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

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

All Implemented Interfaces:

CommandLineModule

public class AmtDatabaseMatcherCLM
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Command linemodule for matching AMT databases to MS1 data from various sources

Field Summary

protected static org.apache.log4j.Logger	_log
protected java.util.Set<java.lang.String>	allMatchedPeptides
protected AmtDatabaseMatcher	amtDatabaseMatcher
protected Fractionation2DUtilities.FractionatedAMTDatabaseStructure	amtDatabaseStructure
protected AmtDatabase	amtDB
protected Feature[]	amtDBBaseFeatures
protected java.io.File	amtDBFile
protected boolean	calcFDR
protected boolean	calibrateMassesUsingMatches
static double	DEFAULT_MIN_EMBEDDED_MS2_PEPTIDE_PROPHET
static MS2Modification[]	defaultMS2ModificationsForMatching
protected int	deltaMassType
protected FeatureSet	embeddedMs2FeatureSet
protected java.io.File	inDir
protected float	looseDeltaElution
protected float	looseDeltaMass
protected int	maxEntriesInMassMatchedDatabase
protected int	maxRunsInMassMatchedDatabase
protected int	maxRunsToKeep
protected double	minMS2PeptideProphet
protected int	minRunPeptideMatchPercent
protected int	minRunsToKeep
protected int	mode
protected static int	MODE_MATCH_AGAINST_MS1
protected static int	MODE_MATCH_AGAINST_MS1_DIR
protected static java.lang.String[]	modeExplanations
protected static java.lang.String[]	modeStrings
protected FeatureSet	ms1FeatureSet
protected java.io.File	ms2Dir
protected MS2Modification[]	ms2ModificationsForMatching
protected java.io.File	mzXmlDir
protected boolean	nonlinearAlignment
protected int	nonlinearMappingPolynomialDegree
protected java.io.File	outDir
protected java.io.File	outFile
protected boolean	populateMs2Times
protected boolean	removeFractions
protected boolean	restrictDatabaseRuns
protected MSRun	run
protected java.io.File	saveChartsDir
protected boolean	showCharts
protected java.util.Set<java.lang.String>	thisRunMatchedPeptides
protected boolean	useAmtDBMods

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

AmtDatabaseMatcherCLM()

Method Summary

protected void	annotateFractionConcordanceForMatches(AmtDatabase amtDatabase, Feature[] ms2Features, FeatureSetMatcher.FeatureMatchingResult matchingResult)
void	assignArgumentValues() the first step in invoking your module.
void	execute() Called by msInspect after assignArgumentValues.
protected FeatureSet	findCorrespondingFeatureSet(java.io.File ms1File, java.io.File directory)
protected java.io.File	findCorrespondingMzXmlFile(java.io.File ms2File)
AmtDatabaseMatcher	getAmtDatabaseMatcher()
FeatureSet	getMs1FeatureSet()
protected void	init()
void	setMs1FeatureSet(FeatureSet ms1FeatureSet)

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

outFile

protected java.io.File outFile

outDir

protected java.io.File outDir

inDir

protected java.io.File inDir

ms2Dir

protected java.io.File ms2Dir

mzXmlDir

protected java.io.File mzXmlDir

amtDBFile

protected java.io.File amtDBFile

amtDB

protected AmtDatabase amtDB

amtDatabaseMatcher

protected AmtDatabaseMatcher amtDatabaseMatcher

ms1FeatureSet

protected FeatureSet ms1FeatureSet

embeddedMs2FeatureSet

protected FeatureSet embeddedMs2FeatureSet

amtDBBaseFeatures

protected Feature[] amtDBBaseFeatures

looseDeltaMass

protected float looseDeltaMass

deltaMassType

protected int deltaMassType

looseDeltaElution

protected float looseDeltaElution

useAmtDBMods

protected boolean useAmtDBMods

ms2ModificationsForMatching

protected MS2Modification[] ms2ModificationsForMatching

calibrateMassesUsingMatches

protected boolean calibrateMassesUsingMatches

calcFDR

protected boolean calcFDR

defaultMS2ModificationsForMatching

public static final MS2Modification[] defaultMS2ModificationsForMatching

DEFAULT_MIN_EMBEDDED_MS2_PEPTIDE_PROPHET

public static final double DEFAULT_MIN_EMBEDDED_MS2_PEPTIDE_PROPHET

See Also:

Constant Field Values

minMS2PeptideProphet

protected double minMS2PeptideProphet

run

protected MSRun run

removeFractions

protected boolean removeFractions

minRunPeptideMatchPercent

protected int minRunPeptideMatchPercent

maxEntriesInMassMatchedDatabase

protected int maxEntriesInMassMatchedDatabase

maxRunsInMassMatchedDatabase

protected int maxRunsInMassMatchedDatabase

restrictDatabaseRuns

protected boolean restrictDatabaseRuns

amtDatabaseStructure

protected Fractionation2DUtilities.FractionatedAMTDatabaseStructure amtDatabaseStructure

mode

protected int mode

modeStrings

protected static final java.lang.String[] modeStrings

modeExplanations

protected static final java.lang.String[] modeExplanations

MODE_MATCH_AGAINST_MS1

protected static final int MODE_MATCH_AGAINST_MS1

See Also:

Constant Field Values

MODE_MATCH_AGAINST_MS1_DIR

protected static final int MODE_MATCH_AGAINST_MS1_DIR

See Also:

Constant Field Values

nonlinearMappingPolynomialDegree

protected int nonlinearMappingPolynomialDegree

showCharts

protected boolean showCharts

saveChartsDir

protected java.io.File saveChartsDir

nonlinearAlignment

protected boolean nonlinearAlignment

minRunsToKeep

protected int minRunsToKeep

maxRunsToKeep

protected int maxRunsToKeep

thisRunMatchedPeptides

protected java.util.Set<java.lang.String> thisRunMatchedPeptides

allMatchedPeptides

protected java.util.Set<java.lang.String> allMatchedPeptides

populateMs2Times

protected boolean populateMs2Times

Constructor Detail

AmtDatabaseMatcherCLM

public AmtDatabaseMatcherCLM()

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

findCorrespondingFeatureSet

protected FeatureSet findCorrespondingFeatureSet(java.io.File ms1File,
                                                 java.io.File directory)
                                          throws java.io.IOException

Throws:

java.io.IOException

findCorrespondingMzXmlFile

protected java.io.File findCorrespondingMzXmlFile(java.io.File ms2File)
                                           throws java.io.IOException

Throws:

java.io.IOException

annotateFractionConcordanceForMatches

protected void annotateFractionConcordanceForMatches(AmtDatabase amtDatabase,
                                                     Feature[] ms2Features,
                                                     FeatureSetMatcher.FeatureMatchingResult matchingResult)

getMs1FeatureSet

public FeatureSet getMs1FeatureSet()

setMs1FeatureSet

public void setMs1FeatureSet(FeatureSet ms1FeatureSet)

getAmtDatabaseMatcher

public AmtDatabaseMatcher getAmtDatabaseMatcher()