org.fhcrc.cpl.viewer.qa.commandline
Class QAExperimentCLM

java.lang.Object
  org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl
      org.fhcrc.cpl.viewer.commandline.modules.BaseViewerCommandLineModuleImpl
          org.fhcrc.cpl.viewer.qa.commandline.QAExperimentCLM

All Implemented Interfaces:

CommandLineModule

public class QAExperimentCLM
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

test

Field Summary

protected static org.apache.log4j.Logger	_log
protected java.io.File	allPepXmlFile
protected java.io.File	allProtXmlFile
protected float	filteredMaxKL
protected float	filteredMaxMz
protected float	filteredMinMz
protected int	filteredMinPeaks
protected boolean	force
protected java.util.List<java.util.Set<java.lang.String>>	genesInEachRun
protected float	labelMassDiff
protected float	minPeptideProphet
protected float	minProteinProphet
protected java.io.File	mzXmlDir
protected int	numTotalPeptideIdentifications
protected int	numTotalQuantitatedPeptideIdentifications
protected java.util.List<java.util.Set<java.lang.String>>	peptidesInEachRun
protected java.util.List<java.util.Set<java.lang.String>>	proteinsInEachRun
protected java.io.File	protGeneFile
protected java.io.File	qaDir
protected java.util.List<java.util.Set<java.lang.String>>	quantGenesInEachRun
protected java.util.List<java.util.Set<java.lang.String>>	quantPeptidesInEachRun
protected java.util.List<java.util.Set<java.lang.String>>	quantProteinsInEachRun
protected java.util.List<java.util.Map<java.lang.String,java.lang.String>>	runSummaryDataMaps
protected boolean	shouldAnalyzeMS1

Fields inherited from class org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl

mArgumentDefs, mArgumentValues, mArgumentValueStrings, mCommandName, mHelpMessage, mShortDescription, mUsageMessage

Fields inherited from interface org.fhcrc.cpl.toolbox.commandline.CommandLineModule

MODULE_HELP_AUTOMATIC, MODULE_USAGE_AUTOMATIC, UNNAMED_ARG_SERIES_SEPARATOR

Constructor Summary

QAExperimentCLM()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
protected java.io.File	createAllPepText(java.io.File allPepTextFile)
protected java.io.File	createAllProtText(java.io.File allProtTextFile)
protected java.io.File	createSummaryText(java.io.File summaryTextFile)
void	execute() do the actual work
protected void	init()
protected java.util.List<java.lang.String>	ms1QA()
protected void	ms2QA()

Methods inherited from class org.fhcrc.cpl.viewer.commandline.modules.BaseViewerCommandLineModuleImpl

createUnnamedFeatureFileArgumentDefinition, createUnnamedSeriesFeatureFileArgumentDefinition, getFastaFileArgumentValue, getFeatureSetArgumentValue, getModificationListArgumentValue

Methods inherited from class org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl

addArgumentDefinition, addArgumentDefinitions, addArgumentDefinitions, assertArgumentAbsent, assertArgumentAbsent, assertArgumentPresent, assertArgumentPresent, createArgsTableHTML, createUnnamedFileArgumentDefinition, createUnnamedSeriesFileArgumentDefinition, digestArguments, getAdvancedArgumentDefinitions, getArgumentDefinition, getArgumentDefinitions, getArgumentDefinitionsSortedForDisplay, getArgumentValue, getArgumentValues, getArgumentValueStrings, getBasicArgumentDefinitions, getBooleanArgumentValue, getCommandName, getDeltaMassArgumentValue, getDoubleArgumentValue, getDoubleArrayArgumentValue, getFileArgumentValue, getFileArrayArgumentValue, getFloatArgumentValue, getFullHelp, getHelpMessage, getHtmlHelpFragment, getIntegerArgumentValue, getPrintWriter, getShortDescription, getStringArgumentValue, getUnnamedArgumentValue, getUnnamedFileArgumentValue, getUnnamedSeriesArgumentValues, getUnnamedSeriesFileArgumentValues, getUsage, hasAdvancedArguments, hasArgumentValue, hasUnnamedArgumentValue, hasUnnamedSeriesArgumentValue, invoke, makeHtmlSafe, sortArgDefsForDisplay, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.fhcrc.cpl.toolbox.commandline.CommandLineModule

