owltools.gaf.inference
Class BasicAnnotationPropagator

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

public class BasicAnnotationPropagator
extends AbstractAnnotationPredictor
implements AnnotationPredictor

TODO: this class has not yet been tested! This performs basic annotation inferences involving propagation between the 3 sub-ontologies in GO

TODO: reimplement using OWL semantics and reasoning

Author:
cjm

Field Summary
protected static org.apache.log4j.Logger LOG
           
 
Constructor Summary
BasicAnnotationPropagator(GafDocument gafDocument, OWLGraphWrapper graph)
           
 
Method Summary
protected  Prediction getPrediction(org.semanticweb.owlapi.model.OWLClass c, String bioentity, String with)
           
 Set<Prediction> predict(String bioentity)
           
 
Methods inherited from class owltools.gaf.inference.AbstractAnnotationPredictor
getAllPredictions, getGafDocument, getGraph, 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
getAllPredictions
 

Field Detail

LOG

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

BasicAnnotationPropagator

public BasicAnnotationPropagator(GafDocument gafDocument,
                                 OWLGraphWrapper graph)
Method Detail

predict

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

getPrediction

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


Copyright © 2010-2011. All Rights Reserved.