Package | Description |
---|---|
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 |
Modifier and Type | Method and Description |
---|---|
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() |
Modifier and Type | Method and Description |
---|---|
Collection<Bioentity> |
GafDocument.getBioentities()
Get all registered
Bioentity objects. |
List<Bioentity> |
BioentityDocument.getBioentities()
Get all
Bioentity objects. |
Modifier and Type | Method and Description |
---|---|
Bioentity |
GafDocument.addBioentity(Bioentity bioentity)
Add a
Bioentity object to the document. |
void |
BioentityDocument.addBioentity(Bioentity bioentity)
Add a
Bioentity object to the document. |
void |
GeneAnnotation.setBioentityObject(Bioentity bioentityObject) |
Constructor and Description |
---|
BioentityDocument(String id,
String documentPath,
List<Bioentity> bioentities) |
GafDocument(String id,
String documentPath,
Map<String,Bioentity> bioentities)
Create a new document instance.
|
Modifier and Type | Method and Description |
---|---|
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 |
---|---|
void |
OpenAnnotationRDFWriter.add(Bioentity bioentity)
Adds a single
Bioentity to a model |
void |
GpiWriter.write(Bioentity bioentity)
Write a single
Bioentity . |
Modifier and Type | Method and Description |
---|---|
void |
GpiWriter.write(Collection<Bioentity> bioentities)
Write a full GAF.
|
void |
GpiWriter.writeHeader(Collection<Bioentity> bioentities)
Write a header of a GPI.
|
void |
GpiWriter.writeHeader(List<String> comments,
Collection<Bioentity> bioentities)
Write a header for a GAF, header comments are optional.
|
Modifier and Type | Method and Description |
---|---|
protected void |
GAFOWLBridge.translateBioentity(Bioentity e) |
Modifier and Type | Method and Description |
---|---|
protected void |
BasicABox.translateBioentity(Bioentity e) |
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