owltools.gaf.owl
Class AnnotationExtensionUnfolder
java.lang.Object
owltools.gaf.owl.GAFOWLBridge
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
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 |
isReplaceGenus
public boolean isReplaceGenus
isThrowOnMultipleExpressions
public boolean isThrowOnMultipleExpressions
AnnotationExtensionUnfolder
public AnnotationExtensionUnfolder(OWLGraphWrapper g)
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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