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

java.lang.Object
  org.fhcrc.cpl.toolbox.commandline.arguments.BaseArgumentDefinitionImpl
      org.fhcrc.cpl.toolbox.proteomics.commandline.arguments.ModificationListArgumentDefinition

All Implemented Interfaces:

CommandLineArgumentDefinition

public class ModificationListArgumentDefinition
extends BaseArgumentDefinitionImpl
implements CommandLineArgumentDefinition

Treats an argument as a comma-separated list of modifications. Each mod should have the format: [V] where V (case-insensitive) is an optional character indicating variable (default is static) for example: M16.5V means a variable modification on Methionine with deltamass 16.5

Field Summary

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

ModificationListArgumentDefinition(java.lang.String argumentName)

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

ModificationListArgumentDefinition(java.lang.String argumentName, boolean required, java.lang.String help, MS2Modification[] defaultValue)

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

Method Summary

javax.swing.JComponent	addComponentsForGUI(java.awt.Container parent, javax.swing.JDialog parentDialog, java.lang.String defaultValue) Same as base method, but resize the text field
MS2Modification[]	convertArgumentValue(java.lang.String argumentValue) Try to match the argument against the set of allowed values, either with or without case-sensitivity
static MS2Modification	createModificationFromString(java.lang.String modString)
java.lang.String	getDefaultValueAsString() Need to override default handling, since we're working with an array, here.
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
static MS2Modification	safeCreateModificationFromString(java.lang.String modString)

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

addComponentsForGUISeries, getArgumentDisplayName, getArgumentName, getDefaultValue, 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

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

Constructor Detail

ModificationListArgumentDefinition

public ModificationListArgumentDefinition(java.lang.String argumentName)

ModificationListArgumentDefinition

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

ModificationListArgumentDefinition

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

ModificationListArgumentDefinition

public ModificationListArgumentDefinition(java.lang.String argumentName,
                                          boolean required,
                                          java.lang.String help,
                                          MS2Modification[] defaultValue)

Method Detail

convertArgumentValue

public MS2Modification[] convertArgumentValue(java.lang.String argumentValue)
                                       throws ArgumentValidationException

Try to match the argument against the set of allowed values, either with or without case-sensitivity

Specified by:

convertArgumentValue in interface CommandLineArgumentDefinition

Specified by:

convertArgumentValue in class BaseArgumentDefinitionImpl

Parameters:

argumentValue -

Returns:

the argument as a String

Throws:

ArgumentValidationException - if the argument doesn't validate

safeCreateModificationFromString

public static MS2Modification safeCreateModificationFromString(java.lang.String modString)

createModificationFromString

public static MS2Modification createModificationFromString(java.lang.String modString)
                                                    throws ArgumentValidationException

Throws:

ArgumentValidationException

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 BaseArgumentDefinitionImpl

Returns:

getDefaultValueAsString

public java.lang.String getDefaultValueAsString()

Need to override default handling, since we're working with an array, here.

Specified by:

getDefaultValueAsString in interface CommandLineArgumentDefinition

Overrides:

getDefaultValueAsString in class BaseArgumentDefinitionImpl

Returns:

addComponentsForGUI

public javax.swing.JComponent addComponentsForGUI(java.awt.Container parent,
                                                  javax.swing.JDialog parentDialog,
                                                  java.lang.String defaultValue)

Same as base method, but resize the text field

Specified by:

addComponentsForGUI in interface CommandLineArgumentDefinition

Overrides:

addComponentsForGUI in class BaseArgumentDefinitionImpl

Parameters:

parent -

parentDialog -

defaultValue -

Returns: