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

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

All Implemented Interfaces:

CommandLineModule

public class PeptideQuantVisualizationCLM
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

test

Field Summary

protected static org.apache.log4j.Logger	_log
protected static java.lang.String	DUMMY_PROTEIN_NAME
protected float	maxCombineFeatureRatioDiff
protected java.io.File	outTsvFile
protected java.util.Set<java.lang.String>	peptidesFound
protected java.io.File	pepXmlFile
protected QuantitationVisualizer	quantVisualizer
protected int	sidebarWidth
protected boolean	writeHTMLAndText

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

PeptideQuantVisualizationCLM()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
void	execute() do the actual work
java.io.File	getOutTsvFile()
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

pepXmlFile

protected java.io.File pepXmlFile

maxCombineFeatureRatioDiff

protected float maxCombineFeatureRatioDiff

writeHTMLAndText

protected boolean writeHTMLAndText

peptidesFound

protected java.util.Set<java.lang.String> peptidesFound

sidebarWidth

protected int sidebarWidth

DUMMY_PROTEIN_NAME

protected static final java.lang.String DUMMY_PROTEIN_NAME

See Also:

Constant Field Values

quantVisualizer

protected QuantitationVisualizer quantVisualizer

outTsvFile

protected java.io.File outTsvFile

Constructor Detail

PeptideQuantVisualizationCLM

public PeptideQuantVisualizationCLM()

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

getOutTsvFile

public java.io.File getOutTsvFile()