owltools.gaf.rules

Class AnnotationRulesFactoryImpl

java.lang.Object

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

Fields

Modifier and Type	Field and Description
static ThreadLocal<DateFormat>	status_df

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AnnotationRulesFactoryImpl(String path, OWLGraphWrapper graph)

Method Summary

Methods

Modifier and Type	Method and Description
protected AnnotationRule	getClassForName(String className)
List<AnnotationRule>	getExperimentalInferenceRules() Get the list of rules, which check for inferred annotations.
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, List<AnnotationRule> experimentalInferenceRules)
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,
                         List<AnnotationRule> experimentalInferenceRules)

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

getExperimentalInferenceRules

public List<AnnotationRule> getExperimentalInferenceRules()

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:

getExperimentalInferenceRules 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