvl2index - Variable in class umich.ms.datatypes.scancollection.ScanIndexRoot
 
MSNumpress - Class in umich.ms.external.msnumpress
 
MSNumpress() - Constructor for class umich.ms.external.msnumpress.MSNumpress
 
MsSoftware - Class in umich.ms.datatypes.lcmsrun
 
MsSoftware(String, String) - Constructor for class umich.ms.datatypes.lcmsrun.MsSoftware
 
MultiSpectraParser - Class in umich.ms.fileio.filetypes.xmlbased
Base class for parsers used by mzXML/mzML files.
MultiSpectraParser(InputStream, LCMSDataSubset) - Constructor for class umich.ms.fileio.filetypes.xmlbased.MultiSpectraParser
 
mz - Variable in class umich.ms.datatypes.spectrum.impl.SpectrumDefault
 
mz - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
MzIdentMlExample - Class in umich.ms.fileio.filetypes.mzidentml.example
As simple as it gets.
MzIdentMlExample() - Constructor for class umich.ms.fileio.filetypes.mzidentml.example.MzIdentMlExample
 
MzIdentMLParser - Class in umich.ms.fileio.filetypes.mzidentml
A parser for MzIdentML (mzid) files.
MzIdentMlReadWriteExample - Class in umich.ms.fileio.filetypes.mzidentml.example
 
MzIdentMlReadWriteExample() - Constructor for class umich.ms.fileio.filetypes.mzidentml.example.MzIdentMlReadWriteExample
 
MZMLFile - Class in umich.ms.fileio.filetypes.mzml
 
MZMLFile(String) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLFile
 
MZMLIndex - Class in umich.ms.fileio.filetypes.mzml
 
MZMLIndex() - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLIndex
 
MZMLIndexBuilder - Class in umich.ms.fileio.filetypes.mzml
 
MZMLIndexBuilder(IndexBuilder.Info, ObjectPool<XMLStreamReaderImpl>) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLIndexBuilder
 
MZMLIndexElement - Class in umich.ms.fileio.filetypes.mzml
 
MZMLIndexElement(int, int, String, OffsetLength) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLIndexElement
 
MZMLIndexParser - Class in umich.ms.fileio.filetypes.mzml
 
MZMLIndexParser(MZMLFile) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
MZMLIndexParser.OffsetId - Class in umich.ms.fileio.filetypes.mzml
 
MZMLMultiSpectraParser - Class in umich.ms.fileio.filetypes.mzml
Parses multiple spectra read from mzML file.
MZMLMultiSpectraParser(InputStream, LCMSDataSubset, MZMLFile) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
MZMLMultiSpectraParser.ATTR - Enum in umich.ms.fileio.filetypes.mzml
 
MZMLMultiSpectraParser.TAG - Enum in umich.ms.fileio.filetypes.mzml
 
MZMLPeaksDecoder - Class in umich.ms.fileio.filetypes.mzml
 
MZMLPeaksDecoder() - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLPeaksDecoder
 
MZMLPeaksDecoder.DecodedData - Class in umich.ms.fileio.filetypes.mzml
 
MZMLRunHeaderParser - Class in umich.ms.fileio.filetypes.mzml
Parses the run header of an mzML file.
MZMLRunHeaderParser(MZMLFile) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
MZMLRunInfo - Class in umich.ms.fileio.filetypes.mzml
 
MZMLRunInfo(LCMSRunInfo) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLRunInfo
 
MZMLRunInfo(MzMLType) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLRunInfo
 
MzmlVars - Class in umich.ms.fileio.filetypes.mzml
 
MzmlVars() - Constructor for class umich.ms.fileio.filetypes.mzml.MzmlVars
 
MzmlVars.BIN_DATA_TYPE - Enum in umich.ms.fileio.filetypes.mzml
 
mzs - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLPeaksDecoder.DecodedData
 
MZXMLFile - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLFile(String) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
MZXMLFile(String, boolean) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLFile
MzXML file constructor.
MZXMLIndex - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLIndex() - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLIndex
 
MZXMLIndexBuilder - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLIndexBuilder(IndexBuilder.Info, ObjectPool<XMLStreamReaderImpl>) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLIndexBuilder
 
MZXMLIndexElement - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLIndexElement(int, int, OffsetLength) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLIndexElement
 
MZXMLIndexParser - Class in umich.ms.fileio.filetypes.mzxml
Parses the index portion of an MZXML file.
MZXMLIndexParser(MZXMLFile) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
MZXMLMultiSpectraParser - Class in umich.ms.fileio.filetypes.mzxml
Parses several spectra using Javolution XML streaming parser.
MZXMLMultiSpectraParser.ATTR - Enum in umich.ms.fileio.filetypes.mzxml
 
MZXMLMultiSpectraParser.TAG - Enum in umich.ms.fileio.filetypes.mzxml
 
MZXMLPeaksDecoder - Class in umich.ms.fileio.filetypes.mzxml
Author: Dmitry Avtonomov (dmitriya)
MZXMLPeaksDecoder.DecodedData - Class in umich.ms.fileio.filetypes.mzxml
 
MZXMLRunHeaderParser - Class in umich.ms.fileio.filetypes.mzxml
Parses the header of the file to get isntrument information.
MZXMLRunHeaderParser(MZXMLFile) - Constructor for class umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser
 

N

name - Variable in class umich.ms.datatypes.lcmsrun.MsSoftware
 
name - Variable in class umich.ms.datatypes.lcmsrun.OriginalFile
 
name - Variable in enum umich.ms.datatypes.scan.props.ScanType
 
name - Variable in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.ATTR
 
name - Variable in enum umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser.TAG
 
name - Variable in class umich.ms.fileio.filetypes.mzml.util.CVTerm
 
name - Variable in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
 
name - Variable in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.ATTR
 
name - Variable in enum umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser.TAG
 
NAME_accession - Static variable in class umich.ms.fileio.filetypes.mzml.util.CvAttrs
 
NAME_cvRef - Static variable in class umich.ms.fileio.filetypes.mzml.util.CvAttrs
 
NAME_name - Static variable in class umich.ms.fileio.filetypes.mzml.util.CvAttrs
 
NAME_unitAccession - Static variable in class umich.ms.fileio.filetypes.mzml.util.CvAttrs
 
NAME_unitCvRef - Static variable in class umich.ms.fileio.filetypes.mzml.util.CvAttrs
 
NAME_unitName - Static variable in class umich.ms.fileio.filetypes.mzml.util.CvAttrs
 
NAME_value - Static variable in class umich.ms.fileio.filetypes.mzml.util.CvAttrs
 
next() - Method in class umich.ms.fileio.chunk.ChunkedFile
 
next() - Method in interface umich.ms.fileio.chunk.FileChunkSource
 
next(LCMSDataSubset, boolean) - Method in interface umich.ms.fileio.filetypes.SequentialScanReader
Gets the next scan.
num - Variable in class umich.ms.datatypes.index.impl.IndexElementDefault
Internal scan number.
num - Variable in class umich.ms.datatypes.scan.AbstractScan
Serial number of this scan in an LC/MS run
num2scan - Variable in class umich.ms.datatypes.scancollection.ScanIndex
 
NUM_BYTES_TO_CHECK_INDEX - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
NUM_BYTES_TO_CHECK_INDEX - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
numRaw - Variable in class umich.ms.datatypes.index.impl.IndexElementDefault
Raw scan number from raw file.
numScansToProcess - Variable in class umich.ms.fileio.filetypes.xmlbased.MultiSpectraParser
this will serve as a hint only, not required

O

offlen - Variable in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedIndexElement
The offset and length of scan entry in the XML file.
offset - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser.OffsetId
 
offset - Variable in class umich.ms.util.OffsetLength
Offset
OffsetId(long, String) - Constructor for class umich.ms.fileio.filetypes.mzml.MZMLIndexParser.OffsetId
 
offsetInFile - Variable in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
Global offset of the read-buffer (which is shared by multiple parsers) relative to the start of the file.
OffsetLength - Class in umich.ms.util
Simple holder for an offset and length of an entry.
OffsetLength(long, int) - Constructor for class umich.ms.util.OffsetLength
 
ONTOLOGY - Static variable in enum umich.ms.fileio.filetypes.mzml.util.PSIMSCV
 
optimalLinearFixedPoint(double[], int) - Static method in class umich.ms.external.msnumpress.MSNumpress
 
optimalSlofFixedPoint(double[], int) - Static method in class umich.ms.external.msnumpress.MSNumpress
 
Opts - Class in umich.ms.fileio
Package options.
OriginalFile - Class in umich.ms.datatypes.lcmsrun
 
OriginalFile(String, String, Hash) - Constructor for class umich.ms.datatypes.lcmsrun.OriginalFile
 
originalFiles - Variable in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
OutOfMemoryException - Exception in umich.ms.fileio.exceptions
An indicator, that file parsing had troubles because of not enough memory.
OutOfMemoryException() - Constructor for exception umich.ms.fileio.exceptions.OutOfMemoryException
 
OutOfMemoryException(String) - Constructor for exception umich.ms.fileio.exceptions.OutOfMemoryException
 
OutOfMemoryException(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.OutOfMemoryException
 
OutOfMemoryException(Throwable) - Constructor for exception umich.ms.fileio.exceptions.OutOfMemoryException
 
OutOfMemoryException(String, Throwable, boolean, boolean) - Constructor for exception umich.ms.fileio.exceptions.OutOfMemoryException
 
overlapAbsolute(DoubleRange) - Method in class umich.ms.util.DoubleRange
If the interval contains just a single point (i.e.
overlapRelative(DoubleRange) - Method in class umich.ms.util.DoubleRange
Relative overlap, that is the overlap, divided by the length of the largest interval.

P

PAD - Variable in class umich.ms.util.base64.Base64
 
PAD_DEFAULT - Static variable in class umich.ms.util.base64.Base64
Byte used to pad output.
parse(String) - Static method in enum umich.ms.datatypes.scan.props.Polarity
Parse Polarity from a string.
parse() - Method in class umich.ms.fileio.filetypes.gpmdb.GPMDBFile
 
parse(Path) - Static method in class umich.ms.fileio.filetypes.gpmdb.GPMDBParser
 
parse(LCMSDataSubset) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Parse a range of scan numbers.
parse(List<Integer>) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
The storage strategy should always be StorageStrategy.STRONG, the receiver then can set it to whatever it needs.
parse(Path) - Static method in class umich.ms.fileio.filetypes.mzidentml.MzIdentMLParser
Will parse the whole file.
parse() - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
parse() - Method in class umich.ms.fileio.filetypes.mzml.MZMLRunHeaderParser
 
parse() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
parse() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLRunHeaderParser
 
parse() - Method in interface umich.ms.fileio.filetypes.mzxml.XmlBasedRunHeaderParser
 
parse(Path) - Static method in class umich.ms.fileio.filetypes.pepxml.PepXmlParser
The simplest method to parse the whole MsmsPipelineAnalysis from a file.
parse(InputStream) - Static method in class umich.ms.fileio.filetypes.pepxml.PepXmlParser
This is helpful for huge combined pepxml files where identification results from several runs are merged together.
parse(Path) - Static method in class umich.ms.fileio.filetypes.protxml.ProtXmlParser
 
parse(LCMSDataSubset) - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parse(List<Integer>) - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parse(LCMSDataSubset) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
parse(List<Integer>) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
Deprecated.
this method has not been updated to the new parsing version
parsedScans - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
parseIndex() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
 
parseIndex() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
parseIndex() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
parseIndex() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parseIndexEntries(byte[], TreeMap<Integer, MZMLIndexParser.OffsetId>) - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
parseIndexEntries(byte[], TreeMap<Integer, Long>) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
parseIonSignature() - Method in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
parseRunInfo() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
 
parseRunInfo() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
parseRunInfo() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
parseRunInfo() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parseScan(int, boolean) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Parse a single scan from file on disk by it's number.
parseScan(int, boolean) - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parseScan(int, boolean) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
parseScanNumFromIndex(CharArray) - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
parseSpectrum(int) - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
Parse a single spectrumRef from file on disk by it's number.
parseSpectrum(int) - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
parseSpectrum(int) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
parsingTimeout - Variable in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
Timeout In seconds.
passivateObject(PooledObject<XMLStreamReaderImpl>) - Method in class umich.ms.fileio.filetypes.xmlbased.XMLStreamReaderFactory
 
passivateObject(PooledObject<ByteArrayHolder>) - Method in class umich.ms.util.ByteArrayHolderFactory
 
path - Variable in class umich.ms.util.file.AbstractFile
 
path - Variable in class umich.ms.util.file.FileListing
 
PeaksCompression - Enum in umich.ms.datatypes.scan
Peaks (m/z and intensity) compression methods used in mzML and mzXML files.
PEM_CHUNK_SIZE - Static variable in class umich.ms.util.base64.Base64
 
PepXmlAnalysisSummaryExample - Class in umich.ms.fileio.filetypes.pepxml.example
Unfortunately, the declarations of different "analyses" are say nothing about the elements in the XML they might be contained in.
PepXmlAnalysisSummaryExample() - Constructor for class umich.ms.fileio.filetypes.pepxml.example.PepXmlAnalysisSummaryExample
 
PepXmlExample - Class in umich.ms.fileio.filetypes.pepxml.example
Simple parsing of all MsmsRunSummary entries in a pep.xml file.
PepXmlExample() - Constructor for class umich.ms.fileio.filetypes.pepxml.example.PepXmlExample
 
