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

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

All Implemented Interfaces:

CommandLineModule

public class PlotMassCalibrationCLM
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Command linemodule for plotting the mass calibration of a feature file

Field Summary

protected static org.apache.log4j.Logger	_log
protected PanelWithBoxAndWhiskerChart	boxWhiskersChartPanel
protected boolean	displayPPMLine
protected FeatureSet[]	featureSets
protected java.io.File	outBoxWhiskersPlotFile
protected java.io.File	outFile
protected double	ppmForLine
protected PanelWithScatterPlot	scatterPlotChartPanel
protected boolean	showCharts
protected double	theoreticalMassWavelength
protected boolean	useMz

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

PlotMassCalibrationCLM()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
void	execute() do the actual work
PanelWithBoxAndWhiskerChart	getBoxWhiskersChartPanel()
PanelWithScatterPlot	getScatterPlotChartPanel()
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

featureSets

protected FeatureSet[] featureSets

outFile

protected java.io.File outFile

outBoxWhiskersPlotFile

protected java.io.File outBoxWhiskersPlotFile

theoreticalMassWavelength

protected double theoreticalMassWavelength

displayPPMLine

protected boolean displayPPMLine

ppmForLine

protected double ppmForLine

showCharts

protected boolean showCharts

useMz

protected boolean useMz

scatterPlotChartPanel

protected PanelWithScatterPlot scatterPlotChartPanel

boxWhiskersChartPanel

protected PanelWithBoxAndWhiskerChart boxWhiskersChartPanel

Constructor Detail

PlotMassCalibrationCLM

public PlotMassCalibrationCLM()

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

getBoxWhiskersChartPanel

public PanelWithBoxAndWhiskerChart getBoxWhiskersChartPanel()

getScatterPlotChartPanel

public PanelWithScatterPlot getScatterPlotChartPanel()