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

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

All Implemented Interfaces:

org.fhcrc.cpl.toolbox.commandline.CommandLineModule

Direct Known Subclasses:

QuantCommandLineModule

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

Command linemodule for deconvolution. The "quant" and "icat" commands subclass this module... all the work is done here.

Field Summary

protected static org.apache.log4j.Logger	_log
protected boolean	deconvolute
protected java.io.File[]	files
protected float	heavyTagWeight
protected int	intensityType
protected static java.lang.String[]	intensityTypeStrings
protected char	labeledResidue
protected float	lightTagWeight
protected float	massTolerance
protected int	massToleranceType
protected double	massWindow
protected int	maxLabelCount
protected java.io.File	outDir
protected java.io.File	outFile
protected boolean	quant
protected MSRun	run
protected int	scanWindow
protected boolean	showCharts
protected boolean	sumIntensities
protected float	timeTolerance

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

DeconvoluteCommandLineModule()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
protected org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition[]	createCommonArgDefs()
void	execute() Called by msInspect after assignArgumentValues.
protected void	init()
void	processFile(java.io.File inputFile, java.io.File outputFile) do the actual work

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

files

protected java.io.File[] files

outFile

protected java.io.File outFile

outDir

protected java.io.File outDir

deconvolute

protected boolean deconvolute

quant

protected boolean quant

scanWindow

protected int scanWindow

massWindow

protected double massWindow

lightTagWeight

protected float lightTagWeight

heavyTagWeight

protected float heavyTagWeight

labeledResidue

protected char labeledResidue

maxLabelCount

protected int maxLabelCount

run

protected MSRun run

intensityType

protected int intensityType

massTolerance

protected float massTolerance

massToleranceType

protected int massToleranceType

timeTolerance

protected float timeTolerance

sumIntensities

protected boolean sumIntensities

showCharts

protected boolean showCharts

intensityTypeStrings

protected static final java.lang.String[] intensityTypeStrings

Constructor Detail

DeconvoluteCommandLineModule

public DeconvoluteCommandLineModule()

Method Detail

createCommonArgDefs

protected org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition[] createCommonArgDefs()

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

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

Called by msInspect after assignArgumentValues. Executes your functionality. Any communication with the user about execution status should be done by this method.

Specified by:

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

Throws:

org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException

processFile

public void processFile(java.io.File inputFile,
                        java.io.File outputFile)
                 throws org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException

do the actual work

Throws:

org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException