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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.io | |
owltools.gaf.owl | |
owltools.gaf.owl.mapping | |
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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Method parameters in owltools.gaf with type arguments of type GeneAnnotation | |
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void |
GafDocument.setGeneAnnotations(List<GeneAnnotation> newAnns)
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Constructors in owltools.gaf with parameters of type GeneAnnotation | |
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GeneAnnotation(GeneAnnotation ann)
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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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protected Prediction |
BasicAnnotationPropagator.createPrediction(org.semanticweb.owlapi.model.OWLClass c,
String aspect,
String with,
GeneAnnotation source)
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protected Prediction |
FoldBasedPredictor.getPrediction(GeneAnnotation ann,
org.semanticweb.owlapi.model.OWLClass c,
String bioentity,
String with)
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Method parameters in owltools.gaf.inference with type arguments of type GeneAnnotation | |
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List<Prediction> |
FoldBasedPredictor.predictForBioEntity(Bioentity e,
Collection<GeneAnnotation> anns)
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List<Prediction> |
CompositionalClassPredictor.predictForBioEntity(Bioentity e,
Collection<GeneAnnotation> anns)
Deprecated. |
List<Prediction> |
BasicAnnotationPropagator.predictForBioEntity(Bioentity entity,
Collection<GeneAnnotation> annotations)
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List<Prediction> |
AnnotationPredictor.predictForBioEntity(Bioentity e,
Collection<GeneAnnotation> annotations)
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Constructors in owltools.gaf.inference with parameters of type GeneAnnotation | |
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Prediction(GeneAnnotation geneAnnotation)
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Uses of GeneAnnotation in owltools.gaf.io |
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Methods in owltools.gaf.io with parameters of type GeneAnnotation | |
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void |
AbstractGafWriter.write(GeneAnnotation ann)
Write a single GeneAnnotation . |
Uses of GeneAnnotation in owltools.gaf.owl |
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Methods in owltools.gaf.owl that return types with arguments of type GeneAnnotation | |
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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)
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Set<GeneAnnotation> |
SimpleABoxToGAF.generateAssociations(org.semanticweb.owlapi.model.OWLOntology ont)
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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 | |
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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)
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void |
GAFOWLBridge.translateGeneAnnotation(GeneAnnotation a)
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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 |
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Methods in owltools.gaf.owl.mapping with parameters of type GeneAnnotation | |
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void |
BasicABox.translateGeneAnnotation(GeneAnnotation a)
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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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