org.fhcrc.cpl.viewer.ms2.commandline
Class CalculateFDRCLM

java.lang.Object
  org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl
      org.fhcrc.cpl.viewer.commandline.modules.BaseViewerCommandLineModuleImpl
          org.fhcrc.cpl.viewer.ms2.commandline.CalculateFDRCLM

All Implemented Interfaces:

CommandLineModule

public class CalculateFDRCLM
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Commandline module for FDR calculation and filtering This allows the user to take a feature file (which can be a pepXML file) and do an FDR calculation based on reverse database hits (rev_ prefix), using some single peptide quality score (PeptideProphet probability, or any arbitrary search_score). The results are then filtered according to some maximum FDR threshold and output to a new file, with all filtered results having a PeptideProphet probability of some specified value.

Nested Class Summary

class

CalculateFDRCLM.SearchScoreComparator

Field Summary

protected static org.apache.log4j.Logger	_log
protected boolean	byCharge
protected boolean	calcAllRunsFDRTogether
static java.lang.String	DEFAULT_REV_PROTEIN_PREFIX
static java.lang.String	DEFAULT_SEARCH_SCORE_NAME
protected java.io.File[]	featureFiles
protected boolean	higherIsBetter
protected float	maxFDRToKeep
static int	MIN_FEATURES_FOR_FDR_CALC
protected static int	MODE_PPROPHET
protected static int	MODE_SEARCH_SCORE
protected static int	OUT_FORMAT_APML
protected static int	OUT_FORMAT_INPUT
protected static int	OUT_FORMAT_MSINSPECT
protected static int	OUT_FORMAT_PEPXML
protected java.io.File	outDir
protected java.io.File	outFile
protected int	outFormat
protected static java.lang.String[]	outFormatExplanations
protected static java.lang.String[]	outFormatStrings
protected float	passingFeaturePeptideProphetValue
protected java.lang.String	reverseProteinPrefix
protected java.io.File	saveChartsDir
protected int	scoreType
protected static java.lang.String[]	scoreTypeExplanations
protected static java.lang.String[]	scoreTypeStrings
protected java.lang.String	searchScoreName
protected boolean	setPeptideProphet1MinusFDR
protected boolean	showCharts
protected float	targetDecoyDBSizeRatio

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

CalculateFDRCLM()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
protected Feature[]	calcFDROnFeatures(Feature[] features, java.lang.String chartNameSuffix)
protected int	calcOutputFormat(java.io.File featureFile)
void	execute() do the actual work
protected double	getSearchScoreValue(Feature feature)
protected void	init()
protected boolean	isInputPepXML(java.io.File featureFile)
protected java.util.List<FeatureSet>	loadFeatureSetsFromFile(java.io.File featureFile)
protected java.util.Map<java.lang.Integer,java.util.List<Feature>>	splitFeaturesByCharge(Feature[] features)
void	writeFeatureSet(FeatureSet featureSet, java.io.File outputFile, int outputFormat)
protected void	writeFile(java.util.List<FeatureSet> featureSets, java.io.File outputFile, int thisFileOutFormat)

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

MIN_FEATURES_FOR_FDR_CALC

public static final int MIN_FEATURES_FOR_FDR_CALC

See Also:

Constant Field Values

featureFiles

protected java.io.File[] featureFiles

searchScoreName

protected java.lang.String searchScoreName

outFile

protected java.io.File outFile

outDir

protected java.io.File outDir

higherIsBetter

protected boolean higherIsBetter

showCharts

protected boolean showCharts

maxFDRToKeep

protected float maxFDRToKeep

passingFeaturePeptideProphetValue

protected float passingFeaturePeptideProphetValue

setPeptideProphet1MinusFDR

protected boolean setPeptideProphet1MinusFDR

targetDecoyDBSizeRatio

protected float targetDecoyDBSizeRatio

scoreType

protected int scoreType

outFormat

protected int outFormat

byCharge

protected boolean byCharge

calcAllRunsFDRTogether

protected boolean calcAllRunsFDRTogether

DEFAULT_REV_PROTEIN_PREFIX

public static final java.lang.String DEFAULT_REV_PROTEIN_PREFIX

See Also:

Constant Field Values

reverseProteinPrefix

protected java.lang.String reverseProteinPrefix

saveChartsDir

protected java.io.File saveChartsDir

DEFAULT_SEARCH_SCORE_NAME

public static final java.lang.String DEFAULT_SEARCH_SCORE_NAME

See Also:

Constant Field Values

scoreTypeStrings

protected static final java.lang.String[] scoreTypeStrings

scoreTypeExplanations

protected static final java.lang.String[] scoreTypeExplanations

MODE_PPROPHET

protected static final int MODE_PPROPHET

See Also:

Constant Field Values

MODE_SEARCH_SCORE

protected static final int MODE_SEARCH_SCORE

See Also:

Constant Field Values

outFormatStrings

protected static final java.lang.String[] outFormatStrings

outFormatExplanations

protected static final java.lang.String[] outFormatExplanations

OUT_FORMAT_PEPXML

protected static final int OUT_FORMAT_PEPXML

See Also:

Constant Field Values

OUT_FORMAT_MSINSPECT

protected static final int OUT_FORMAT_MSINSPECT

See Also:

Constant Field Values

OUT_FORMAT_APML

protected static final int OUT_FORMAT_APML

See Also:

Constant Field Values

OUT_FORMAT_INPUT

protected static final int OUT_FORMAT_INPUT

See Also:

Constant Field Values

Constructor Detail

CalculateFDRCLM

public CalculateFDRCLM()

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

isInputPepXML

protected boolean isInputPepXML(java.io.File featureFile)
                         throws java.io.IOException

Throws:

java.io.IOException

loadFeatureSetsFromFile

protected java.util.List<FeatureSet> loadFeatureSetsFromFile(java.io.File featureFile)
                                                      throws java.lang.Exception

Throws:

java.lang.Exception

calcOutputFormat

protected int calcOutputFormat(java.io.File featureFile)
                        throws java.io.IOException

Throws:

java.io.IOException

splitFeaturesByCharge

protected java.util.Map<java.lang.Integer,java.util.List<Feature>> splitFeaturesByCharge(Feature[] features)

execute

public void execute()
             throws CommandLineModuleExecutionException

do the actual work

Specified by:

execute in interface CommandLineModule

Throws:

CommandLineModuleExecutionException

writeFile

protected void writeFile(java.util.List<FeatureSet> featureSets,
                         java.io.File outputFile,
                         int thisFileOutFormat)
                  throws CommandLineModuleExecutionException

Throws:

CommandLineModuleExecutionException

calcFDROnFeatures

protected Feature[] calcFDROnFeatures(Feature[] features,
                                      java.lang.String chartNameSuffix)
                               throws CommandLineModuleExecutionException

Parameters:

features -

Returns:

forward features passing FDR cutoff

Throws:

CommandLineModuleExecutionException

writeFeatureSet

public void writeFeatureSet(FeatureSet featureSet,
                            java.io.File outputFile,
                            int outputFormat)
                     throws CommandLineModuleExecutionException

Throws:

CommandLineModuleExecutionException

getSearchScoreValue

protected double getSearchScoreValue(Feature feature)