PepXmlParser - Class in umich.ms.fileio.filetypes.pepxml
A very simple parser for PepXML files.
PepXmlSimpleExample - Class in umich.ms.fileio.filetypes.pepxml.example
Created by Dmitry Avtonomov on 2016-04-13.
PepXmlSimpleExample() - Constructor for class umich.ms.fileio.filetypes.pepxml.example.PepXmlSimpleExample
 
PepXmlStream - Class in umich.ms.fileio.filetypes.pepxml
 
PepXmlStream() - Constructor for class umich.ms.fileio.filetypes.pepxml.PepXmlStream
 
PepXmlWriteExample - Class in umich.ms.fileio.filetypes.pepxml.example
An example of how a pepxml file can be written using the provided bindings Created by Dmitry Avtonomov on 2015-10-17.
PepXmlWriteExample() - Constructor for class umich.ms.fileio.filetypes.pepxml.example.PepXmlWriteExample
 
polarity - Variable in class umich.ms.datatypes.scan.AbstractScan
 
Polarity - Enum in umich.ms.datatypes.scan.props
Author: Dmitry Avtonomov (dmitriya)
polarity - Variable in enum umich.ms.datatypes.scan.props.Polarity
 
pool - Variable in class umich.ms.util.base64.Base64ContextPooled
 
PooledByteArrayHolders - Class in umich.ms.util
A singleton pool of ByteArrayHolders.
POSITION - Enum in umich.ms.util.xml
Describes if the beginning or the end of a text element should be reported as location.
ppm2amu(double, double) - Static method in class umich.ms.util.SpectrumUtils
Given an m/z value, calculates what a certain ppm accuracy converts to in terms of m/z.
precursor - Variable in class umich.ms.datatypes.scan.AbstractScan
If this is an MS1 scan, this field is left null, indicating there was no precursor
PrecursorInfo - Class in umich.ms.datatypes.scan.props
Author: Dmitry Avtonomov (dmitriya)
PrecursorInfo() - Constructor for class umich.ms.datatypes.scan.props.PrecursorInfo
 
prettyPrint() - Method in class umich.ms.util.IntervalST
Print out the current tree from left to right.
ProtXmlJaxbExample - Class in umich.ms.fileio.filetypes.protxml.example
 
ProtXmlJaxbExample() - Constructor for class umich.ms.fileio.filetypes.protxml.example.ProtXmlJaxbExample
 
ProtXmlParser - Class in umich.ms.fileio.filetypes.protxml
A very simple parser for ProtXML files.
ProtXmlSimpleExample - Class in umich.ms.fileio.filetypes.protxml.example
 
ProtXmlSimpleExample() - Constructor for class umich.ms.fileio.filetypes.protxml.example.ProtXmlSimpleExample
 
PSIMSCV - Enum in umich.ms.fileio.filetypes.mzml.util
Commonly used Ontology terms in mzML files.
put(Interval1D<K>, V) - Method in class umich.ms.util.IntervalST
Insert a new node in the tree.

R

RE_END_OF_RUN - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
RE_END_OF_RUN - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
RE_INDEX_ENTRY - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
Not used since started using Javolution instead of regular expressions for parsing index
RE_INDEX_ENTRY_SIMPLE - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
RE_INDEX_ENTRY_SIMPLE - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
RE_INDEX_OFFSET - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
RE_INDEX_OFFSET - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
RE_PEAK_DESCRIPTION - Static variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
read() - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
read(byte[]) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
read(byte[], int, int) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
read() - Method in class umich.ms.external.BufferedRandomAccessFile
Reads one byte form the current position
read(byte[], int, int) - Method in class umich.ms.external.BufferedRandomAccessFile
Reads the set number of bytes into the passed buffer.
read() - Method in class umich.ms.util.ReverseLineInputStream
 
readContinuousBatchOfSpectra(Iterator<? extends Map.Entry<Integer, ? extends XMLBasedIndexElement>>, RandomAccessFile, byte[], ArrayList<OffsetLength>, int) - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
readerPool - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
readerPool - Variable in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
readResults() - Method in class umich.ms.util.base64.Base64Context
 
releaseMemory() - Method in class umich.ms.datatypes.LCMSData
Releases all memory by calling LCMSDataSource.releaseMemory() and IScanCollection.reset().
releaseMemory() - Method in interface umich.ms.fileio.filetypes.LCMSDataSource
The intent is to be able to free the memory, e.g.
releaseMemory() - Method in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 
releaseMemory() - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
 
