Package org.incenp.obofoundry.odk

Class CheckAlignmentCommand

java.lang.Object

org.incenp.obofoundry.odk.BasePlugin

org.incenp.obofoundry.odk.CheckAlignmentCommand

All Implemented Interfaces:

org.obolibrary.robot.Command

public class CheckAlignmentCommand
extends BasePlugin

A command to check the alignment of an ontology against another, upper-level ontology. The ontology is said to be “aligned” if all its classes are subclasses of one of the upper ontology’s classes.

The command can also check “self-alignment” (option --use-self true): the ontology is “self-aligned” if all its classes are subclasses of one of the self-declared “preferred roots” (declared within the ontology itself with the IAO:0000700 annotation).

Lastly, the command can check alignment against arbitrary root terms which can be specified with the --term or --term-file options.

Field Summary

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

ioHelper, options

Fields inherited from interface org.obolibrary.robot.Command

global, missingFileError

Constructor Summary

Constructors

Constructor	Description
CheckAlignmentCommand()

Method Summary

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

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

execute, getDescription, 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

CheckAlignmentCommand

public CheckAlignmentCommand()

Method Details

performOperation

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

Description copied from class: BasePlugin

Performs 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 occurs when attempting to execute the operation.