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Packages that use Bioentity | |
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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 |
Uses of Bioentity in owltools.gaf |
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Methods in owltools.gaf that return Bioentity | |
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Bioentity |
GafDocument.addBioentity(Bioentity bioentity)
Add a Bioentity object to the document. |
Bioentity |
GafDocument.getBioentity(String id)
Retrieve the Bioentity object for the given id. |
Bioentity |
GeneAnnotation.getBioentityObject()
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Methods in owltools.gaf that return types with arguments of type Bioentity | |
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Collection<Bioentity> |
GafDocument.getBioentities()
Get all registered Bioentity objects. |
Methods in owltools.gaf with parameters of type Bioentity | |
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Bioentity |
GafDocument.addBioentity(Bioentity bioentity)
Add a Bioentity object to the document. |
void |
GeneAnnotation.setBioentityObject(Bioentity bioentityObject)
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Constructor parameters in owltools.gaf with type arguments of type Bioentity | |
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GafDocument(String id,
String documentPath,
Map<String,Bioentity> bioentities)
Create a new document instance. |
Uses of Bioentity in owltools.gaf.inference |
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Methods in owltools.gaf.inference with parameters of type Bioentity | |
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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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Uses of Bioentity in owltools.gaf.io |
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Methods in owltools.gaf.io with parameters of type Bioentity | |
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void |
GpiWriter.write(Bioentity bioentity)
Write a single Bioentity . |
Method parameters in owltools.gaf.io with type arguments of type Bioentity | |
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void |
GpiWriter.write(Iterable<Bioentity> bioentities)
Write a full GAF. |
Uses of Bioentity in owltools.gaf.owl |
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Methods in owltools.gaf.owl with parameters of type Bioentity | |
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protected void |
GAFOWLBridge.translateBioentity(Bioentity e)
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Uses of Bioentity in owltools.gaf.owl.mapping |
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Methods in owltools.gaf.owl.mapping with parameters of type Bioentity | |
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protected void |
BasicABox.translateBioentity(Bioentity e)
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