org.fhcrc.cpl.viewer.commandline.modules
Class DumpWindow2DCommandLineModule

java.lang.Object
  org.fhcrc.cpl.viewer.commandline.modules.BaseCommandLineModuleImpl
      org.fhcrc.cpl.viewer.commandline.modules.DumpWindow2DCommandLineModule

All Implemented Interfaces:

org.fhcrc.cpl.toolbox.commandline.CommandLineModule

public class DumpWindow2DCommandLineModule
extends BaseCommandLineModuleImpl
implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule

Dump a 2D window (scans in rows, m/z in columns) around each feature. Only for use by D0/D3 quantitation code; this will be going away.

Field Summary

protected static org.apache.log4j.Logger	_log
protected java.io.File	featureFile
protected java.io.File	mzXmlFile
protected java.io.File	outFile

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

DumpWindow2DCommandLineModule()

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.BaseCommandLineModuleImpl

addArgumentDefinition, addArgumentDefinitions, addArgumentDefinitions, assertArgumentAbsent, assertArgumentAbsent, assertArgumentPresent, assertArgumentPresent, createArgsTableHTML, createArgumentDefinition, createArgumentDefinition, createBooleanArgumentDefinition, createBooleanArgumentDefinition, createDecimalArgumentDefinition, createDecimalArgumentDefinition, createDecimalListArgumentDefinition, createDecimalListArgumentDefinition, createDecimalListArgumentDefinition, createDeltaMassArgumentDefinition, createDeltaMassArgumentDefinition, createDirectoryToReadArgumentDefinition, createEnumeratedArgumentDefinition, createEnumeratedArgumentDefinition, createEnumeratedArgumentDefinition, createEnumeratedArgumentDefinition, createFastaFileArgumentDefinition, createFeatureFileArgumentDefinition, createFileToReadArgumentDefinition, createFileToReadListArgumentDefinition, createFileToWriteArgumentDefinition, createIntegerArgumentDefinition, createIntegerArgumentDefinition, createModificationListArgumentDefinition, createModificationListArgumentDefinition, createStringArgumentDefinition, createStringArgumentDefinition, createUnnamedArgumentDefinition, createUnnamedFileArgumentDefinition, createUnnamedSeriesArgumentDefinition, createUnnamedSeriesFileArgumentDefinition, digestArguments, getAdvancedArgumentDefinitions, getArgumentDefinition, getArgumentDefinitions, getArgumentDefinitionsSortedForDisplay, getArgumentValue, getArgumentValues, getArgumentValueStrings, getBasicArgumentDefinitions, getBooleanArgumentValue, getCommandName, getDeltaMassArgumentValue, getDoubleArgumentValue, getDoubleArrayArgumentValue, getFastaFileArgumentValue, getFeatureSetArgumentValue, getFileArgumentValue, getFileArrayArgumentValue, getFloatArgumentValue, getFullHelp, getHelpMessage, getHtmlHelpFragment, getIntegerArgumentValue, getModificationListArgumentValue, 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

mzXmlFile

protected java.io.File mzXmlFile

featureFile

protected java.io.File featureFile

outFile

protected java.io.File outFile

Constructor Detail

DumpWindow2DCommandLineModule

public DumpWindow2DCommandLineModule()

Method Detail

init

protected void init()

assignArgumentValues

public void assignArgumentValues()
                          throws org.fhcrc.cpl.toolbox.commandline.arguments.ArgumentValidationException

Description copied from interface: org.fhcrc.cpl.toolbox.commandline.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 org.fhcrc.cpl.toolbox.commandline.CommandLineModule

Throws:

org.fhcrc.cpl.toolbox.commandline.arguments.ArgumentValidationException

execute

public void execute()
             throws org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException

do the actual work

Specified by:

execute in interface org.fhcrc.cpl.toolbox.commandline.CommandLineModule

Throws:

org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException