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

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.amt.commandline.AmtDatabaseCreatorCommandLineModule

All Implemented Interfaces:

CommandLineModule

public class AmtDatabaseCreatorCommandLineModule
extends FeatureSelectionParamsCommandLineModule
implements CommandLineModule

Command line module for creating AMT databases, either from pepXml (or other feature) files, or from other AMT databases, or from random peptides pulled out of a FASTA file

Field Summary

protected static org.apache.log4j.Logger	_log
protected boolean	align
protected static int	CREATE_AMTXML_FROM_DIRECTORIES_MODE
protected static int	CREATE_AMTXML_FROM_MS2_FEATURES_MODE
protected static int	CREATE_AMTXML_FROM_MULTIPLE_AMT_XMLS_MODE
protected static int	CREATE_AMTXML_FROM_PROTEIN_TRYPTIC_PEPTIDES_MODE
protected static int	CREATE_AMTXML_FROM_RANDOM_PEPTIDES_MODE
protected AmtDatabaseBuilder	databaseBuilder
protected int	maxMissedCleavages
protected int	maxPeptideLength
protected double	maxStudentizedResidualForInclusion
protected double	maxStudentizedResidualForRegression
protected int	minPeptideLength
protected int	mode
protected static java.lang.String[]	modeExplanations
protected static java.lang.String[]	modeStrings
protected java.io.File	ms1FeaturesDir
protected java.io.File	ms2FeaturesDir
protected java.io.File	mzXmlDir
protected int	numRandomPeptides
protected java.io.File	outFile
protected boolean	populateMs2Times
protected Protein[]	proteinsFromFasta
protected java.util.List<Protein>	proteinsToDigest
protected boolean	robustRegression
protected int	scanOrTimeMode

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

AmtDatabaseCreatorCommandLineModule()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
void	execute() do the actual work
protected void	init()
protected static void	writeAmtDatabase(AmtDatabase amtDatabase, java.io.File outAmtXmlFile)

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

mzXmlDir

protected java.io.File mzXmlDir

ms2FeaturesDir

protected java.io.File ms2FeaturesDir

ms1FeaturesDir

protected java.io.File ms1FeaturesDir

outFile

protected java.io.File outFile

scanOrTimeMode

protected int scanOrTimeMode

robustRegression

protected boolean robustRegression

maxStudentizedResidualForRegression

protected double maxStudentizedResidualForRegression

maxStudentizedResidualForInclusion

protected double maxStudentizedResidualForInclusion

mode

protected int mode

CREATE_AMTXML_FROM_DIRECTORIES_MODE

protected static final int CREATE_AMTXML_FROM_DIRECTORIES_MODE

See Also:

Constant Field Values

CREATE_AMTXML_FROM_MS2_FEATURES_MODE

protected static final int CREATE_AMTXML_FROM_MS2_FEATURES_MODE

See Also:

Constant Field Values

CREATE_AMTXML_FROM_MULTIPLE_AMT_XMLS_MODE

protected static final int CREATE_AMTXML_FROM_MULTIPLE_AMT_XMLS_MODE

See Also:

Constant Field Values

CREATE_AMTXML_FROM_RANDOM_PEPTIDES_MODE

protected static final int CREATE_AMTXML_FROM_RANDOM_PEPTIDES_MODE

See Also:

Constant Field Values

CREATE_AMTXML_FROM_PROTEIN_TRYPTIC_PEPTIDES_MODE

protected static final int CREATE_AMTXML_FROM_PROTEIN_TRYPTIC_PEPTIDES_MODE

See Also:

Constant Field Values

minPeptideLength

protected int minPeptideLength

maxPeptideLength

protected int maxPeptideLength

modeStrings

protected static final java.lang.String[] modeStrings

modeExplanations

protected static final java.lang.String[] modeExplanations

align

protected boolean align

numRandomPeptides

protected int numRandomPeptides

proteinsFromFasta

protected Protein[] proteinsFromFasta

proteinsToDigest

protected java.util.List<Protein> proteinsToDigest

maxMissedCleavages

protected int maxMissedCleavages

populateMs2Times

protected boolean populateMs2Times

databaseBuilder

protected AmtDatabaseBuilder databaseBuilder

Constructor Detail

AmtDatabaseCreatorCommandLineModule

public AmtDatabaseCreatorCommandLineModule()

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

writeAmtDatabase

protected static void writeAmtDatabase(AmtDatabase amtDatabase,
                                       java.io.File outAmtXmlFile)

Parameters:

amtDatabase -

outAmtXmlFile -