releaseResources() - Method in class umich.ms.fileio.filetypes.mzml.MZMLFile
 
releaseResources() - Method in class umich.ms.fileio.filetypes.mzxml.MZXMLFile
 
releaseResources() - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedDataSource
This method will be called by AbstractXMLBasedDataSource.releaseMemory() in addition to cleaning up resources, used by this abstract implementation.
remove(Interval1D<K>) - Method in class umich.ms.util.IntervalST
Remove and return value associated with given interval.
removeFromAll(LCMSRange) - Method in class umich.ms.datatypes.LCMSRangeSet.MsLevelRangeSet
Remove the range from all range sets in this ms level.
removeFromSpecific(LCMSRange) - Method in class umich.ms.datatypes.LCMSRangeSet.MsLevelRangeSet
Remove range from all specific precursor ranges at this ms level.
removeInstrument(String) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
removeInstrument(Instrument) - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
reset() - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
reset() - Method in interface umich.ms.datatypes.scancollection.IScanCollection
Bring the collection back to initial empty state.
reset() - Method in class umich.ms.fileio.filetypes.mzml.MzmlVars
Resets all held variables to their default values.
reset() - Method in class umich.ms.util.ByteArrayHolder
Resets the count field of this byte array output stream to zero, so that all currently accumulated output in the output stream is discarded.
Result(IndexBuilder.Info) - Constructor for class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Result
 
reverseBase64Chars - Static variable in class umich.ms.util.base64.Base64Slow
Reverse lookup table for the Base64 alphabet.
ReverseLineInputStream - Class in umich.ms.util
 
ReverseLineInputStream(RandomAccessFile) - Constructor for class umich.ms.util.ReverseLineInputStream
 
rt - Variable in class umich.ms.datatypes.scan.AbstractScan
Retention time in minutes
rt - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
RT in minutes.
rt - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentMSPeak
 
rt2scan - Variable in class umich.ms.datatypes.scancollection.ScanIndex
 
rtHi - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
rtLo - Variable in class umich.ms.fileio.filetypes.agilent.cef.example.AgilentCompound
 
RunHeaderBoundsNotFound - Exception in umich.ms.fileio.exceptions
Created by Dmitry Avtonomov on 2015-10-26.
RunHeaderBoundsNotFound() - Constructor for exception umich.ms.fileio.exceptions.RunHeaderBoundsNotFound
 
RunHeaderBoundsNotFound(String) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderBoundsNotFound
 
RunHeaderBoundsNotFound(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderBoundsNotFound
 
RunHeaderBoundsNotFound(Throwable) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderBoundsNotFound
 
RunHeaderParsingException - Exception in umich.ms.fileio.exceptions
Used in areas, where run header info is parsed.
RunHeaderParsingException() - Constructor for exception umich.ms.fileio.exceptions.RunHeaderParsingException
 
RunHeaderParsingException(String) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderParsingException
 
RunHeaderParsingException(String, Throwable) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderParsingException
 
RunHeaderParsingException(Throwable) - Constructor for exception umich.ms.fileio.exceptions.RunHeaderParsingException
 
runInfo - Variable in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
runInfo - Variable in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
 
runInfo - Variable in class umich.ms.fileio.filetypes.mzml.MZMLMultiSpectraParser
 
runInfo - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLMultiSpectraParser
 
runInfo - Variable in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 

S

ScanCollectionDefault - Class in umich.ms.datatypes.scancollection.impl
The default implementation of IScanCollection.
ScanCollectionDefault() - Constructor for class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
ScanCollectionDefault(boolean) - Constructor for class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
With this constructor you can pre-configure the scan collection to automatically load spectra if they were not parsed in the first place.
ScanCollectionHelper - Class in umich.ms.datatypes.scancollection
Helper utils for ScanCollections.
ScanDefault - Class in umich.ms.datatypes.scan.impl
All the constructors produce Scans that have StorageStrategy set to StorageStrategy.STRONG, it's up to the client to reset this to anything else.
ScanDefault(int) - Constructor for class umich.ms.datatypes.scan.impl.ScanDefault
 
ScanDefault(IScanCollection, int) - Constructor for class umich.ms.datatypes.scan.impl.ScanDefault
 
ScanDefault(int, double, int, boolean) - Constructor for class umich.ms.datatypes.scan.impl.ScanDefault
 
ScanDefault(IScanCollection, int, double, int, boolean) - Constructor for class umich.ms.datatypes.scan.impl.ScanDefault
 
ScanIndex - Class in umich.ms.datatypes.scancollection
 
ScanIndex() - Constructor for class umich.ms.datatypes.scancollection.ScanIndex
 
ScanIndexRoot - Class in umich.ms.datatypes.scancollection
 
ScanIndexRoot() - Constructor for class umich.ms.datatypes.scancollection.ScanIndexRoot
 
