Uses of Class
owltools.gaf.GeneAnnotation

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

Uses of GeneAnnotation in owltools.gaf
 

Fields in owltools.gaf with type parameters of type GeneAnnotation
protected  List<GeneAnnotation> GafDocument.annotations
           
 

Methods in owltools.gaf that return types with arguments of type GeneAnnotation
 List<GeneAnnotation> GafDocument.getGeneAnnotations()
           
 Set<GeneAnnotation> GafDocument.getGeneAnnotations(String bioentity)
           
 List<GeneAnnotation> GafDocument.getGeneAnnotationsByDirectGoCls(String cls)
           
 

Methods in owltools.gaf with parameters of type GeneAnnotation
 void GafDocument.addGeneAnnotation(GeneAnnotation ga)
           
 

Method parameters in owltools.gaf with type arguments of type GeneAnnotation
 void GafDocument.setGeneAnnotations(List<GeneAnnotation> newAnns)
           
 

Constructors in owltools.gaf with parameters of type GeneAnnotation
GeneAnnotation(GeneAnnotation ann)
           
 

Uses of GeneAnnotation in owltools.gaf.inference
 

Methods in owltools.gaf.inference that return GeneAnnotation
 GeneAnnotation Prediction.getGeneAnnotation()
           
 

Methods in owltools.gaf.inference with parameters of type GeneAnnotation
protected  Prediction FoldBasedPredictor.getPrediction(GeneAnnotation ann, org.semanticweb.owlapi.model.OWLClass c, String bioentity, String with)
           
 void Prediction.setGeneAnnotation(GeneAnnotation geneAnnotation)
           
 

Uses of GeneAnnotation in owltools.gaf.io
 

Methods in owltools.gaf.io with parameters of type GeneAnnotation
 void GafWriter.write(GeneAnnotation ann)
           
 

Uses of GeneAnnotation in owltools.gaf.owl
 

Methods in owltools.gaf.owl that return types with arguments of type GeneAnnotation
 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
 Set<GeneAnnotation> SimpleABoxToGAF.generateAssociations(org.semanticweb.owlapi.model.OWLNamedIndividual ind, org.semanticweb.owlapi.model.OWLOntology ont)
           
 Set<GeneAnnotation> SimpleABoxToGAF.generateAssociations(org.semanticweb.owlapi.model.OWLOntology ont)
           
 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
 

Methods in owltools.gaf.owl with parameters of type GeneAnnotation
 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
protected  GAFOWLBridge.GAFDescription GAFOWLBridge.getDescription(GeneAnnotation a)
           
 void GAFOWLBridge.translateGeneAnnotation(GeneAnnotation a)
           
 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 GeneAnnotation in owltools.gaf.owl.mapping
 

Methods in owltools.gaf.owl.mapping with parameters of type GeneAnnotation
 void BasicABox.translateGeneAnnotation(GeneAnnotation a)
           
 

Uses of GeneAnnotation in owltools.gaf.rules
 

Methods in owltools.gaf.rules that return GeneAnnotation
 GeneAnnotation AnnotationRuleViolation.getSourceAnnotation()
           
 

Methods in owltools.gaf.rules that return types with arguments of type GeneAnnotation
 Set<GeneAnnotation> AnnotationRuleViolation.getSuggestedReplacements()
           
 

Methods in owltools.gaf.rules with parameters of type GeneAnnotation
 Set<AnnotationRuleViolation> GenericReasonerValidationCheck.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> AnnotationTaxonRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> AnnotationRule.getRuleViolations(GeneAnnotation a)
          Given an annotation, find the set of violations using the rule
 Set<AnnotationRuleViolation> AnnotationRegularExpressionFromXMLRule.getRuleViolations(GeneAnnotation a)
           
abstract  Set<AnnotationRuleViolation> AbstractAnnotationRule.getRuleViolations(GeneAnnotation a)
           
 void AnnotationRuleViolation.setSourceAnnotation(GeneAnnotation sourceAnnotation)
           
 

Method parameters in owltools.gaf.rules with type arguments of type GeneAnnotation
 void AnnotationRuleViolation.setSuggestedReplacements(Set<GeneAnnotation> suggestedReplacements)
           
 

Constructors in owltools.gaf.rules with parameters of type GeneAnnotation
AnnotationRuleViolation(String ruleId, String message, GeneAnnotation sourceAnnotation)
          Create a violation object with a message and a the corresponding source annotation.
AnnotationRuleViolation(String ruleId, String message, GeneAnnotation sourceAnnotation, AnnotationRuleViolation.ViolationType type)
          Create a violation object with a message and a the corresponding source annotation.
 

Uses of GeneAnnotation in owltools.gaf.rules.go
 

Methods in owltools.gaf.rules.go with parameters of type GeneAnnotation
 Set<AnnotationRuleViolation> GOReciprocalAnnotationRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoNoISSProteinBindingRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoNoHighLevelTermAnnotationRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoNDAnnotationRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoMultipleTaxonRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoIPICatalyticActivityRestrictionsRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoIPIAnnotationRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoIEPRestrictionsRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoIDAAnnotationRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoICAnnotationRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoClassReferenceAnnotationRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> GoBindingCheckWithFieldRule.getRuleViolations(GeneAnnotation a)
           
 Set<AnnotationRuleViolation> BasicChecksRule.getRuleViolations(GeneAnnotation a)
           
 



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