owltools.gaf.inference

Class CompositionalClassPredictor

java.lang.Object

owltools.gaf.inference.AbstractAnnotationPredictor

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

Fields

Modifier and Type	Field and Description
protected static org.apache.log4j.Logger	LOG Deprecated.

Constructor Summary

Constructors

Constructor and Description
CompositionalClassPredictor(GafDocument gafDocument, OWLGraphWrapper graph) Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
protected org.semanticweb.owlapi.model.OWLClass	getOWLClass(String id) Deprecated.
protected Prediction	getPrediction(org.semanticweb.owlapi.model.OWLClass c, String bioentity, String with) Deprecated.
boolean	isInitialized() 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.

isInitialized

public boolean isInitialized()

Deprecated.

Specified by:

isInitialized in interface AnnotationPredictor

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.