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

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

All Implemented Interfaces:

CommandLineModule

public class ProteinRollupCommandLineModule
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Command linemodule to help roll up peptide information to the protein level. Includes some naive mechanisms for generating lists of possible proteins given a list of peptides and a Fasta file. More usefully, includes some mechanisms for generating pepXml files that can be used by ProteinProphet, given some peptide IDs and a Fasta file

Field Summary

protected static org.apache.log4j.Logger	_log
protected AmtDatabase	amtDB
protected boolean	expanded
protected java.io.File	fastaFile
protected java.io.File	geneLookupFile
protected java.io.File	inDir
protected java.io.File	inTabFile
protected int	minPeptides
protected double	minProtXmlProbability
protected int	minUniquePeptides
protected int	mode
protected static int	MODE_COLLAPSE_PEPTIDES
protected static int	MODE_CREATE_PEPXML_FOR_TABFILE
protected static int	MODE_DIGEST_PROTXML
protected static int	MODE_ROLLUP_GENES
protected static int	MODE_ROLLUP_PEPTIDES_TO_GENES
protected static int	MODE_TABFILE
protected static java.lang.String[]	modeExplanations
protected static java.lang.String[]	modeStrings
protected FeatureSet[]	ms1FeatureSets
protected java.io.File	outDir
protected java.io.File	outFile
protected FeatureSet	pepXmlFeatureSet
protected Protein[]	proteinsInFasta
protected java.io.File[]	protXmlFiles

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

ProteinRollupCommandLineModule()

Method Summary

protected java.lang.String	assembleStringFromCollection(java.util.Collection<java.lang.String> stringCollection)
void	assignArgumentValues() the first step in invoking your module.
protected void	createPepXmlForTabFile()
void	execute() Called by msInspect after assignArgumentValues.
protected void	init()
protected void	peptideGeneRollup()
protected void	peptideGeneRollupExpanded()
protected void	rollupTabFile() roll up tab file to protein level naively (and natively)

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

mode

protected int mode

modeStrings

protected static final java.lang.String[] modeStrings

modeExplanations

protected static final java.lang.String[] modeExplanations

MODE_DIGEST_PROTXML

protected static final int MODE_DIGEST_PROTXML

See Also:

Constant Field Values

MODE_TABFILE

protected static final int MODE_TABFILE

See Also:

Constant Field Values

MODE_CREATE_PEPXML_FOR_TABFILE

protected static final int MODE_CREATE_PEPXML_FOR_TABFILE

See Also:

Constant Field Values

MODE_COLLAPSE_PEPTIDES

protected static final int MODE_COLLAPSE_PEPTIDES

See Also:

Constant Field Values

MODE_ROLLUP_GENES

protected static final int MODE_ROLLUP_GENES

See Also:

Constant Field Values

MODE_ROLLUP_PEPTIDES_TO_GENES

protected static final int MODE_ROLLUP_PEPTIDES_TO_GENES

See Also:

Constant Field Values

ms1FeatureSets

protected FeatureSet[] ms1FeatureSets

proteinsInFasta

protected Protein[] proteinsInFasta

fastaFile

protected java.io.File fastaFile

protXmlFiles

protected java.io.File[] protXmlFiles

pepXmlFeatureSet

protected FeatureSet pepXmlFeatureSet

minUniquePeptides

protected int minUniquePeptides

minProtXmlProbability

protected double minProtXmlProbability

outFile

protected java.io.File outFile

outDir

protected java.io.File outDir

inDir

protected java.io.File inDir

inTabFile

protected java.io.File inTabFile

geneLookupFile

protected java.io.File geneLookupFile

expanded

protected boolean expanded

minPeptides

protected int minPeptides

amtDB

protected AmtDatabase amtDB

Constructor Detail

ProteinRollupCommandLineModule

public ProteinRollupCommandLineModule()

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

Description copied from interface: 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 CommandLineModule

Throws:

CommandLineModuleExecutionException

peptideGeneRollupExpanded

protected void peptideGeneRollupExpanded()
                                  throws CommandLineModuleExecutionException

Throws:

CommandLineModuleExecutionException

assembleStringFromCollection

protected java.lang.String assembleStringFromCollection(java.util.Collection<java.lang.String> stringCollection)

peptideGeneRollup

protected void peptideGeneRollup()
                          throws CommandLineModuleExecutionException

Throws:

CommandLineModuleExecutionException

createPepXmlForTabFile

protected void createPepXmlForTabFile()
                               throws CommandLineModuleExecutionException

Throws:

CommandLineModuleExecutionException

rollupTabFile

protected void rollupTabFile()
                      throws CommandLineModuleExecutionException

roll up tab file to protein level naively (and natively)

Throws:

CommandLineModuleExecutionException