A B C D E F G H I K L M N O P R S T U V W

A

ACC_NUMPRESS_LINEAR - Static variable in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

ACC_NUMPRESS_PIC - Static variable in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

ACC_NUMPRESS_SLOF - Static variable in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

acceptsDirectory() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

acceptsDirectory() - Method in interface io.github.bigbio.pgatk.io.common.MzReader

Indicates whether the given peak list parser supports the parsing of directories.

acceptsDirectory() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

acceptsDirectory() - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

acceptsDirectory() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

acceptsDirectory() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader

acceptsFile() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

acceptsFile() - Method in interface io.github.bigbio.pgatk.io.common.MzReader

Indicates whether the given peak list parser supports the parsing of single files.

acceptsFile() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

acceptsFile() - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

acceptsFile() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

acceptsFile() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader

accessChannel - Variable in class io.github.bigbio.pgatk.io.common.MzIterableChannelReader

ACCESSCOUNTER - Static variable in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

The access counter.

AccessionLocalization - Class in io.github.bigbio.pgatk.io.pride

AccessionLocalization() - Constructor for class io.github.bigbio.pgatk.io.pride.AccessionLocalization

AccessionLocalization(String, long, long) - Constructor for class io.github.bigbio.pgatk.io.pride.AccessionLocalization

acquire() - Method in class io.github.bigbio.pgatk.io.objectdb.SimpleSemaphore

Acquires.

activationMethod - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

addAttribute(String, String) - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

addErrorTag(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

Adds an error tolerant tag.

addETag(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

Adds an error tolerant tag.

addMGFProperties(Properties, String) - Static method in class io.github.bigbio.pgatk.io.properties.KnownProperties

parse an mgf line like SEQ or USER00..USER12

addMod(int, String) - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

addModification(IModification) - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFilePSM

addModifications(Collection<IModification>) - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFilePSM

addObject(Long, Object) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Adds an object to the cache.

addObject(long, Object) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Adds an object into the database.

addObjects(Map<Long, Object>) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Adds an object to the cache.

addObjects(HashMap<Long, Object>, WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Adds a list of objects into the database.

addPeak(Double, Double) - Method in class io.github.bigbio.pgatk.io.apl.AplSpectrum

Adds a peak to the spectrum.

addPeak(Double, Double) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

Adds a peak to the spectrum.

addPeak(double, double) - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

addPeaksFromString(String, String) - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

Adds peaks to the spectrum based on the m/z and intensity value string

addPeaksFromString(String, String) - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

addPosition(int, Set<CvParam>) - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

addProperty(Map<Long, Object>) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Add a set of SpectrumProperty

addProteinAccessionNumber(String) - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

addScores(String, String) - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

addSequenceQualifier(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

Ads a sequence qualifier.

addSpectrumProperty(long, SpectrumProperty) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Adds a SpectrumProperty.

addSpectrumProperty(String, SpectrumProperty) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Adds a SpectrumProperty.

addTag(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

Adds a tag.

addUrParam(UrParameter) - Method in class io.github.bigbio.pgatk.io.objectdb.LongObject

Adds a user refinement parameter.

AminoAcid - Enum in io.github.bigbio.pgatk.io.utils

AnnotatedSpectrum - Class in io.github.bigbio.pgatk.io.pride

AnnotatedSpectrum() - Constructor for class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

AnnotatedSpectrum(String, String, String, List<String>, List<String>, List<AccessionLocalization>, List<GeneCoordinates>, String, String, List<AvroTuple>, List<AvroTuple>, double, Integer, List<AvroModification>, List<Double>, List<Double>, Double, Integer, Integer, List<AvroTerm>, List<AvroTuple>, String, Boolean, Double) - Constructor for class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

AnySimpleTypeAdapter - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util

AnySimpleTypeAdapter() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util.AnySimpleTypeAdapter

AplIndexedReader - Class in io.github.bigbio.pgatk.io.apl

This class implement the JmzReader Interface to provide the information of apl spectra.

AplIndexedReader() - Constructor for class io.github.bigbio.pgatk.io.apl.AplIndexedReader

Default constructor generating an empty APL file object.

AplIndexedReader(File) - Constructor for class io.github.bigbio.pgatk.io.apl.AplIndexedReader

Creates the APL file object from an existing APL file.

AplIndexedReader(File, List<IndexElement>) - Constructor for class io.github.bigbio.pgatk.io.apl.AplIndexedReader

Creates the APL file object from an existing APL file with a pre-parsed index of ms2 spectra.

AplSpectrum - Class in io.github.bigbio.pgatk.io.apl

AplSpectrum(String, Long) - Constructor for class io.github.bigbio.pgatk.io.apl.AplSpectrum

appendReport(String, boolean, boolean) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Append text to the report.

appendReportEndLine() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Append a new line to the report.

appendReportNewLineNoDate() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Append two tabs to the report.

ArchiveSpectrum - Class in io.github.bigbio.pgatk.io.pride

ArchiveSpectrum() - Constructor for class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

ArchiveSpectrum(String, String, String, String, String, String, Double[], Double[], Integer, Integer, Integer, Double, Double, Set<CvParam>, String, Integer, Collection<IdentifiedModification>, List<String>, Boolean, Set<CvParam>, Boolean, List<String>, List<String>) - Constructor for class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

asLongHash(String) - Static method in class io.github.bigbio.pgatk.io.objectdb.LongObject

Creating a unique 64 bit hash key from the original key of arbitrary length.

attributePattern - Static variable in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

Regex to recognize a attribute and extract its name and value

attributePattern - Static variable in class io.github.bigbio.pgatk.io.mgf.MgfUtils

Regex to recognize a attribute and extract its name and value

AvroModification - Class in io.github.bigbio.pgatk.io.pride

AvroModification() - Constructor for class io.github.bigbio.pgatk.io.pride.AvroModification

AvroModification(List<AvroTerm>, String, String, Integer) - Constructor for class io.github.bigbio.pgatk.io.pride.AvroModification

AvroTerm - Class in io.github.bigbio.pgatk.io.pride

AvroTerm() - Constructor for class io.github.bigbio.pgatk.io.pride.AvroTerm

AvroTerm(String, String, String) - Constructor for class io.github.bigbio.pgatk.io.pride.AvroTerm

AvroTuple - Class in io.github.bigbio.pgatk.io.pride

AvroTuple() - Constructor for class io.github.bigbio.pgatk.io.pride.AvroTuple

AvroTuple(String, String) - Constructor for class io.github.bigbio.pgatk.io.pride.AvroTuple

B

basePeakIntensity - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

basePeakMz - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

BinaryPeaks - Class in io.github.bigbio.pgatk.io.pride

BinaryPeaks() - Constructor for class io.github.bigbio.pgatk.io.pride.BinaryPeaks

BinaryPeaks(byte[], byte[]) - Constructor for class io.github.bigbio.pgatk.io.pride.BinaryPeaks

BinaryPeaks(List<Double>, List<Double>) - Constructor for class io.github.bigbio.pgatk.io.pride.BinaryPeaks

BinaryPropertyStorage - Class in io.github.bigbio.pgatk.io.properties

buffer - Variable in class io.github.bigbio.pgatk.io.common.MzIterableChannelReader

BUFFER_SIZE - Static variable in class io.github.bigbio.pgatk.io.mgf.MgfUtils

BufferedRandomAccessFile - Class in io.github.bigbio.pgatk.io.braf

This is an optimized version of the RandomAccessFile class as described by Nick Zhang on JavaWorld.com.

BufferedRandomAccessFile(String, String, int) - Constructor for class io.github.bigbio.pgatk.io.braf.BufferedRandomAccessFile

Creates a new instance of the BufferedRandomAccessFile.

BufferedRandomAccessFile(File, String, int) - Constructor for class io.github.bigbio.pgatk.io.braf.BufferedRandomAccessFile

buildDynamicEcacheStorage(File) - Static method in class io.github.bigbio.pgatk.io.properties.PropertyStorageFactory

Get a Static Property Storage with s predefined number of entries.

buildDynamicLevelDBPropertyStorage(File) - Static method in class io.github.bigbio.pgatk.io.properties.PropertyStorageFactory

Get a Static Property Storage with s predefined number of entries.

buildDynamicMapDBStorage(File) - Static method in class io.github.bigbio.pgatk.io.properties.PropertyStorageFactory

Get a Static Property Storage with s predefined number of entries.

buildDynamicSparkKeyStorage(File) - Static method in class io.github.bigbio.pgatk.io.properties.PropertyStorageFactory

Get a Static Property Storage with s predefined number of entries.

buildInMemoryPropertyStorage() - Static method in class io.github.bigbio.pgatk.io.properties.PropertyStorageFactory

Get InMemoryPropertyStorage for the Storage

buildStaticPropertyStorage(File) - Static method in class io.github.bigbio.pgatk.io.properties.PropertyStorageFactory

Get a Static Property Storage with default version MAX_NUMBER_FEATURES

buildStaticPropertyStorage(File, int) - Static method in class io.github.bigbio.pgatk.io.properties.PropertyStorageFactory

Get a Static Property Storage with s predefined number of entries.

byteOrder - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

C

category - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.OntologyEntry

centroided - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

centroided - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

CHARGE - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

chargeDeconvoluted - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

chargeDeconvoluted - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

ChronicleMapPropertyStorage<T> - Class in io.github.bigbio.pgatk.io.properties

ChronicleMapPropertyStorage(File, long) - Constructor for class io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage

Create a ChronicleMap for storing properties

ChronicleMapPropertyStorage(File) - Constructor for class io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage

Create a ChronicleMap for storing properties using the MAX_NUMBER_FEATURES = 100M.

cidGasPressure - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

cleanFilePersistence(File) - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

Clean if some persistence of the Maps in files is present

cleanStorage() - Method in interface io.github.bigbio.pgatk.io.mapcache.IMapStorage

Delete all the information from the Storage

cleanStorage() - Method in class io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage

cleanStorage() - Method in class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage

cleanStorage() - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

cleanStorage() - Method in class io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage

cleanStorage() - Method in class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage

cleanStorage() - Method in class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

clear() - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

clearCache() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Clears the cache.

clearModifications() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFilePSM

clearParametersMap() - Method in class io.github.bigbio.pgatk.io.objectdb.LongObject

Clears the loaded parameters.

close() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

close() - Method in class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader

close() - Method in interface io.github.bigbio.pgatk.io.common.MzIterableReader

Close the respective channel and File use to parse the Spectra

close() - Method in interface io.github.bigbio.pgatk.io.mapcache.IMapStorage

Close a MapStore

close() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

close() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIterableReader

close() - Method in class io.github.bigbio.pgatk.io.msp.MspIterableReader

close() - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

close() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIterableReader

close() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Closes the db connection.

close(boolean) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Closes the db connection.

close() - Method in class io.github.bigbio.pgatk.io.pride.PrideAvroReader

close() - Method in class io.github.bigbio.pgatk.io.pride.PrideAvroWriter

close() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIterableReader

close() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonWriter

close() - Method in class io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage

Close the DB on Disk and delete it.

close() - Method in class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage

close() - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

Close the storage Map

close() - Method in class io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage

Close the DB on Disk and delete it.

close() - Method in class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage

close() - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Closes the database connection.

close() - Method in class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

closeRandomAccess() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

A method to close the RandomAccessFile that is used to access the data in the data file.

ClusteringFileCluster - Class in io.github.bigbio.pgatk.io.common.cluster

ClusteringFileCluster(double, double, List<ISpectrumReference>, List<Double>, List<Double>, List<Integer>, String, String) - Constructor for class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

ClusteringFileIndex - Class in io.github.bigbio.pgatk.io.clustering.indexing

Represents the index to a .clustering file.

ClusteringFileIndex(Map<String, ClusteringIndexElement>) - Constructor for class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringFileIndex

ClusteringFileIndexer - Class in io.github.bigbio.pgatk.io.clustering.indexing

Indexer to index .clustering files.

ClusteringFileIndexer() - Constructor for class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringFileIndexer

ClusteringFileModification - Class in io.github.bigbio.pgatk.io.common.cluster

Created by jg on 24.09.14.

ClusteringFileModification(int, String) - Constructor for class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileModification

ClusteringFilePSM - Class in io.github.bigbio.pgatk.io.common.cluster

Created by jg on 24.09.14.

ClusteringFilePSM(String) - Constructor for class io.github.bigbio.pgatk.io.common.cluster.ClusteringFilePSM

ClusteringFileReader - Class in io.github.bigbio.pgatk.io.clustering

Created by jg on 10.07.14.

ClusteringFileReader(File) - Constructor for class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader

ClusteringFileReader(File, ClusteringFileIndex) - Constructor for class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader

ClusteringFileSpectrumReference - Class in io.github.bigbio.pgatk.io.common.cluster

Created by jg on 01.08.14.

ClusteringFileSpectrumReference(String, int, double, String, float, String, String) - Constructor for class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

ClusteringFileSpectrumReference(String) - Constructor for class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

ClusteringFileSpectrumReference.Peak - Class in io.github.bigbio.pgatk.io.common.cluster

ClusteringIndexElement - Class in io.github.bigbio.pgatk.io.clustering.indexing

IndexElement used to index .clustering files.

ClusteringIndexElement(String, float, long, int) - Constructor for class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringIndexElement

collisionEnergy - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

collisionGas - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

commit() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Committing all changes into the database.

compare(ClusteringFileSpectrumReference.Peak, ClusteringFileSpectrumReference.Peak) - Method in class io.github.bigbio.pgatk.io.clustering.PeakMzComparator

Deprecated.

compareTo(IModification) - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileModification

compensationVoltage - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

completionTime - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

compressedLen - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

compressionType - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

contains(long) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Checks if database contains a certain object.

contentType - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

convertPeaksToMap(Peaks) - Static method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Extracts the peak list from the given Peaks object and returns it as a Map with the m/z as key and the intensity as value.

convertPeaksToMap(String, String, String, Integer) - Static method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIterableReader

Extracts the peak list from the given Peaks object and returns it as a Map with the m/z as key and the intensity as value.

createDataProcessing() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of DataProcessing

createMaldi() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Maldi

createMsInstrument() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of MsInstrument

createMsManufacturer() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of MsManufacturer

createMsMassAnalyzer() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of MsMassAnalyzer

createMsRun() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of MsRun

createNameValue() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of NameValue

createOntologyEntry() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of OntologyEntry

createOperator() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Operator

createOrientation() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Orientation

createParentFile() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of ParentFile

createPattern() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Pattern

createPeaks() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Peaks

createPlate() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Plate

createPrecursorMz() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of PrecursorMz

createRobot() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Robot

createScan() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Scan

createScanOrigin() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of ScanOrigin

createSeparation() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Separation

createSeparationTechnique() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of SeparationTechnique

createSeparationTechnique(SeparationTechnique) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of JAXBElement<SeparationTechnique>}

createSoftware() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Software

createSpot() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Spot

createSpotting() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create an instance of Spotting

CvParam - Class in io.github.bigbio.pgatk.io.common

A CvParam object.

CvParam(String, String, String, String) - Constructor for class io.github.bigbio.pgatk.io.common.CvParam

CvParam - Class in io.github.bigbio.pgatk.io.pride

CvParam is the default implementation of CvParam.

CvParam() - Constructor for class io.github.bigbio.pgatk.io.pride.CvParam

The Default Constructor

CvParam(CvParam) - Constructor for class io.github.bigbio.pgatk.io.pride.CvParam

Create a new CvParam from original one.

CvParam(String, String, String, String) - Constructor for class io.github.bigbio.pgatk.io.pride.CvParam

Default constructor fof the term including all the attributes.

CvParam(String, String) - Constructor for class io.github.bigbio.pgatk.io.pride.CvParam

The minimun constructor most contains accession and name of the property.

D

DataProcessing - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

DataProcessing() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

dataProcessing - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

dbDirectory - Variable in class io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage

dbFile - Static variable in class io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage

dbFile - Static variable in class io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage

DbMutex - Class in io.github.bigbio.pgatk.io.objectdb

Placeholder for the db mutex.

DbMutex() - Constructor for class io.github.bigbio.pgatk.io.objectdb.DbMutex

dbMutex - Static variable in class io.github.bigbio.pgatk.io.objectdb.DbMutex

The db mutex.

DbObject - Class in io.github.bigbio.pgatk.io.objectdb

All classes that are stored in the backend need a unique identifier, all further classes inherit from this class.

DbObject() - Constructor for class io.github.bigbio.pgatk.io.objectdb.DbObject

deadVolume - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

decode(String, byte[], int) - Static method in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

Convenience function for decoding binary data encoded by MSNumpress.

decodeFixedPoint(byte[]) - Static method in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

decodeLinear(byte[], int, double[]) - Static method in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

Decodes data encoded by encodeLinear.

decodePic(byte[], int, double[]) - Static method in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

Decodes data encoded by encodePic

decodeSlof(byte[], int, double[]) - Static method in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

Decodes data encoded by encodeSlof

decreaseRWCounter() - Static method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Function for decreasing the counter of processes accessing objects from the db.

DEFAULT_ALLOW_CUSTOM_TAGS - Static variable in class io.github.bigbio.pgatk.io.mgf.MgfUtils

DEFAULT_IGNORE_WRONG_PEAKS - Static variable in class io.github.bigbio.pgatk.io.mgf.MgfUtils

DefaultSpectrum - Class in io.github.bigbio.pgatk.io.common

DefaultSpectrum(String, long, int, double, double, Map<Double, Double>, Integer, List<CvParam>) - Constructor for class io.github.bigbio.pgatk.io.common.DefaultSpectrum

deisotoped - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

deisotoped - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

dumpToDB() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Triggers a dump of all objects within the cache into the database.

E

EcachePropertyStorage<V> - Class in io.github.bigbio.pgatk.io.properties

EcachePropertyStorage(File) - Constructor for class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage

email - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

encodeFixedPoint(double, byte[]) - Static method in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

encodeInt(long, byte[], int) - Static method in class io.github.bigbio.pgatk.io.utils.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 io.github.bigbio.pgatk.io.utils.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 io.github.bigbio.pgatk.io.utils.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 io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

Encodes ion counts by taking the natural logarithm, and storing a fixed point representation of this.

endMz - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

endTime - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

equals(Object) - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileModification

equals(Object) - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFilePSM

equals(Object) - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

equals(Object) - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference.Peak

equals(Object) - Method in class io.github.bigbio.pgatk.io.common.CvParam

equals(Object) - Method in class io.github.bigbio.pgatk.io.common.DefaultSpectrum

equals(Object) - Method in class io.github.bigbio.pgatk.io.pride.CvParam

equals(Object) - Method in class io.github.bigbio.pgatk.io.pride.ExonInfo

equals(Object) - Method in class io.github.bigbio.pgatk.io.pride.GeneCoordinates

equals(Object) - Method in class io.github.bigbio.pgatk.io.utils.Triple

equals(Object) - Method in class io.github.bigbio.pgatk.io.utils.Tuple

establishConnection(boolean) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Establishes connection to the database.

ExonInfo - Class in io.github.bigbio.pgatk.io.pride

ExonInfo() - Constructor for class io.github.bigbio.pgatk.io.pride.ExonInfo

ExonInfo(int, int, int, String) - Constructor for class io.github.bigbio.pgatk.io.pride.ExonInfo

F

FILE_INDEX - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

FILE_SCAN - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

fileName - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

fileSha1 - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

fileType - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

filterLine - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

finalize() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

first - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

firstSpotID - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Orientation

flush() - Method in interface io.github.bigbio.pgatk.io.mapcache.IMapStorage

Write all changes to disk.

flush() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonWriter

flush() - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

flush() - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

flush() - Method in class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

G

geMS1ScanIterator() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Returns an iterator over all the MS 1 scan objects.

GeneCoordinates - Class in io.github.bigbio.pgatk.io.pride

GeneCoordinates() - Constructor for class io.github.bigbio.pgatk.io.pride.GeneCoordinates

GeneCoordinates(int, int, boolean, boolean, String, String, String, String, String, String, List<ExonInfo>) - Constructor for class io.github.bigbio.pgatk.io.pride.GeneCoordinates

get(String) - Method in interface io.github.bigbio.pgatk.io.mapcache.IMapStorage

Retrieve a stored property for a defined item.

get(String, String) - Method in class io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage

get(String, String) - Method in class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage

get(String) - Method in class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage

get(String, String) - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

Get the Value for an specific combination of itemId and propertyName

get(String) - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

Get a value for a key in the Map

get(String, String) - Method in interface io.github.bigbio.pgatk.io.properties.IPropertyStorage

The key in the Property Storage is the combination of itemId + PropertyName For example:

get(String, String) - Method in class io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage

get(String, String) - Method in class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage

get(String) - Method in class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage

get(String, String) - Method in class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

get(String) - Method in class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

getAccess() - Method in enum io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader.MZML_PARAMS

getAccession() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileModification

getAccession() - Method in class io.github.bigbio.pgatk.io.common.CvParam

getAccession() - Method in interface io.github.bigbio.pgatk.io.common.modification.IModification

getAccession() - Method in class io.github.bigbio.pgatk.io.pride.CvParam

getAccessions() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getActivationMethod() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Gets the value of the activationMethod property.

getAdditional() - Method in class io.github.bigbio.pgatk.io.apl.AplSpectrum

getAdditional() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getAdditional() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getAdditional() - Method in class io.github.bigbio.pgatk.io.common.DefaultSpectrum

getAdditional() - Method in interface io.github.bigbio.pgatk.io.common.spectra.Spectrum

Retrieves file format specific variables as parameters.

getAdditional() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

Get Attributes as CvParam

getAdditional() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getAdditional() - Method in class io.github.bigbio.pgatk.io.mzml.MzMLSpectrum

getAdditional() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

getAdditional() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

getAdditional() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

getAdditionalAttributesStrings() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

getAdditionalAttributesStrings() - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

getAttributes() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

getAttributes() - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

getAvailableProperties() - Method in class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage

getAvailableProperties() - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

Properties available in the Map

getAvailableProperties() - Method in class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage

getAvailableProperties() - Method in class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

getBasePeakIntensity() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the basePeakIntensity property.

getBasePeakMz() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the basePeakMz property.

getByteOrder() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Gets the value of the byteOrder property.

getCacheSize() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Returns the cache size in number of objects.

getCategory() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.OntologyEntry

Gets the value of the category property.

getCharge() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getCharge() - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

getChargeState() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getCidGasPressure() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the cidGasPressure property.

getClassObjects(Class) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Returns an iterator of all objects of a given class.

getClassObjects(Class) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Returns the keys of the objects of the given class,

getClassType() - Method in enum io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXmlElement

getCollisionEnergy() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the collisionEnergy property.

getCombinedKey(String, String) - Method in class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage

getCombinedKey(String, String) - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

Get a combined key from an ItemId and Property Name

getCombinedKey(String, String) - Method in class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage

getCombinedKey(String, String) - Method in class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

getCompensationVoltage() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the compensationVoltage property.

getCompletionTime() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

Gets the value of the completionTime property.

getComposition() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getCompressedLen() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Gets the value of the compressedLen property.

getCompressionType() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Gets the value of the compressionType property.

getConsensusCountValues() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getConsensusCountValues() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get number of spectrum that contains the specific peak.

getConsensusIntensValues() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getConsensusIntensValues() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get Consensus Intensity values as List.

getConsensusMzValues() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getConsensusMzValues() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get MzValues as a List

getContentType() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Gets the value of the contentType property.

getCount() - Method in class io.github.bigbio.pgatk.io.common.psms.SequenceCount

getCurrentAdded() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Getter for the current number of added objects.

getCv() - Method in class io.github.bigbio.pgatk.io.common.CvParam

getCvLabel() - Method in class io.github.bigbio.pgatk.io.pride.CvParam

getDatabase() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getDatabaseDirectory() - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Returns the database directory.

getDataProcessing() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Gets the value of the dataProcessing property.

getDataProcessing() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Retrieves the data processings from the file.

getDB() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Getter for the persistence manager.

getDbFile() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Getter for the database file.

getDbFolder() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Getter for the database folder.

getDeadVolume() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

Gets the value of the deadVolume property.

getDisplayProgress() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Returns if the waiting handler is to show the progress for the current process or not.

getEmail() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Gets the value of the email property.

getEndMz() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the endMz property.

getEndTime() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Gets the value of the endTime property.

getEnzyme() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getErrorTolerantTags() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getFileName() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getFileName() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

Gets the value of the fileName property.

getFilePointer() - Method in class io.github.bigbio.pgatk.io.braf.BufferedRandomAccessFile

Returns the current position of the pointer in the file.

getFileSha1() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

Gets the value of the fileSha1 property.

getFileType() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

Gets the value of the fileType property.

getFilterLine() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the filterLine property.

getFirst() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Gets the value of the first property.

getFirst() - Method in class io.github.bigbio.pgatk.io.utils.Triple

getFirstLevel() - Method in class io.github.bigbio.pgatk.io.objectdb.DbObject

getFirstSpotID() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Orientation

Gets the value of the firstSpotID property.

getFixedMofications() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getFormat() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

getFormat() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getFragmentIonTolerance() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getFragmentIonToleranceUnit() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getFrames() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getHighMz() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the highMz property.

getId() - Method in class io.github.bigbio.pgatk.io.apl.AplSpectrum

getId() - Method in class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringIndexElement

getId() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getId() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getId() - Method in class io.github.bigbio.pgatk.io.common.DefaultSpectrum

getId() - Method in interface io.github.bigbio.pgatk.io.common.spectra.Spectrum

The textual representation of an ID of a scan.

getId() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

Gets the ID.

getId() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getId() - Method in class io.github.bigbio.pgatk.io.mzml.MzMLSpectrum

getId() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

getId() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

getId() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

getIdentifiedSpecCount() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getIdentifiedSpecCount() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get the Identified Spectrum Count

getIdMap() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Getter for the id map mapping the hashed keys into zoo db ids.

getIndex() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

Returns the index of ms2 queries in the APL file.

getIndex() - Method in class io.github.bigbio.pgatk.io.apl.AplSpectrum

getIndex() - Method in class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringFileIndex

getIndex() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getIndex() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getIndex() - Method in class io.github.bigbio.pgatk.io.common.DefaultSpectrum

getIndex() - Method in interface io.github.bigbio.pgatk.io.common.spectra.Spectrum

Internal Spectrum in the corresponding file MGF or mzXML or mzML, starting from 1, incrementing by one for each consecutive spectrum.

getIndex() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Returns the index of ms2 queries in the mgf file.

getIndex() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getIndex() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getIndex() - Method in class io.github.bigbio.pgatk.io.mzml.MzMLSpectrum

getIndex() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

getIndex() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

getIndex() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

getIndexedSpectrum(File, IndexElement) - Static method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

Loads a (MS2) spectrum from an APL file who's position in the file is already known.

getIndexedSpectrum(File, IndexElement, boolean, boolean) - Static method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getIndexedSpectrum(File, IndexElement, boolean) - Static method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Loads a (MS2) spectrum from an MGF file who's position in the file is already known.

getIndexedSpectrum(File, IndexElement) - Static method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

getIndexElementForIds() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

getIndexElementForIds() - Method in interface io.github.bigbio.pgatk.io.common.MzReader

Returns a Map containing the spectra ids as keys and the associated IndexElementS as values.

getIndexElementForIds() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getIndexElementForIds() - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

getIndexElementForIds() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

getIndexElementForIds() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader

getInstance() - Static method in class io.github.bigbio.pgatk.io.mzxml.mzxml.unmarshaller.MzXMLUnmarshallerFactory

getInstrument() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getInstrument() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getIntensities() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

getIntensity() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference.Peak

getIntensityCutoff() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Gets the value of the intensityCutoff property.

getIonisationEnergy() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the ionisationEnergy property.

getIsErrorTolerant() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getIterator(Class, String) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Returns an iterator of all objects of a given class

getKey() - Method in class io.github.bigbio.pgatk.io.common.SpectrumProperty

getKey() - Method in class io.github.bigbio.pgatk.io.properties.BinaryPropertyStorage

getKey() - Method in interface io.github.bigbio.pgatk.io.utils.ITuple

getKey() - Method in class io.github.bigbio.pgatk.io.utils.Tuple

getLaserFrequency() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Gets the value of the laserFrequency property.

getLaserIntensity() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Gets the value of the laserIntensity property.

getLaserShootCount() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Gets the value of the laserShootCount property.

getLast() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Gets the value of the last property.

getLowMz() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the lowMz property.

getMaldi() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the maldi property.

getMaldiMatrix() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

Gets the value of the maldiMatrix property.

getMasses() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

getMassType() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getMaxHitsToReport() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getMaxPrimaryProgressCounter() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Returns the max primary progress counter.

getMaxRatio() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getMaxRatio() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get Max Ratio

getMaxSecondaryProgressCounter() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Returns the max secondary progress counter.

getMaxSequence() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getMaxSequence() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get Max Sequence

getMemoryShare() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Returns the share of heap size which can be used before emptying the cache.

getModification() - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

getModificationCvTerm() - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

getModificationNames() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

getModifications() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFilePSM

getModifications() - Method in interface io.github.bigbio.pgatk.io.common.psms.IPeptideSpectrumMatch

getMods() - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

getMostCommonPSM() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getMostCommonPSM() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

getMS1ScanCount() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Returns the number of MS1 scans in the file

getMs2Query(int, boolean) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Returns the MS2 query with the given (0-based) index in the file.

getMs2QueryCount() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Returns the number of Ms2 queries in the file.

getMS2ScanCount() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Returns the number of MS2 scans in the file.

getMS2ScanIterator() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Returns an iterator over all the MS 2 scan objects.

getMsDetector() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Gets the value of the msDetector property.

getMsInstrument() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Gets the value of the msInstrument property.

getMsInstrument() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Retrieves the msInstruments from the file.

getMsInstrumentID() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Gets the value of the msInstrumentID property.

getMsInstrumentID() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the msInstrumentID property.

getMsIonisation() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Gets the value of the msIonisation property.

getMsLevel() - Method in class io.github.bigbio.pgatk.io.apl.AplSpectrum

getMsLevel() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getMsLevel() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getMsLevel() - Method in class io.github.bigbio.pgatk.io.common.DefaultSpectrum

getMsLevel() - Method in interface io.github.bigbio.pgatk.io.common.spectra.Spectrum

Returns the msLevel of the spectrum.

getMsLevel() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getMsLevel() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getMsLevel() - Method in class io.github.bigbio.pgatk.io.mzml.MzMLSpectrum

getMsLevel() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the msLevel property.

getMsLevel() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

getMsLevel() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

getMsLevels() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

getMsLevels() - Method in interface io.github.bigbio.pgatk.io.common.MzReader

Returns a list of ms levels (as integers) found in the parsed file.

getMsLevels() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getMsLevels() - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

getMsLevels() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

getMsLevels() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader

getMsManufacturer() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Gets the value of the msManufacturer property.

getMsMassAnalyzer() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Gets the value of the msMassAnalyzer property.

getMsModel() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Gets the value of the msModel property.

getMsNIndexes(int) - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

getMsNIndexes(int) - Method in interface io.github.bigbio.pgatk.io.common.MzReader

Returns a list of IndexElements for the spectra of the given MS level in the file.

getMsNIndexes(int) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getMsNIndexes(int) - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

getMsNIndexes(int) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

getMsNIndexes(int) - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader

getMsResolution() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Gets the value of the msResolution property.

getMz() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference.Peak

getName() - Method in class io.github.bigbio.pgatk.io.common.CvParam

getName() - Method in interface io.github.bigbio.pgatk.io.common.Param

Returns the parameter's name.

getName() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

Gets the value of the name property.

getName() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

Gets the value of the name property.

getName() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Returns the database name.

getName() - Method in class io.github.bigbio.pgatk.io.pride.CvParam

getNameValueAndComment() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Gets the value of the nameValueAndComment property.

getNameValueAndComment() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the nameValueAndComment property.

getNeutralLoss() - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

getNextLine() - Method in class io.github.bigbio.pgatk.io.braf.BufferedRandomAccessFile

Returns the next line from the file.

getNum() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the num property.

getNum() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ScanOrigin

Gets the value of the num property.

getNumber(Class) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Returns the number of instances of a given class stored in the db.

getNumber(Class) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Returns the number of objects of a given class

getNumberModifiedSites() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

getObject(Long) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Returns the objects if present in the cache.

getObjectId() - Method in class io.github.bigbio.pgatk.io.objectdb.DbObject

getObjectsCache() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Returns the cache used by this database.

getObjectsDB() - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Returns the objects database used in this class.

getObjectsIterator(Class, String) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Returns an iterator of all objects of a given class.

getOperator() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Gets the value of the operator property.

getOrientation() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Pattern

Gets the value of the orientation property.

getOriginalSpectrumTitle() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getOriginalSpectrumTitle() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

If the spectrum source file and source index were reported using the special format, this function returns the original spectrum's title without the added information.

getParameterKey() - Method in interface io.github.bigbio.pgatk.io.objectdb.UrParameter

This method returns the key of the parameter.

getParentFile() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Gets the value of the parentFile property.

getParentFile() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Retrieves the parent files specified in the mzXML file.

getParentFileID() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ScanOrigin

Gets the value of the parentFileID property.

getPartials() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getPath() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Returns the path to the database.

getPattern() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Gets the value of the pattern property.

getPeakList(int) - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

Returns the MS2 query with the given (0-based) index in the file.

getPeakList() - Method in class io.github.bigbio.pgatk.io.apl.AplSpectrum

getPeakList() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getPeakList() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getPeakList() - Method in class io.github.bigbio.pgatk.io.common.DefaultSpectrum

getPeakList() - Method in interface io.github.bigbio.pgatk.io.common.spectra.Spectrum

Returns the spectrum's peak list as a HashMap with the m/z values as keys and the corresponding intensities as values.

getPeakList() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getPeakList() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getPeakList() - Method in class io.github.bigbio.pgatk.io.mzml.MzMLSpectrum

getPeakList() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

getPeakList() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

getPeakList() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

getPeakListCount() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

Returns the number of Ms2 queries in the file.

getPeaks() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getPeaks() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

getPeaks() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the peaks property.

getPeaksCount() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the peaksCount property.

getPeptideIntensity() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getPeptideIsotopeError() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getPeptideMass() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getPeptideMassTolerance() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getPeptideMassToleranceUnit() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getPeptideSequence() - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

getPeptideSequence() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getPerformDecoySearch() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getPhone() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Gets the value of the phone property.

getPlate() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spotting

Gets the value of the plate property.

getPlateID() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Gets the value of the plateID property.

getPlateID() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Gets the value of the plateID property.

getPlateManufacturer() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Gets the value of the plateManufacturer property.

getPlateModel() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Gets the value of the plateModel property.

getPolarity() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the polarity property.

getPosition() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileModification

getPosition() - Method in interface io.github.bigbio.pgatk.io.common.modification.IModification

getPositionMap() - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

getPossibleCharges() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Gets the value of the possibleCharges property.

getPrecision() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Gets the value of the precision property.

getPrecursor() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getPrecursorCharge() - Method in class io.github.bigbio.pgatk.io.apl.AplSpectrum

getPrecursorCharge() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getPrecursorCharge() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getPrecursorCharge() - Method in class io.github.bigbio.pgatk.io.common.DefaultSpectrum

getPrecursorCharge() - Method in interface io.github.bigbio.pgatk.io.common.spectra.Spectrum

Returns the spectrum's charge or null in case the charge is not available.

getPrecursorCharge() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

Gets the precursor charge.

getPrecursorCharge() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getPrecursorCharge() - Method in class io.github.bigbio.pgatk.io.mzml.MzMLSpectrum

getPrecursorCharge() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Gets the value of the precursorCharge property.

getPrecursorCharge() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

getPrecursorCharge() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.apl.AplSpectrum

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.common.DefaultSpectrum

getPrecursorIntensity() - Method in interface io.github.bigbio.pgatk.io.common.spectra.Spectrum

Returns the precursor's intensity or null in case it it not available.

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.mzml.MzMLSpectrum

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Gets the value of the precursorIntensity property.

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

getPrecursorIntensity() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

getPrecursorMZ() - Method in class io.github.bigbio.pgatk.io.apl.AplSpectrum

getPrecursorMz() - Method in class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringIndexElement

getPrecursorMZ() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getPrecursorMZ() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getPrecursorMZ() - Method in class io.github.bigbio.pgatk.io.common.DefaultSpectrum

getPrecursorMZ() - Method in interface io.github.bigbio.pgatk.io.common.spectra.Spectrum

Returns the precursor's m/z or null in case the precursor's m/z is not available.

getPrecursorMZ() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getPrecursorMz() - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

getPrecursorMZ() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getPrecursorMZ() - Method in class io.github.bigbio.pgatk.io.mzml.MzMLSpectrum

getPrecursorMz() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the precursorMz property.

getPrecursorMZ() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

getPrecursorMZ() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

getPrecursorMZ() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

getPrecursorRemoval() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getPrecursorScanNum() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Gets the value of the precursorScanNum property.

getPrimaryProgressCounter() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Returns the primary progress counter.

getProcessingOperationAndComment() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Gets the value of the processingOperationAndComment property.

getProperties() - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

getProperties() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getPropertyId() - Method in class io.github.bigbio.pgatk.io.common.SpectrumProperty

getPropertyName() - Method in class io.github.bigbio.pgatk.io.properties.BinaryPropertyStorage

getPropertyStorageSize() - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Returns the number of clusters identifications.

getProteinMass() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getProteins() - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

getProteins() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getPsmCount() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getPsmCount() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Returns the total number of PSMs.

getPSMs() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getPSMs() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

getPsmSequenceCounts() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getPsmSequenceCounts() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Returns a Map with the PSM sequence as key and its occurrence as value.

getPtms() - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

getPtms() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getQuantitation() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getReportType() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getRetentionTime() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getRetentionTime() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the retentionTime property.

getRobot() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spotting

Gets the value of the robot property.

getRobotManufacturer() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

Gets the value of the robotManufacturer property.

getRobotModel() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

Gets the value of the robotModel property.

getRunAttributes() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Returns the run's attributes.

getScan() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getScan() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Gets the value of the scan property.

getScan() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the scan property.

getScanByNum(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Unmarshals a given scan based on its num attribute.

getScanByStringNum(String) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Unmarshals a given scan based on its num attribute.

getScanCount() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Gets the value of the scanCount property.

getScanIterator() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Returns and iterator over all level 1 scans in the mzXML file.

getScanNumbers() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Returns a list of all scan numbers found in the file.

getScanOrigin() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the scanOrigin property.

getScanType() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the scanType property.

getScores() - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

getScores() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

getSearchTitle() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getSearchType() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getSecond() - Method in class io.github.bigbio.pgatk.io.utils.Triple

getSecondaryProgressCounter() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Returns the secondary progress counter.

getSecondSpotID() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Orientation

Gets the value of the secondSpotID property.

getSeparation() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Gets the value of the separation property.

getSeparationTechnique() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Separation

Gets the value of the separationTechnique property.

getSequence() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFilePSM

getSequence() - Method in interface io.github.bigbio.pgatk.io.common.psms.IPeptideSpectrumMatch

getSequence() - Method in class io.github.bigbio.pgatk.io.common.psms.SequenceCount

getSequenceCounts() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getSequenceCounts() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get number of SequenceCounts.

getSequenceQualifiers() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getSequences() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getSequences() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get Peptide Sequences for the cluster

getSha1() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Gets the value of the sha1 property.

getSimilarityScore() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getSimilarityScore() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

getSize() - Method in class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringIndexElement

getSize() - Method in interface io.github.bigbio.pgatk.io.common.IndexElement

Returns the size of the indexed object in the file.

getSize() - Method in class io.github.bigbio.pgatk.io.common.IndexElementImpl

getSoftware() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Software used to convert the data.

getSoftware() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Gets the value of the software property.

getSourceFilename() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getSourceFilename() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

Spectrum source filenames may be reported using a special id format.

getSourceId() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getSourceId() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

Spectrum source filename and original id within may be reported using a special id format.

getSpearation() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Retrieves the separation object.

getSpecCount() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getSpecCount() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get Spectrum Count

getSpecies() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getSpecies() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

getSpecies() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

getSpecies() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

getSpectraCount() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

Functions required by the PeakListParser interface.

getSpectraCount() - Method in interface io.github.bigbio.pgatk.io.common.MzReader

Returns the number of spectra in the given file / directory.

getSpectraCount() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Functions required by the PeakListParser interface.

getSpectraCount() - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

getSpectraCount() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

getSpectraCount() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader

getSpectraIds() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

getSpectraIds() - Method in interface io.github.bigbio.pgatk.io.common.MzReader

Returns a list of Strings that hold the spectra's ids.

getSpectraIds() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getSpectraIds() - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

getSpectraIds() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

getSpectraIds() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader

getSpectrumById(String) - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

getSpectrumById(String) - Method in interface io.github.bigbio.pgatk.io.common.MzReader

Returns the spectrum with the given id.

getSpectrumById(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getSpectrumById(String) - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

getSpectrumById(String) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

getSpectrumById(String) - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader

getSpectrumByIndex(int) - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

getSpectrumByIndex(int) - Method in interface io.github.bigbio.pgatk.io.common.MzReader

Returns the spectrum based on its 1-based index in the file.

getSpectrumByIndex(int) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getSpectrumByIndex(int) - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

getSpectrumByIndex(int) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Retruns the spectrum based on its 1-based index in the mzXML file.

getSpectrumByIndex(int) - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader

getSpectrumId() - Method in class io.github.bigbio.pgatk.io.common.SpectrumProperty

getSpectrumPrecursorMzRange() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getSpectrumPrecursorMzRange() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get precursor MzRange

getSpectrumProperty(long) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Returns the spectrum match with the given key.

getSpectrumReferences() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getSpectrumReferences() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get List of Spectrum References

getSpot() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Gets the value of the spot property.

getSpotDiameter() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

Gets the value of the spotDiameter property.

getSpotID() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Gets the value of the spotID property.

getSpotID() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

Gets the value of the spotID property.

getSpotting() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Gets the value of the spotting property.

getSpotting() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Retrieves the spotting object.

getSpottingPattern() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Pattern

Gets the value of the spottingPattern property.

getSpotXCount() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Gets the value of the spotXCount property.

getSpotXPosition() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

Gets the value of the spotXPosition property.

getSpotYCount() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Gets the value of the spotYCount property.

getSpotYPosition() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

Gets the value of the spotYPosition property.

getStart() - Method in class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringIndexElement

getStart() - Method in interface io.github.bigbio.pgatk.io.common.IndexElement

Returns the starting position (in bytes) of the indexed object.

getStart() - Method in class io.github.bigbio.pgatk.io.common.IndexElementImpl

getStartMz() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the startMz property.

getStartTime() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Gets the value of the startTime property.

getSymbol() - Method in enum io.github.bigbio.pgatk.io.utils.AminoAcid

getTags() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getTaxonomy() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getTheValue() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

Gets the value of the theValue property.

getTheValue() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.OntologyEntry

Gets the value of the theValue property.

getThird() - Method in class io.github.bigbio.pgatk.io.utils.Triple

getTimePerSpot() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

Gets the value of the timePerSpot property.

getTitle() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getTolerance() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getToleranceUnit() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getTotIonCurrent() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the totIonCurrent property.

getType() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

Gets the value of the type property.

getType() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

Gets the value of the type property.

getUnidentifiedSpecCount() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileCluster

getUnidentifiedSpecCount() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ICluster

Get Unidentified Spectrum Count

getURI() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Gets the value of the uri property.

getUrParam(UrParameter) - Method in class io.github.bigbio.pgatk.io.objectdb.LongObject

Returns the refinement parameter of the same type than the one provided.

getUrParams() - Method in class io.github.bigbio.pgatk.io.objectdb.LongObject

Returns the user parameters map.

getUserMail() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getUserName() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getUserParameter() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getUserTags() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getValue() - Method in class io.github.bigbio.pgatk.io.common.CvParam

getValue() - Method in interface io.github.bigbio.pgatk.io.common.Param

Return's the parameter's value.

getValue() - Method in class io.github.bigbio.pgatk.io.common.SpectrumProperty

getValue() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

Gets the value of the value property.

getValue() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Gets the value of the value property.

getValue() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

Gets the value of the value property.

getValue() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Gets the value of the value property.

getValue() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Gets the value of the value property.

getValue() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

Gets the value of the value property.

getValue() - Method in class io.github.bigbio.pgatk.io.pride.CvParam

getValue() - Method in class io.github.bigbio.pgatk.io.properties.BinaryPropertyStorage

getValue() - Method in interface io.github.bigbio.pgatk.io.utils.ITuple

getValue() - Method in class io.github.bigbio.pgatk.io.utils.Tuple

getVariableModifications() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

getVariableModifications() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

getVersion() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

Gets the value of the version property.

getWindowWideness() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Gets the value of the windowWideness property.

getXpath() - Method in enum io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXmlElement

getXpaths() - Static method in enum io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXmlElement

globalTrim(String) - Static method in class io.github.bigbio.pgatk.io.utils.StringUtils

H

hashCode() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileModification

hashCode() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFilePSM

hashCode() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

hashCode() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference.Peak

hashCode() - Method in class io.github.bigbio.pgatk.io.common.CvParam

hashCode() - Method in class io.github.bigbio.pgatk.io.common.DefaultSpectrum

hashCode() - Method in class io.github.bigbio.pgatk.io.pride.CvParam

hashCode() - Method in class io.github.bigbio.pgatk.io.pride.ExonInfo

hashCode() - Method in class io.github.bigbio.pgatk.io.pride.GeneCoordinates

hashCode() - Method in class io.github.bigbio.pgatk.io.utils.Triple

hashCode() - Method in class io.github.bigbio.pgatk.io.utils.Tuple

hasNext() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

hasNext() - Method in class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader

hasNext() - Method in interface io.github.bigbio.pgatk.io.common.MzIterableReader

This method returns if the collection has more spectra after read the current Spectrum

hasNext() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

hasNext() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIterableReader

hasNext() - Method in class io.github.bigbio.pgatk.io.msp.MspIterableReader

hasNext() - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

hasNext() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader.MzXMLScanIterator

hasNext() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader.SpectrumIterator

hasNext() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIterableReader

hasNext() - Method in class io.github.bigbio.pgatk.io.pride.PrideAvroReader

hasNext() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIterableReader

hasPeaks() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

hasPeaks() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

highMz - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

I

ICluster - Interface in io.github.bigbio.pgatk.io.common.cluster

Created by jg on 10.07.14.

IClusterSourceListener - Interface in io.github.bigbio.pgatk.io.clustering

Created by jg on 10.07.14.

IClusterSourceReader - Interface in io.github.bigbio.pgatk.io.clustering

Created by jg on 10.07.14.

IdentifiedModification - Class in io.github.bigbio.pgatk.io.pride

IdentifiedModification() - Constructor for class io.github.bigbio.pgatk.io.pride.IdentifiedModification

Default constructor

IdentifiedModification(CvParam, List<Tuple<Integer, List<CvParam>>>, CvParam, Set<CvParam>) - Constructor for class io.github.bigbio.pgatk.io.pride.IdentifiedModification

Constructor with all parameters

IIndexer - Interface in io.github.bigbio.pgatk.io.clustering.indexing

Interface representing classes to index clustering result files.

IMapStorage<V> - Interface in io.github.bigbio.pgatk.io.mapcache

This interface provides general methods to retrieve information from A cache Map implementation such as LevelDBPropertyStorage or ChronicleMap

IModification - Interface in io.github.bigbio.pgatk.io.common.modification

Created by jg on 24.09.14.

inCache(long) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Check if key in cache.

inCache(long) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Indicates whether an object is loaded in cache.

increasePrimaryProgressCounter() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Increase the primary progress counter by one "counter".

increasePrimaryProgressCounter(int) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Increase the primary progress counter by the given increment.

increaseRWCounter() - Static method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Function for increasing the counter of processes accessing objects from the db.

increaseSecondaryProgressCounter() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Increase the secondary progress counter by one "counter".

increaseSecondaryProgressCounter(int) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Increase the secondary progress counter by the given value.

inDB(long) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Indicates whether an object is in the cache or the database.

