owltools.gaf.rules
Class AnnotationTaxonRule
java.lang.Object
owltools.gaf.rules.AbstractAnnotationRule
owltools.gaf.rules.AnnotationTaxonRule
- All Implemented Interfaces:
- AnnotationRule
- Direct Known Subclasses:
- GoAnnotationTaxonRule
public class AnnotationTaxonRule
- extends AbstractAnnotationRule
Checks if an annotation is valid according to taxon constraints.
Methods inherited from class owltools.gaf.rules.AbstractAnnotationRule |
getDate, getDescription, getGrandFatheringDate, getName, getPredictedAnnotations, getRuleId, getRuleViolations, getStatus, hasGrandFathering, isAnnotationLevel, isDocumentLevel, isInferringAnnotations, setDate, setDescription, setGrandFatheringDate, setName, setRuleId, setStatus |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AnnotationTaxonRule
public AnnotationTaxonRule(OWLGraphWrapper graph)
- Parameters:
graph
-
getRuleViolations
public Set<AnnotationRuleViolation> getRuleViolations(GeneAnnotation a)
- Description copied from interface:
AnnotationRule
- Given an annotation, find the set of violations using the rule
- Specified by:
getRuleViolations
in interface AnnotationRule
- Specified by:
getRuleViolations
in class AbstractAnnotationRule
- Parameters:
a
- annotation
- Returns:
- set of violations
- See Also:
AnnotationRule.isAnnotationLevel()
isOwlDocumentLevel
public boolean isOwlDocumentLevel()
- Specified by:
isOwlDocumentLevel
in interface AnnotationRule
- Overrides:
isOwlDocumentLevel
in class AbstractAnnotationRule
- Returns:
- true if the rule has to be applied to the whole OWL document.
- See Also:
AnnotationRule.getRuleViolations(GafDocument, OWLGraphWrapper)
getRuleViolations
public Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc,
OWLGraphWrapper graph)
- Description copied from interface:
AnnotationRule
- Given a whole
GafDocument
in OWL, find the set of violations using the rule
- Specified by:
getRuleViolations
in interface AnnotationRule
- Overrides:
getRuleViolations
in class AbstractAnnotationRule
- Returns:
- set of violations
- See Also:
AnnotationRule.isOwlDocumentLevel()
handleUnsatisfiable
protected void handleUnsatisfiable(Set<org.semanticweb.owlapi.model.OWLClass> unsatisfiable,
org.semanticweb.owlapi.model.OWLOntology ontology)
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