org.obolibrary.robot

Class RemoveCommand

java.lang.Object

org.obolibrary.robot.RemoveCommand

All Implemented Interfaces:

Command

public class RemoveCommand
extends Object
implements Command

Remove axioms from an ontology based on a series of inputs.

Author:

Becky Tauber

Field Summary

Fields inherited from interface org.obolibrary.robot.Command

global, missingFileError

Constructor Summary

Constructors

Constructor and Description
RemoveCommand() Initialze the command.

Method Summary

Modifier and Type	Method and Description
CommandState	execute(CommandState state, String[] args) Given an input state and command line arguments, create a new ontology with removed axioms and return a new state.
String	getDescription() Brief description of the command.
String	getName() Name of the command.
protected static Set<org.semanticweb.owlapi.model.OWLObject>	getObjects(org.apache.commons.cli.CommandLine line, IOHelper ioHelper, org.semanticweb.owlapi.model.OWLOntology ontology, List<List<String>> selectGroups) Given a command line, an IOHelper, an ontology, and a list of select groups, return the objects from the ontology based on the select groups.
org.apache.commons.cli.Options	getOptions() Command-line options for the command.
String	getUsage() Command-line usage for the command.
void	main(String[] args) Handle the command-line and file operations.

Methods inherited from class java.lang.Object

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

Constructor Detail

RemoveCommand

public RemoveCommand()

Initialze the command.

Method Detail

getName

public String getName()

Name of the command.

Specified by:

getName in interface Command

Returns:

name

getDescription

public String getDescription()

Brief description of the command.

Specified by:

getDescription in interface Command

Returns:

description

getUsage

public String getUsage()

Command-line usage for the command.

Specified by:

getUsage in interface Command

Returns:

usage

getOptions

public org.apache.commons.cli.Options getOptions()

Command-line options for the command.

Specified by:

getOptions in interface Command

Returns:

options

main

public void main(String[] args)

Handle the command-line and file operations.

Specified by:

main in interface Command

Parameters:

args - strings to use as arguments

execute

public CommandState execute(CommandState state,
                            String[] args)
                     throws Exception

Given an input state and command line arguments, create a new ontology with removed axioms and return a new state. The input ontology is not changed.

Specified by:

execute in interface Command

Parameters:

state - the state from the previous command, or null

args - the command-line arguments

Returns:

a new state with the new ontology

Throws:

Exception - on any problem

getObjects

protected static Set<org.semanticweb.owlapi.model.OWLObject> getObjects(org.apache.commons.cli.CommandLine line,
                                                                        IOHelper ioHelper,
                                                                        org.semanticweb.owlapi.model.OWLOntology ontology,
                                                                        List<List<String>> selectGroups)
                                                                 throws Exception

Given a command line, an IOHelper, an ontology, and a list of select groups, return the objects from the ontology based on the select groups.

Parameters:

line - CommandLine to get options from

ioHelper - IOHelper to get IRIs

ontology - OWLOntology to get objects from

selectGroups - List of select groups (lists of select options)

Returns:

set of selected objects from the ontology

Throws:

Exception - on issue getting terms or processing selects