owltools.gaf.rules
Class AnnotationRulesFactoryImpl

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

public class AnnotationRulesFactoryImpl
extends Object
implements AnnotationRulesFactory

This class reads the annotation_qc.xml file and builds AnnotationRule objects from the qc file.

Author:
shahidmanzoor

Field Summary
static ThreadLocal<DateFormat> status_df
           
 
Constructor Summary
protected AnnotationRulesFactoryImpl(String path, OWLGraphWrapper graph)
           
 
Method Summary
protected  AnnotationRule getClassForName(String className)
           
 List<AnnotationRule> getGafDocumentRules()
          Get the list of rules, which require a global view of the GAF (GafDocument).
 List<AnnotationRule> getGeneAnnotationRules()
          Get the list of rules to be applied for each GeneAnnotation
 OWLGraphWrapper getGraph()
          Get the underlying ontology graph for this rule factory.
 List<AnnotationRule> getInferenceRules()
          Get the list of rules, which check for inferred annotations.
 List<AnnotationRule> getOwlRules()
          Get the list of rules, which require a global view of the GAF (GafDocument) and OWL.
protected  void handleAdditionalRules(List<AnnotationRule> annotationRules, List<AnnotationRule> documentRules, List<AnnotationRule> owlRules, List<AnnotationRule> inferenceRules)
           
 void init()
          Initialize the factory.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

status_df

public static final ThreadLocal<DateFormat> status_df
Constructor Detail

AnnotationRulesFactoryImpl

protected AnnotationRulesFactoryImpl(String path,
                                     OWLGraphWrapper graph)
Parameters:
path - location of the annotation_qc.xml file
graph -
Method Detail

init

public void init()
Description copied from interface: AnnotationRulesFactory
Initialize the factory.

Specified by:
init in interface AnnotationRulesFactory

handleAdditionalRules

protected void handleAdditionalRules(List<AnnotationRule> annotationRules,
                                     List<AnnotationRule> documentRules,
                                     List<AnnotationRule> owlRules,
                                     List<AnnotationRule> inferenceRules)

getClassForName

protected AnnotationRule getClassForName(String className)
                                  throws Exception
Parameters:
className -
Returns:
annotation rule (never null)
Throws:
Exception

getGeneAnnotationRules

public List<AnnotationRule> getGeneAnnotationRules()
Description copied from interface: AnnotationRulesFactory
Get the list of rules to be applied for each GeneAnnotation

Specified by:
getGeneAnnotationRules in interface AnnotationRulesFactory
Returns:
rules

getGafDocumentRules

public List<AnnotationRule> getGafDocumentRules()
Description copied from interface: AnnotationRulesFactory
Get the list of rules, which require a global view of the GAF (GafDocument).

Specified by:
getGafDocumentRules in interface AnnotationRulesFactory
Returns:
rules

getOwlRules

public List<AnnotationRule> getOwlRules()
Description copied from interface: AnnotationRulesFactory
Get the list of rules, which require a global view of the GAF (GafDocument) and OWL.

Specified by:
getOwlRules in interface AnnotationRulesFactory
Returns:
rules

getInferenceRules

public List<AnnotationRule> getInferenceRules()
Description copied from interface: AnnotationRulesFactory
Get the list of rules, which check for inferred annotations. These also need the global view of the GAF (GafDocument) and the OWL.

Specified by:
getInferenceRules in interface AnnotationRulesFactory
Returns:
rules

getGraph

public OWLGraphWrapper getGraph()
Description copied from interface: AnnotationRulesFactory
Get the underlying ontology graph for this rule factory.

Specified by:
getGraph in interface AnnotationRulesFactory
Returns:
graph or null


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