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

Class PepXmlReader

java.lang.Object

org.expasy.mzjava.proteomics.io.ms.ident.PepXmlReader

All Implemented Interfaces:

PsmReader

public class PepXmlReader
extends Object
implements PsmReader

Version:

sqrt -1

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PepXmlReader.ModMassStorage
protected static class	PepXmlReader.NamespaceRewriteDelegate

Field Summary

Fields

Modifier and Type	Field and Description
protected static ModificationMatchResolver	CONSTANT_RESOLVER
protected boolean	discardAmbiguous
protected PepXmlReader.ModMassStorage	modMassStorage
protected ModificationMatchResolver	modMatchResolver
protected static BitSet	UNKNOWN_AA

Constructor Summary

Constructors

Constructor and Description
PepXmlReader(PepXmlReader.ModMassStorage modMassStorage, boolean discardAmbiguousSequences)
PepXmlReader(PepXmlReader.ModMassStorage modMassStorage, boolean discardAmbiguousSequences, ModificationMatchResolver modMatchResolver)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	addScanNumber(SpectrumIdentifier identifier, int startScan, int endScan)
protected double	adjustMass(Double mass, AminoAcid residue)
protected double	adjustMass(Double mass, ModAttachment modAttachment)
protected boolean	containsUnknownAA(String peptideSequence)
protected void	copyModInfo(PeptideMatch peptideMatch, MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo modInfo)
protected int	intValue(BigInteger integer, int missingValue)
protected PeptideProteinMatch	newProteinMatch(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein protein)
protected PeptideProteinMatch	newProteinMatch(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit)
void	parse(File file, PSMReaderCallback callback) Parse file and call back PSMReaderCallback on each found PSM
void	parse(InputStream inputStream, PSMReaderCallback callback) Parse inputStream and call back PSMReaderCallback on each found PSM
void	parse(Reader reader, PSMReaderCallback callback) Parse reader and call back PSMReaderCallback on each found PSM
protected void	parse(XMLStreamReader xsr, com.google.common.base.Optional<String> xmlFileName, PSMReaderCallback callback)
protected boolean	parseBoolean(BigInteger value)
protected double	parseDouble(String number)
protected void	processSearchHit(PSMReaderCallback callback, SpectrumIdentifier identifier, MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit)
protected void	readAnalysisResult(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit, PeptideMatch searchResult)
protected void	resolveMod(ModificationMatch modMatch)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

modMassStorage

protected final PepXmlReader.ModMassStorage modMassStorage

discardAmbiguous

protected final boolean discardAmbiguous

modMatchResolver

protected final ModificationMatchResolver modMatchResolver

UNKNOWN_AA

protected static final BitSet UNKNOWN_AA

CONSTANT_RESOLVER

protected static final ModificationMatchResolver CONSTANT_RESOLVER

Constructor Detail

PepXmlReader

public PepXmlReader(PepXmlReader.ModMassStorage modMassStorage,
            boolean discardAmbiguousSequences)

PepXmlReader

public PepXmlReader(PepXmlReader.ModMassStorage modMassStorage,
            boolean discardAmbiguousSequences,
            ModificationMatchResolver modMatchResolver)

Method Detail

parse

public void parse(File file,
         PSMReaderCallback callback)

Description copied from interface: PsmReader

Parse file and call back PSMReaderCallback on each found PSM

Specified by:

parse in interface PsmReader

Parameters:

file - input file

callback - a PSMReaderCallback implementation

parse

public void parse(InputStream inputStream,
         PSMReaderCallback callback)

Description copied from interface: PsmReader

Parse inputStream and call back PSMReaderCallback on each found PSM

Specified by:

parse in interface PsmReader

Parameters:

inputStream - input stream

callback - a PSMReaderCallback implementation

parse

public void parse(Reader reader,
         PSMReaderCallback callback)

Description copied from interface: PsmReader

Parse reader and call back PSMReaderCallback on each found PSM

Specified by:

parse in interface PsmReader

Parameters:

reader - input stream

callback - a PSMReaderCallback implementation

parse

protected void parse(XMLStreamReader xsr,
         com.google.common.base.Optional<String> xmlFileName,
         PSMReaderCallback callback)
              throws XMLStreamException,
                     JAXBException

Throws:

XMLStreamException

JAXBException

addScanNumber

protected void addScanNumber(SpectrumIdentifier identifier,
                 int startScan,
                 int endScan)

processSearchHit

protected void processSearchHit(PSMReaderCallback callback,
                    SpectrumIdentifier identifier,
                    MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit)

containsUnknownAA

protected boolean containsUnknownAA(String peptideSequence)

readAnalysisResult

protected void readAnalysisResult(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit,
                      PeptideMatch searchResult)

newProteinMatch

protected PeptideProteinMatch newProteinMatch(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.AlternativeProtein protein)

newProteinMatch

protected PeptideProteinMatch newProteinMatch(MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit)

copyModInfo

protected void copyModInfo(PeptideMatch peptideMatch,
               MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit.ModificationInfo modInfo)

resolveMod

protected void resolveMod(ModificationMatch modMatch)

adjustMass

protected double adjustMass(Double mass,
                AminoAcid residue)

adjustMass

protected double adjustMass(Double mass,
                ModAttachment modAttachment)

intValue

protected int intValue(BigInteger integer,
           int missingValue)

parseDouble

protected double parseDouble(String number)

parseBoolean

protected boolean parseBoolean(BigInteger value)