Package org.incenp.obofoundry.uberon

Class MergeSpeciesCommand

java.lang.Object

org.incenp.obofoundry.uberon.BasePlugin

org.incenp.obofoundry.uberon.MergeSpeciesCommand

All Implemented Interfaces:

org.obolibrary.robot.Command

public class MergeSpeciesCommand
extends BasePlugin

A command to fold species-specific classes to form a “composite” ontology.

This command is the critical component of Uberon’s “composite-metazoan” pipeline. It replaces OWLTools’s --merge-species-ontology command.

Field Summary

Fields inherited from class org.incenp.obofoundry.uberon.BasePlugin

options

Fields inherited from interface org.obolibrary.robot.Command

global, missingFileError

Constructor Summary

Constructors

Constructor	Description
MergeSpeciesCommand()

Method Summary

Modifier and Type	Method	Description
void	performOperation(org.obolibrary.robot.CommandState state, org.apache.commons.cli.CommandLine line)	Perform whatever operation the command is supposed to do.

Methods inherited from class org.incenp.obofoundry.uberon.BasePlugin

execute, getDescription, getIOHelper, getIRI, getName, getOptions, getUsage, main

Methods inherited from class java.lang.Object

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

Constructor Details

MergeSpeciesCommand

public MergeSpeciesCommand()

Method Details

performOperation

public void performOperation(org.obolibrary.robot.CommandState state,
 org.apache.commons.cli.CommandLine line)
                      throws Exception

Description copied from class: BasePlugin

Perform whatever operation the command is supposed to do.

Specified by:

performOperation in class BasePlugin

Parameters:

state - The internal state of ROBOT.

line - The command line used to invoke the command.

Throws:

Exception - If any error occurred when attempting to execute the operation.