owltools.gaf.rules.go
Class GoAnnotationTaxonRule

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

public class GoAnnotationTaxonRule
extends AnnotationTaxonRule

Checks if an annotation is valid according to GO taxon constraints. Ensure that taxGraphWrapper contains:

 http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
 http://www.geneontology.org/quality_control/annotation_checks/taxon_checks/taxon_go_triggers.obo
 http://www.geneontology.org/quality_control/annotation_checks/taxon_checks/ncbi_taxon_slim.obo
 http://www.geneontology.org/quality_control/annotation_checks/taxon_checks/taxon_union_terms.obo
 
See also: http://www.biomedcentral.com/1471-2105/11/530

Author:
cjm

Field Summary
static String PERMANENT_JAVA_ID
          The string to identify this class in the annotation_qc.xml and related factories.
 
Constructor Summary
GoAnnotationTaxonRule(OWLGraphWrapper graphWrapper)
           
 
Method Summary
 
Methods inherited from class owltools.gaf.rules.AnnotationTaxonRule
check, getRuleViolations, getRuleViolations
 
Methods inherited from class owltools.gaf.rules.AbstractAnnotationRule
getDate, getDescription, getName, getRuleId, getRuleViolations, getRuleViolations, getStatus, isAnnotationLevel, isDocumentLevel, isOwlDocumentLevel, setDate, setDescription, 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

GoAnnotationTaxonRule

public GoAnnotationTaxonRule(OWLGraphWrapper graphWrapper)
Parameters:
graphWrapper -


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