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

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

All Implemented Interfaces:

CommandLineModule

public class FindPeptidesCommandLineModule
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Command Module for feature finding. Not much of the actual work of feature finding is done directly in this class. This class serves mainly to parse user arguments and control the flow of work. This design philosophy is used throughout Command Modules in the msInspect platform dhmay changing 2009/01/02: adding default filtering of minimum 2 peaks and maximum KL 3.0, as well as a "nofilter" parameter that turns this off

Field Summary

protected static org.apache.log4j.Logger	_log
protected int	accurateMassAdjustmentScans
static float	DEFAULT_MAX_KL
static int	DEFAULT_MIN_PEAKS
protected int	dumpWindowSize
protected java.lang.Class<? extends FeatureStrategy>	featureStrategyClass
protected boolean	filterFeatures
protected float	maxKL
protected float	maxMz
protected float	minMz
protected int	minPeaks
protected java.io.File[]	mzXmlFiles
protected boolean	noAccurateMass
protected java.io.File	outDir
protected java.io.File	outFile
protected boolean	peakRidgeWalkSmoothed
protected boolean	plotStatistics
protected int	scanCount
protected int	startScan

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

FindPeptidesCommandLineModule()
Just calls initializer

Method Summary

void	assignArgumentValues() After the lower-level argument validation has taken place, assign the values to variables, and throw an exception if there's any trouble
void	execute() Controller method to oversee the work, which is done in findFeaturesInFile
protected void	findFeaturesInFile(java.io.File mzXmlFile, java.io.File outFile) Workhorse method that operates on a single input file and output file
protected void	init() Define the command name, usage message, help message, and short description, and define all arguments

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

mzXmlFiles

protected java.io.File[] mzXmlFiles

outFile

protected java.io.File outFile

outDir

protected java.io.File outDir

startScan

protected int startScan

scanCount

protected int scanCount

minMz

protected float minMz

maxMz

protected float maxMz

dumpWindowSize

protected int dumpWindowSize

accurateMassAdjustmentScans

protected int accurateMassAdjustmentScans

featureStrategyClass

protected java.lang.Class<? extends FeatureStrategy> featureStrategyClass

peakRidgeWalkSmoothed

protected boolean peakRidgeWalkSmoothed

plotStatistics

protected boolean plotStatistics

noAccurateMass

protected boolean noAccurateMass

DEFAULT_MAX_KL

public static final float DEFAULT_MAX_KL

See Also:

Constant Field Values

DEFAULT_MIN_PEAKS

public static final int DEFAULT_MIN_PEAKS

See Also:

Constant Field Values

maxKL

protected float maxKL

minPeaks

protected int minPeaks

filterFeatures

protected boolean filterFeatures

Constructor Detail

FindPeptidesCommandLineModule

public FindPeptidesCommandLineModule()

Just calls initializer

Method Detail

init

protected void init()

Define the command name, usage message, help message, and short description, and define all arguments

assignArgumentValues

public void assignArgumentValues()
                          throws ArgumentValidationException

After the lower-level argument validation has taken place, assign the values to variables, and throw an exception if there's any trouble

Specified by:

assignArgumentValues in interface CommandLineModule

Throws:

ArgumentValidationException

execute

public void execute()
             throws CommandLineModuleExecutionException

Controller method to oversee the work, which is done in findFeaturesInFile

Specified by:

execute in interface CommandLineModule

Throws:

CommandLineModuleExecutionException

findFeaturesInFile

protected void findFeaturesInFile(java.io.File mzXmlFile,
                                  java.io.File outFile)
                           throws CommandLineModuleExecutionException

Workhorse method that operates on a single input file and output file

Parameters:

mzXmlFile -

outFile -

Throws:

CommandLineModuleExecutionException