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

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

All Implemented Interfaces:

CommandLineModule

Direct Known Subclasses:

AlignCLM, AmtDatabaseDiagnosticCommandLineModule, AmtDatabaseFeatureSetCreatorCLM, AmtDatabaseManagerCommandLineModule, AmtDatabaseMatcherCLM, AmtLabeledQuantCLM, CalculateFDRCLM, CalibrateFeatureMassesCLM, CalibrateMzxmlMassesCLM, CombineAmtMs2FilesCLM, CombinePepXmlFilesCLM, CompareFastasCLM, ConsensusFeatureFileCLM, ConvertFeatureFileCommandLineModule, CorrectPrecursorMzCLM, CreateIndexCommandLineModule, DeconvoluteCommandLineModule, DetectAdductsCLM, DumpWindow2DCommandLineModule, FeatureSelectionParamsCommandLineModule, FeatureSetMatcherCommandLineModule, FilterPeptideRegexpCLM, FilterPepXmlCLM, FilterReverseDBHitsCLM, FindIndistinguishableProteinsCLM, FindPeptidesCommandLineModule, FindSearchScoreCutoffForFARCLM, FlagQuantEventsCLM, FlipPepXMLRatiosCLM, GuessProteinsFromFastaCLM, HydrophobicityAlgorithmAnalyzerCLM, MassAccuracyCommandLineModule, MRMCommandLineModule, MS2ScanViewerCLM, PeptideArrayAnalyzerCommandLineModule, PeptideCompareCommandLineModule, PeptidePeakModellerCLM, PeptideQuantVisualizationCLM, PeptideRatioVariationCLM, PickTargetedMS2CandidatesCLM, PlotDeltaMassesCLM, PlotFeatureAttributesCLM, PlotMassCalibrationCLM, PlotMs1Ms2ScanCountsCLM, PopulateMS2TimesCLM, PostProcessPepXMLCLM, ProteinFractionsSpreadsheetCLM, ProteinQuantChartsCLM, ProteinRollupCommandLineModule, ProtXmlCompareCLM, Q3CommandLineModule, QAExperimentCLM, QAProtXMLCLM, ReverseFastaCLM, ReviewQuantitationCLM, RunCommandFileCommandLineModule, SaveImageCommandLineModule, SaveMzxmlWindowCommandLineModule, SpectralCountCLM, SpreadsheetMergeCLM, SummarizeProtXmlCLM, UserManualCLM, ViewSpectrumChartCLM

public abstract class BaseViewerCommandLineModuleImpl
extends BaseCommandLineModuleImpl

Base class for command line modules. Command line modules do not have to extend this class (they only need to implement CommandLineModule), but it's highly recommended, because this class provides dozens of highly useful convenience methods for argument management

Field Summary

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

BaseViewerCommandLineModuleImpl()

Method Summary

protected FeatureFileArgumentDefinition	createUnnamedFeatureFileArgumentDefinition(boolean required, java.lang.String helpText)
protected FeatureFileArgumentDefinition	createUnnamedSeriesFeatureFileArgumentDefinition(boolean required, java.lang.String helpText)
protected Protein[]	getFastaFileArgumentValue(java.lang.String argumentName)
protected FeatureSet	getFeatureSetArgumentValue(java.lang.String argumentName)
protected MS2Modification[]	getModificationListArgumentValue(java.lang.String argumentName)

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

assignArgumentValues, execute

Constructor Detail

BaseViewerCommandLineModuleImpl

public BaseViewerCommandLineModuleImpl()

Method Detail

getFastaFileArgumentValue

protected Protein[] getFastaFileArgumentValue(java.lang.String argumentName)

Overrides:

getFastaFileArgumentValue in class BaseCommandLineModuleImpl

getFeatureSetArgumentValue

protected FeatureSet getFeatureSetArgumentValue(java.lang.String argumentName)

getModificationListArgumentValue

protected MS2Modification[] getModificationListArgumentValue(java.lang.String argumentName)

Overrides:

getModificationListArgumentValue in class BaseCommandLineModuleImpl

createUnnamedFeatureFileArgumentDefinition

protected FeatureFileArgumentDefinition createUnnamedFeatureFileArgumentDefinition(boolean required,
                                                                                   java.lang.String helpText)

createUnnamedSeriesFeatureFileArgumentDefinition

protected FeatureFileArgumentDefinition createUnnamedSeriesFeatureFileArgumentDefinition(boolean required,
                                                                                         java.lang.String helpText)