owltools.gaf.owl
Class AnnotationExtensionFolder

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

public class AnnotationExtensionFolder
extends GAFOWLBridge

Author:
cjm 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 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
 Map<org.semanticweb.owlapi.model.OWLClass,org.semanticweb.owlapi.model.OWLClassExpression> foldedClassMap
           
 
Fields inherited from class owltools.gaf.owl.GAFOWLBridge
GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI, graph
 
Constructor Summary
AnnotationExtensionFolder(OWLGraphWrapper g)
           
 
Method Summary
 void fold(GafDocument gdoc)
           
 void fold(GafDocument gdoc, boolean isReplace)
           
 Collection<GeneAnnotation> fold(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
 Map<org.semanticweb.owlapi.model.OWLClass,org.semanticweb.owlapi.model.OWLClassExpression> getFoldedClassMap()
           
 org.semanticweb.owlapi.model.OWLClass mapExt(org.semanticweb.owlapi.model.OWLClass annotatedToClass, List<ExtensionExpression> exts)
           
 void setFoldedClassMap(Map<org.semanticweb.owlapi.model.OWLClass,org.semanticweb.owlapi.model.OWLClassExpression> foldedClassMap)
           
 
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

foldedClassMap

public Map<org.semanticweb.owlapi.model.OWLClass,org.semanticweb.owlapi.model.OWLClassExpression> foldedClassMap
Constructor Detail

AnnotationExtensionFolder

public AnnotationExtensionFolder(OWLGraphWrapper g)
Method Detail

fold

public void fold(GafDocument gdoc)

fold

public void fold(GafDocument gdoc,
                 boolean isReplace)

fold

public Collection<GeneAnnotation> fold(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

Parameters:
gdoc -
ann -
Returns:
annotations

mapExt

public org.semanticweb.owlapi.model.OWLClass mapExt(org.semanticweb.owlapi.model.OWLClass annotatedToClass,
                                                    List<ExtensionExpression> exts)

getFoldedClassMap

public Map<org.semanticweb.owlapi.model.OWLClass,org.semanticweb.owlapi.model.OWLClassExpression> getFoldedClassMap()

setFoldedClassMap

public void setFoldedClassMap(Map<org.semanticweb.owlapi.model.OWLClass,org.semanticweb.owlapi.model.OWLClassExpression> foldedClassMap)


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