Uses of Class
owltools.gaf.GafDocument

Packages that use GafDocument
owltools.gaf Processing of GO Gene Association Files 
owltools.gaf.inference Perform inference on Gene Associations 
owltools.gaf.io   
owltools.gaf.owl   
owltools.gaf.rules   
owltools.gaf.rules.go   
 

Uses of GafDocument in owltools.gaf
 

Fields in owltools.gaf declared as GafDocument
protected  GafDocument GeneAnnotation.gafDocumentObject
           
 

Methods in owltools.gaf that return GafDocument
 GafDocument GafObjectsBuilder.buildDocument(File gafFilePath)
           
 GafDocument GafObjectsBuilder.buildDocument(Reader reader, String docId, String path)
           
 GafDocument GafObjectsBuilder.buildDocument(String gafFile)
           
 GafDocument GafObjectsBuilder.buildDocument(String fileName, String docId, String path)
           
 GafDocument GafObjectsBuilder.getGafDocument()
           
 GafDocument GafObjectsBuilder.getNextSplitDocument()
          When this variable reaches the splitSize count, the algorithm in the GafObjectsBuilder.getNextSplitDocument() method stops calling next method of the GafParser and returns the GafDocument object build with the number of rows
 

Uses of GafDocument in owltools.gaf.inference
 

Methods in owltools.gaf.inference that return GafDocument
 GafDocument AbstractAnnotationPredictor.getGafDocument()
           
 

Methods in owltools.gaf.inference with parameters of type GafDocument
 void AbstractAnnotationPredictor.setGafDocument(GafDocument gafDocument)
           
 

Constructors in owltools.gaf.inference with parameters of type GafDocument
AbstractAnnotationPredictor(GafDocument gafDocument, OWLGraphWrapper graph)
           
BasicAnnotationPropagator(GafDocument gafDocument, OWLGraphWrapper graph)
          Create instance.
CompositionalClassPredictor(GafDocument gafDocument, OWLGraphWrapper graph)
          Deprecated.  
FoldBasedPredictor(GafDocument gafDocument, OWLGraphWrapper graph)
           
 

Uses of GafDocument in owltools.gaf.io
 

Methods in owltools.gaf.io with parameters of type GafDocument
 void AbstractGafWriter.write(GafDocument gdoc)
          Write a full GAF.
 void AbstractGafWriter.writeHeader(GafDocument gdoc)
          Write a header of a GAF, use the comments from the GafDocument.
 

Method parameters in owltools.gaf.io with type arguments of type GafDocument
 void XgmmlWriter.write(OutputStream stream, OWLGraphWrapper graph, List<GafDocument> gafs)
          Write a pseudo RDF XML for the given ontology and gene annotations.
 void PseudoRdfXmlWriter.write(OutputStream stream, OWLGraphWrapper graph, List<GafDocument> gafs)
          Write a pseudo RDF XML for the given ontology and gene annotations.
 

Uses of GafDocument in owltools.gaf.owl
 

Methods in owltools.gaf.owl with parameters of type GafDocument
 void AnnotationExtensionFolder.fold(GafDocument gdoc)
           
 void AnnotationExtensionFolder.fold(GafDocument gdoc, boolean isReplace)
           
 Collection<GeneAnnotation> AnnotationExtensionFolder.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
 org.semanticweb.owlapi.model.OWLOntology GAFOWLBridge.translate(GafDocument gafdoc)
           
 void AnnotationExtensionUnfolder.unfold(GafDocument gdoc)
           
 Collection<GeneAnnotation> AnnotationExtensionUnfolder.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
 

Uses of GafDocument in owltools.gaf.rules
 

Methods in owltools.gaf.rules with parameters of type GafDocument
 List<Prediction> AnnotationRule.getPredictedAnnotations(GafDocument gafDoc, OWLGraphWrapper graph)
          Given a whole GafDocument in plan and OWL format, check for possible new inferred annotations (Prediction).
 List<Prediction> AbstractAnnotationRule.getPredictedAnnotations(GafDocument gafDoc, OWLGraphWrapper graph)
           
 Set<AnnotationRuleViolation> AnnotationRule.getRuleViolations(GafDocument gafDoc)
          Given a whole GafDocument , find the set of violations using the rule
 Set<AnnotationRuleViolation> AbstractAnnotationRule.getRuleViolations(GafDocument gafDoc)
           
 AnnotationRulesEngine.AnnotationRulesEngineResult AnnotationRulesEngine.validateAnnotations(GafDocument doc)
          Validate the given GafDocument.
 

Uses of GafDocument in owltools.gaf.rules.go
 

Methods in owltools.gaf.rules.go with parameters of type GafDocument
 List<Prediction> GoAnnotationPredictionRule.getPredictedAnnotations(GafDocument gafDoc, OWLGraphWrapper graph)
           
 Set<AnnotationRuleViolation> GOReciprocalAnnotationRule.getRuleViolations(GafDocument gafDoc)
           
 



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