owltools.gaf.rules
Class AnnotationTaxonRule

java.lang.Object
  extended by owltools.gaf.rules.AbstractAnnotationRule
      extended by 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.


Constructor Summary
AnnotationTaxonRule(OWLGraphWrapper graph)
           
 
Method Summary
 Set<AnnotationRuleViolation> getRuleViolations(GeneAnnotation a)
          Given an annotation, find the set of violations using the rule
 Set<AnnotationRuleViolation> getRuleViolations(OWLGraphWrapper graph)
          Given a whole GafDocument in OWL, find the set of violations using the rule
protected  void handleUnsatisfiable(Set<org.semanticweb.owlapi.model.OWLClass> unsatisfiable, org.semanticweb.owlapi.model.OWLOntology ontology)
           
 boolean isOwlDocumentLevel()
           
 
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
 

Constructor Detail

AnnotationTaxonRule

public AnnotationTaxonRule(OWLGraphWrapper graph)
Parameters:
graph -
Method Detail

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(OWLGraphWrapper)

getRuleViolations

public Set<AnnotationRuleViolation> getRuleViolations(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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