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
Method was added for backwards compatibility, consider using the full signature version AbstractScan.setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean).
setSpectrum(ISpectrum, boolean) - Method in interface umich.ms.datatypes.scan.IScan
Set the spectrumRef for this scan.
setSpectrumImpl(ISpectrum) - Method in class umich.ms.datatypes.scan.AbstractScan
The implementation of IScan.setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean) in this base class will set all the Scan-level variables for you according to the spectrumRef provided, but you need to define how to store the spectrumRef itself.
setSpectrumImpl(ISpectrum) - Method in class umich.ms.datatypes.scan.impl.ScanDefault
 
setStorageStrategy(StorageStrategy) - Method in class umich.ms.datatypes.scan.AbstractScan
 
setStorageStrategy(StorageStrategy) - Method in interface umich.ms.datatypes.scan.IScan
Implementors of IScan interface must respect the value of reftype in constructors and IScan.setSpectrum(umich.ms.datatypes.spectrum.ISpectrum, boolean) implementations in order for memory management to work.
setStorageStrategy(LCMSDataSubset, StorageStrategy) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
setStorageStrategy(LCMSDataSubset, StorageStrategy, StorageStrategy) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
setStorageStrategy(LCMSDataSubset, StorageStrategy) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
 
setStorageStrategy(LCMSDataSubset, StorageStrategy, StorageStrategy) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
 
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.

T

TAG_END_OF_RUN - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
TAG_END_OF_RUN - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
TAG_INDEX - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
TAG_INDEX - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
TAG_INDEXOFFSET - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
TAG_INDEXOFFSET - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
TAG_MSMS_PIPELINE_ANALYSIS - Static variable in class umich.ms.fileio.filetypes.pepxml.PepXmlParser
 
TAG_MSMS_RUN_SUMMARY - Static variable in class umich.ms.fileio.filetypes.pepxml.PepXmlParser
 
TAG_OFFSET - Variable in class umich.ms.fileio.filetypes.mzml.MZMLIndexParser
 
TAG_OFFSET - Variable in class umich.ms.fileio.filetypes.mzxml.MZXMLIndexParser
 
TAG_TYPE - Enum in umich.ms.util.xml
XML tag type.
tasksPerCpuPerBatch - Variable in class umich.ms.fileio.filetypes.AbstractLCMSDataSource
How many spectra each CPU will be given in one batch.
ThermoRawFile - Class in umich.ms.fileio.filetypes.thermo.raw
LC/MS data source for Thermo RAW files.
ThermoRawFile(String) - Constructor for class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
Create a new source with autoload of spectra disabled.
ThermoRawIndex - Class in umich.ms.fileio.filetypes.thermo.raw
There's nothing really special about Thermo index, we're using our default implementation.
ThermoRawIndex() - Constructor for class umich.ms.fileio.filetypes.thermo.raw.ThermoRawIndex
 
ThermoRawIndexElement - Class in umich.ms.fileio.filetypes.thermo.raw
Created by Dmitry Avtonomov on 2016-04-25.
ThermoRawIndexElement(int, int) - Constructor for class umich.ms.fileio.filetypes.thermo.raw.ThermoRawIndexElement
 
ThermoTest - Class in umich.ms.fileio.filetypes.thermo.raw.test
 
ThermoTest() - Constructor for class umich.ms.fileio.filetypes.thermo.raw.test.ThermoTest
 
tic - Variable in class umich.ms.datatypes.scan.AbstractScan
Total ion current
timeUnit - Variable in enum umich.ms.fileio.filetypes.mzml.util.UnitsCV
 
toByteArray() - Method in class umich.ms.util.ByteArrayHolder
Creates a newly allocated byte array.
toByteBuffer() - Method in class umich.ms.util.ByteArrayHolder
 
toDecodedData(double[]) - Static method in class umich.ms.fileio.filetypes.mzml.MZMLPeaksDecoder
 
toString() - Method in class umich.ms.datatypes.index.impl.IndexElementDefault
 
toString() - Method in class umich.ms.datatypes.LCMSDataSubset
 
toString() - Method in class umich.ms.datatypes.lcmsrun.LCMSRunInfo
 
toString() - Method in class umich.ms.datatypes.scan.AbstractScan
 
toString() - Method in class umich.ms.datatypes.scan.props.ActivationInfo
 
toString() - Method in class umich.ms.datatypes.scan.props.Instrument
 
toString() - Method in enum umich.ms.datatypes.scan.props.Polarity
 
toString() - Method in class umich.ms.fileio.filetypes.mzml.MZMLIndexElement
 
toString() - Method in class umich.ms.fileio.filetypes.mzml.util.CVTerm
 
toString() - Method in class umich.ms.fileio.filetypes.mzml.util.InstrumentModelCVTerm
 
