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Packages that use GeneAnnotation | |
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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 |
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Fields in owltools.gaf with type parameters of type GeneAnnotation | |
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protected List<GeneAnnotation> |
GafDocument.annotations
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Methods in owltools.gaf that return types with arguments of type GeneAnnotation | |
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List<GeneAnnotation> |
GafDocument.getGeneAnnotations()
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Set<GeneAnnotation> |
GafDocument.getGeneAnnotations(String bioentity)
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List<GeneAnnotation> |
GafDocument.getGeneAnnotationsByDirectGoCls(String cls)
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Methods in owltools.gaf with parameters of type GeneAnnotation | |
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void |
GafDocument.addGeneAnnotation(GeneAnnotation ga)
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Uses of GeneAnnotation in owltools.gaf.inference |
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Methods in owltools.gaf.inference that return GeneAnnotation | |
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GeneAnnotation |
Prediction.getGeneAnnotation()
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Methods in owltools.gaf.inference with parameters of type GeneAnnotation | |
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void |
Prediction.setGeneAnnotation(GeneAnnotation geneAnnotation)
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Uses of GeneAnnotation in owltools.gaf.rules |
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Methods in owltools.gaf.rules that return GeneAnnotation | |
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GeneAnnotation |
AnnotationRuleViolation.getSourceAnnotation()
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Methods in owltools.gaf.rules that return types with arguments of type GeneAnnotation | |
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Set<GeneAnnotation> |
AnnotationRuleViolation.getSuggestedReplacements()
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Methods in owltools.gaf.rules with parameters of type GeneAnnotation | |
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Set<AnnotationRuleViolation> |
GenericReasonerValidationCheck.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
AnnotationTaxonRule.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
AnnotationRule.getRuleViolations(GeneAnnotation a)
Given an annotation, find the set of violations using the rule |
Set<AnnotationRuleViolation> |
AnnotationRegularExpressionFromXMLRule.getRuleViolations(GeneAnnotation a)
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abstract Set<AnnotationRuleViolation> |
AbstractAnnotationRule.getRuleViolations(GeneAnnotation a)
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void |
AnnotationRuleViolation.setSourceAnnotation(GeneAnnotation sourceAnnotation)
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Method parameters in owltools.gaf.rules with type arguments of type GeneAnnotation | |
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void |
AnnotationRuleViolation.setSuggestedReplacements(Set<GeneAnnotation> suggestedReplacements)
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Constructors in owltools.gaf.rules with parameters of type GeneAnnotation | |
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AnnotationRuleViolation(String ruleId,
String message,
GeneAnnotation sourceAnnotation)
Create a violation object with a message and a the corresponding source annotation. |
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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 |
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Methods in owltools.gaf.rules.go with parameters of type GeneAnnotation | |
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Set<AnnotationRuleViolation> |
GoNoISSProteinBindingRule.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
GoNDAnnotationRule.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
GoIPICatalyticActivityRestrictionsRule.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
GoIPIAnnotationRule.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
GoIEPRestrictionsRule.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
GoIDAAnnotationRule.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
GoICAnnotationRule.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
GoClassReferenceAnnotationRule.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
GoBindingCheckWithFieldRule.getRuleViolations(GeneAnnotation a)
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Set<AnnotationRuleViolation> |
BasicChecksRule.getRuleViolations(GeneAnnotation a)
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