owltools.gaf.rules.go
Class BasicChecksRule

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

public class BasicChecksRule
extends AbstractAnnotationRule

This class performs basic checks. See the GO_AR:0000001 rule in the "http://www.geneontology.org/quality_control/annotation_checks/annotation_qc.xml" file for details about the checks.

Author:
Shahid Manzoor

Field Summary
static ThreadLocal<SimpleDateFormat> dtFormat
           
static String PERMANENT_JAVA_ID
          The string to identify this class in the annotation_qc.xml and related factories.
 
Constructor Summary
BasicChecksRule(String xrefAbbsLocation, TraversingEcoMapper eco)
           
 
Method Summary
 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

dtFormat

public static final ThreadLocal<SimpleDateFormat> dtFormat
Constructor Detail

BasicChecksRule

public BasicChecksRule(String xrefAbbsLocation,
                       TraversingEcoMapper eco)
Parameters:
xrefAbbsLocation -
eco -
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()


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