org.fhcrc.cpl.viewer.quant.commandline
Class Q3CommandLineModule

java.lang.Object
  org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl
      org.fhcrc.cpl.viewer.commandline.modules.BaseViewerCommandLineModuleImpl
          org.fhcrc.cpl.viewer.quant.commandline.Q3CommandLineModule

All Implemented Interfaces:

CommandLineModule

public class Q3CommandLineModule
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Command linemodule for Q3 quantitation

Field Summary

protected static org.apache.log4j.Logger	_log
protected boolean	compatMode
protected boolean	debugMode
protected boolean	forceOutput
protected FeatureSet	inFeatureSet
protected java.io.File[]	inFiles
protected char	labeledResidue
protected float	massDiff
protected float	maxFracDeltaMass
protected boolean	maxFracDeltaMassIsPPM
protected boolean	mimicXpress
protected float	minPeptideProphet
protected boolean	noSentinels
protected java.io.File	outDir
protected java.io.File	outFile
protected boolean	stripExistingQ3

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

Q3CommandLineModule()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
void	execute() do the actual work
protected void	init()
void	processFile(java.io.File inFile, java.io.File outputFile)

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

forceOutput

protected boolean forceOutput

mimicXpress

protected boolean mimicXpress

noSentinels

protected boolean noSentinels

compatMode

protected boolean compatMode

debugMode

protected boolean debugMode

stripExistingQ3

protected boolean stripExistingQ3

labeledResidue

protected char labeledResidue

massDiff

protected float massDiff

minPeptideProphet

protected float minPeptideProphet

maxFracDeltaMass

protected float maxFracDeltaMass

maxFracDeltaMassIsPPM

protected boolean maxFracDeltaMassIsPPM

inFeatureSet

protected FeatureSet inFeatureSet

inFiles

protected java.io.File[] inFiles

outFile

protected java.io.File outFile

outDir

protected java.io.File outDir

Constructor Detail

Q3CommandLineModule

public Q3CommandLineModule()

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

processFile

public void processFile(java.io.File inFile,
                        java.io.File outputFile)
                 throws CommandLineModuleExecutionException

Throws:

CommandLineModuleExecutionException