owltools.gaf.rules
Class AbstractAnnotationRule

java.lang.Object
  extended by owltools.gaf.rules.AbstractAnnotationRule
All Implemented Interfaces:
AnnotationRule
Direct Known Subclasses:
AnnotationRegularExpressionFromXMLRule, AnnotationTaxonRule, BasicChecksRule, GenericReasonerValidationCheck, GoBindingCheckWithFieldRule, GoClassReferenceAnnotationRule, GoICAnnotationRule, GoIDAAnnotationRule, GoIEPRestrictionsRule, GoIPIAnnotationRule, GoIPICatalyticActivityRestrictionsRule, GoNoISSProteinBindingRule

public abstract class AbstractAnnotationRule
extends Object
implements AnnotationRule


Constructor Summary
AbstractAnnotationRule()
           
 
Method Summary
 String getRuleId()
          Get the ruleId.
 Set<AnnotationRuleViolation> getRuleViolations(GafDocument gafDoc)
          Given a whole GafDocument , find the set of violations using the rule
abstract  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
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

AbstractAnnotationRule

public AbstractAnnotationRule()
Method Detail

getRuleViolations

public abstract 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
Parameters:
a - annotation
Returns:
set of violations
See Also:
AnnotationRule.isAnnotationLevel()

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
Returns:
set of violations
See Also:
AnnotationRule.isDocumentLevel()

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
Returns:
set of violations
See Also:
AnnotationRule.isOwlDocumentLevel()

setRuleId

public void setRuleId(String ruleId)
Description copied from interface: AnnotationRule
Set the rule id

Specified by:
setRuleId in interface AnnotationRule

getRuleId

public String getRuleId()
Description copied from interface: AnnotationRule
Get the ruleId.

Specified by:
getRuleId in interface AnnotationRule
Returns:
ruleId

isAnnotationLevel

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

isDocumentLevel

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

isOwlDocumentLevel

public boolean isOwlDocumentLevel()
Specified by:
isOwlDocumentLevel in interface AnnotationRule
Returns:
true if the rule has to be applied to the whole OWL document.
See Also:
AnnotationRule.getRuleViolations(OWLGraphWrapper)


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