owltools.gaf.rules.go

Class GoClassReferenceAnnotationRule

java.lang.Object

owltools.gaf.rules.AbstractAnnotationRule

owltools.gaf.rules.go.GoClassReferenceAnnotationRule

All Implemented Interfaces:

AnnotationRule

public class GoClassReferenceAnnotationRule
extends AbstractAnnotationRule

Checks to see if an annotation uses a class that is not in the current ontology, and that the class has not been obsoleted

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
GoClassReferenceAnnotationRule(OWLGraphWrapper wrapper, String... idPrefixes)

Method Summary

Methods

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

Methods inherited from class owltools.gaf.rules.AbstractAnnotationRule

getDate, getDescription, getGrandFatheringDate, getName, getPredictedAnnotations, getRuleId, getRuleViolations, getRuleViolations, getStatus, hasGrandFathering, isAnnotationLevel, isDocumentLevel, isInferringAnnotations, 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

GoClassReferenceAnnotationRule

public GoClassReferenceAnnotationRule(OWLGraphWrapper wrapper,
                              String... idPrefixes)

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()