digestArguments, getAdvancedArgumentDefinitions, getArgumentDefinition, getArgumentDefinitions, getArgumentDefinitionsSortedForDisplay, getArgumentValueStrings, getBasicArgumentDefinitions, getCommandName, getFullHelp, getHelpMessage, getHtmlHelpFragment, getShortDescription, getUsage, invoke

Field Detail

_log

protected static org.apache.log4j.Logger _log

mzXmlDir

protected java.io.File mzXmlDir

allPepXmlFile

protected java.io.File allPepXmlFile

allProtXmlFile

protected java.io.File allProtXmlFile

protGeneFile

protected java.io.File protGeneFile

qaDir

protected java.io.File qaDir

force

protected boolean force

filteredMaxKL

protected float filteredMaxKL

filteredMinPeaks

protected int filteredMinPeaks

filteredMinMz

protected float filteredMinMz

filteredMaxMz

protected float filteredMaxMz

minPeptideProphet

protected float minPeptideProphet

minProteinProphet

protected float minProteinProphet

labelMassDiff

protected float labelMassDiff

runSummaryDataMaps

protected java.util.List<java.util.Map<java.lang.String,java.lang.String>> runSummaryDataMaps

peptidesInEachRun

protected java.util.List<java.util.Set<java.lang.String>> peptidesInEachRun

quantPeptidesInEachRun

protected java.util.List<java.util.Set<java.lang.String>> quantPeptidesInEachRun

proteinsInEachRun

protected java.util.List<java.util.Set<java.lang.String>> proteinsInEachRun

genesInEachRun

protected java.util.List<java.util.Set<java.lang.String>> genesInEachRun

quantProteinsInEachRun

protected java.util.List<java.util.Set<java.lang.String>> quantProteinsInEachRun

quantGenesInEachRun

protected java.util.List<java.util.Set<java.lang.String>> quantGenesInEachRun

numTotalPeptideIdentifications

protected int numTotalPeptideIdentifications

numTotalQuantitatedPeptideIdentifications

protected int numTotalQuantitatedPeptideIdentifications

shouldAnalyzeMS1

protected boolean shouldAnalyzeMS1

Constructor Detail

QAExperimentCLM

public QAExperimentCLM()

Method Detail

init

protected void init()

assignArgumentValues

public void assignArgumentValues()
                          throws ArgumentValidationException

Description copied from interface: CommandLineModule

the first step in invoking your module. The values assigned to the various arguments by the user are passed to your module for storage and additional validation. Any communication with the user about their argument values should be done by this method.

Specified by:

assignArgumentValues in interface CommandLineModule

Throws:

ArgumentValidationException

execute

public void execute()
             throws CommandLineModuleExecutionException

do the actual work

Specified by:

execute in interface CommandLineModule

Throws:

CommandLineModuleExecutionException

ms1QA

protected java.util.List<java.lang.String> ms1QA()
                                          throws java.lang.Exception

Throws:

java.lang.Exception

ms2QA

protected void ms2QA()
              throws CommandLineModuleExecutionException

Throws:

CommandLineModuleExecutionException

createSummaryText

protected java.io.File createSummaryText(java.io.File summaryTextFile)
                                  throws java.io.IOException,
                                         javax.xml.stream.XMLStreamException

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

createAllPepText

protected java.io.File createAllPepText(java.io.File allPepTextFile)
                                 throws java.io.IOException,
                                        javax.xml.stream.XMLStreamException

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException

createAllProtText

protected java.io.File createAllProtText(java.io.File allProtTextFile)
                                  throws java.lang.Exception

Throws:

java.lang.Exception