Uses of Class
owltools.gaf.Bioentity

Packages that use Bioentity
owltools.gaf Processing of GO Gene Association Files 
owltools.gaf.inference Perform inference on Gene Associations 
owltools.gaf.io   
owltools.gaf.owl   
owltools.gaf.owl.mapping   
 

Uses of Bioentity in owltools.gaf
 

Methods in owltools.gaf that return Bioentity
 Bioentity GafDocument.addBioentity(Bioentity bioentity)
          Add a Bioentity object to the document.
 Bioentity GafDocument.getBioentity(String id)
          Retrieve the Bioentity object for the given id.
 Bioentity GeneAnnotation.getBioentityObject()
           
 

Methods in owltools.gaf that return types with arguments of type Bioentity
 Collection<Bioentity> GafDocument.getBioentities()
          Get all registered Bioentity objects.
 

Methods in owltools.gaf with parameters of type Bioentity
 Bioentity GafDocument.addBioentity(Bioentity bioentity)
          Add a Bioentity object to the document.
 void GeneAnnotation.setBioentityObject(Bioentity bioentityObject)
           
 

Constructor parameters in owltools.gaf with type arguments of type Bioentity
GafDocument(String id, String documentPath, Map<String,Bioentity> bioentities)
          Create a new document instance.
 

Uses of Bioentity in owltools.gaf.inference
 

Methods in owltools.gaf.inference with parameters of type Bioentity
 List<Prediction> FoldBasedPredictor.predictForBioEntity(Bioentity e, Collection<GeneAnnotation> anns)
           
 List<Prediction> CompositionalClassPredictor.predictForBioEntity(Bioentity e, Collection<GeneAnnotation> anns)
          Deprecated.  
 List<Prediction> BasicAnnotationPropagator.predictForBioEntity(Bioentity entity, Collection<GeneAnnotation> annotations)
           
 List<Prediction> AnnotationPredictor.predictForBioEntity(Bioentity e, Collection<GeneAnnotation> annotations)
           
 

Uses of Bioentity in owltools.gaf.io
 

Methods in owltools.gaf.io with parameters of type Bioentity
 void GpiWriter.write(Bioentity bioentity)
          Write a single Bioentity.
 

Method parameters in owltools.gaf.io with type arguments of type Bioentity
 void GpiWriter.write(Iterable<Bioentity> bioentities)
          Write a full GAF.
 

Uses of Bioentity in owltools.gaf.owl
 

Methods in owltools.gaf.owl with parameters of type Bioentity
protected  void GAFOWLBridge.translateBioentity(Bioentity e)
           
 

Uses of Bioentity in owltools.gaf.owl.mapping
 

Methods in owltools.gaf.owl.mapping with parameters of type Bioentity
protected  void BasicABox.translateBioentity(Bioentity e)
           
 



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