org.fhcrc.cpl.viewer.commandline.modules
Class CalibrateMzxmlMassesCLM
java.lang.Object
org.fhcrc.cpl.viewer.commandline.modules.BaseCommandLineModuleImpl
org.fhcrc.cpl.viewer.commandline.modules.CalibrateMzxmlMassesCLM
- All Implemented Interfaces:
- org.fhcrc.cpl.toolbox.commandline.CommandLineModule
public class CalibrateMzxmlMassesCLM
- extends BaseCommandLineModuleImpl
- implements org.fhcrc.cpl.toolbox.commandline.CommandLineModule
Command linemodule for Saving pieces of mzXML files
| Fields inherited from interface org.fhcrc.cpl.toolbox.commandline.CommandLineModule |
MODULE_HELP_AUTOMATIC, MODULE_USAGE_AUTOMATIC, UNNAMED_ARG_SERIES_SEPARATOR |
| 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 |
_log
protected static org.apache.log4j.Logger _log
outFile
protected java.io.File outFile
outDir
protected java.io.File outDir
inFiles
protected java.io.File[] inFiles
calibrationParameters
protected org.fhcrc.cpl.toolbox.Pair<java.lang.Integer,org.fhcrc.cpl.toolbox.Pair<java.lang.Double,java.lang.Double>>[] calibrationParameters
outFeatureFile
protected java.io.File outFeatureFile
ms2PrecursorMassesOnly
protected boolean ms2PrecursorMassesOnly
numPartitions
protected int numPartitions
initialMassFilterPPM
protected int initialMassFilterPPM
CalibrateMzxmlMassesCLM
public CalibrateMzxmlMassesCLM()
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
- Description copied from interface:
org.fhcrc.cpl.toolbox.commandline.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 org.fhcrc.cpl.toolbox.commandline.CommandLineModule
- Throws:
org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException
handleFile
public void handleFile(MSRun run,
java.io.File outputFile,
FeatureSet featureSetForCalibration,
FeatureSet scanChargeFeatures)
throws org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException
- do the actual work
- Throws:
org.fhcrc.cpl.toolbox.commandline.CommandLineModuleExecutionException
Fred Hutchinson Cancer Research Center