org.fhcrc.cpl.toolbox.proteomics.filehandler
Class BasePepXmlWriter

java.lang.Object
  org.fhcrc.cpl.toolbox.proteomics.filehandler.BasePepXmlWriter

Direct Known Subclasses:

FeaturePepXmlWriter

public abstract class BasePepXmlWriter
extends java.lang.Object

An abstract base class for use as a wrapper for writing PepXml files. We take advantage of XmlBeans to build the structure of the pepxml file, and search_summaries (for modifications), but we stitch the XmlBeans XML output for features together by hand, writing out to a file as we go, so that we don't have to hold the whole structure in memory. This class is abstract because different implementations are likely to want to use different objects to populate the individual spectrum_queries that are written out. The only implementing class at the time of this comment is viewer.feature.FeaturePepXmlWriter, which uses an array of viewer.Feature.Feature to populate the spectrum_queries. I can foresee at least two issues arising when another implementation needs to be created (likely on the CPAS side): 1. More file-level data may need to be written out at the top of the file. In that case, please discuss with me (Damon) and we'll make sure that anything that's useful for everybody gets stuck in this abstract base class 2. Something other than MS2Modifications might be desired to populate the modifications. In that case, this abstract base class can turn into two levels of abstract base classes. :) Also I think there may be some weirdness with where the MS2Modifications are declared, in the case that there's more than one fraction. We'll burn that bridge when we come to it.

Field Summary

protected java.lang.String	_baseName
protected java.lang.String	_documentPostscript
protected java.lang.String	_documentPrefix
protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary	_firstRunSummary
protected MS2Modification[]	_modifications
protected org.apache.xmlbeans.XmlOptions	_optionsForPrinting
protected java.lang.String	_precursorMassType
protected java.lang.String	_searchEngine
protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary	_searchSummary
protected java.lang.String	_spectrumBaseString
protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis	_xmlBeansAnalysis
protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument	_xmlBeansPepXmlDoc
protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary[]	_xmlBeansRunSummaryArray
static java.lang.String	PRECURSOR_MASS_TYPE_MONOISOTOPIC
static java.lang.String	SEARCH_ENGINE_XTANDEM_COMET

Constructor Summary

BasePepXmlWriter()
Constructor creates the XmlBeans representing the shell of a PepXml document, and creates the "prefix" and "postscript" strings representing that shell

BasePepXmlWriter(MS2Modification[] modifications)
Create doc structure, populate features and modifications

Method Summary

protected void	addModificationsToSearchHit(net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit, java.util.List<ModifiedAminoAcid>[] modifiedAminoAcids, float nTermModMass, float cTermModMass) Utility method for adding modified aminoacids
protected void	addModificationsToXML() Add modifications to the xml output We assume a reasonably small number of modifications.
protected void	addPeptideProphet(net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit, float pprophet, java.lang.String allNttProb, float fval) Adds an AnalysisResult representing the peptide prophet score
protected void	addSearchScore(net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit, java.lang.String searchScoreName, java.lang.String searchScoreValue) Add a search score.
protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery	addSpectrumQuery(int scanFirst, int scanLast, int charge, int index) Utility method to create a spectrumQuery, added to the first run summary
java.lang.String	get_precursorMassType()
java.lang.String	get_searchEngine()
net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary	getSearchSummary()
java.lang.String	getSpectrumBaseString()
protected void	preWrite()
void	set_precursorMassType(java.lang.String _precursorMassType)
void	set_searchEngine(java.lang.String _searchEngine)
void	setBaseName(java.lang.String baseName) setter for basename
void	setModifications(MS2Modification[] modifications) setter for modifications
void	setSearchConstraints(int maxCleavages, int minTermini) Better only call once.
void	setSearchDatabase(java.lang.String databasePath) Better only call once
void	setSpectrumBaseString(java.lang.String spectrumBaseString)
void	write(java.io.File file) Write out the full document, with all modifications and features, to a file
protected abstract void	writeSpectrumQueries(java.io.PrintWriter pw) Write out all features immediately

Methods inherited from class java.lang.Object

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

Field Detail

_xmlBeansPepXmlDoc

protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument _xmlBeansPepXmlDoc

_xmlBeansAnalysis

protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis _xmlBeansAnalysis

_xmlBeansRunSummaryArray

protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary[] _xmlBeansRunSummaryArray

