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

java.lang.Object
  org.fhcrc.cpl.viewer.commandline.modules.BaseCommandLineModuleImpl
      org.fhcrc.cpl.viewer.commandline.modules.DetectAdductsCLM

All Implemented Interfaces:

org.fhcrc.cpl.toolbox.commandline.CommandLineModule

public class DetectAdductsCLM
extends BaseCommandLineModuleImpl
implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule

Command linemodule for adduct detection. Quick and dirty. Lots of hacks.

Field Summary

protected static org.apache.log4j.Logger	_log
protected double	massWavelength
protected float	matcherMassTolerance
protected int	matcherMassToleranceType
protected int	matcherScanTolerance
protected int	maxRelativeDaltons
protected int	maxRelativeSeconds
protected int	minRelativeDaltons
protected int	minRelativeSeconds
protected java.io.File[]	ms1FeatureFiles
protected java.io.File	outZeroBucketFeatureFileDir
protected int	scanWindowSize
protected int	secondsIncrement

Fields inherited from class org.fhcrc.cpl.viewer.commandline.modules.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

DetectAdductsCLM()

Method Summary

void	assignArgumentValues() the first step in invoking your module.
void	execute() do the actual work
protected void	init()

Methods inherited from class org.fhcrc.cpl.viewer.commandline.modules.BaseCommandLineModuleImpl

addArgumentDefinition, addArgumentDefinitions, addArgumentDefinitions, assertArgumentAbsent, assertArgumentAbsent, assertArgumentPresent, assertArgumentPresent, createArgsTableHTML, createArgumentDefinition, createArgumentDefinition, createBooleanArgumentDefinition, createBooleanArgumentDefinition, createDecimalArgumentDefinition, createDecimalArgumentDefinition, createDecimalListArgumentDefinition, createDecimalListArgumentDefinition, createDecimalListArgumentDefinition, createDeltaMassArgumentDefinition, createDeltaMassArgumentDefinition, createDirectoryToReadArgumentDefinition, createEnumeratedArgumentDefinition, createEnumeratedArgumentDefinition, createEnumeratedArgumentDefinition, createEnumeratedArgumentDefinition, createFastaFileArgumentDefinition, createFeatureFileArgumentDefinition, createFileToReadArgumentDefinition, createFileToReadListArgumentDefinition, createFileToWriteArgumentDefinition, createIntegerArgumentDefinition, createIntegerArgumentDefinition, createModificationListArgumentDefinition, createModificationListArgumentDefinition, createStringArgumentDefinition, createStringArgumentDefinition, createUnnamedArgumentDefinition, createUnnamedFileArgumentDefinition, createUnnamedSeriesArgumentDefinition, createUnnamedSeriesFileArgumentDefinition, digestArguments, getAdvancedArgumentDefinitions, getArgumentDefinition, getArgumentDefinitions, getArgumentDefinitionsSortedForDisplay, getArgumentValue, getArgumentValues, getArgumentValueStrings, getBasicArgumentDefinitions, getBooleanArgumentValue, getCommandName, getDeltaMassArgumentValue, getDoubleArgumentValue, getDoubleArrayArgumentValue, getFastaFileArgumentValue, getFeatureSetArgumentValue, getFileArgumentValue, getFileArrayArgumentValue, getFloatArgumentValue, getFullHelp, getHelpMessage, getHtmlHelpFragment, getIntegerArgumentValue, getModificationListArgumentValue, 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

ms1FeatureFiles

protected java.io.File[] ms1FeatureFiles

massWavelength

protected double massWavelength

scanWindowSize

protected int scanWindowSize

maxRelativeDaltons

protected int maxRelativeDaltons

minRelativeDaltons

protected int minRelativeDaltons

matcherMassTolerance

protected float matcherMassTolerance

matcherMassToleranceType

protected int matcherMassToleranceType

matcherScanTolerance

protected int matcherScanTolerance

outZeroBucketFeatureFileDir

protected java.io.File outZeroBucketFeatureFileDir

minRelativeSeconds

protected int minRelativeSeconds

maxRelativeSeconds

protected int maxRelativeSeconds

secondsIncrement

protected int secondsIncrement

Constructor Detail

DetectAdductsCLM

public DetectAdductsCLM()

Method Detail

init

protected void init()

assignArgumentValues

public void assignArgumentValues()
                          throws org.fhcrc.cpl.toolbox.commandline.arguments.ArgumentValidationException

Description copied from interface: org.fhcrc.cpl.toolbox.commandline.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 org.fhcrc.cpl.toolbox.commandline.CommandLineModule

Throws:

org.fhcrc.cpl.toolbox.commandline.arguments.ArgumentValidationException

execute

public void execute()
             throws org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException

do the actual work

Specified by:

execute in interface org.fhcrc.cpl.toolbox.commandline.CommandLineModule

Throws:

org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException