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

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

All Implemented Interfaces:

CommandLineModule

public class AmtDatabaseManagerCommandLineModule
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Command linemodule for refining AMT databases

Field Summary

protected static org.apache.log4j.Logger	_log
protected static int	ADJUST_ACRYLAMIDE_MODE
protected static int	ALIGN_ALL_RUNS_MODE
protected AmtDatabase	amtDatabase
protected java.io.File	fastaFile
protected static int	FILTER_OBSERVATIONS_BY_PPROPHET_MODE
protected float	massMatchDeltaMass
protected int	massMatchDeltaMassType
protected int	matchingDegree
protected int	maxEntriesInMassMatchedDatabase
protected int	maxRunsInMassMatchedDatabase
protected int	minMassMatchPercent
protected int	minObservations
protected float	minPeptideProphet
protected int	mode
protected static java.lang.String[]	modeExplanations
protected static java.lang.String[]	modeStrings
protected FeatureSet	ms1FeatureSet
protected java.io.File	outFile
protected float	predictedHOutlierDeviationMultipleCutoff
protected static int	REMOVE_FASTA_PEPTIDES_MODE
protected static int	REMOVE_FEW_OBSERVATIONS_MODE
protected static int	REMOVE_OUTLIER_OBSERVATIONS_MODE
protected static int	REMOVE_PEPTIDES_WITH_RESIDUE_MODE
protected static int	REMOVE_PREDICTED_H_OUTLIERS_MODE
protected static int	REMOVE_RUNS_WITHOUT_MASS_MATCHES_MODE
protected java.lang.String	residueToRemove
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

AmtDatabaseManagerCommandLineModule()

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

amtDatabase

protected AmtDatabase amtDatabase

outFile

protected java.io.File outFile

fastaFile

protected java.io.File fastaFile

minPeptideProphet

protected float minPeptideProphet

mode

protected int mode

REMOVE_OUTLIER_OBSERVATIONS_MODE

protected static final int REMOVE_OUTLIER_OBSERVATIONS_MODE

See Also:

Constant Field Values

REMOVE_PREDICTED_H_OUTLIERS_MODE

protected static final int REMOVE_PREDICTED_H_OUTLIERS_MODE

See Also:

Constant Field Values

REMOVE_FEW_OBSERVATIONS_MODE

protected static final int REMOVE_FEW_OBSERVATIONS_MODE

See Also:

Constant Field Values

REMOVE_RUNS_WITHOUT_MASS_MATCHES_MODE

protected static final int REMOVE_RUNS_WITHOUT_MASS_MATCHES_MODE

See Also:

Constant Field Values

ALIGN_ALL_RUNS_MODE

protected static final int ALIGN_ALL_RUNS_MODE

See Also:

Constant Field Values

ADJUST_ACRYLAMIDE_MODE

protected static final int ADJUST_ACRYLAMIDE_MODE

See Also:

Constant Field Values

REMOVE_PEPTIDES_WITH_RESIDUE_MODE

protected static final int REMOVE_PEPTIDES_WITH_RESIDUE_MODE

See Also:

Constant Field Values

REMOVE_FASTA_PEPTIDES_MODE

protected static final int REMOVE_FASTA_PEPTIDES_MODE

See Also:

Constant Field Values

FILTER_OBSERVATIONS_BY_PPROPHET_MODE

protected static final int FILTER_OBSERVATIONS_BY_PPROPHET_MODE

See Also:

Constant Field Values

matchingDegree

protected int matchingDegree

predictedHOutlierDeviationMultipleCutoff

protected float predictedHOutlierDeviationMultipleCutoff

modeStrings

protected static final java.lang.String[] modeStrings

modeExplanations

protected static final java.lang.String[] modeExplanations

minObservations

protected int minObservations

minMassMatchPercent

protected int minMassMatchPercent

maxEntriesInMassMatchedDatabase

protected int maxEntriesInMassMatchedDatabase

maxRunsInMassMatchedDatabase

protected int maxRunsInMassMatchedDatabase

ms1FeatureSet

protected FeatureSet ms1FeatureSet

showCharts

protected boolean showCharts

residueToRemove

protected java.lang.String residueToRemove

massMatchDeltaMass

protected float massMatchDeltaMass

massMatchDeltaMassType

protected int massMatchDeltaMassType

Constructor Detail

AmtDatabaseManagerCommandLineModule

public AmtDatabaseManagerCommandLineModule()

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

writeAmtDatabase

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

Parameters:

amtDatabase -

outAmtXmlFile -