org.fhcrc.cpl.viewer.mrm.commandline
Class MRMCommandLineModule

java.lang.Object
  org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl
      org.fhcrc.cpl.viewer.commandline.modules.BaseViewerCommandLineModuleImpl
          org.fhcrc.cpl.viewer.mrm.commandline.MRMCommandLineModule

All Implemented Interfaces:

CommandLineModule

public class MRMCommandLineModule
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Commandline module for MRM viewer

Field Summary

protected static org.apache.log4j.Logger	_log
protected java.io.File	file
protected java.io.File	outFile
protected java.lang.Class	peakStrategyClass
protected boolean	readSIMs
static java.lang.String[]	strategies
protected boolean	syncLH
protected boolean	traceAllFragments

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

MRMCommandLineModule()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
void	execute() do the actual work
protected void	init()

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

file

protected java.io.File file

outFile

protected java.io.File outFile

readSIMs

protected boolean readSIMs

traceAllFragments

protected boolean traceAllFragments

peakStrategyClass

protected java.lang.Class peakStrategyClass

syncLH

protected boolean syncLH

strategies

public static final java.lang.String[] strategies

Constructor Detail

MRMCommandLineModule

public MRMCommandLineModule()

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