org.fhcrc.cpl.viewer.amt.commandline
Class CombineAmtMs2FilesCLM

java.lang.Object
  org.fhcrc.cpl.toolbox.commandline.BaseCommandLineModuleImpl
      org.fhcrc.cpl.viewer.commandline.modules.BaseViewerCommandLineModuleImpl
          org.fhcrc.cpl.viewer.amt.commandline.CombineAmtMs2FilesCLM

All Implemented Interfaces:

CommandLineModule

public class CombineAmtMs2FilesCLM
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Command linemodule for feature finding

Field Summary

protected static org.apache.log4j.Logger	_log
protected java.io.File	amtDir
protected java.io.File	fastaFile
protected Protein[]	fastaProteins
protected static int	FORMAT_FEATURE
protected static int	FORMAT_PEPXML
protected static java.lang.String[]	formatExplanations
protected static java.lang.String[]	formatStrings
protected boolean	guessProteins
protected java.io.File	ms2Dir
protected java.io.File	outDir
protected java.io.File	outFile
protected int	outFormat
protected java.io.File[]	pepXMLFiles
protected boolean	restrictCharge
protected boolean	runRefreshParser
protected boolean	showCharts

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

CombineAmtMs2FilesCLM()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
protected FeatureSet	createCombinedSet(java.io.File[] files, java.io.File outputFile)
void	execute() do the actual work
protected java.util.List<Pair<java.io.File,java.io.File>>	findFilePairs() Pick pairs of files from directories by name, without extension
protected void	handleFiles(java.io.File[] files, java.io.File outputFile)
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

fastaProteins

protected Protein[] fastaProteins

outFile

protected java.io.File outFile

outDir

protected java.io.File outDir

pepXMLFiles

protected java.io.File[] pepXMLFiles

ms2Dir

protected java.io.File ms2Dir

amtDir

protected java.io.File amtDir

guessProteins

protected boolean guessProteins

fastaFile

protected java.io.File fastaFile

outFormat

protected int outFormat

FORMAT_PEPXML

protected static final int FORMAT_PEPXML

See Also:

Constant Field Values

FORMAT_FEATURE

protected static final int FORMAT_FEATURE

See Also:

Constant Field Values

showCharts

protected boolean showCharts

runRefreshParser

protected boolean runRefreshParser

restrictCharge

protected boolean restrictCharge

formatStrings

protected static final java.lang.String[] formatStrings

formatExplanations

protected static final java.lang.String[] formatExplanations

Constructor Detail

CombineAmtMs2FilesCLM

public CombineAmtMs2FilesCLM()

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

handleFiles

protected void handleFiles(java.io.File[] files,
                           java.io.File outputFile)
                    throws CommandLineModuleExecutionException

Throws:

CommandLineModuleExecutionException

findFilePairs

protected java.util.List<Pair<java.io.File,java.io.File>> findFilePairs()

Pick pairs of files from directories by name, without extension

Returns:

createCombinedSet

protected FeatureSet createCombinedSet(java.io.File[] files,
                                       java.io.File outputFile)
                                throws CommandLineModuleExecutionException

Throws:

CommandLineModuleExecutionException