Uses of Class
org.expasy.mzjava.proteomics.ms.ident.PeptideMatch

Packages that use PeptideMatch

Package	Description
org.expasy.mzjava.proteomics.io.ms.ident
org.expasy.mzjava.proteomics.ms.ident

Uses of PeptideMatch in org.expasy.mzjava.proteomics.io.ms.ident

Fields in org.expasy.mzjava.proteomics.io.ms.ident with type parameters of type PeptideMatch

Modifier and Type	Field and Description
protected List<PeptideMatch>	MODaPsmReader.psmBuffer

Methods in org.expasy.mzjava.proteomics.io.ms.ident that return PeptideMatch

Modifier and Type	Method and Description
PeptideMatch	MODaPsmReader.PSMInfoParser.parse(String line, SpectrumIdentifier identifier)
protected PeptideMatch	MzIdentMlReader.readPeptide(String peptideRef, SequenceCollectionType sequenceCollection)

Methods in org.expasy.mzjava.proteomics.io.ms.ident that return types with arguments of type PeptideMatch

Modifier and Type	Method and Description
com.google.common.base.Optional<PeptideMatch>	MaxQuantPsmReader.makePeptideMatch(ResultSet results)
protected com.google.common.base.Optional<PeptideMatch>	ProteinPilotPsmReader.makePeptideMatch(ResultSet results)
protected abstract com.google.common.base.Optional<PeptideMatch>	AbstractPsmCsvReader.makePeptideMatch(ResultSet results) Create a new PeptideMatch from a given ResultSet

Methods in org.expasy.mzjava.proteomics.io.ms.ident with parameters of type PeptideMatch

Modifier and Type	Method and Description
void	PepXmlWriter.add(MsnSpectrum spectrum, PeptideMatch... peptideMatch) Collect the list of peptide identifications for the given spectrum
void	MODaPsmReader.PeptideInfoParser.addModifs(PeptideMatch peptideMatch, double massDiff)
protected void	PepXmlReader.copyModInfo(PeptideMatch peptideMatch, MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo modInfo)
protected void	PepXmlReader.readAnalysisResult(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit, PeptideMatch searchResult)
void	PSMReaderCallback.resultRead(SpectrumIdentifier identifier, PeptideMatch searchResult) Handle a peptide spectrum match
protected void	MaxQuantPsmReader.setValues(PeptideMatch peptideMatch, ResultSet results)
protected void	ProteinPilotPsmReader.setValues(PeptideMatch peptideMatch, ResultSet results)
protected abstract void	AbstractPsmCsvReader.setValues(PeptideMatch peptideMatch, ResultSet results) Set PeptideMatch score values

Method parameters in org.expasy.mzjava.proteomics.io.ms.ident with type arguments of type PeptideMatch

Modifier and Type	Method and Description
void	PepXmlWriter.add(MsnSpectrum spectrum, List<PeptideMatch> peptideMatchList) Collect the list of peptide identifications for the given spectrum
static PepXmlWriterBuilder.Builder	PepXmlWriterBuilder.create(EngineType engineType, Comparator<PeptideMatch> peptideMatchComparator) Main entry point to build PepXmlWriter
static PepXmlWriter	PepXmlWriter.newStrictWriter(EngineType engineType, Comparator<PeptideMatch> peptideMatchComparator) Create an instance of PepXmlWriter that strictly checks for inconsistencies
static PepXmlWriter	PepXmlWriter.newTolerantWriter(EngineType engineType, Comparator<PeptideMatch> peptideMatchComparator) Create an instance of PepXmlWriter that does not check for inconsistencies

Uses of PeptideMatch in org.expasy.mzjava.proteomics.ms.ident

Methods in org.expasy.mzjava.proteomics.ms.ident that return types with arguments of type PeptideMatch

Modifier and Type	Method and Description
List<PeptideMatch>	ScanNumberSearchResultMap.getResults(MsnSpectrum spectrum)
List<PeptideMatch>	TitleSearchResultMap.getResults(MsnSpectrum spectrum)
List<PeptideMatch>	ScanNumberIndexSearchResultMap.getResults(MsnSpectrum spectrum)
abstract List<PeptideMatch>	SearchResultMap.getResults(MsnSpectrum spectrum)

Methods in org.expasy.mzjava.proteomics.ms.ident with parameters of type PeptideMatch

Modifier and Type	Method and Description
int	PeptideMatchComparator.compare(PeptideMatch m1, PeptideMatch m2)
int	PeptideMatch.compareTo(PeptideMatch o)
protected void	ScanNumberSearchResultMap.doPut(SpectrumIdentifier identifier, PeptideMatch searchResult)
protected void	TitleSearchResultMap.doPut(SpectrumIdentifier spectrumIdentifier, PeptideMatch searchResult)
void	ScanNumberIndexSearchResultMap.doPut(SpectrumIdentifier identifier, PeptideMatch searchResult)
protected abstract void	SearchResultMap.doPut(SpectrumIdentifier identifier, PeptideMatch searchResult)
com.google.common.base.Optional<SpectrumIdentifier>	SearchResultMap.getIdentifier(PeptideMatch searchResult)
void	SearchResultMap.put(SpectrumIdentifier identifier, PeptideMatch searchResult)
boolean	PeptideMatch.sameModPeptide(PeptideMatch match) Returns true if this PeptideMatch and match have the same peptide sequence and modifications.