owltools.gaf.rules.go
Class GoAnnotationPredictionRule
java.lang.Object
owltools.gaf.rules.AbstractAnnotationRule
owltools.gaf.rules.go.GoAnnotationPredictionRule
- All Implemented Interfaces:
- AnnotationRule
public class GoAnnotationPredictionRule
- extends AbstractAnnotationRule
Field Summary |
static String |
PERMANENT_JAVA_ID
The string to identify this class in the annotation_qc.xml and related factories. |
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 |
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
GoAnnotationPredictionRule
public GoAnnotationPredictionRule(OWLGraphWrapper source)
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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