owltools.gaf.rules.go
Class GoAnnotationRulesFactoryImpl

java.lang.Object
  extended by owltools.gaf.rules.AnnotationRulesFactoryImpl
      extended by owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
All Implemented Interfaces:
AnnotationRulesFactory

public class GoAnnotationRulesFactoryImpl
extends AnnotationRulesFactoryImpl


Field Summary
 
Fields inherited from class owltools.gaf.rules.AnnotationRulesFactoryImpl
status_df
 
Constructor Summary
GoAnnotationRulesFactoryImpl(OWLGraphWrapper graph, TraversingEcoMapper eco, boolean createOntologyModules)
           
GoAnnotationRulesFactoryImpl(ParserWrapper parserWrapper, boolean createOntologyModules)
           
GoAnnotationRulesFactoryImpl(String qcfile, String xrfabbslocation, OWLGraphWrapper graph, TraversingEcoMapper eco, boolean createOntologyModules)
           
GoAnnotationRulesFactoryImpl(String qcfile, String xrfabbslocation, ParserWrapper p, List<String> ont, String eco, boolean createOntologyModules)
           
GoAnnotationRulesFactoryImpl(String qcfile, String xrfabbslocation, ParserWrapper p, String go, String gorel, String eco)
          Deprecated. 
 
Method Summary
protected  AnnotationRule getClassForName(String className)
           
protected  void handleAdditionalRules(List<AnnotationRule> annotationRules, List<AnnotationRule> documentRules, List<AnnotationRule> owlRules, List<AnnotationRule> inferenceRules, List<AnnotationRule> experimentalInferenceRules)
           
 
Methods inherited from class owltools.gaf.rules.AnnotationRulesFactoryImpl
getExperimentalInferenceRules, getGafDocumentRules, getGeneAnnotationRules, getGraph, getInferenceRules, getOwlRules, init
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GoAnnotationRulesFactoryImpl

public GoAnnotationRulesFactoryImpl(ParserWrapper parserWrapper,
                                    boolean createOntologyModules)

GoAnnotationRulesFactoryImpl

@Deprecated
public GoAnnotationRulesFactoryImpl(String qcfile,
                                               String xrfabbslocation,
                                               ParserWrapper p,
                                               String go,
                                               String gorel,
                                               String eco)
Deprecated. 


GoAnnotationRulesFactoryImpl

public GoAnnotationRulesFactoryImpl(String qcfile,
                                    String xrfabbslocation,
                                    ParserWrapper p,
                                    List<String> ont,
                                    String eco,
                                    boolean createOntologyModules)

GoAnnotationRulesFactoryImpl

public GoAnnotationRulesFactoryImpl(OWLGraphWrapper graph,
                                    TraversingEcoMapper eco,
                                    boolean createOntologyModules)

GoAnnotationRulesFactoryImpl

public GoAnnotationRulesFactoryImpl(String qcfile,
                                    String xrfabbslocation,
                                    OWLGraphWrapper graph,
                                    TraversingEcoMapper eco,
                                    boolean createOntologyModules)
Method Detail

handleAdditionalRules

protected void handleAdditionalRules(List<AnnotationRule> annotationRules,
                                     List<AnnotationRule> documentRules,
                                     List<AnnotationRule> owlRules,
                                     List<AnnotationRule> inferenceRules,
                                     List<AnnotationRule> experimentalInferenceRules)
Overrides:
handleAdditionalRules in class AnnotationRulesFactoryImpl

getClassForName

protected AnnotationRule getClassForName(String className)
                                  throws Exception
Overrides:
getClassForName in class AnnotationRulesFactoryImpl
Returns:
annotation rule (never null)
Throws:
Exception


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