toString() - Method in class umich.ms.fileio.filetypes.xmlbased.AbstractXMLBasedIndexElement
 
toString() - Method in class umich.ms.fileio.filetypes.xmlbased.IndexBuilder.Info
 
toString() - Method in class umich.ms.util.base64.Base64Context
Returns a String useful for debugging (especially within a debugger.)
toString() - Method in class umich.ms.util.ByteArrayHolder
Converts the buffer's contents into a string decoding bytes using the platform's default character set.
toString(String) - Method in class umich.ms.util.ByteArrayHolder
Converts the buffer's contents into a string by decoding the bytes using the specified charsetName.
toString(int) - Method in class umich.ms.util.ByteArrayHolder
Deprecated.
This method does not properly convert bytes into characters. As of JDK 1.1, the preferred way to do this is via the toString(String enc) method, which takes an encoding-name argument, or the toString() method, which uses the platform's default character encoding.
toString() - Method in class umich.ms.util.Interval1D
 
toString() - Method in class umich.ms.util.IntervalST.Node
 
toString() - Method in class umich.ms.util.OffsetLength
 
type - Variable in class umich.ms.datatypes.lcmsrun.Hash
 

U

umich.ms.datatypes - package umich.ms.datatypes
 
umich.ms.datatypes.index - package umich.ms.datatypes.index
 
umich.ms.datatypes.index.impl - package umich.ms.datatypes.index.impl
 
umich.ms.datatypes.lcmsrun - package umich.ms.datatypes.lcmsrun
 
umich.ms.datatypes.scan - package umich.ms.datatypes.scan
 
umich.ms.datatypes.scan.impl - package umich.ms.datatypes.scan.impl
 
umich.ms.datatypes.scan.props - package umich.ms.datatypes.scan.props
 
umich.ms.datatypes.scancollection - package umich.ms.datatypes.scancollection
 
umich.ms.datatypes.scancollection.impl - package umich.ms.datatypes.scancollection.impl
 
umich.ms.datatypes.spectrum - package umich.ms.datatypes.spectrum
 
umich.ms.datatypes.spectrum.impl - package umich.ms.datatypes.spectrum.impl
 
umich.ms.external - package umich.ms.external
 
umich.ms.external.apache.cassandra.io - package umich.ms.external.apache.cassandra.io
 
umich.ms.external.msnumpress - package umich.ms.external.msnumpress
 
umich.ms.fileio - package umich.ms.fileio
 
umich.ms.fileio.chunk - package umich.ms.fileio.chunk
 
umich.ms.fileio.exceptions - package umich.ms.fileio.exceptions
 
umich.ms.fileio.filetypes - package umich.ms.fileio.filetypes
 
umich.ms.fileio.filetypes.agilent.cef - package umich.ms.fileio.filetypes.agilent.cef
 
umich.ms.fileio.filetypes.agilent.cef.example - package umich.ms.fileio.filetypes.agilent.cef.example
 
umich.ms.fileio.filetypes.gpmdb - package umich.ms.fileio.filetypes.gpmdb
 
umich.ms.fileio.filetypes.mzidentml - package umich.ms.fileio.filetypes.mzidentml
 
umich.ms.fileio.filetypes.mzidentml.example - package umich.ms.fileio.filetypes.mzidentml.example
 
umich.ms.fileio.filetypes.mzml - package umich.ms.fileio.filetypes.mzml
 
umich.ms.fileio.filetypes.mzml.util - package umich.ms.fileio.filetypes.mzml.util
 
umich.ms.fileio.filetypes.mzxml - package umich.ms.fileio.filetypes.mzxml
 
umich.ms.fileio.filetypes.mzxml.example - package umich.ms.fileio.filetypes.mzxml.example
 
umich.ms.fileio.filetypes.pepxml - package umich.ms.fileio.filetypes.pepxml
There are 3 packages generated with JAXB: umich.ms.fileio.filetypes.pepxml.jaxb.primitive umich.ms.fileio.filetypes.pepxml.jaxb.standard nested was generated with default xjc parameters, which results in very ugly nesting of classes, but there are 100% no name clashes.
umich.ms.fileio.filetypes.pepxml.example - package umich.ms.fileio.filetypes.pepxml.example
 
umich.ms.fileio.filetypes.protxml - package umich.ms.fileio.filetypes.protxml
 
umich.ms.fileio.filetypes.protxml.example - package umich.ms.fileio.filetypes.protxml.example
 
