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.owl   
owltools.gaf.rules   
 

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 at splitSize then the algorithm in the getNextSplitDocument method stops calling next method of the GafParser and return 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)
           
CompositionalClassPredictor(GafDocument gafDocument, OWLGraphWrapper graph)
           
 

Uses of GafDocument in owltools.gaf.owl
 

Methods in owltools.gaf.owl with parameters of type GafDocument
 org.semanticweb.owlapi.model.OWLOntology GAFOWLBridge.translate(GafDocument gafdoc)
           
 

Uses of GafDocument in owltools.gaf.rules
 

Methods in owltools.gaf.rules with parameters of type GafDocument
 Map<String,List<AnnotationRuleViolation>> AnnotationRulesEngine.validateAnnotations(GafDocument doc)
           
 



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