org.fhcrc.cpl.toolbox.proteomics.feature
Class FeaturePepXmlWriter

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

public class FeaturePepXmlWriter
extends BasePepXmlWriter

A restrictive wrapper for writing PepXml files, using a Feature array to populate the spectrum_queries

Field Summary

protected Feature[]	_features
protected AnalyzeICAT.IsotopicLabel	_isotopicLabel
protected boolean	featureSetHasRatioDeclaration
protected int	firstSpectrumQueryIndex
int	RATIO_MODE_Q3
int	RATIO_MODE_XPRESS
protected int	ratioMode
protected boolean	writeIntensitiesAsXpressResults

Fields inherited from class org.fhcrc.cpl.toolbox.proteomics.filehandler.BasePepXmlWriter

_baseName, _documentPostscript, _documentPrefix, _firstRunSummary, _modifications, _optionsForPrinting, _precursorMassType, _searchEngine, _searchSummary, _spectrumBaseString, _xmlBeansAnalysis, _xmlBeansPepXmlDoc, _xmlBeansRunSummaryArray, PRECURSOR_MASS_TYPE_MONOISOTOPIC, SEARCH_ENGINE_XTANDEM_COMET

Constructor Summary

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

FeaturePepXmlWriter(FeatureSet featureSet)

Method Summary

int	getFirstSpectrumQueryIndex() Write out the full document, with all modifications and features, to a file It's too bad I have to override the superclass version here.
int	getRatioMode()
protected void	preWrite() Make absolutely sure that we write a quantitative summary declaration at the top of the file, if either: -the incoming FeatureFile told us it had ratios, or -any feature in the file has ratios
void	setFeatures(Feature[] features) setter for features
void	setFirstSpectrumQueryIndex(int firstSpectrumQueryIndex)
void	setRatioMode(int ratioMode)
void	setWriteIntensitiesAsXpressResults(boolean writeIntensitiesAsXpressResults)
boolean	willWriteIntensitiesAsXpressResults()
protected void	writeFeature(int featureIndex, java.io.PrintWriter pw) Add a SearchResult representing the passed-in feature to the first run of the file.
protected void	writeSpectrumQueries(java.io.PrintWriter pw) Write out all features immediately

Methods inherited from class org.fhcrc.cpl.toolbox.proteomics.filehandler.BasePepXmlWriter

addModificationsToSearchHit, addModificationsToXML, addPeptideProphet, addSearchScore, addSpectrumQuery, get_precursorMassType, get_searchEngine, getSearchSummary, getSpectrumBaseString, set_precursorMassType, set_searchEngine, setBaseName, setModifications, setSearchConstraints, setSearchDatabase, setSpectrumBaseString, write

Methods inherited from class java.lang.Object

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

Field Detail

_features

protected Feature[] _features

writeIntensitiesAsXpressResults

protected boolean writeIntensitiesAsXpressResults

firstSpectrumQueryIndex

protected int firstSpectrumQueryIndex

RATIO_MODE_XPRESS

public final int RATIO_MODE_XPRESS

See Also:

Constant Field Values

RATIO_MODE_Q3

public final int RATIO_MODE_Q3

See Also:

Constant Field Values

ratioMode

protected int ratioMode

featureSetHasRatioDeclaration

protected boolean featureSetHasRatioDeclaration

_isotopicLabel

protected AnalyzeICAT.IsotopicLabel _isotopicLabel

Constructor Detail

FeaturePepXmlWriter

public FeaturePepXmlWriter(Feature[] features,
                           MS2Modification[] modifications)

Create doc structure, populate features and modifications

Parameters:

features -

modifications -

FeaturePepXmlWriter

public FeaturePepXmlWriter(FeatureSet featureSet)

Method Detail

setFeatures

public void setFeatures(Feature[] features)

setter for features

Parameters:

features -

willWriteIntensitiesAsXpressResults

public boolean willWriteIntensitiesAsXpressResults()

setWriteIntensitiesAsXpressResults

public void setWriteIntensitiesAsXpressResults(boolean writeIntensitiesAsXpressResults)

writeSpectrumQueries

protected void writeSpectrumQueries(java.io.PrintWriter pw)

Write out all features immediately

Specified by:

writeSpectrumQueries in class BasePepXmlWriter

Parameters:

pw -

writeFeature

protected void writeFeature(int featureIndex,
                            java.io.PrintWriter pw)

Add a SearchResult representing the passed-in feature to the first run of the file. Write out the XML for that search result

preWrite

protected void preWrite()

Make absolutely sure that we write a quantitative summary declaration at the top of the file, if either: -the incoming FeatureFile told us it had ratios, or -any feature in the file has ratios

Overrides:

preWrite in class BasePepXmlWriter

getFirstSpectrumQueryIndex

public int getFirstSpectrumQueryIndex()

Write out the full document, with all modifications and features, to a file It's too bad I have to override the superclass version here. The only reason that's necessary is to strip out the "pep:" stuff, because programs like RefreshParser only _pretend_ to parse XML. In practice they're looking for actual strings like "/msms_run_summary"

Throws:

java.io.IOException

setFirstSpectrumQueryIndex

public void setFirstSpectrumQueryIndex(int firstSpectrumQueryIndex)

getRatioMode

public int getRatioMode()

setRatioMode

public void setRatioMode(int ratioMode)