owltools.gaf.rules
Interface AnnotationRule

All Known Implementing Classes:
AbstractAnnotationRule, AnnotationRegularExpressionFromXMLRule, AnnotationTaxonRule, BasicChecksRule, GenericReasonerValidationCheck, GoAnnotationTaxonRule, GoBindingCheckWithFieldRule, GoClassReferenceAnnotationRule, GoICAnnotationRule, GoIDAAnnotationRule, GoIEPRestrictionsRule, GoIPIAnnotationRule, GoIPICatalyticActivityRestrictionsRule, GoNoISSProteinBindingRule

public interface AnnotationRule


Method Summary
 String getRuleId()
          Get the ruleId.
 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
 Set<AnnotationRuleViolation> getRuleViolations(OWLGraphWrapper graph)
          Given a whole GafDocument in OWL, find the set of violations using the rule
 boolean isAnnotationLevel()
           
 boolean isDocumentLevel()
           
 boolean isOwlDocumentLevel()
           
 void setRuleId(String ruleId)
          Set the rule id
 

Method Detail

getRuleViolations

Set<AnnotationRuleViolation> getRuleViolations(GeneAnnotation a)
Given an annotation, find the set of violations using the rule

Parameters:
a - annotation
Returns:
set of violations
See Also:
isAnnotationLevel()

getRuleViolations

Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc)
Given a whole GafDocument , find the set of violations using the rule

Parameters:
gafDoc -
Returns:
set of violations
See Also:
isDocumentLevel()

getRuleViolations

Set<AnnotationRuleViolation> getRuleViolations(OWLGraphWrapper graph)
Given a whole GafDocument in OWL, find the set of violations using the rule

Parameters:
graph -
Returns:
set of violations
See Also:
isOwlDocumentLevel()

setRuleId

void setRuleId(String ruleId)
Set the rule id

Parameters:
ruleId -

getRuleId

String getRuleId()
Get the ruleId.

Returns:
ruleId

isAnnotationLevel

boolean isAnnotationLevel()
Returns:
true if the rule has to be applied to a GeneAnnotation.
See Also:
getRuleViolations(GeneAnnotation)

isDocumentLevel

boolean isDocumentLevel()
Returns:
true if the rule has to be applied to the whole GA document.
See Also:
getRuleViolations(GafDocument)

isOwlDocumentLevel

boolean isOwlDocumentLevel()
Returns:
true if the rule has to be applied to the whole OWL document.
See Also:
getRuleViolations(OWLGraphWrapper)


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