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

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

All Implemented Interfaces:

CommandLineModule

public class AmtDatabaseFeatureSetCreatorCLM
extends BaseViewerCommandLineModuleImpl
implements CommandLineModule

Command linemodule for creating featuresets that represent AMT databases

Field Summary

protected static org.apache.log4j.Logger	_log
protected boolean	adjustFeatureMasses
protected AmtDatabase	amtDB
protected float	featureMassAdjustment
protected java.util.List<MS2Modification>	ms2Modifications
protected java.io.File	outFile

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

AmtDatabaseFeatureSetCreatorCLM()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
void	execute() Called by msInspect after assignArgumentValues.
protected void	init()

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

featureMassAdjustment

protected float featureMassAdjustment

adjustFeatureMasses

protected boolean adjustFeatureMasses

amtDB

protected AmtDatabase amtDB

ms2Modifications

protected java.util.List<MS2Modification> ms2Modifications

Constructor Detail

AmtDatabaseFeatureSetCreatorCLM

public AmtDatabaseFeatureSetCreatorCLM()

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