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

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

All Implemented Interfaces:

org.fhcrc.cpl.toolbox.commandline.CommandLineModule

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

Command linemodule for Saving pieces of mzXML files

Field Summary

protected static org.apache.log4j.Logger	_log
protected org.fhcrc.cpl.toolbox.Pair<java.lang.Integer,org.fhcrc.cpl.toolbox.Pair<java.lang.Double,java.lang.Double>>[]	calibrationParameters
protected java.io.File[]	inFiles
protected int	initialMassFilterPPM
protected boolean	ms2PrecursorMassesOnly
protected int	numPartitions
protected java.io.File	outDir
protected java.io.File	outFeatureFile
protected java.io.File	outFile

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

CalibrateMzxmlMassesCLM()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
void	execute() Called by msInspect after assignArgumentValues.
void	handleFile(MSRun run, java.io.File outputFile, FeatureSet featureSetForCalibration, FeatureSet scanChargeFeatures) do the actual work
protected void	init()

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

outFile

protected java.io.File outFile

outDir

protected java.io.File outDir

inFiles

protected java.io.File[] inFiles

calibrationParameters

protected org.fhcrc.cpl.toolbox.Pair<java.lang.Integer,org.fhcrc.cpl.toolbox.Pair<java.lang.Double,java.lang.Double>>[] calibrationParameters

outFeatureFile

protected java.io.File outFeatureFile

ms2PrecursorMassesOnly

protected boolean ms2PrecursorMassesOnly

numPartitions

protected int numPartitions

initialMassFilterPPM

protected int initialMassFilterPPM

Constructor Detail

CalibrateMzxmlMassesCLM

public CalibrateMzxmlMassesCLM()

Method Detail

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

handleFile

public void handleFile(MSRun run,
                       java.io.File outputFile,
                       FeatureSet featureSetForCalibration,
                       FeatureSet scanChargeFeatures)
                throws org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException

do the actual work

Throws:

org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException