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> getOwlRules()
          Get the list of rules, which require a global view of the GAF (GafDocument) and OWL.
 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

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

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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