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.

Author:
cjm

Constructor Summary
AnnotationTaxonRule(OWLGraphWrapper graph, String neverId, String onlyId)
           
 
Method Summary
 boolean check(String annotationCls, String taxonCls)
           
 Set<AnnotationRuleViolation> getRuleViolations(GeneAnnotation a)
          Given an annotation, find the set of violations using the rule
 Set<AnnotationRuleViolation> getRuleViolations(String annotationCls, String taxonCls)
           
 
Methods inherited from class owltools.gaf.rules.AbstractAnnotationRule
getRuleId, getRuleViolations, getRuleViolations, isAnnotationLevel, isDocumentLevel, isOwlDocumentLevel, setRuleId
 
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,
                           String neverId,
                           String onlyId)
Parameters:
graph - The OWLGraphWrapper with merged-in taxon constraints
neverId -
onlyId -
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()

check

public boolean check(String annotationCls,
                     String taxonCls)

getRuleViolations

public Set<AnnotationRuleViolation> getRuleViolations(String annotationCls,
                                                      String taxonCls)


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