Package | Description |
---|---|
owltools.gaf.inference |
Perform inference on Gene Associations
|
owltools.gaf.rules | |
owltools.gaf.rules.go |
Modifier and Type | Method and Description |
---|---|
protected Prediction |
BasicAnnotationPropagator.createPrediction(org.semanticweb.owlapi.model.OWLClass c,
String aspect,
String with,
GeneAnnotation source) |
protected Prediction |
FoldBasedPredictor.getPrediction(GeneAnnotation ann,
org.semanticweb.owlapi.model.OWLClass c,
String bioentity,
String with) |
protected Prediction |
CompositionalClassPredictor.getPrediction(org.semanticweb.owlapi.model.OWLClass c,
String bioentity,
String with)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
List<Prediction> |
AnnotationPredictor.getAllPredictions() |
List<Prediction> |
AbstractAnnotationPredictor.getAllPredictions() |
List<Prediction> |
AnnotationPredictor.predict(String bioentity) |
List<Prediction> |
AbstractAnnotationPredictor.predict(String bioentity) |
List<Prediction> |
FoldBasedPredictor.predictForBioEntity(Bioentity e,
Collection<GeneAnnotation> anns) |
List<Prediction> |
CompositionalClassPredictor.predictForBioEntity(Bioentity e,
Collection<GeneAnnotation> anns)
Deprecated.
|
List<Prediction> |
BasicAnnotationPropagator.predictForBioEntity(Bioentity entity,
Collection<GeneAnnotation> annotations) |
List<Prediction> |
AnnotationPredictor.predictForBioEntity(Bioentity e,
Collection<GeneAnnotation> annotations) |
Modifier and Type | Method and Description |
---|---|
protected void |
AbstractAnnotationPredictor.setAndFilterRedundantPredictions(Set<Prediction> predictions,
Set<org.semanticweb.owlapi.model.OWLClass> aClasses)
side-effects: removes redundant predictions over all relationships
|
protected void |
AbstractAnnotationPredictor.setAndFilterRedundantPredictions(Set<Prediction> predictions,
Set<org.semanticweb.owlapi.model.OWLClass> aClasses,
Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)
side-effects: removes redundant predictions over a set of relationships.
|
Modifier and Type | Method and Description |
---|---|
List<Prediction> |
AnnotationRule.getPredictedAnnotations(GafDocument gafDoc,
OWLGraphWrapper graph)
Given a whole
GafDocument in plan and OWL format, check for
possible new inferred annotations (Prediction ). |
List<Prediction> |
AbstractAnnotationRule.getPredictedAnnotations(GafDocument gafDoc,
OWLGraphWrapper graph) |
Modifier and Type | Method and Description |
---|---|
void |
AnnotationRulesEngine.AnnotationRulesEngineResult.addExperimentalInferences(List<Prediction> predictions) |
void |
AnnotationRulesEngine.AnnotationRulesEngineResult.addInferences(List<Prediction> predictions) |
Modifier and Type | Method and Description |
---|---|
List<Prediction> |
GoAnnotationPredictionRule.getPredictedAnnotations(GafDocument gafDoc,
OWLGraphWrapper graph) |
List<Prediction> |
GoAnnotationExperimentalPredictionRule.getPredictedAnnotations(GafDocument gafDoc,
OWLGraphWrapper graph) |
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