owltools.gaf.owl
Class AnnotationExtensionUnfolder

java.lang.Object
  extended by owltools.gaf.owl.GAFOWLBridge
      extended by owltools.gaf.owl.AnnotationExtensionUnfolder

public class AnnotationExtensionUnfolder
extends GAFOWLBridge

Author:
cjm given an annotation to a pre-existing term, this will add to the annotation extension field based on existing logical definitions. optionally, the original annotation can be replaced with the more basic term (genus) In OWL terminology, this operation is known as "unfolding" - we are unfolding or unpacking a composite class into its constituent components. See: http://code.google.com/p/owltools/wiki/AnnotationExtensionFolding

Nested Class Summary
 
Nested classes/interfaces inherited from class owltools.gaf.owl.GAFOWLBridge
GAFOWLBridge.BioentityMapping, GAFOWLBridge.GAFDescription, GAFOWLBridge.Vocab
 
Field Summary
 boolean isReplaceGenus
           
 boolean isThrowOnMultipleExpressions
           
 
Fields inherited from class owltools.gaf.owl.GAFOWLBridge
GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI, graph
 
Constructor Summary
AnnotationExtensionUnfolder(OWLGraphWrapper g)
           
 
Method Summary
 void unfold(GafDocument gdoc)
           
 Collection<GeneAnnotation> unfold(GafDocument gdoc, GeneAnnotation ann)
          given an annotation to a pre-existing term, this will return a set of zero or more annotations to new terms that are generated from folding the annotation extensions into newly created term
 
Methods inherited from class owltools.gaf.owl.GAFOWLBridge
addAxioms, getBioentityMapping, getDescription, getObjectPropertyByShorthand, getOWLClass, getTargetOntology, isBasicAboxMapping, isGenerateIndividuals, setBasicAboxMapping, setBioentityMapping, setGenerateIndividuals, setTargetOntology, translate, translateBioentity, translateGeneAnnotation
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

isReplaceGenus

public boolean isReplaceGenus

isThrowOnMultipleExpressions

public boolean isThrowOnMultipleExpressions
Constructor Detail

AnnotationExtensionUnfolder

public AnnotationExtensionUnfolder(OWLGraphWrapper g)
Method Detail

unfold

public void unfold(GafDocument gdoc)
            throws owltools.gaf.owl.AnnotationExtensionUnfolder.MultipleUnfoldOptionsException
Throws:
owltools.gaf.owl.AnnotationExtensionUnfolder.MultipleUnfoldOptionsException

unfold

public Collection<GeneAnnotation> unfold(GafDocument gdoc,
                                         GeneAnnotation ann)
                                  throws owltools.gaf.owl.AnnotationExtensionUnfolder.MultipleUnfoldOptionsException
given an annotation to a pre-existing term, this will return a set of zero or more annotations to new terms that are generated from folding the annotation extensions into newly created term

Parameters:
gdoc -
ann -
Returns:
annotations
Throws:
MultipleUnfoldOptionsException
owltools.gaf.owl.AnnotationExtensionUnfolder.MultipleUnfoldOptionsException


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