|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use GafDocument | |
---|---|
owltools.gaf | Processing of GO Gene Association Files |
owltools.gaf.inference | Perform inference on Gene Associations |
owltools.gaf.io | |
owltools.gaf.lego | |
owltools.gaf.owl | |
owltools.gaf.rules | |
owltools.gaf.rules.go |
Uses of GafDocument in owltools.gaf |
---|
Fields in owltools.gaf declared as GafDocument | |
---|---|
protected GafDocument |
GeneAnnotation.gafDocumentObject
|
Methods in owltools.gaf that return GafDocument | |
---|---|
GafDocument |
GafObjectsBuilder.buildDocument(File gafFilePath)
|
GafDocument |
GafObjectsBuilder.buildDocument(Reader reader,
String docId,
String path)
|
GafDocument |
GafObjectsBuilder.buildDocument(String gafFile)
|
GafDocument |
GafObjectsBuilder.buildDocument(String fileName,
String docId,
String path)
|
GafDocument |
GafObjectsBuilder.getGafDocument()
|
GafDocument |
GafObjectsBuilder.getNextSplitDocument()
When this variable reaches the splitSize count, the algorithm in the GafObjectsBuilder.getNextSplitDocument() method stops calling next method of the GafParser
and returns the GafDocument object build with the number of rows |
Uses of GafDocument in owltools.gaf.inference |
---|
Methods in owltools.gaf.inference that return GafDocument | |
---|---|
GafDocument |
AbstractAnnotationPredictor.getGafDocument()
|
Methods in owltools.gaf.inference with parameters of type GafDocument | |
---|---|
void |
AbstractAnnotationPredictor.setGafDocument(GafDocument gafDocument)
|
Constructors in owltools.gaf.inference with parameters of type GafDocument | |
---|---|
AbstractAnnotationPredictor(GafDocument gafDocument,
OWLGraphWrapper graph)
|
|
BasicAnnotationPropagator(GafDocument gafDocument,
OWLGraphWrapper graph)
Create instance. |
|
CompositionalClassPredictor(GafDocument gafDocument,
OWLGraphWrapper graph)
Deprecated. |
|
FoldBasedPredictor(GafDocument gafDocument,
OWLGraphWrapper graph)
|
Uses of GafDocument in owltools.gaf.io |
---|
Methods in owltools.gaf.io with parameters of type GafDocument | |
---|---|
void |
AbstractGafWriter.write(GafDocument gdoc)
Write a full GAF. |
void |
AbstractGafWriter.writeHeader(GafDocument gdoc)
Write a header of a GAF, use the comments from the GafDocument . |
Method parameters in owltools.gaf.io with type arguments of type GafDocument | |
---|---|
void |
XgmmlWriter.write(OutputStream stream,
OWLGraphWrapper graph,
List<GafDocument> gafs)
Write a pseudo RDF XML for the given ontology and gene annotations. |
void |
PseudoRdfXmlWriter.write(OutputStream stream,
OWLGraphWrapper graph,
List<GafDocument> gafs)
Write a pseudo RDF XML for the given ontology and gene annotations. |
Uses of GafDocument in owltools.gaf.lego |
---|
Methods in owltools.gaf.lego with parameters of type GafDocument | |
---|---|
void |
NetworkInferenceEngine.initialize(GafDocument gafdoc,
OWLGraphWrapper g)
|
void |
LegoModelGenerator.initialize(GafDocument gafdoc,
OWLGraphWrapper g)
|
org.semanticweb.owlapi.model.OWLOntology |
GafToLegoTranslator.minimizedTranslate(GafDocument gaf)
Translate the given GafDocument into an OWL representation of the LEGO model. |
org.semanticweb.owlapi.model.OWLOntology |
GafToLegoTranslator.translate(GafDocument gaf)
Translate the given GafDocument into an OWL representation of the LEGO model. |
Uses of GafDocument in owltools.gaf.owl |
---|
Methods in owltools.gaf.owl with parameters of type GafDocument | |
---|---|
void |
AnnotationExtensionFolder.fold(GafDocument gdoc)
|
void |
AnnotationExtensionFolder.fold(GafDocument gdoc,
boolean isReplace)
|
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 |
org.semanticweb.owlapi.model.OWLOntology |
GAFOWLBridge.translate(GafDocument gafdoc)
|
void |
AnnotationExtensionUnfolder.unfold(GafDocument gdoc)
|
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 GafDocument in owltools.gaf.rules |
---|
Uses of GafDocument in owltools.gaf.rules.go |
---|
Methods in owltools.gaf.rules.go with parameters of type GafDocument | |
---|---|
List<Prediction> |
GoAnnotationPredictionRule.getPredictedAnnotations(GafDocument gafDoc,
OWLGraphWrapper graph)
|
List<Prediction> |
GoAnnotationExperimentalPredictionRule.getPredictedAnnotations(GafDocument gafDoc,
OWLGraphWrapper graph)
|
Set<AnnotationRuleViolation> |
GOReciprocalAnnotationRule.getRuleViolations(GafDocument gafDoc)
|
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |