org.fhcrc.cpl.toolbox.proteomics.commandline.arguments
Class FastaFileArgumentDefinition

java.lang.Object
  org.fhcrc.cpl.toolbox.commandline.arguments.BaseArgumentDefinitionImpl
      org.fhcrc.cpl.toolbox.commandline.arguments.FileArgumentDefinition
          org.fhcrc.cpl.toolbox.commandline.arguments.FileToReadArgumentDefinition
              org.fhcrc.cpl.toolbox.proteomics.commandline.arguments.FastaFileArgumentDefinition

All Implemented Interfaces:

CommandLineArgumentDefinition

public class FastaFileArgumentDefinition
extends FileToReadArgumentDefinition
implements CommandLineArgumentDefinition

Nested Class Summary

Nested classes/interfaces inherited from class org.fhcrc.cpl.toolbox.commandline.arguments.FileArgumentDefinition

FileArgumentDefinition.GUIFileChooserButtonListener

Field Summary

Fields inherited from class org.fhcrc.cpl.toolbox.commandline.arguments.FileArgumentDefinition

FILE_TYPE_FEATURE, FILE_TYPE_IMAGE, FILE_TYPE_UNKNOWN, fileType

Fields inherited from class org.fhcrc.cpl.toolbox.commandline.arguments.BaseArgumentDefinitionImpl

mArgumentHelpText, mArgumentName, mDefaultValue, mDisplayName, mIsAdvanced, mRequired

Fields inherited from interface org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition

UNNAMED_PARAMETER_VALUE_ARGUMENT, UNNAMED_PARAMETER_VALUE_SERIES_ARGUMENT

Constructor Summary

FastaFileArgumentDefinition(java.lang.String argumentName)

FastaFileArgumentDefinition(java.lang.String argumentName, boolean required, java.lang.String help)

FastaFileArgumentDefinition(java.lang.String argumentName, java.lang.String help)

Method Summary

java.lang.Object	convertArgumentValue(java.lang.String filePath) Create a file for the filepath and then try to load it as a FeatureSet.
java.lang.String	getValueDescriptor() Return a String that will be used as a generic example for the value to be used for this argument, in auto-generated usage

Methods inherited from class org.fhcrc.cpl.toolbox.commandline.arguments.FileToReadArgumentDefinition

addComponentsForGUI, addComponentsForGUISeries, checkFileForReading

Methods inherited from class org.fhcrc.cpl.toolbox.commandline.arguments.FileArgumentDefinition

addComponentsForGUI, getFileType, setFileType

Methods inherited from class org.fhcrc.cpl.toolbox.commandline.arguments.BaseArgumentDefinitionImpl

addComponentsForGUISeries, getArgumentDisplayName, getArgumentName, getDefaultValue, getDefaultValueAsString, getDisplayName, getHelpText, getValueFromGUIComponent, hasDefaultValue, isAdvanced, isRequired, setAdvanced, setArgumentDisplayName, setDefaultValue, setDisplayName, setHelpText, setRequired, valueToString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.fhcrc.cpl.toolbox.commandline.arguments.CommandLineArgumentDefinition

addComponentsForGUI, addComponentsForGUISeries, getArgumentDisplayName, getArgumentName, getDefaultValue, getDefaultValueAsString, getHelpText, getValueFromGUIComponent, hasDefaultValue, isAdvanced, isRequired, setAdvanced, setArgumentDisplayName, setDefaultValue, setHelpText, setRequired, valueToString

Constructor Detail

FastaFileArgumentDefinition

public FastaFileArgumentDefinition(java.lang.String argumentName)

FastaFileArgumentDefinition

public FastaFileArgumentDefinition(java.lang.String argumentName,
                                   java.lang.String help)

FastaFileArgumentDefinition

public FastaFileArgumentDefinition(java.lang.String argumentName,
                                   boolean required,
                                   java.lang.String help)

Method Detail

convertArgumentValue

public java.lang.Object convertArgumentValue(java.lang.String filePath)
                                      throws ArgumentValidationException

Create a file for the filepath and then try to load it as a FeatureSet. Note: this loading happens at individual argument validation time, before the module has a chance to view all the arguments together. This can be pretty bad from a usability perspective: if the arguments as a whole don't mesh, you've wasted a bunch of time loading feature files. Only use this when you're pretty sure the user's gonna get the arguments right most of the time.

Specified by:

convertArgumentValue in interface CommandLineArgumentDefinition

Overrides:

convertArgumentValue in class FileToReadArgumentDefinition

Parameters:

filePath -

Returns:

a FeatureSet containing the features loaded from the file.

Throws:

ArgumentValidationException - if the argument doesn't validate

getValueDescriptor

public java.lang.String getValueDescriptor()

Description copied from interface: CommandLineArgumentDefinition

Return a String that will be used as a generic example for the value to be used for this argument, in auto-generated usage

Specified by:

getValueDescriptor in interface CommandLineArgumentDefinition

Overrides:

getValueDescriptor in class FileArgumentDefinition

Returns: