owltools.gaf.inference
Class AbstractAnnotationPredictor

java.lang.Object
  extended by owltools.gaf.inference.AbstractAnnotationPredictor
All Implemented Interfaces:
AnnotationPredictor
Direct Known Subclasses:
BasicAnnotationPropagator, CompositionalClassPredictor, FoldBasedPredictor

public abstract class AbstractAnnotationPredictor
extends Object
implements AnnotationPredictor

Author:
cjm

Constructor Summary
AbstractAnnotationPredictor(GafDocument gafDocument, OWLGraphWrapper graph)
           
 
Method Summary
 void dispose()
           
 List<Prediction> getAllPredictions()
           
 GafDocument getGafDocument()
           
 OWLGraphWrapper getGraph()
           
 List<Prediction> predict(String bioentity)
           
protected  void setAndFilterRedundantPredictions(Set<Prediction> predictions, Set<org.semanticweb.owlapi.model.OWLClass> aClasses)
          side-effects: removes redundant predictions over all relationships
protected  void setAndFilterRedundantPredictions(Set<Prediction> predictions, Set<org.semanticweb.owlapi.model.OWLClass> aClasses, Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)
          side-effects: removes redundant predictions over a set of relationships.
 void setGafDocument(GafDocument gafDocument)
           
 void setGraph(OWLGraphWrapper graph)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface owltools.gaf.inference.AnnotationPredictor
predictForBioEntity
 

Constructor Detail

AbstractAnnotationPredictor

public AbstractAnnotationPredictor(GafDocument gafDocument,
                                   OWLGraphWrapper graph)
Method Detail

getGafDocument

public GafDocument getGafDocument()

setGafDocument

public void setGafDocument(GafDocument gafDocument)

getGraph

public OWLGraphWrapper getGraph()

setGraph

public void setGraph(OWLGraphWrapper graph)

setAndFilterRedundantPredictions

protected void setAndFilterRedundantPredictions(Set<Prediction> predictions,
                                                Set<org.semanticweb.owlapi.model.OWLClass> aClasses)
side-effects: removes redundant predictions over all relationships

Parameters:
predictions -
aClasses -

setAndFilterRedundantPredictions

protected void setAndFilterRedundantPredictions(Set<Prediction> predictions,
                                                Set<org.semanticweb.owlapi.model.OWLClass> aClasses,
                                                Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)
side-effects: removes redundant predictions over a set of relationships. If overProps set is empty, only the subClassOf hierarchy is used, if it's null all relationships are used.

Parameters:
predictions -
aClasses -
overProps -

predict

public List<Prediction> predict(String bioentity)
Specified by:
predict in interface AnnotationPredictor

getAllPredictions

public List<Prediction> getAllPredictions()
Specified by:
getAllPredictions in interface AnnotationPredictor

dispose

public void dispose()
Specified by:
dispose in interface AnnotationPredictor


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