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Packages that use GafDocument | |
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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.rules |
Uses of GafDocument in owltools.gaf |
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Fields in owltools.gaf declared as GafDocument | |
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protected GafDocument |
GeneAnnotation.gafDocumentObject
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Methods in owltools.gaf that return GafDocument | |
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GafDocument |
GafObjectsBuilder.buildDocument(File gafFilePath)
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GafDocument |
GafObjectsBuilder.buildDocument(Reader reader,
String docId,
String path)
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GafDocument |
GafObjectsBuilder.buildDocument(String gafFile)
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GafDocument |
GafObjectsBuilder.buildDocument(String fileName,
String docId,
String path)
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GafDocument |
GafObjectsBuilder.getGafDocument()
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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 |
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Methods in owltools.gaf.inference that return GafDocument | |
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GafDocument |
AbstractAnnotationPredictor.getGafDocument()
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Methods in owltools.gaf.inference with parameters of type GafDocument | |
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void |
AbstractAnnotationPredictor.setGafDocument(GafDocument gafDocument)
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Constructors in owltools.gaf.inference with parameters of type GafDocument | |
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AbstractAnnotationPredictor(GafDocument gafDocument,
OWLGraphWrapper graph)
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BasicAnnotationPropagator(GafDocument gafDocument,
OWLGraphWrapper graph)
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CompositionalClassPredictor(GafDocument gafDocument,
OWLGraphWrapper graph)
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Uses of GafDocument in owltools.gaf.io |
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Method parameters in owltools.gaf.io with type arguments of type GafDocument | |
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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.owl |
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Methods in owltools.gaf.owl with parameters of type GafDocument | |
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org.semanticweb.owlapi.model.OWLOntology |
GAFOWLBridge.translate(GafDocument gafdoc)
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Uses of GafDocument in owltools.gaf.rules |
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Methods in owltools.gaf.rules with parameters of type GafDocument | |
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Set<AnnotationRuleViolation> |
AnnotationRule.getRuleViolations(GafDocument gafDoc)
Given a whole GafDocument , find the set of violations using the rule |
Set<AnnotationRuleViolation> |
AbstractAnnotationRule.getRuleViolations(GafDocument gafDoc)
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AnnotationRulesEngine.AnnotationRulesEngineResult |
AnnotationRulesEngine.validateAnnotations(GafDocument doc)
Validate the given GafDocument . |
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