owltools.gaf.rules.go
Class GOReciprocalAnnotationRule

java.lang.Object
  extended by owltools.gaf.rules.AbstractAnnotationRule
      extended by owltools.gaf.rules.go.GOReciprocalAnnotationRule
All Implemented Interfaces:
AnnotationRule

public class GOReciprocalAnnotationRule
extends AbstractAnnotationRule

GO_AR:0000004


Field Summary
static String PERMANENT_JAVA_ID
          The string to identify this class in the annotation_qc.xml and related factories.
 
Constructor Summary
GOReciprocalAnnotationRule(OWLGraphWrapper graph, OWLGraphWrapper eco)
           
 
Method Summary
 Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc)
          Given a whole GafDocument , find the set of violations using the rule
 Set<AnnotationRuleViolation> getRuleViolations(GeneAnnotation a)
          Given an annotation, find the set of violations using the rule
 boolean isAnnotationLevel()
           
 boolean isDocumentLevel()
           
 
Methods inherited from class owltools.gaf.rules.AbstractAnnotationRule
getDate, getDescription, getGrandFatheringDate, getName, getRuleId, getRuleViolations, getStatus, hasGrandFathering, isOwlDocumentLevel, setDate, setDescription, setGrandFatheringDate, setName, setRuleId, setStatus
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

PERMANENT_JAVA_ID

public static final String PERMANENT_JAVA_ID
The string to identify this class in the annotation_qc.xml and related factories. This is not supposed to be changed.

See Also:
Constant Field Values
Constructor Detail

GOReciprocalAnnotationRule

public GOReciprocalAnnotationRule(OWLGraphWrapper graph,
                                  OWLGraphWrapper eco)
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()

isAnnotationLevel

public boolean isAnnotationLevel()
Specified by:
isAnnotationLevel in interface AnnotationRule
Overrides:
isAnnotationLevel in class AbstractAnnotationRule
Returns:
true if the rule has to be applied to a GeneAnnotation.
See Also:
AnnotationRule.getRuleViolations(GeneAnnotation)

getRuleViolations

public Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc)
Description copied from interface: AnnotationRule
Given a whole GafDocument , 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.isDocumentLevel()

isDocumentLevel

public boolean isDocumentLevel()
Specified by:
isDocumentLevel in interface AnnotationRule
Overrides:
isDocumentLevel in class AbstractAnnotationRule
Returns:
true if the rule has to be applied to the whole GA document.
See Also:
AnnotationRule.getRuleViolations(GafDocument)


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