public class BasicAnnotationPropagator extends AbstractAnnotationPredictor implements AnnotationPredictor
Modifier and Type | Field and Description |
---|---|
protected static org.apache.log4j.Logger |
LOG |
protected static boolean |
SKIP_IEA |
Constructor and Description |
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BasicAnnotationPropagator(GafDocument gafDocument,
OWLGraphWrapper graph,
boolean throwExceptions)
Create instance.
|
Modifier and Type | Method and Description |
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protected Map<String,String> |
createDefaultAspectMap(OWLGraphWrapper graph)
Create the mapping from the sub ontology to the aspect in the GAF.
|
protected Prediction |
createPrediction(org.semanticweb.owlapi.model.OWLClass c,
String aspect,
String with,
GeneAnnotation source) |
protected Map<String,Set<org.semanticweb.owlapi.model.OWLClass>> |
createPropagationRules(OWLGraphWrapper graph,
org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
Create the default propagation rule set tailored for the GeneOntology.
|
void |
dispose() |
protected static Set<org.semanticweb.owlapi.model.OWLClass> |
getDirectLinkedClasses(org.semanticweb.owlapi.model.OWLClass c,
Set<org.semanticweb.owlapi.model.OWLObjectProperty> properties,
OWLGraphWrapper g,
Set<org.semanticweb.owlapi.model.OWLClass> superSet)
Lookup relation super classes in graph g for a given sub class c and property p.
|
protected static Set<org.semanticweb.owlapi.model.OWLClass> |
getDirectLinkedClasses(org.semanticweb.owlapi.model.OWLClass c,
String property,
OWLGraphWrapper g)
Lookup relation super classes in graph g for a given sub class c and property p.
|
protected String |
getGoSubOntology(org.semanticweb.owlapi.model.OWLClass c,
OWLGraphWrapper g)
Get the specific sub ontology.
|
protected static Set<org.semanticweb.owlapi.model.OWLClass> |
getIsaPartofSuperClassClosure(Collection<org.semanticweb.owlapi.model.OWLClass> annotations,
OWLGraphWrapper graph,
org.semanticweb.owlapi.reasoner.OWLReasoner r) |
protected static Set<org.semanticweb.owlapi.model.OWLClass> |
getNonRedundantLinkedClasses(org.semanticweb.owlapi.model.OWLClass c,
Set<org.semanticweb.owlapi.model.OWLObjectProperty> properties,
OWLGraphWrapper g,
org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
Set<org.semanticweb.owlapi.model.OWLClass> superSet,
Map<Set<org.semanticweb.owlapi.model.OWLClass>,Set<org.semanticweb.owlapi.model.OWLClass>> cache)
Retrieve the non redundant set of linked classes using the given
relation.
|
protected String |
getSubOntology(org.semanticweb.owlapi.model.OWLClass c) |
boolean |
isInitialized() |
List<Prediction> |
predictForBioEntity(Bioentity entity,
Collection<GeneAnnotation> annotations) |
protected static Set<org.semanticweb.owlapi.model.OWLClass> |
reduceToNonRedundant(Set<org.semanticweb.owlapi.model.OWLClass> classes,
org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
Given a set of classes, create a new non-redundant set with respect to
the inferred super class hierarchy.
|
getAllPredictions, getGafDocument, getGraph, predict, setAndFilterRedundantPredictions, setAndFilterRedundantPredictions, setGafDocument, setGraph
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getAllPredictions, predict
protected static org.apache.log4j.Logger LOG
protected static boolean SKIP_IEA
public BasicAnnotationPropagator(GafDocument gafDocument, OWLGraphWrapper graph, boolean throwExceptions)
gafDocument
- graph
- throwExceptions
- public boolean isInitialized()
isInitialized
in interface AnnotationPredictor
protected Map<String,Set<org.semanticweb.owlapi.model.OWLClass>> createPropagationRules(OWLGraphWrapper graph, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
graph
- reasoner
- protected static Set<org.semanticweb.owlapi.model.OWLClass> getNonRedundantLinkedClasses(org.semanticweb.owlapi.model.OWLClass c, Set<org.semanticweb.owlapi.model.OWLObjectProperty> properties, OWLGraphWrapper g, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, Set<org.semanticweb.owlapi.model.OWLClass> superSet, Map<Set<org.semanticweb.owlapi.model.OWLClass>,Set<org.semanticweb.owlapi.model.OWLClass>> cache)
reduceToNonRedundant(Set, OWLReasoner)
. Therefore the results of
that method are cached in a map.c
- properties
- g
- reasoner
- superSet
- cache
- protected static Set<org.semanticweb.owlapi.model.OWLClass> getDirectLinkedClasses(org.semanticweb.owlapi.model.OWLClass c, String property, OWLGraphWrapper g)
c
- property
- g
- protected static Set<org.semanticweb.owlapi.model.OWLClass> getDirectLinkedClasses(org.semanticweb.owlapi.model.OWLClass c, Set<org.semanticweb.owlapi.model.OWLObjectProperty> properties, OWLGraphWrapper g, Set<org.semanticweb.owlapi.model.OWLClass> superSet)
c
- properties
- g
- superSet
- protected static Set<org.semanticweb.owlapi.model.OWLClass> reduceToNonRedundant(Set<org.semanticweb.owlapi.model.OWLClass> classes, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
classes
- reasoner
- protected Map<String,String> createDefaultAspectMap(OWLGraphWrapper graph)
graph
- protected String getGoSubOntology(org.semanticweb.owlapi.model.OWLClass c, OWLGraphWrapper g)
c
- g
- public List<Prediction> predictForBioEntity(Bioentity entity, Collection<GeneAnnotation> annotations)
predictForBioEntity
in interface AnnotationPredictor
protected static Set<org.semanticweb.owlapi.model.OWLClass> getIsaPartofSuperClassClosure(Collection<org.semanticweb.owlapi.model.OWLClass> annotations, OWLGraphWrapper graph, org.semanticweb.owlapi.reasoner.OWLReasoner r)
protected String getSubOntology(org.semanticweb.owlapi.model.OWLClass c)
protected Prediction createPrediction(org.semanticweb.owlapi.model.OWLClass c, String aspect, String with, GeneAnnotation source)
public void dispose()
dispose
in interface AnnotationPredictor
dispose
in class AbstractAnnotationPredictor
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