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

Packages that use SpectrumIdentifier

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

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

Fields in org.expasy.mzjava.proteomics.io.ms.ident declared as SpectrumIdentifier

Modifier and Type	Field and Description
protected SpectrumIdentifier	MODaPsmReader.spectrumIdentifier

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

Modifier and Type	Method and Description
protected SpectrumIdentifier	MaxQuantPsmReader.getSpectrumId(ResultSet results)
protected SpectrumIdentifier	ProteinPilotPsmReader.getSpectrumId(ResultSet results)
protected abstract SpectrumIdentifier	AbstractPsmCsvReader.getSpectrumId(ResultSet results) Create a new SpectrumIdentifier from a given ResultSet
SpectrumIdentifier	MODaPsmReader.SpectrumInfoParser.parse(String line)

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

Modifier and Type	Method and Description
protected void	PepXmlReader.addScanNumber(SpectrumIdentifier identifier, int startScan, int endScan)
PeptideMatch	MODaPsmReader.PSMInfoParser.parse(String line, SpectrumIdentifier identifier)
protected void	PepXmlReader.processSearchHit(PSMReaderCallback callback, SpectrumIdentifier identifier, MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit)
void	PSMReaderCallback.resultRead(SpectrumIdentifier identifier, PeptideMatch searchResult) Handle a peptide spectrum match

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

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

Modifier and Type	Method and Description
com.google.common.base.Optional<SpectrumIdentifier>	SearchResultMap.getIdentifier(PeptideMatch searchResult)

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

Modifier and Type	Method and Description
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)
void	SearchResultMap.put(SpectrumIdentifier identifier, PeptideMatch searchResult)