org.mindswap.pellet.utils

Class AnnotationClasses

java.lang.Object

org.mindswap.pellet.utils.AnnotationClasses

public class AnnotationClasses
extends Object

In some ontologies, such as the ones from OBO, annotations may be nested and contain type assertions on annotation values. Such type assertions will be treated as regular assertions and processed by the reasoner. This causes many superfluous logical axioms to be considered by the reasoner which might have significant impact on performance. The PelletOptions.IGNORE_ANNOTATION_CLASSES option tells Pellet to ignore such annotations. The set of classes that will be treated as annotation classes are stored in this class. This set can be modified by adding new classes or removing existing classes.

Annotation classes from OBO are included by default. These are obo:DbXref, obo:Definition, obo:Subset, obo:Synonym, obo:SynonymType where obo namespace refers to http://www.geneontology.org/formats/oboInOwl.

Author:

Evren Sirin

Constructor Summary

Constructors

Constructor and Description
AnnotationClasses()

Method Summary

Modifier and Type	Method and Description
static void	add(aterm.ATermAppl cls) Adds the specified class to the set of annotation classes.
static boolean	contains(aterm.ATermAppl cls) Returns true if the specified class is defined to be an annotation class AND PelletOptions.IGNORE_ANNOTATION_CLASSES option is set to true.
static Set<aterm.ATermAppl>	getAll() Returns an unmodifiable copy of the annotation classes regardless of the PelletOptions.IGNORE_ANNOTATION_CLASSES option.
static void	remove(aterm.ATermAppl cls) Removes the specified class form set of annotation classes.

Methods inherited from class java.lang.Object

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

Constructor Detail

AnnotationClasses

public AnnotationClasses()

Method Detail

add

public static void add(aterm.ATermAppl cls)

Adds the specified class to the set of annotation classes.

Parameters:

cls - class to add

contains

public static boolean contains(aterm.ATermAppl cls)

Returns true if the specified class is defined to be an annotation class AND PelletOptions.IGNORE_ANNOTATION_CLASSES option is set to true. If the configuration option is false this function will return false for every class.

Parameters:

cls - class to check

remove

public static void remove(aterm.ATermAppl cls)

Removes the specified class form set of annotation classes.

Parameters:

cls - class to remove.

getAll

public static Set<aterm.ATermAppl> getAll()

Returns an unmodifiable copy of the annotation classes regardless of the PelletOptions.IGNORE_ANNOTATION_CLASSES option.