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 | |
owltools.gaf.parser | |
owltools.gaf.rules | |
owltools.gaf.rules.go |
Modifier and Type | Method and Description |
---|---|
GeneAnnotation |
GafDocument.getGeneAnnotationByLineNumber(int lineNumber)
Retrieve the (first) annotation for the given line number or null.
|
Modifier and Type | Method and Description |
---|---|
List<GeneAnnotation> |
Bioentity.getAnnotations() |
List<GeneAnnotation> |
GafDocument.getGeneAnnotations()
Get all annotations from this document.
|
Collection<GeneAnnotation> |
GafDocument.getGeneAnnotations(String bioentity)
Get all annotations for a given
Bioentity id. |
List<GeneAnnotation> |
GafDocument.getGeneAnnotationsByDirectGoCls(String cls)
Search for all annotations with the given cls String.
|
Modifier and Type | Method and Description |
---|---|
void |
Bioentity.addAnnotation(GeneAnnotation assoc) |
void |
GafDocument.addGeneAnnotation(GeneAnnotation ga)
Add a single annotation to the document.
|
Modifier and Type | Method and Description |
---|---|
void |
Bioentity.setAnnotations(List<GeneAnnotation> annotations) |
void |
GafDocument.setGeneAnnotations(List<GeneAnnotation> annotations)
Replace the current set of annotations with the given list.
|
Constructor and Description |
---|
GeneAnnotation(GeneAnnotation ann) |
Modifier and Type | Method and Description |
---|---|
GeneAnnotation |
Prediction.getGeneAnnotation() |
Modifier and Type | Method and Description |
---|---|
protected Prediction |
BasicAnnotationPropagator.createPrediction(org.semanticweb.owlapi.model.OWLClass c,
String aspect,
String with,
GeneAnnotation source) |
protected Prediction |
FoldBasedPredictor.getPrediction(GeneAnnotation ann,
org.semanticweb.owlapi.model.OWLClass c,
String bioentity,
String with) |
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) |
Constructor and Description |
---|
Prediction(GeneAnnotation geneAnnotation) |
Modifier and Type | Method and Description |
---|---|
void |
OpenAnnotationRDFWriter.add(GeneAnnotation ann)
Adds a single
GeneAnnotation to a model |
void |
GpadWriter.write(GeneAnnotation ann)
Write a single
GeneAnnotation . |
void |
AbstractGafWriter.write(GeneAnnotation ann)
Write a single
GeneAnnotation . |
Modifier and Type | Method and Description |
---|---|
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
|
Set<GeneAnnotation> |
SimpleABoxToGAF.generateAssociations(org.semanticweb.owlapi.model.OWLNamedIndividual ind,
org.semanticweb.owlapi.model.OWLOntology ont) |
Set<GeneAnnotation> |
SimpleABoxToGAF.generateAssociations(org.semanticweb.owlapi.model.OWLOntology ont) |
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 |
---|---|
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
|
protected List<GAFOWLBridge.GAFDescription> |
GAFOWLBridge.getDescription(GeneAnnotation a) |
void |
GAFOWLBridge.translateGeneAnnotation(GeneAnnotation a) |
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 |
---|---|
void |
BasicABox.translateGeneAnnotation(GeneAnnotation a) |
Modifier and Type | Method and Description |
---|---|
static String |
BuilderTools.buildGafQualifierString(GeneAnnotation ann) |
static String |
BuilderTools.buildGpadQualifierString(GeneAnnotation ann) |
static void |
BuilderTools.parseQualifiers(GeneAnnotation ga,
String qualifierString,
owltools.gaf.parser.AnnotationParserMessages reporter) |
Modifier and Type | Method and Description |
---|---|
GeneAnnotation |
AnnotationRuleViolation.getSourceAnnotation() |
Modifier and Type | Method and Description |
---|---|
Set<GeneAnnotation> |
AnnotationRuleViolation.getSuggestedReplacements() |
Modifier and Type | Method and Description |
---|---|
Set<AnnotationRuleViolation> |
GenericReasonerValidationCheck.getRuleViolations(GeneAnnotation a) |
Set<AnnotationRuleViolation> |
AnnotationTaxonRule.getRuleViolations(GeneAnnotation a) |
Set<AnnotationRuleViolation> |
AnnotationRule.getRuleViolations(GeneAnnotation a)
Given an annotation, find the set of violations using the rule
|
Set<AnnotationRuleViolation> |
AnnotationRegularExpressionFromXMLRule.getRuleViolations(GeneAnnotation a) |
abstract Set<AnnotationRuleViolation> |
AbstractAnnotationRule.getRuleViolations(GeneAnnotation a) |
void |
AnnotationRuleViolation.setSourceAnnotation(GeneAnnotation sourceAnnotation) |
Modifier and Type | Method and Description |
---|---|
void |
AnnotationRuleViolation.setSuggestedReplacements(Set<GeneAnnotation> suggestedReplacements) |
Constructor and Description |
---|
AnnotationRuleViolation(String ruleId,
String message,
GeneAnnotation sourceAnnotation)
Create a violation object with a message and a the corresponding source
annotation.
|
AnnotationRuleViolation(String ruleId,
String message,
GeneAnnotation sourceAnnotation,
AnnotationRuleViolation.ViolationType type)
Create a violation object with a message and a the corresponding source
annotation.
|
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