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

Class PepXmlWriter

java.lang.Object

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

public class PepXmlWriter
extends Object

This Writer writes peptide identifications in PepXML format. Use PepXmlWriterBuilder to make instances of this class, add peptide identifications by calling method add(spectrum, peptideMatches), and write to a OutputStream or a file.

Author:

fnikitin Date: 1/8/14

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PepXmlWriter.ConsistencyCheck

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	PepXmlWriter(PepXmlWriterBuilder.Builder builder)

Method Summary

Methods

Modifier and Type	Method and Description
void	add(MsnSpectrum spectrum, List<PeptideMatch> peptideMatchList) Collect the list of peptide identifications for the given spectrum
void	add(MsnSpectrum spectrum, PeptideMatch... peptideMatch) Collect the list of peptide identifications for the given spectrum
protected String	buildSpectrumQuerySpectrumAttribute(MsnSpectrum spectrum) Format MsnSpectrum id for element spectrum attribute of spectrum_query element.
static PepXmlWriter	newStrictWriter(EngineType engineType, Comparator<PeptideMatch> peptideMatchComparator) Create an instance of PepXmlWriter that strictly checks for inconsistencies
static PepXmlWriter	newStrictWriter(EngineType engineType, String scoreName) Create an instance of PepXmlWriter that strictly checks for inconsistencies
static PepXmlWriter	newTolerantWriter(EngineType engineType, Comparator<PeptideMatch> peptideMatchComparator) Create an instance of PepXmlWriter that does not check for inconsistencies
static PepXmlWriter	newTolerantWriter(EngineType engineType, String scoreName) Create an instance of PepXmlWriter that does not check for inconsistencies
void	removeConsistencyChecks(Set<PepXmlWriter.ConsistencyCheck> ccs)
static String	toDefaultSpectrumQuerySpectrumAttribute(MsnSpectrum spectrum) Create the following spectrum format 'basename.scanNumberStart.scanNumberEnd.charge' or 'basename.scanNumberIndex.scanNumberIndex.charge' if no scan numbers
protected MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery	toSpectrumQuery(MsnSpectrum spectrum) Convert MsnSpectrum to PepXml element SpectrumQuery
void	write(File pepXmlFile) Write the PepXml after peptide identifications been collected (see add(spectrum, peptideMatches))
void	write(OutputStream os, URI pepXmlURI) Write the PepXml after peptide identifications been collected (see add(spectrum, peptideMatches))

Methods inherited from class java.lang.Object

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

Constructor Detail

PepXmlWriter

protected PepXmlWriter(PepXmlWriterBuilder.Builder builder)

Method Detail

newStrictWriter

public static PepXmlWriter newStrictWriter(EngineType engineType,
                           Comparator<PeptideMatch> peptideMatchComparator)

Create an instance of PepXmlWriter that strictly checks for inconsistencies

Parameters:

engineType - the engine type was used for MS identification

peptideMatchComparator - the peptide match comparator

Returns:

PepXmlWriter object

newStrictWriter

public static PepXmlWriter newStrictWriter(EngineType engineType,
                           String scoreName)

Create an instance of PepXmlWriter that strictly checks for inconsistencies

Parameters:

engineType - the engine type was used for MS identification

scoreName - the score name used to compare peptide matches

Returns:

PepXmlWriter object

newTolerantWriter

public static PepXmlWriter newTolerantWriter(EngineType engineType,
                             Comparator<PeptideMatch> peptideMatchComparator)

Create an instance of PepXmlWriter that does not check for inconsistencies

Parameters:

engineType - the engine type was used for MS identification

peptideMatchComparator - the peptide match comparator

Returns:

PepXmlWriter object

newTolerantWriter

public static PepXmlWriter newTolerantWriter(EngineType engineType,
                             String scoreName)

Create an instance of PepXmlWriter that does not check for inconsistencies

Parameters:

engineType - the engine type was used for MS identification

scoreName - the score name used to compare peptide matches

Returns:

PepXmlWriter object

removeConsistencyChecks

public void removeConsistencyChecks(Set<PepXmlWriter.ConsistencyCheck> ccs)

toSpectrumQuery

protected MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery toSpectrumQuery(MsnSpectrum spectrum)

Convert MsnSpectrum to PepXml element SpectrumQuery

Parameters:

spectrum - the MsnSpectrum to convert

Returns:

SpectrumQuery

Throws:

IllegalStateException - if spectrum does not contain scan number and this writer expect have one (see removeConsistencyChecks() to disable the check)

buildSpectrumQuerySpectrumAttribute

protected String buildSpectrumQuerySpectrumAttribute(MsnSpectrum spectrum)

Format MsnSpectrum id for element spectrum attribute of spectrum_query element. The default format is defined in PepXmlWriter.toDefaultSpectrumQuerySpectrumAttribute() that this method is calling Needs to be overriden to change format.

toDefaultSpectrumQuerySpectrumAttribute

public static String toDefaultSpectrumQuerySpectrumAttribute(MsnSpectrum spectrum)

Create the following spectrum format 'basename.scanNumberStart.scanNumberEnd.charge' or 'basename.scanNumberIndex.scanNumberIndex.charge' if no scan numbers

Parameters:

spectrum - the spectrum to create the id from

Returns:

the spectrum attribute value

add

public void add(MsnSpectrum spectrum,
       List<PeptideMatch> peptideMatchList)

Collect the list of peptide identifications for the given spectrum

Parameters:

spectrum - the spectrum

peptideMatchList - the list of peptide identifications

add

public void add(MsnSpectrum spectrum,
       PeptideMatch... peptideMatch)

Collect the list of peptide identifications for the given spectrum

Parameters:

spectrum - the spectrum

peptideMatch - the peptide identification(s)

write

public void write(OutputStream os,
         URI pepXmlURI)
           throws IOException

Write the PepXml after peptide identifications been collected (see add(spectrum, peptideMatches))

Parameters:

os - the output stream to flush PepXml into

pepXmlURI - the PepXml URI

Throws:

IOException

write

public void write(File pepXmlFile)
           throws IOException

Write the PepXml after peptide identifications been collected (see add(spectrum, peptideMatches))

Parameters:

pepXmlFile - the output file to flush PepXml into

Throws:

IOException