owltools.gaf.inference
Class CompositionalClassPredictor

java.lang.Object
  extended by owltools.gaf.inference.AbstractAnnotationPredictor
      extended by owltools.gaf.inference.CompositionalClassPredictor
All Implemented Interfaces:
AnnotationPredictor

Deprecated.

@Deprecated
public class CompositionalClassPredictor
extends AbstractAnnotationPredictor
implements AnnotationPredictor

Given an annotation to classes c1, c2, ..., cn, we generate suggestions of annotations to class D if D EquivalentTo d1 and d2 and dm and forall d in d1..dm, there exists a class c in c1...cn such that: Path(c,d) OR d = r some e, and Path(c,e) (i.e. we ignore the relation in the differentia) note the list c1..cn is drawn from direct annotations, AND the set of classes that are the subject of relations in c16. here Path means there is some positive path (TODO: include has_part?) TODO: reimplement using OWL semantics and reasoning

Author:
cjm

Field Summary
protected static org.apache.log4j.Logger LOG
          Deprecated.  
 
Constructor Summary
CompositionalClassPredictor(GafDocument gafDocument, OWLGraphWrapper graph)
          Deprecated.  
 
Method Summary
protected  org.semanticweb.owlapi.model.OWLClass getOWLClass(String id)
          Deprecated.  
protected  Prediction getPrediction(org.semanticweb.owlapi.model.OWLClass c, String bioentity, String with)
          Deprecated.  
 List<Prediction> predictForBioEntity(Bioentity e, Collection<GeneAnnotation> anns)
          Deprecated.  
 
Methods inherited from class owltools.gaf.inference.AbstractAnnotationPredictor
dispose, getAllPredictions, getGafDocument, getGraph, predict, setAndFilterRedundantPredictions, setAndFilterRedundantPredictions, setGafDocument, setGraph
 
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
dispose, getAllPredictions, predict
 

Field Detail

LOG

protected static org.apache.log4j.Logger LOG
Deprecated. 
Constructor Detail

CompositionalClassPredictor

public CompositionalClassPredictor(GafDocument gafDocument,
                                   OWLGraphWrapper graph)
Deprecated. 
Method Detail

getOWLClass

protected org.semanticweb.owlapi.model.OWLClass getOWLClass(String id)
Deprecated. 

predictForBioEntity

public List<Prediction> predictForBioEntity(Bioentity e,
                                            Collection<GeneAnnotation> anns)
Deprecated. 
Specified by:
predictForBioEntity in interface AnnotationPredictor

getPrediction

protected Prediction getPrediction(org.semanticweb.owlapi.model.OWLClass c,
                                   String bioentity,
                                   String with)
Deprecated. 


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