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

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

All Implemented Interfaces:

CommandLineModule

Direct Known Subclasses:

IcatCommandLineModule

public class QuantCommandLineModule
extends DeconvoluteCommandLineModule
implements CommandLineModule

Quantitation. Same as DeconvoluteCommandLineModule, but with the "quant" argument set to true, and allowing you to tweak the "deconvolute" argument

Field Summary

protected static org.apache.log4j.Logger

_log

Fields inherited from class org.fhcrc.cpl.viewer.commandline.modules.DeconvoluteCommandLineModule

deconvolute, files, heavyTagWeight, intensityType, intensityTypeStrings, labeledResidue, lightTagWeight, massTolerance, massToleranceType, massWindow, maxLabelCount, outDir, outFile, quant, run, scanWindow, showCharts, sumIntensities, timeTolerance

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

QuantCommandLineModule()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
protected void	init()

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

createCommonArgDefs, execute, processFile

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

Field Detail

_log

protected static org.apache.log4j.Logger _log

Constructor Detail

QuantCommandLineModule

public QuantCommandLineModule()

Method Detail

init

protected void init()

Overrides:

init in class DeconvoluteCommandLineModule

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

Overrides:

assignArgumentValues in class DeconvoluteCommandLineModule

Throws:

ArgumentValidationException