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

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

All Implemented Interfaces:

CommandLineModule

public class ViewSpectrumChartCLM
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

test

Field Summary

protected static org.apache.log4j.Logger	_log
protected int	dialogHeight
protected int	dialogWidth
protected float	maxMz
protected int	maxScan
protected int	maxScansImageHeight
protected float	minMz
protected int	minScan
protected java.io.File	outFile
protected java.io.File	outScansFile
protected int	resolution
protected MSRun	run
protected int	scanLine1
protected int	scanLine2
protected int	scansFileImageHeight
protected boolean	showCharts
protected boolean	showScans
protected boolean	staticMode

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

ViewSpectrumChartCLM()

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

run

protected MSRun run

minScan

protected int minScan

maxScan

protected int maxScan

minMz

protected float minMz

maxMz

protected float maxMz

resolution

protected int resolution

scanLine1

protected int scanLine1

scanLine2

protected int scanLine2

staticMode

protected boolean staticMode

showScans

protected boolean showScans

showCharts

protected boolean showCharts

outFile

protected java.io.File outFile

outScansFile

protected java.io.File outScansFile

dialogWidth

protected int dialogWidth

dialogHeight

protected int dialogHeight

scansFileImageHeight

protected int scansFileImageHeight

maxScansImageHeight

protected int maxScansImageHeight

Constructor Detail

ViewSpectrumChartCLM

public ViewSpectrumChartCLM()

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