INDEX_CHARGE - Variable in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

INDEX_ID - Variable in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

INDEX_MODIFICATIONS - Variable in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

INDEX_PRECURSOR_MZ - Variable in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

INDEX_SEQUENCE - Variable in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

INDEX_SIMILARITY_SCORE - Variable in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

INDEX_SPECIES - Variable in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

IndexElement - Interface in io.github.bigbio.pgatk.io.common

Interface describing IndexElements that represent the position of an object in a file.

IndexElementImpl - Class in io.github.bigbio.pgatk.io.common

Simple implementation of the IndexElement interface.

IndexElementImpl(long, int) - Constructor for class io.github.bigbio.pgatk.io.common.IndexElementImpl

indexFile(File) - Method in class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringFileIndexer

indexFile(File) - Method in interface io.github.bigbio.pgatk.io.clustering.indexing.IIndexer

Index the defined result file and returns a map containing the cluster's ids as keys and the ClusteringIndexElementS representing these clusters as values.

initializeUnmarshaller() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.unmarshaller.MzXMLUnmarshallerFactory

InMemoryPropertyStorage - Class in io.github.bigbio.pgatk.io.properties

This implementation store a set of keys into a java HashMap.

InMemoryPropertyStorage() - Constructor for class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

insertObject(long, Object) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Stores an object in the desired table.

insertObjects(Map<Long, Object>, WaitingHandler) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Inserts a set of objects in the given table.

intensityCutoff - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

io.github.bigbio.pgatk.io.apl - package io.github.bigbio.pgatk.io.apl

io.github.bigbio.pgatk.io.braf - package io.github.bigbio.pgatk.io.braf

io.github.bigbio.pgatk.io.clustering - package io.github.bigbio.pgatk.io.clustering

io.github.bigbio.pgatk.io.clustering.indexing - package io.github.bigbio.pgatk.io.clustering.indexing

io.github.bigbio.pgatk.io.common - package io.github.bigbio.pgatk.io.common

io.github.bigbio.pgatk.io.common.cluster - package io.github.bigbio.pgatk.io.common.cluster

io.github.bigbio.pgatk.io.common.modification - package io.github.bigbio.pgatk.io.common.modification

io.github.bigbio.pgatk.io.common.psms - package io.github.bigbio.pgatk.io.common.psms

io.github.bigbio.pgatk.io.common.spectra - package io.github.bigbio.pgatk.io.common.spectra

io.github.bigbio.pgatk.io.mapcache - package io.github.bigbio.pgatk.io.mapcache

io.github.bigbio.pgatk.io.mgf - package io.github.bigbio.pgatk.io.mgf

io.github.bigbio.pgatk.io.msp - package io.github.bigbio.pgatk.io.msp

io.github.bigbio.pgatk.io.mzml - package io.github.bigbio.pgatk.io.mzml

io.github.bigbio.pgatk.io.mzxml - package io.github.bigbio.pgatk.io.mzxml

io.github.bigbio.pgatk.io.mzxml.mzxml.model - package io.github.bigbio.pgatk.io.mzxml.mzxml.model

io.github.bigbio.pgatk.io.mzxml.mzxml.unmarshaller - package io.github.bigbio.pgatk.io.mzxml.mzxml.unmarshaller

io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util - package io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util

io.github.bigbio.pgatk.io.objectdb - package io.github.bigbio.pgatk.io.objectdb

io.github.bigbio.pgatk.io.pride - package io.github.bigbio.pgatk.io.pride

io.github.bigbio.pgatk.io.properties - package io.github.bigbio.pgatk.io.properties

io.github.bigbio.pgatk.io.utils - package io.github.bigbio.pgatk.io.utils

io.github.bigbio.pgatk.io.utils.msnumpress - package io.github.bigbio.pgatk.io.utils.msnumpress

ionisationEnergy - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

IPeptideSpectrumMatch - Interface in io.github.bigbio.pgatk.io.common.psms

Created by jg on 24.09.14.

IPropertyStorage - Interface in io.github.bigbio.pgatk.io.properties

This interface describes a property storage in HashMap.

isCentroided() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Gets the value of the centroided property.

isCentroided() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the centroided property.

isChargeDeconvoluted() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Gets the value of the chargeDeconvoluted property.

isChargeDeconvoluted() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the chargeDeconvoluted property.

isCollisionGas() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Gets the value of the collisionGas property.

isConnectionActive() - Static method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Indicates whether the connection to the DB is active.

isConnectionActive() - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Indicates whether the connection to the DB is active.

isDecoy() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

isDeisotoped() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Gets the value of the deisotoped property.

isDeisotoped() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Gets the value of the deisotoped property.

isEmpty() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Indicates whether the cache is empty.

isIdentified() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

isIdentified() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

isIdentifiedAsMultiplePeptides() - Method in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

isIdentifiedAsMultiplePeptides() - Method in interface io.github.bigbio.pgatk.io.common.cluster.ISpectrumReference

isInteger(String) - Static method in class io.github.bigbio.pgatk.io.utils.StringUtils

Helper method to check if a String is a valid integer or not (0-9 digits).

ISpectrumReference - Interface in io.github.bigbio.pgatk.io.common.cluster

Created by jg on 01.08.14.

isReport() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Indicates whether this waiting handler supports reports.

isRunCanceled() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Returns true if the run is canceled.

isRunFinished() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Returns true if the process is finished.

isSpotIntegration() - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Gets the value of the spotIntegration property.

isUnambiguous() - Method in enum io.github.bigbio.pgatk.io.utils.AminoAcid

Returns true if this amino acid symbol unambiguously refers to only one amino acid.

isUseCache() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

isValid() - Method in class io.github.bigbio.pgatk.io.pride.ArchiveSpectrum

iterator() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader.MzXMLScanIterator

ITuple<K,V> - Interface in io.github.bigbio.pgatk.io.utils

This code is licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.

K

KnownProperties - Class in io.github.bigbio.pgatk.io.properties

uk.ac.ebi.pride.spectracluster.spectrum.KnownProperties This class has properties of spectra and clusters known well enough to be hard coded and hints about how they are writtem to MGF and CGF files see http://www.matrixscience.com/help/data_file_help.html for defined MGF Keys

KnownProperties() - Constructor for class io.github.bigbio.pgatk.io.properties.KnownProperties

L

laserFrequency - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

laserIntensity - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

laserShootCount - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

last - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

LEVELDB_CACHE_SIZE - Static variable in class io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage

LevelDBPropertyStorage<T> - Class in io.github.bigbio.pgatk.io.properties

Implementation of LevelDB for InMemoryPropertyStorage using levelDB database.

LevelDBPropertyStorage(File) - Constructor for class io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage

The LevelDB Property Storage allows to store key-values in Map and Cache

LibrarySpectrumBuilder - Class in io.github.bigbio.pgatk.io.msp

LibrarySpectrumBuilder() - Constructor for class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

loadFromFile(File) - Static method in class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringFileIndex

Loads a .clustering file's index from a binary index file.

loadObjectMutex - Static variable in class io.github.bigbio.pgatk.io.objectdb.DbMutex

The cache load objects mutex.

loadObjects(Collection<Long>, WaitingHandler) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Loads objects from a table in the cache.

loadObjects(Class, WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Loads all objects from a given class.

loadObjects(Class, WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Loads all objects of the class in cache.

loadObjects(ArrayList<Long>, WaitingHandler) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Loads all objects of given keys in cache.

lock(WaitingHandler) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Locking the db for storing.

LongObject - Class in io.github.bigbio.pgatk.io.objectdb

This abstract class provides customization facilities.

LongObject() - Constructor for class io.github.bigbio.pgatk.io.objectdb.LongObject

lowMz - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

M

Maldi - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Maldi() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

maldi - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

maldiMatrix - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

MapDBPropertyStorage<T> - Class in io.github.bigbio.pgatk.io.properties

MapDBPropertyStorage(File) - Constructor for class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage

marshal(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util.AnySimpleTypeAdapter

marshal(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util.NonNegativeIntegerAdapter

marshallToFile(File) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Marshalls the mgf file object to a file.

MAX_NUMBER_FEATURES - Static variable in class io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage

mgfCommentRegex - Static variable in class io.github.bigbio.pgatk.io.mgf.MgfUtils

Regex to capture mgf comments in mgf files.

MgfIndexedReader - Class in io.github.bigbio.pgatk.io.mgf

Represents a MgfIndexedReader.

MgfIndexedReader() - Constructor for class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Default constructor generating an empty mgf file object.

MgfIndexedReader(File) - Constructor for class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Creates the mgf file object from an existing mgf file.

MgfIndexedReader(File, List<IndexElement>) - Constructor for class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Creates the mgf file object from an existing mgf file with a pre-parsed index of ms2 spectra.

MgfIndexedReader(File, boolean, boolean) - Constructor for class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Creates the mgf file object from an existing mgf file.

MgfIndexedReader(File, List<IndexElement>, boolean, boolean) - Constructor for class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Creates the mgf file object from an existing mgf file with a pre-parsed index of ms2 spectra.

MgfIterableReader - Class in io.github.bigbio.pgatk.io.mgf

This implementation only allows to iterate over all the spectra in a file and retrieve the corresponding spectra.

MgfIterableReader(File, boolean, boolean, boolean) - Constructor for class io.github.bigbio.pgatk.io.mgf.MgfIterableReader

MgfUtils - Class in io.github.bigbio.pgatk.io.mgf

MgfUtils() - Constructor for class io.github.bigbio.pgatk.io.mgf.MgfUtils

MgfUtils.FragmentToleranceUnits - Enum in io.github.bigbio.pgatk.io.mgf

MgfUtils.MassType - Enum in io.github.bigbio.pgatk.io.mgf

MgfUtils.PeptideToleranceUnit - Enum in io.github.bigbio.pgatk.io.mgf

MgfUtils.ReportType - Enum in io.github.bigbio.pgatk.io.mgf

MgfUtils.SearchType - Enum in io.github.bigbio.pgatk.io.mgf

MODEL_PKG - Static variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ModelConstants

ModelConstants - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

ModelConstants() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ModelConstants

MOST_COMMON_PEPTIDE_KEY - Static variable in class io.github.bigbio.pgatk.io.properties.KnownProperties

Ms2Query - Class in io.github.bigbio.pgatk.io.mgf

This class reads the MS2 information in the MGF.

Ms2Query(boolean) - Constructor for class io.github.bigbio.pgatk.io.mgf.Ms2Query

Default constructor generating an empty Ms2Query

Ms2Query(String, int, boolean, boolean) - Constructor for class io.github.bigbio.pgatk.io.mgf.Ms2Query

Generates a Ms2Query from a mgf part representing an Ms2Query (including "BEGIN IONS" and "END IONS")

msDetector - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

MsInstrument - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

MsInstrument() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

msInstrument - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

msInstrumentID - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

msInstrumentID - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

msIonisation - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

msLevel - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

msManufacturer - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

MsManufacturer - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

MsManufacturer() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsManufacturer

msMassAnalyzer - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

MsMassAnalyzer - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

MsMassAnalyzer() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsMassAnalyzer

msModel - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

MSNumpress - Class in io.github.bigbio.pgatk.io.utils.msnumpress

MSNumpress() - Constructor for class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

MspAttributeReader - Class in io.github.bigbio.pgatk.io.msp

MspAttributeReader() - Constructor for class io.github.bigbio.pgatk.io.msp.MspAttributeReader

MspIterableReader - Class in io.github.bigbio.pgatk.io.msp

An IterativeReader that can read nist msp files.

MspIterableReader(File) - Constructor for class io.github.bigbio.pgatk.io.msp.MspIterableReader

MspSpectrum - Class in io.github.bigbio.pgatk.io.msp

MspSpectrum() - Constructor for class io.github.bigbio.pgatk.io.msp.MspSpectrum

Default Constructor

MspSpectrum(String, Integer) - Constructor for class io.github.bigbio.pgatk.io.msp.MspSpectrum

msResolution - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

MsRun - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

MsRun() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

MzIterableChannelReader - Class in io.github.bigbio.pgatk.io.common

MzIterableChannelReader(File) - Constructor for class io.github.bigbio.pgatk.io.common.MzIterableChannelReader

MzIterableReader - Interface in io.github.bigbio.pgatk.io.common

The MzIterableReader is an interface that only provides methods to read one Spectrum after another This interface and the classes behind allow to read an entire file without needs to index the entire file.