umich.ms.fileio.filetypes.thermo.raw - package umich.ms.fileio.filetypes.thermo.raw
 
umich.ms.fileio.filetypes.thermo.raw.test - package umich.ms.fileio.filetypes.thermo.raw.test
 
umich.ms.fileio.filetypes.xmlbased - package umich.ms.fileio.filetypes.xmlbased
 
umich.ms.logging - package umich.ms.logging
 
umich.ms.msfiletoolbox - package umich.ms.msfiletoolbox
 
umich.ms.util - package umich.ms.util
 
umich.ms.util.base64 - package umich.ms.util.base64
 
umich.ms.util.file - package umich.ms.util.file
 
umich.ms.util.xml - package umich.ms.util.xml
 
UnitsCV - Enum in umich.ms.fileio.filetypes.mzml.util
Used to convert retention times in mzML files.
UNKNOWN_ANALYZER - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
UNKNOWN_DETECTOR - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
UNKNOWN_IONISATION - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
UNKNOWN_MANUFACTURER - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
UNKNOWN_METHOD - Static variable in class umich.ms.fileio.filetypes.mzml.util.ActivationCVTerm
 
UNKNOWN_MODEL - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
UNKNOWN_SERIAL_NUMBER - Static variable in class umich.ms.datatypes.scan.props.Instrument
 
unload(LCMSDataSubset) - Method in class umich.ms.datatypes.LCMSData
Unloads spectra matched by this subset.
unload(LCMSDataSubset, Object, Set<LCMSDataSubset>) - Method in class umich.ms.datatypes.LCMSData
Unloads spectra matched by this subset.
unloadData(LCMSDataSubset) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
unloadData(LCMSDataSubset, Set<LCMSDataSubset>) - Method in class umich.ms.datatypes.scancollection.impl.ScanCollectionDefault
 
unloadData(LCMSDataSubset) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
IMPLEMENTATIONS MUST BE SYNCHRONIZED Unloads SPECTRA from the underlying ScanCollection.
unloadData(LCMSDataSubset, Set<LCMSDataSubset>) - Method in interface umich.ms.datatypes.scancollection.IScanCollection
IMPLEMENTATIONS MUST BE SYNCHRONIZED Unloads SPECTRA from the underlying ScanCollection.
User(Object) - Constructor for class umich.ms.datatypes.LCMSData.User
 

V

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

W

WHOLE_RUN - Static variable in class umich.ms.datatypes.LCMSDataSubset
Sets up the parsing parameters to parse all the scans and spectra in a run.
WHOLE_RUN - Static variable in class umich.ms.datatypes.LCMSRange
 
WHOLE_RUN_MS1 - Static variable in class umich.ms.datatypes.LCMSRange
 
WHOLE_RUN_MS2 - Static variable in class umich.ms.datatypes.LCMSRange
 
WHOLE_RUN_STRUCTURE - Static variable in class umich.ms.datatypes.LCMSRange
 
wrap(XMLStreamReaderImpl) - Method in class umich.ms.fileio.filetypes.xmlbased.XMLStreamReaderFactory
 
wrap(ByteArrayHolder) - Method in class umich.ms.util.ByteArrayHolderFactory
 
write(int) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
write(byte[]) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
write(byte[], int, int) - Method in class umich.ms.external.apache.cassandra.io.BufferedRandomAccessFile
 
write(int) - Method in class umich.ms.util.ByteArrayHolder
Writes the specified byte to this byte array output stream.
write(byte[], int, int) - Method in class umich.ms.util.ByteArrayHolder
Writes len bytes from the specified byte array starting at offset off to this byte array output stream.
writeTo(OutputStream) - Method in class umich.ms.util.ByteArrayHolder
Writes the complete contents of this byte array output stream to the specified output stream argument, as if by calling the output stream's write method using out.write(buf, 0, count).

X

XMLBasedIndexElement - Interface in umich.ms.fileio.filetypes.xmlbased
 
XmlBasedRunHeaderParser - Interface in umich.ms.fileio.filetypes.mzxml
For example look at source of MZXMLRunHeaderParser and MZMLRunHeaderParser.
XMLStreamReaderFactory - Class in umich.ms.fileio.filetypes.xmlbased
Produces XMLStreamReaderImpl objects for reuse in XML parser-workers.
XMLStreamReaderFactory() - Constructor for class umich.ms.fileio.filetypes.xmlbased.XMLStreamReaderFactory
 
XmlUtils - Class in umich.ms.util.xml
 
xRawfile5 - Variable in class umich.ms.fileio.filetypes.thermo.raw.ThermoRawFile
 

Z

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