owltools.gaf.rules.go
Class GoAnnotationExperimentalPredictionRule

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

public class GoAnnotationExperimentalPredictionRule
extends AbstractAnnotationRule


Field Summary
static String PERMANENT_JAVA_ID
          The string to identify this class in the annotation_qc.xml and related factories.
 
Constructor Summary
GoAnnotationExperimentalPredictionRule(OWLGraphWrapper source)
           
 
Method Summary
 List<Prediction> getPredictedAnnotations(GafDocument gafDoc, OWLGraphWrapper graph)
          Given a whole GafDocument in plan and OWL format, check for possible new inferred annotations (Prediction).
 Set<AnnotationRuleViolation> getRuleViolations(GeneAnnotation a)
          Given an annotation, find the set of violations using the rule
 boolean isAnnotationLevel()
           
 boolean isInferringAnnotations()
           
 
Methods inherited from class owltools.gaf.rules.AbstractAnnotationRule
getDate, getDescription, getGrandFatheringDate, getName, getRuleId, getRuleViolations, getRuleViolations, getStatus, hasGrandFathering, isDocumentLevel, 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

GoAnnotationExperimentalPredictionRule

public GoAnnotationExperimentalPredictionRule(OWLGraphWrapper source)
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)

getPredictedAnnotations

public List<Prediction> getPredictedAnnotations(GafDocument gafDoc,
                                                OWLGraphWrapper graph)
Description copied from interface: AnnotationRule
Given a whole GafDocument in plan and OWL format, check for possible new inferred annotations (Prediction).

Specified by:
getPredictedAnnotations in interface AnnotationRule
Overrides:
getPredictedAnnotations in class AbstractAnnotationRule
Returns:
set of inferred annotation predictions

isInferringAnnotations

public boolean isInferringAnnotations()
Specified by:
isInferringAnnotations in interface AnnotationRule
Overrides:
isInferringAnnotations in class AbstractAnnotationRule
Returns:
true, if the rule is also capable of inferring new annotations.
See Also:
AnnotationRule.getPredictedAnnotations(GafDocument, OWLGraphWrapper)


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