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java.lang.Objectowltools.gaf.inference.AbstractAnnotationPredictor
owltools.gaf.inference.BasicAnnotationPropagator
public class BasicAnnotationPropagator
This performs basic annotation inferences involving propagation between the 3 sub-ontologies in GO
Field Summary | |
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protected static org.apache.log4j.Logger |
LOG
|
protected static boolean |
SKIP_IEA
|
Constructor Summary | |
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BasicAnnotationPropagator(GafDocument gafDocument,
OWLGraphWrapper graph)
Create instance. |
Method Summary | |
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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)
|
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. |
Methods inherited from class owltools.gaf.inference.AbstractAnnotationPredictor |
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getAllPredictions, getGafDocument, getGraph, predict, setAndFilterRedundantPredictions, setAndFilterRedundantPredictions, setGafDocument, setGraph |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface owltools.gaf.inference.AnnotationPredictor |
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getAllPredictions, predict |
Field Detail |
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protected static org.apache.log4j.Logger LOG
protected static boolean SKIP_IEA
Constructor Detail |
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public BasicAnnotationPropagator(GafDocument gafDocument, OWLGraphWrapper graph)
gafDocument
- graph
- Method Detail |
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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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