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

Class MODaPsmReader

java.lang.Object

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

All Implemented Interfaces:

PsmReader

public class MODaPsmReader
extends Object
implements PsmReader

Version:

0.0

Author:

Markus Muller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	MODaPsmReader.PeptideInfoParser
protected class	MODaPsmReader.PSMInfoParser
protected class	MODaPsmReader.SpectrumInfoParser

Field Summary

Fields

Modifier and Type	Field and Description
protected Pattern	excludeProteinPattern
protected List<AminoAcid>	fixedModResidues
protected Pattern	includeProteinPattern
protected int	lineNr
static String	MODA_PROB
static String	MODA_SCORE
protected List<PeptideMatch>	psmBuffer
protected MODaPsmReader.PSMInfoParser	psmInfoParser
protected String	readFile
protected com.google.common.collect.Multimap<Integer,Modification>	sideChainFixedModMap
protected SpectrumIdentifier	spectrumIdentifier
protected MODaPsmReader.SpectrumInfoParser	spectrumInfoParser
protected com.google.common.collect.Multimap<ModAttachment,Modification>	termFixedModMap

Constructor Summary

Constructors

Constructor and Description
MODaPsmReader()
MODaPsmReader(List<AminoAcid> fixedModResidues, com.google.common.collect.Multimap<Integer,Modification> sideChainFixedModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termFixedModMap)

Method Summary

Methods

Modifier and Type	Method and Description
protected String[]	getTabValues(String line)
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	setRanks()
protected void	submit(PSMReaderCallback callback)

Methods inherited from class java.lang.Object

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

Field Detail

MODA_SCORE

public static final String MODA_SCORE

See Also:

Constant Field Values

MODA_PROB

public static final String MODA_PROB

See Also:

Constant Field Values

lineNr

protected int lineNr

readFile

protected String readFile

psmBuffer

protected List<PeptideMatch> psmBuffer

spectrumIdentifier

protected SpectrumIdentifier spectrumIdentifier

fixedModResidues

protected List<AminoAcid> fixedModResidues

sideChainFixedModMap

protected com.google.common.collect.Multimap<Integer,Modification> sideChainFixedModMap

termFixedModMap

protected com.google.common.collect.Multimap<ModAttachment,Modification> termFixedModMap

excludeProteinPattern

protected Pattern excludeProteinPattern

includeProteinPattern

protected Pattern includeProteinPattern

psmInfoParser

protected final MODaPsmReader.PSMInfoParser psmInfoParser

spectrumInfoParser

protected final MODaPsmReader.SpectrumInfoParser spectrumInfoParser

Constructor Detail

MODaPsmReader

public MODaPsmReader(List<AminoAcid> fixedModResidues,
             com.google.common.collect.Multimap<Integer,Modification> sideChainFixedModMap,
             com.google.common.collect.Multimap<ModAttachment,Modification> termFixedModMap)

MODaPsmReader

public MODaPsmReader()

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

setRanks

protected void setRanks()

submit

protected void submit(PSMReaderCallback callback)

getTabValues

protected String[] getTabValues(String line)

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