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.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)
           
 

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
 void Prediction.setGeneAnnotation(GeneAnnotation geneAnnotation)
           
 

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> GoNoISSProteinBindingRule.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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