MzMlIndexedReader - Class in io.github.bigbio.pgatk.io.mzml

Wrapper class around the jmzml parser library that's implementing the JMzReader interface.

MzMlIndexedReader(File) - Constructor for class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

Creates a new MzMlIndexedReader object parsing the passed mzML file.

MzMlIndexedReader.MZML_PARAMS - Enum in io.github.bigbio.pgatk.io.mzml

MzML cvParams to be used to extract required parameters from the spectra.

MzMLSpectrum - Class in io.github.bigbio.pgatk.io.mzml

A wrapper class around the jmzml Spectrum class implementing the Spectrum interface from the peak-list-parser library.

MzMLSpectrum(Spectrum, Long) - Constructor for class io.github.bigbio.pgatk.io.mzml.MzMLSpectrum

Creates a new MzMlWrapperSpectrum based on the passed mzML Spectrum object.

MzReader - Interface in io.github.bigbio.pgatk.io.common

Parser for a peak list formats.

MZXML_NAMESPACE - Static variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ModelConstants

MzXmlElement - Enum in io.github.bigbio.pgatk.io.mzxml.mzxml.model

MzXMLIndexedReader - Class in io.github.bigbio.pgatk.io.mzxml

The main class to parse mzXML files.

MzXMLIndexedReader(File) - Constructor for class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader

Creates a new MzXMLIndexedReader object based on the given mzXML file.

MzXMLIndexedReader.MzXMLScanIterator - Class in io.github.bigbio.pgatk.io.mzxml

An iterator over all the scans in the given mzXML file.

MzXMLIndexedReader.SpectrumIterator - Class in io.github.bigbio.pgatk.io.mzxml

A Wrapper around the MzXMLScanIterator.

MzXMLIterableReader - Class in io.github.bigbio.pgatk.io.mzxml

MzXMLIterableReader(File) - Constructor for class io.github.bigbio.pgatk.io.mzxml.MzXMLIterableReader

MzXMLObject - Interface in io.github.bigbio.pgatk.io.mzxml.mzxml.model

MzXMLParsingException - Exception in io.github.bigbio.pgatk.io.mzxml

MzXMLParsingException() - Constructor for exception io.github.bigbio.pgatk.io.mzxml.MzXMLParsingException

MzXMLParsingException(String) - Constructor for exception io.github.bigbio.pgatk.io.mzxml.MzXMLParsingException

MzXMLParsingException(Throwable) - Constructor for exception io.github.bigbio.pgatk.io.mzxml.MzXMLParsingException

MzXMLParsingException(String, Throwable) - Constructor for exception io.github.bigbio.pgatk.io.mzxml.MzXMLParsingException

MzXMLSpectrum - Class in io.github.bigbio.pgatk.io.mzxml

This class wraps Scan elements into PeakListParser compatible Spectrum objects.

MzXMLSpectrum() - Constructor for class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

Default Spectrum for mzXML scans

MzXMLSpectrum(Scan) - Constructor for class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

Create a new MzXMLSpectrum object wrapping the given Scan object.

MzXMLUnmarshaller - Interface in io.github.bigbio.pgatk.io.mzxml.mzxml.unmarshaller

MzXMLUnmarshallerFactory - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.unmarshaller

N

N_HIGHEST_PEAKS - Static variable in class io.github.bigbio.pgatk.io.properties.KnownProperties

name - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

name - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

NameValue - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for namevalueType complex type.

NameValue() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

nameValueAndComment - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

nameValueAndComment - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

next() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

next() - Method in class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader

next() - Method in interface io.github.bigbio.pgatk.io.common.MzIterableReader

Return the next Spectra

next() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

next() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIterableReader

next() - Method in class io.github.bigbio.pgatk.io.msp.MspIterableReader

next() - Method in class io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader

next() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader.MzXMLScanIterator

next() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader.SpectrumIterator

next() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIterableReader

next() - Method in class io.github.bigbio.pgatk.io.pride.PrideAvroReader

next() - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonIterableReader

nextPosition - Variable in class io.github.bigbio.pgatk.io.common.MzIterableChannelReader

NO_KEY - Static variable in class io.github.bigbio.pgatk.io.objectdb.LongObject

NonNegativeIntegerAdapter - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util

Created by IntelliJ IDEA.

NonNegativeIntegerAdapter() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util.NonNegativeIntegerAdapter

num - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

num - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ScanOrigin

O

ObjectDBPropertyStorage - Class in io.github.bigbio.pgatk.io.properties

This class interacts with the back-end database to manage identification objects.

ObjectDBPropertyStorage(ObjectsDB) - Constructor for class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Default constructor

ObjectFactory - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

This object contains factory methods for each Java content interface and Java element interface generated in the uk.ac.ebi.pride.tools.mzxml.mzxml.model package.

ObjectFactory() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ObjectFactory

Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: uk.ac.ebi.pride.tools.mzxml.mzxml.model

ObjectsCache - Class in io.github.bigbio.pgatk.io.objectdb

An object cache can be combined to an ObjectsDB to improve its performance.

ObjectsCache(ObjectsDB) - Constructor for class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Constructor.

ObjectsCache() - Constructor for class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Empty default constructor

ObjectsDB - Class in io.github.bigbio.pgatk.io.objectdb

ObjectsDB() - Constructor for class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Empty default constructor.

ObjectsDB(String, String) - Constructor for class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Constructor.

ObjectsDB(String, boolean) - Constructor for class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Constructor.

ObjectsDB(String, String, boolean) - Constructor for class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Constructor.

onNewClusterRead(ICluster) - Method in interface io.github.bigbio.pgatk.io.clustering.IClusterSourceListener

OntologyEntry - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for ontologyEntryType complex type.

OntologyEntry() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.OntologyEntry

operator - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Operator - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Operator() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

optimalLinearFixedPoint(double[], int) - Static method in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

optimalSlofFixedPoint(double[], int) - Static method in class io.github.bigbio.pgatk.io.utils.msnumpress.MSNumpress

ORG_FILENAME - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

Orientation - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Orientation() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Orientation

orientation - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Pattern

ORIGINAL_PEAKS_INTENS - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

ORIGINAL_PEAKS_MZ - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

P

Param - Interface in io.github.bigbio.pgatk.io.common

Describes a param used to report additional data found in the supported file formats.

parentFile - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

ParentFile - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

ParentFile() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

parentFileID - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ScanOrigin

parseComment(String, LibrarySpectrumBuilder) - Static method in class io.github.bigbio.pgatk.io.msp.MspAttributeReader

parseModsComment(String, LibrarySpectrumBuilder) - Static method in class io.github.bigbio.pgatk.io.msp.MspAttributeReader

parseName(String, LibrarySpectrumBuilder) - Static method in class io.github.bigbio.pgatk.io.msp.MspAttributeReader

parsePeakLine(String) - Static method in class io.github.bigbio.pgatk.io.mgf.MgfUtils

parsePeptideFromPeptidoform(String, LibrarySpectrumBuilder) - Static method in class io.github.bigbio.pgatk.io.msp.MspAttributeReader

parseProteinComment(String, LibrarySpectrumBuilder) - Static method in class io.github.bigbio.pgatk.io.msp.MspAttributeReader

parseUnknownCommentTag(String, String, LibrarySpectrumBuilder) - Static method in class io.github.bigbio.pgatk.io.msp.MspAttributeReader

Pattern - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Pattern() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Pattern

pattern - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Peak(double, double) - Constructor for class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference.Peak

PeakMzComparator - Class in io.github.bigbio.pgatk.io.clustering

Deprecated.

PeakMzComparator() - Constructor for class io.github.bigbio.pgatk.io.clustering.PeakMzComparator

Deprecated.

Peaks - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Peaks() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

peaks - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

peaksCount - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

PEPTIDE_PURITY_STRING - Static variable in class io.github.bigbio.pgatk.io.properties.KnownProperties

PEPTIDES_LIST_COMMA_DELIMITED - Static variable in class io.github.bigbio.pgatk.io.properties.KnownProperties

PgatkIOException - Exception in io.github.bigbio.pgatk.io.common

PgatkIOException(String, Exception) - Constructor for exception io.github.bigbio.pgatk.io.common.PgatkIOException

PgatkIOException(String) - Constructor for exception io.github.bigbio.pgatk.io.common.PgatkIOException

PgatkIOException(Throwable) - Constructor for exception io.github.bigbio.pgatk.io.common.PgatkIOException

PgatkIOException(String, Throwable) - Constructor for exception io.github.bigbio.pgatk.io.common.PgatkIOException

phone - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Plate - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Plate() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

plate - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spotting

plateID - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

plateID - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

plateManufacturer - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

plateModel - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

polarity - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

possibleCharges - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

precision - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

PRECURSOR_MZ - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

precursorCharge - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

precursorIntensity - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

PrecursorMz - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

PrecursorMz() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

precursorMz - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

precursorScanNum - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

PrideAvroReader - Class in io.github.bigbio.pgatk.io.pride

PrideAvroReader(File) - Constructor for class io.github.bigbio.pgatk.io.pride.PrideAvroReader

PrideAvroWriter - Class in io.github.bigbio.pgatk.io.pride

Write a list of AnnotatedSpectrum into Avro format.

PrideAvroWriter(File) - Constructor for class io.github.bigbio.pgatk.io.pride.PrideAvroWriter

PrideJsonIndexedReader - Class in io.github.bigbio.pgatk.io.pride

PrideJsonIndexedReader(File, boolean) - Constructor for class io.github.bigbio.pgatk.io.pride.PrideJsonIndexedReader

Constructor of PrideJsonIndexedReader

PrideJsonIterableReader - Class in io.github.bigbio.pgatk.io.pride

PrideJsonIterableReader(File, Class) - Constructor for class io.github.bigbio.pgatk.io.pride.PrideJsonIterableReader

Constructor of PrideJsonIndexedReader

PrideJsonWriter - Class in io.github.bigbio.pgatk.io.pride

PrideJsonWriter(File) - Constructor for class io.github.bigbio.pgatk.io.pride.PrideJsonWriter

Create a BufferedWriter from a source File

processingOperationAndComment - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

propertyNames - Variable in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

propertyStorage - Variable in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

PropertyStorageFactory - Class in io.github.bigbio.pgatk.io.properties

This code is licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.

PropertyStorageFactory() - Constructor for class io.github.bigbio.pgatk.io.properties.PropertyStorageFactory

PTMS - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

put(String, V) - Method in interface io.github.bigbio.pgatk.io.mapcache.IMapStorage

Store a particular key and value in the Storage

put(String, String, String) - Method in class io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage

put(String, String, String) - Method in class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage

put(String, Object) - Method in class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage

put(String, String, String) - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

This function store a particular property from the store system, in this case the key is the combination of the itemId and the propertyName

put(String, Object) - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

Put a key, value in the storage

put(String, String, String) - Method in interface io.github.bigbio.pgatk.io.properties.IPropertyStorage

The key in the Property Storage is the combination of itemId + PropertyName For example:

put(String, String, String) - Method in class io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage

put(String, String, String) - Method in class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage

put(String, Object) - Method in class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage

put(String, String, String) - Method in class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

put(String, Object) - Method in class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

R

read() - Method in class io.github.bigbio.pgatk.io.braf.BufferedRandomAccessFile

Reads one byte form the current position

read(byte[], int, int) - Method in class io.github.bigbio.pgatk.io.braf.BufferedRandomAccessFile

Reads the set number of bytes into the passed buffer.

readAllClusters() - Method in class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader

readAllClusters() - Method in interface io.github.bigbio.pgatk.io.clustering.IClusterSourceReader

This function reads all clusters from the clustering source.

readBuffer() - Method in class io.github.bigbio.pgatk.io.common.MzIterableChannelReader

readCluster(String) - Method in class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader

Reads the specified cluster from the file.

readCluster(String) - Method in interface io.github.bigbio.pgatk.io.clustering.IClusterSourceReader

Read a specific cluster.

readClustersIteratively(Collection<IClusterSourceListener>) - Method in class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader

readClustersIteratively(Collection<IClusterSourceListener>) - Method in interface io.github.bigbio.pgatk.io.clustering.IClusterSourceReader

This function includes spectra if they are available.

readDBMode() - Method in class io.github.bigbio.pgatk.io.objectdb.DbObject

release() - Method in class io.github.bigbio.pgatk.io.objectdb.SimpleSemaphore

Releases.

remove() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader.MzXMLScanIterator

remove() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader.SpectrumIterator

removeBOMString(String) - Static method in class io.github.bigbio.pgatk.io.utils.StringUtils

Some files started with BOM character, we should remove that from the reader.

removeObject(long) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Removes an object from the cache.

removeObject(long) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Removing an object from the cache and database.

removeObject(long) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Removes an object from the database.

removeObjects(Collection<Long>, WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Removing an object from the cache and database.

removeObjects(ArrayList<Long>, WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Remove a list of objects from the database.

removeUrParam(long) - Method in class io.github.bigbio.pgatk.io.objectdb.LongObject

Removes a user parameter from the user parameters map.

resetPrimaryProgressCounter() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Reset the primary progress counter to 0.

resetSecondaryProgressCounter() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Reset the secondary progress counter to 0.

