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

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

All Implemented Interfaces:

CommandLineModule

public class FilterFeaturesCommandLineModule
extends FeatureSelectionParamsCommandLineModule
implements CommandLineModule

Command Module for feature filtering

Field Summary

protected static org.apache.log4j.Logger	_log
protected java.io.File[]	inFeatureFiles
protected double	maxSearchScore
protected double	minSearchScore
static int	OUT_FORMAT_MSINSPECT
static int	OUT_FORMAT_PEPXML
protected java.io.File	outDir
protected java.io.File	outFile
protected int	outFormat
protected static java.lang.String[]	outFormatExplanations
protected static java.lang.String[]	outFormatStrings
protected java.lang.String	searchScoreName

Fields inherited from class org.fhcrc.cpl.viewer.commandline.modules.FeatureSelectionParamsCommandLineModule

featureSelector

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

FilterFeaturesCommandLineModule()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
static java.lang.String	createFilteredFeatureFileFilename(java.lang.String inputFileName, int outFormat) Decide the filename of the output file, if not specified by user
void	execute() do the actual work
protected void	filterFeatureFile(FeatureSet inFeatureSet, java.io.File outputFile)
protected static java.io.PrintWriter	getPrintWriter(java.io.File outFile)
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, 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

inFeatureFiles

protected java.io.File[] inFeatureFiles

outFile

protected java.io.File outFile

outDir

protected java.io.File outDir

minSearchScore

protected double minSearchScore

maxSearchScore

protected double maxSearchScore

searchScoreName

protected java.lang.String searchScoreName

OUT_FORMAT_MSINSPECT

public static final int OUT_FORMAT_MSINSPECT

See Also:

Constant Field Values

OUT_FORMAT_PEPXML

public static final int OUT_FORMAT_PEPXML

See Also:

Constant Field Values

outFormat

protected int outFormat

outFormatStrings

protected static final java.lang.String[] outFormatStrings

outFormatExplanations

protected static final java.lang.String[] outFormatExplanations

Constructor Detail

FilterFeaturesCommandLineModule

public FilterFeaturesCommandLineModule()

Method Detail

init

protected void init()

Overrides:

init in class FeatureSelectionParamsCommandLineModule

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

Overrides:

assignArgumentValues in class FeatureSelectionParamsCommandLineModule

Throws:

ArgumentValidationException

execute

public void execute()
             throws CommandLineModuleExecutionException

do the actual work

Specified by:

execute in interface CommandLineModule

Throws:

CommandLineModuleExecutionException

createFilteredFeatureFileFilename

public static java.lang.String createFilteredFeatureFileFilename(java.lang.String inputFileName,
                                                                 int outFormat)

Decide the filename of the output file, if not specified by user

Parameters:

inputFileName -

Returns:

filterFeatureFile

protected void filterFeatureFile(FeatureSet inFeatureSet,
                                 java.io.File outputFile)
                          throws CommandLineModuleExecutionException

Throws:

CommandLineModuleExecutionException

getPrintWriter

protected static java.io.PrintWriter getPrintWriter(java.io.File outFile)
                                             throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException