owltools.gaf.rules.go

Class GoAnnotationExperimentalPredictionRule

java.lang.Object

owltools.gaf.rules.AbstractAnnotationRule

owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule

All Implemented Interfaces:

AnnotationRule

public class GoAnnotationExperimentalPredictionRule
extends AbstractAnnotationRule

Field Summary

Fields

Modifier and Type	Field and Description
static String	PERMANENT_JAVA_ID The string to identify this class in the annotation_qc.xml and related factories.

Constructor Summary

Constructors

Constructor and Description
GoAnnotationExperimentalPredictionRule(OWLGraphWrapper source)

Method Summary

Methods

Modifier and Type	Method and Description
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)