RETENTION_TIME - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

retentionTime - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

retrieveObject(long) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Retrieves an object from the database or cache.

retrieveObject(long) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Returns an array of all objects of a given list of keys

retrieveObjects(Collection<Long>, WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Retrieves some objects from the database or cache.

retrieveObjects(Class, WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Retrieves all objects from a given class.

retrieveObjects(Collection<Long>, WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Returns an array of all objects of a given list of keys

retrieveObjects(Class, WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.properties.ObjectDBPropertyStorage

Returns an array of all objects of a given class

Robot - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Robot() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

robot - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spotting

robotManufacturer - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

robotModel - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

S

saveAttribute(String, String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

Stores the attribute in the respective member variable.

saveCache(WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Saves the cache content in the database.

saveObjects(int) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Saves an entry in the database if modified and clears it from the cache.

saveObjects(int, WaitingHandler, boolean) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Saves an entry in the database if modified.

saveToFile(File) - Method in class io.github.bigbio.pgatk.io.clustering.indexing.ClusteringFileIndex

Save the current index object to a binary file.

scan - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Scan - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Scan() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

scan - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

scanCount - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

scanOrigin - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

ScanOrigin - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

ScanOrigin() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ScanOrigin

scanType - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

SEARCH_ENGINE_SCORE_TYPES - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

A "," delimited string of search engine score types / names

SEARCH_ENGINE_SCORES - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

A "," delimited string of search engine scores

secondSpotID - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Orientation

seek(long) - Method in class io.github.bigbio.pgatk.io.braf.BufferedRandomAccessFile

Moves the internal pointer to the passed (byte) position in the file.

separation - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Separation - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Separation() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Separation

separationTechnique - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Separation

SeparationTechnique - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for separationTechniqueType complex type.

SeparationTechnique() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.SeparationTechnique

SEPARATOR - Variable in class io.github.bigbio.pgatk.io.common.cluster.ClusteringFileSpectrumReference

SEQUENCE - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

SequenceCount - Class in io.github.bigbio.pgatk.io.common.psms

Created by jg on 10.07.14.

SequenceCount(String, int) - Constructor for class io.github.bigbio.pgatk.io.common.psms.SequenceCount

setAccession(String) - Method in class io.github.bigbio.pgatk.io.common.CvParam

setAccessions(List<String>) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setActivationMethod(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Sets the value of the activationMethod property.

setActivationMethod(String) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setAllowCustomTags(boolean) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setAttributes(Set<? extends CvParam>) - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

setBasePeakIntensity(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the basePeakIntensity property.

setBasePeakMz(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the basePeakMz property.

setByteOrder(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Sets the value of the byteOrder property.

setCategory(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.OntologyEntry

Sets the value of the category property.

setCentroid(Boolean) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setCentroided(Boolean) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Sets the value of the centroided property.

setCentroided(Boolean) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the centroided property.

setCharge(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setCharge(Integer) - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

setChargeDeconvoluted(Boolean) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Sets the value of the chargeDeconvoluted property.

setChargeDeconvoluted(Boolean) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the chargeDeconvoluted property.

setChargeDeconvoluted() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setChargeState(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setCidGasPressure(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the cidGasPressure property.

setCidgasPressure(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setCollisionEnergy(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the collisionEnergy property.

setCollisionGas(Boolean) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Sets the value of the collisionGas property.

setCollitionEnergy(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setCompensationVoltage(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the compensationVoltage property.

setCompletionTime(XMLGregorianCalendar) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

Sets the value of the completionTime property.

setComposition(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setCompressedLen(int) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Sets the value of the compressedLen property.

setCompressionType(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Sets the value of the compressionType property.

setContentType(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Sets the value of the contentType property.

setCv(String) - Method in class io.github.bigbio.pgatk.io.common.CvParam

setDatabase(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setDeadVolume(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

Sets the value of the deadVolume property.

setDebugInteractions(boolean) - Static method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Turn the debugging of interactions on or off.

setDeisotoped(Boolean) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Sets the value of the deisotoped property.

setDeisotoped(Boolean) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the deisotoped property.

setDeisotoped(Boolean) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setDisableCommentSupport(boolean) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setDisplayProgress(boolean) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Set if the waiting handler is to show the progress for the current process or not.

setEmail(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Sets the value of the email property.

setEndMz(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the endMz property.

setEndTime(Duration) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Sets the value of the endTime property.

setEnzyme(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setErrorTolerantTags(List<String>) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setFileName(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

Sets the value of the fileName property.

setFileSha1(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

Sets the value of the fileSha1 property.

setFileType(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

Sets the value of the fileType property.

setFilterLine(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the filterLine property.

setFilterLine(String) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setFirst(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Sets the value of the first property.

setFirst(K) - Method in class io.github.bigbio.pgatk.io.utils.Triple

setFirstLevel(boolean) - Method in class io.github.bigbio.pgatk.io.objectdb.DbObject

setFirstSpotID(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Orientation

Sets the value of the firstSpotID property.

setFixedMofications(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setFormat(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setFragmentIonTolerance(Double) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setFragmentIonToleranceUnit(MgfUtils.FragmentToleranceUnits) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setFrames(List<Integer>) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setHighMz(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the highMz property.

setId(String) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setId(long) - Method in class io.github.bigbio.pgatk.io.objectdb.DbObject

setIndex(long) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setIndex(long) - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

setIndex(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setInstrument(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setInstrument(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setIntensityCutoff(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Sets the value of the intensityCutoff property.

setIonCurrent(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setIonisationEnergy(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the ionisationEnergy property.

setIonizationEnergy(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setIsErrorTolerant(Boolean) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setKey(String) - Method in class io.github.bigbio.pgatk.io.common.SpectrumProperty

setKey(String) - Method in class io.github.bigbio.pgatk.io.properties.BinaryPropertyStorage

setKey(K) - Method in class io.github.bigbio.pgatk.io.utils.Tuple

setLaserFrequency(Duration) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Sets the value of the laserFrequency property.

setLaserIntensity(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Sets the value of the laserIntensity property.

setLaserShootCount(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Sets the value of the laserShootCount property.

setLast(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Sets the value of the last property.

setLowMz(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the lowMz property.

setMaldi(Maldi) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the maldi property.

setMaldiMatrix(OntologyEntry) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

Sets the value of the maldiMatrix property.

setMassType(MgfUtils.MassType) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setMaxHitsToReport(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setMaxPrimaryProgressCounter(int) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Set the maximum value for the primary progress counter.

setMaxSecondaryProgressCounter(int) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Set the maximum value for the secondary progress counter.

setMemoryShare(double) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Sets the share of heap size which can be used before emptying the cache.

setModification(CvParam) - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

setMs2Queries(List<Ms2Query>) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

Set the MS2 queries of the MGF file.

setMsDetector(OntologyEntry) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Sets the value of the msDetector property.

setMsInstrumentID(Integer) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Sets the value of the msInstrumentID property.

setMsInstrumentID(Integer) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the msInstrumentID property.

setMsIonisation(OntologyEntry) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Sets the value of the msIonisation property.

setMsLevel(Integer) - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

setMsLevel(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the msLevel property.

setMsLevel(int) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setMsManufacturer(MsManufacturer) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Sets the value of the msManufacturer property.

setMsMassAnalyzer(MsMassAnalyzer) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Sets the value of the msMassAnalyzer property.

setMsModel(OntologyEntry) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Sets the value of the msModel property.

setMsResolution(OntologyEntry) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Sets the value of the msResolution property.

setName(String) - Method in class io.github.bigbio.pgatk.io.common.CvParam

setName(String) - Method in interface io.github.bigbio.pgatk.io.common.Param

Sets the parameter's name.

setName(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

Sets the value of the name property.

setName(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

Sets the value of the name property.

setNeutralLoss(CvParam) - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

setNum(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the num property.

setNum(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ScanOrigin

Sets the value of the num property.

setObjectCache(ObjectsCache) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Sets the object cache to be used by this database.

setOperator(Operator) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Sets the value of the operator property.

setOrientation(Orientation) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Pattern

Sets the value of the orientation property.

setParentFileID(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ScanOrigin

Sets the value of the parentFileID property.

setPartials(Integer) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setPattern(Pattern) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Sets the value of the pattern property.

setPeakList(Map<Double, Double>) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setPeakList(Map<Double, Double>) - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

setPeakLists(List<AplSpectrum>) - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

Set the MS2 queries of the APL file.

setPeaks(Map<Double, Double>) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setPeaksCount(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the peaksCount property.

setPeptideIntensity(Double) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setPeptideIsotopeError(Double) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setPeptideMass(Double) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setPeptideMassTolerance(Double) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setPeptideMassToleranceUnit(MgfUtils.PeptideToleranceUnit) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setPeptideSequence(String) - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

setPerformDecoySearch(Boolean) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setPhone(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Sets the value of the phone property.

setPlateID(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Sets the value of the plateID property.

setPlateID(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Sets the value of the plateID property.

setPlateManufacturer(OntologyEntry) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Sets the value of the plateManufacturer property.

setPlateModel(OntologyEntry) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Sets the value of the plateModel property.

setPolarity(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the polarity property.

setPolarity(String) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setPositionMap(List<Tuple<Integer, List<CvParam>>>) - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

setPossibleCharges(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Sets the value of the possibleCharges property.

setPrecision(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Sets the value of the precision property.

setPrecursor(Double) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setPrecursorCharge(Integer) - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

setPrecursorCharge(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Sets the value of the precursorCharge property.

setPrecursorCharge(int) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setPrecursorIntensity(Double) - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

setPrecursorIntensity(float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Sets the value of the precursorIntensity property.

setPrecursorIntesity(double) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setPrecursorMz(Double) - Method in class io.github.bigbio.pgatk.io.msp.LibrarySpectrumBuilder

setPrecursorMz(Double) - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

setPrecursorMz(Double) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setPrecursorRemoval(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setPrecursorScanNum(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Sets the value of the precursorScanNum property.

setPrimaryProgressCounter(int) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Sets the primary progress counter to the given value.

setPrimaryProgressCounterIndeterminate(boolean) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Sets whether the primary progress counter is indeterminate or not.

setProperties(LibrarySpectrumBuilder) - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

setPropertyId(String) - Method in class io.github.bigbio.pgatk.io.common.SpectrumProperty

setPropertyName(String) - Method in class io.github.bigbio.pgatk.io.properties.BinaryPropertyStorage

setProteinMass(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setQuantitation(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setReadOnly(boolean) - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsCache

Sets the cache in read only.

setReportType(MgfUtils.ReportType) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setRetentionTime(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setRetentionTime(Duration) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the retentionTime property.

setRetentionTime(Duration) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setRetentionTime(String) - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

setRobot(Robot) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spotting

Sets the value of the robot property.

setRobotManufacturer(OntologyEntry) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

Sets the value of the robotManufacturer property.

setRobotModel(OntologyEntry) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

Sets the value of the robotModel property.

setRunCanceled() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Set the process as canceled.

setRunFinished() - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Set the process as finished.

setScan(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setScanCount(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Sets the value of the scanCount property.

setScanType(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the scanType property.

setSearchTitle(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setSearchType(MgfUtils.SearchType) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setSecond(V) - Method in class io.github.bigbio.pgatk.io.utils.Triple

setSecondaryProgressCounter(int) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Sets the secondary progress counter to the given value.

setSecondaryProgressCounterIndeterminate(boolean) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Sets the secondary progress counter to indeterminate or not.

setSecondaryProgressText(String) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Set the secondary progress counter text.

setSecondSpotID(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Orientation

Sets the value of the secondSpotID property.

setSeparation(Separation) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Sets the value of the separation property.

setSequenceQualifiers(List<String>) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setSha1(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Sets the value of the sha1 property.

setSize(int) - Method in class io.github.bigbio.pgatk.io.common.IndexElementImpl

setSoftware(Software) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Sets the value of the software property.

setSoftware(Software) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Sets the value of the software property.

setSpectrumId(String) - Method in class io.github.bigbio.pgatk.io.common.SpectrumProperty

setSpotDiameter(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

Sets the value of the spotDiameter property.

setSpotID(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

Sets the value of the spotID property.

setSpotID(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

Sets the value of the spotID property.

setSpotIntegration(Boolean) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

Sets the value of the spotIntegration property.

setSpotting(Spotting) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Sets the value of the spotting property.

setSpottingPattern(OntologyEntry) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Pattern

Sets the value of the spottingPattern property.

setSpotXCount(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Sets the value of the spotXCount property.

setSpotXPosition(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

Sets the value of the spotXPosition property.

setSpotYCount(Long) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Sets the value of the spotYCount property.

setSpotYPosition(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

Sets the value of the spotYPosition property.

setStart(long) - Method in class io.github.bigbio.pgatk.io.common.IndexElementImpl

setStartMz(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the startMz property.

setStartTime(Duration) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Sets the value of the startTime property.

setTags(List<String>) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setTaxonomy(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setTheValue(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

Sets the value of the theValue property.

setTheValue(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.OntologyEntry

Sets the value of the theValue property.

setThird(T) - Method in class io.github.bigbio.pgatk.io.utils.Triple

setTimePerSpot(Duration) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

Sets the value of the timePerSpot property.

setTitle(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setTolerance(Double) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setToleranceUnit(MgfUtils.PeptideToleranceUnit) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setTotIonCurrent(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Sets the value of the totIonCurrent property.

setType(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

Sets the value of the type property.

setType(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

Sets the value of the type property.

setURI(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Sets the value of the uri property.

setUrParams(HashMap<Long, UrParameter>) - Method in class io.github.bigbio.pgatk.io.objectdb.LongObject

Sets the user parameters map.

setUseCache(boolean) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setUserMail(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setUserName(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setUserParameter(List<String>) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setUserTags(Map<Integer, String>) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setUsi(String) - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

setValue(String) - Method in class io.github.bigbio.pgatk.io.common.CvParam

setValue(String) - Method in interface io.github.bigbio.pgatk.io.common.Param

Sets the parameter's value.

setValue(String) - Method in class io.github.bigbio.pgatk.io.common.SpectrumProperty

setValue(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

Sets the value of the value property.

setValue(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

Sets the value of the value property.

setValue(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

Sets the value of the value property.

setValue(byte[]) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

Sets the value of the value property.

setValue(float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Sets the value of the value property.

setValue(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

Sets the value of the value property.

setValue(String) - Method in class io.github.bigbio.pgatk.io.pride.CvParam

setValue(String) - Method in class io.github.bigbio.pgatk.io.properties.BinaryPropertyStorage

setValue(V) - Method in class io.github.bigbio.pgatk.io.utils.Tuple

setVariableModifications(String) - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

setVariableModifications(String) - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

setVersion(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

Sets the value of the version property.

setWaitingText(String) - Method in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Sets the text describing what is currently being waited for.

setWindowWideness(Float) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

Sets the value of the windowWideness property.

sha1 - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

SIMPLE_DATA_FORMAT - Static variable in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

Convenience date format.

SimpleSemaphore - Class in io.github.bigbio.pgatk.io.objectdb

A simple semaphore where thread interrupted exception are thrown as runtime exception.

SimpleSemaphore(int, boolean) - Constructor for class io.github.bigbio.pgatk.io.objectdb.SimpleSemaphore

Constructor.

SimpleSemaphore(int) - Constructor for class io.github.bigbio.pgatk.io.objectdb.SimpleSemaphore

Constructor.

smartParseDouble(String) - Static method in class io.github.bigbio.pgatk.io.utils.StringUtils

Smart parse of Double values in the way ##.##.##

software - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

software - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsInstrument

Software - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Software() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

SparkeyPropertyStorage<T> - Class in io.github.bigbio.pgatk.io.properties

SparkeyPropertyStorage(File) - Constructor for class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

Spectrum - Interface in io.github.bigbio.pgatk.io.common.spectra

Represents a spectrum in the parsed peak list file.

SpectrumIterator() - Constructor for class io.github.bigbio.pgatk.io.mzxml.MzXMLIndexedReader.SpectrumIterator

SpectrumProperty - Class in io.github.bigbio.pgatk.io.common

This class storage the properties for a single spectrum such as Retention time, mz value, etc.

SpectrumProperty() - Constructor for class io.github.bigbio.pgatk.io.common.SpectrumProperty

SpectrumProperty(String, String, String, String) - Constructor for class io.github.bigbio.pgatk.io.common.SpectrumProperty

spot - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

Spot - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Spot() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

spotDiameter - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

spotID - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Maldi

spotID - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

spotIntegration - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.DataProcessing

spotting - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

Spotting - Class in io.github.bigbio.pgatk.io.mzxml.mzxml.model

Java class for anonymous complex type.

Spotting() - Constructor for class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spotting

spottingPattern - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Pattern

spotXCount - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

spotXPosition - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

spotYCount - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Plate

spotYPosition - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Spot

startMz - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

startTime - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.MsRun

storageSize() - Method in interface io.github.bigbio.pgatk.io.mapcache.IMapStorage

Get size of the storage

storageSize() - Method in class io.github.bigbio.pgatk.io.properties.ChronicleMapPropertyStorage

storageSize() - Method in class io.github.bigbio.pgatk.io.properties.EcachePropertyStorage

storageSize() - Method in class io.github.bigbio.pgatk.io.properties.InMemoryPropertyStorage

Get the Size of the Storage

storageSize() - Method in class io.github.bigbio.pgatk.io.properties.LevelDBPropertyStorage

storageSize() - Method in class io.github.bigbio.pgatk.io.properties.MapDBPropertyStorage

storageSize() - Method in class io.github.bigbio.pgatk.io.properties.SparkeyPropertyStorage

StoredProperties - Class in io.github.bigbio.pgatk.io.properties

Defined the stored properties.

StringUtils - Class in io.github.bigbio.pgatk.io.utils

This code is licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.

StringUtils() - Constructor for class io.github.bigbio.pgatk.io.utils.StringUtils

supportsReadAllClusters() - Method in class io.github.bigbio.pgatk.io.clustering.ClusteringFileReader

supportsReadAllClusters() - Method in interface io.github.bigbio.pgatk.io.clustering.IClusterSourceReader

T

TAB_HTML - Static variable in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

The tab space to add when using HTML.

TAB_NON_HTML - Static variable in interface io.github.bigbio.pgatk.io.objectdb.WaitingHandler

The tab space to add when not using HTML.

theValue - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

theValue - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.OntologyEntry

timePerSpot - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Robot

TITLE - Static variable in class io.github.bigbio.pgatk.io.properties.StoredProperties

toMGFLine(String, String) - Static method in class io.github.bigbio.pgatk.io.properties.KnownProperties

take property - value pair to a line to insert in MGF USER12 is any unknown

toString() - Method in class io.github.bigbio.pgatk.io.apl.AplIndexedReader

toString() - Method in class io.github.bigbio.pgatk.io.apl.AplSpectrum

toString() - Method in class io.github.bigbio.pgatk.io.mgf.MgfIndexedReader

toString() - Method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.PeptideToleranceUnit

toString() - Method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.ReportType

toString() - Method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.SearchType

toString() - Method in class io.github.bigbio.pgatk.io.mgf.Ms2Query

Compiles all the information from this Ms2Query object.

toString() - Method in class io.github.bigbio.pgatk.io.msp.MspSpectrum

toString() - Method in class io.github.bigbio.pgatk.io.mzxml.MzXMLSpectrum

Compiles all the information from this Ms2Query object.

toString() - Method in class io.github.bigbio.pgatk.io.pride.AnnotatedSpectrum

toString() - Method in class io.github.bigbio.pgatk.io.pride.CvParam

toString() - Method in class io.github.bigbio.pgatk.io.pride.ExonInfo

toString() - Method in class io.github.bigbio.pgatk.io.pride.GeneCoordinates

toString() - Method in class io.github.bigbio.pgatk.io.pride.IdentifiedModification

toString() - Method in class io.github.bigbio.pgatk.io.utils.Tuple

totIonCurrent - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Scan

Triple<K,V,T> - Class in io.github.bigbio.pgatk.io.utils

Data structure contains three elements

Triple(K, V, T) - Constructor for class io.github.bigbio.pgatk.io.utils.Triple

Tuple<K,V> - Class in io.github.bigbio.pgatk.io.utils

Tuple stores two elements.

Tuple() - Constructor for class io.github.bigbio.pgatk.io.utils.Tuple

Tuple(K, V) - Constructor for class io.github.bigbio.pgatk.io.utils.Tuple

type - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

type - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

U

unlock() - Method in class io.github.bigbio.pgatk.io.objectdb.ObjectsDB

Unlocking the db after storing.

unmarshal(String, MzXmlElement) - Method in interface io.github.bigbio.pgatk.io.mzxml.mzxml.unmarshaller.MzXMLUnmarshaller

unmarshal(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util.AnySimpleTypeAdapter

unmarshal(String) - Method in class io.github.bigbio.pgatk.io.mzxml.mzxml.xml.util.NonNegativeIntegerAdapter

uri - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

UrParameter - Interface in io.github.bigbio.pgatk.io.objectdb

This interface is used to reference refinement parameters.

V

value - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.NameValue

value - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Operator

value - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.ParentFile

value - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Peaks

value - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

value - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

valueOf(String) - Static method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.FragmentToleranceUnits

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.MassType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.PeptideToleranceUnit

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.ReportType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.SearchType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader.MZML_PARAMS

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXmlElement

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum io.github.bigbio.pgatk.io.utils.AminoAcid

Returns the enum constant of this type with the specified name.

valueOf(char) - Static method in enum io.github.bigbio.pgatk.io.utils.AminoAcid

values() - Static method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.FragmentToleranceUnits

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.MassType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.PeptideToleranceUnit

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.ReportType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.bigbio.pgatk.io.mgf.MgfUtils.SearchType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.bigbio.pgatk.io.mzml.MzMlIndexedReader.MZML_PARAMS

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.bigbio.pgatk.io.mzxml.mzxml.model.MzXmlElement

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum io.github.bigbio.pgatk.io.utils.AminoAcid

Returns an array containing the constants of this enum type, in the order they are declared.

version - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.Software

W

WaitingHandler - Interface in io.github.bigbio.pgatk.io.objectdb

windowWideness - Variable in class io.github.bigbio.pgatk.io.mzxml.mzxml.model.PrecursorMz

write(AnnotatedSpectrum) - Method in class io.github.bigbio.pgatk.io.pride.PrideAvroWriter

write(Spectrum) - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonWriter

Write an ArchiveSpectrum to a file output

writeDBMode() - Method in class io.github.bigbio.pgatk.io.objectdb.DbObject

writeList(List<Spectrum>) - Method in class io.github.bigbio.pgatk.io.pride.PrideJsonWriter

Write a list of ArchiveSpectrum to a file output

A B C D E F G H I K L M N O P R S T U V W