Package | Description |
---|---|
owltools.gaf.godb |
This will replace go-db-perl MySQL loader
|
owltools.gaf.inference |
Perform inference on Gene Associations
|
owltools.gaf.io | |
owltools.gaf.lego | |
owltools.gaf.lego.legacy | |
owltools.gaf.owl | |
owltools.gaf.parser | |
owltools.gaf.rules | |
owltools.gaf.rules.go |
Modifier and Type | Field and Description |
---|---|
protected Set<GafDocument> |
Dumper.gafdocs |
Modifier and Type | Method and Description |
---|---|
Set<GafDocument> |
Dumper.getGafdocs() |
Modifier and Type | Method and Description |
---|---|
void |
Dumper.addGafDocument(GafDocument gd) |
void |
GoMySQLDatabaseDumper.dumpAssociationRowsForGaf(PrintStream s,
GafDocument gafdoc) |
void |
GoMySQLDatabaseDumper.dumpGeneProductRowsForGaf(PrintStream s,
GafDocument gafdoc) |
Modifier and Type | Method and Description |
---|---|
void |
Dumper.setGafdocs(Set<GafDocument> gafdocs) |
Modifier and Type | Method and Description |
---|---|
GafDocument |
AbstractAnnotationPredictor.getGafDocument() |
Modifier and Type | Method and Description |
---|---|
void |
AbstractAnnotationPredictor.setGafDocument(GafDocument gafDocument) |
Constructor and Description |
---|
AbstractAnnotationPredictor(GafDocument gafDocument,
OWLGraphWrapper graph) |
BasicAnnotationPropagator(GafDocument gafDocument,
OWLGraphWrapper graph,
boolean throwExceptions)
Create instance.
|
CompositionalClassPredictor(GafDocument gafDocument,
OWLGraphWrapper graph)
Deprecated.
|
FoldBasedPredictor(GafDocument gafDocument,
OWLGraphWrapper graph,
boolean throwExceptions) |
Modifier and Type | Method and Description |
---|---|
void |
OpenAnnotationRDFWriter.addHeaderInfo(GafDocument gdoc)
Adds header info from a GAF, use the comments from the
GafDocument . |
void |
OpenAnnotationRDFWriter.createModel(GafDocument gdoc)
Generate an RDF model from a GAF Document
|
void |
GpadWriter.write(GafDocument gdoc)
Write a full GAF.
|
void |
AbstractGafWriter.write(GafDocument gdoc)
Write a full GAF.
|
void |
OpenAnnotationRDFWriter.write(GafDocument gdoc,
File ttl) |
void |
OpenAnnotationRDFWriter.write(GafDocument gdoc,
PrintStream out)
Writes associations from GAF document as RDF on out
|
void |
OpenAnnotationRDFWriter.write(GafDocument gdoc,
String path) |
void |
GpadWriter.writeHeader(GafDocument gdoc)
Write a header of a GAF, use the comments from the
GafDocument . |
void |
AbstractGafWriter.writeHeader(GafDocument gdoc)
Write a header of a GAF, use the comments from the
GafDocument . |
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
GafDocument |
FileBasedMolecularModelManager.getGaf(String db) |
GafDocument |
FileBasedMolecularModelManager.loadGaf(String db)
loads/register a Gaf document
|
GafDocument |
FileBasedMolecularModelManager.loadGaf(String db,
File gafFile)
Loads and caches a GAF document from a specified location
|
Modifier and Type | Method and Description |
---|---|
void |
NetworkInferenceEngine.initialize(GafDocument gafdoc,
OWLGraphWrapper g)
Deprecated.
|
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. |
Modifier and Type | Method and Description |
---|---|
void |
LegoToGeneAnnotationTranslator.translate(org.semanticweb.owlapi.model.OWLOntology modelAbox,
GafDocument annotations,
BioentityDocument entities,
List<String> additionalRefs) |
void |
LegoAllIndividualToGeneAnnotationTranslator.translate(org.semanticweb.owlapi.model.OWLOntology modelAbox,
GafDocument annotations,
BioentityDocument entities,
List<String> additionalRefs) |
Modifier and Type | Method and Description |
---|---|
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
|
Modifier and Type | Method and Description |
---|---|
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.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 |
Modifier and Type | Method and Description |
---|---|
org.apache.commons.lang3.tuple.Pair<BioentityDocument,GafDocument> |
GpadGpiObjectsBuilder.loadGpadGpi(File gpad,
File gpi) |
Modifier and Type | Method and Description |
---|---|
List<Prediction> |
GoAnnotationPredictionRule.getPredictedAnnotations(GafDocument gafDoc,
OWLGraphWrapper graph) |
List<Prediction> |
GoAnnotationExperimentalPredictionRule.getPredictedAnnotations(GafDocument gafDoc,
OWLGraphWrapper graph) |
Set<AnnotationRuleViolation> |
GOReciprocalAnnotationRule.getRuleViolations(GafDocument gafDoc) |
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