_firstRunSummary

protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary _firstRunSummary

_searchSummary

protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary _searchSummary

_documentPrefix

protected java.lang.String _documentPrefix

_documentPostscript

protected java.lang.String _documentPostscript

_optionsForPrinting

protected org.apache.xmlbeans.XmlOptions _optionsForPrinting

_modifications

protected MS2Modification[] _modifications

_spectrumBaseString

protected java.lang.String _spectrumBaseString

_baseName

protected java.lang.String _baseName

PRECURSOR_MASS_TYPE_MONOISOTOPIC

public static final java.lang.String PRECURSOR_MASS_TYPE_MONOISOTOPIC

See Also:

Constant Field Values

_precursorMassType

protected java.lang.String _precursorMassType

SEARCH_ENGINE_XTANDEM_COMET

public static final java.lang.String SEARCH_ENGINE_XTANDEM_COMET

See Also:

Constant Field Values

_searchEngine

protected java.lang.String _searchEngine

Constructor Detail

BasePepXmlWriter

public BasePepXmlWriter()

Constructor creates the XmlBeans representing the shell of a PepXml document, and creates the "prefix" and "postscript" strings representing that shell

BasePepXmlWriter

public BasePepXmlWriter(MS2Modification[] modifications)

Create doc structure, populate features and modifications

Parameters:

modifications -

Method Detail

getSearchSummary

public net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SearchSummary getSearchSummary()

setModifications

public void setModifications(MS2Modification[] modifications)

setter for modifications

Parameters:

modifications -

setBaseName

public void setBaseName(java.lang.String baseName)

setter for basename

Parameters:

baseName -

addModificationsToXML

protected void addModificationsToXML()

Add modifications to the xml output We assume a reasonably small number of modifications. No need to write them each out individually and then dispose of the java object

writeSpectrumQueries

protected abstract void writeSpectrumQueries(java.io.PrintWriter pw)

Write out all features immediately

Parameters:

pw -

addPeptideProphet

protected void addPeptideProphet(net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit,
                                 float pprophet,
                                 java.lang.String allNttProb,
                                 float fval)

Adds an AnalysisResult representing the peptide prophet score

Parameters:

searchHit -

pprophet -

allNttProb -

fval - 0 is a sentinel value meaning absent

addSearchScore

protected void addSearchScore(net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit,
                              java.lang.String searchScoreName,
                              java.lang.String searchScoreValue)

Add a search score. Doesn't make any attempt to prevent duplicates

Parameters:

searchHit -

searchScoreName -

searchScoreValue -

addSpectrumQuery

protected net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery addSpectrumQuery(int scanFirst,
                                                                                                                                             int scanLast,
                                                                                                                                             int charge,
                                                                                                                                             int index)

Utility method to create a spectrumQuery, added to the first run summary

Parameters:

scanFirst -

scanLast -

charge -

Returns:

addModificationsToSearchHit

protected void addModificationsToSearchHit(net.systemsbiology.regisWeb.pepXML.MsmsPipelineAnalysisDocument.MsmsPipelineAnalysis.MsmsRunSummary.SpectrumQuery.SearchResult.SearchHit searchHit,
                                           java.util.List<ModifiedAminoAcid>[] modifiedAminoAcids,
                                           float nTermModMass,
                                           float cTermModMass)

Utility method for adding modified aminoacids

Parameters:

searchHit -

modifiedAminoAcids -

setSearchDatabase

public void setSearchDatabase(java.lang.String databasePath)

Better only call once

Parameters:

databasePath -

setSearchConstraints

public void setSearchConstraints(int maxCleavages,
                                 int minTermini)

Better only call once. TODO: un-hardcode trypsin

Parameters:

maxCleavages -

minTermini -

preWrite

protected void preWrite()

write

public void write(java.io.File file)
           throws java.io.IOException

Write out the full document, with all modifications and features, to a file

Parameters:

file -

Throws:

java.io.IOException

getSpectrumBaseString

public java.lang.String getSpectrumBaseString()

setSpectrumBaseString

public void setSpectrumBaseString(java.lang.String spectrumBaseString)

get_precursorMassType

public java.lang.String get_precursorMassType()

set_precursorMassType

public void set_precursorMassType(java.lang.String _precursorMassType)

get_searchEngine

public java.lang.String get_searchEngine()

set_searchEngine

public void set_searchEngine(java.lang.String _searchEngine)