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java.lang.Objectorg.mindswap.pellet.utils.AnnotationClasses
public class AnnotationClasses
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
.
Constructor Summary | |
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AnnotationClasses()
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Method Summary | |
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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 java.util.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 |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public AnnotationClasses()
Method Detail |
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public static void add(aterm.ATermAppl cls)
cls
- class to addpublic static boolean contains(aterm.ATermAppl cls)
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.
cls
- class to checkpublic static void remove(aterm.ATermAppl cls)
cls
- class to remove.public static java.util.Set<aterm.ATermAppl> getAll()
PelletOptions.IGNORE_ANNOTATION_CLASSES
option.
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