org.coode.owlapi.obo.parser

Class OBOConsumer

java.lang.Object

org.coode.owlapi.obo.parser.OBOConsumer

All Implemented Interfaces:

OBOParserHandler

public class OBOConsumer
extends Object
implements OBOParserHandler

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 10-Jan-2007

Constructor Summary

Constructors

Constructor and Description
OBOConsumer(OWLOntologyManager owlOntologyManager, OWLOntology ontology, OWLOntologyLoaderConfiguration configuration, IRI baseIRI)
OBOConsumer(OWLOntology ontology, OWLOntologyLoaderConfiguration configuration, IRI baseIRI)

Method Summary

Methods

Modifier and Type	Method and Description
void	addIntersectionOfOperand(OWLClassExpression classExpression)
void	addSymbolicIdMapping(String symbolicName, IRI fullIRI)
void	addUnionOfOperand(OWLClassExpression classExpression)
void	endFrame()
void	endHeader()
OWLClass	getCurrentClass()
OWLEntity	getCurrentEntity()
String	getCurrentId()
String	getDefaultNamespaceTagValue() Gets the default-namespace tag value for the current ontology.
IDSpaceManager	getIdSpaceManager() Gets a COPY of the IDSpaceManager held by this OBOConsumer.
IRI	getIRIFromOBOId(String oboId) Gets an IRI from an OBO ID.
IRI	getIRIFromTagName(String tagName) Gets an IRI from a tag name.
OWLOntology	getOntology()
OWLOntologyManager	getOWLOntologyManager()
IRI	getRelationIRIFromSymbolicIdOrOBOId(String symbolicIdOrOBOId)
String	getStanzaType()
void	handleTagValue(String tag, String value, String qualifierBlock, String comment)
boolean	isInstanceType()
boolean	isTerm()
boolean	isTypedef()
OWLAnnotation	parseXRef(String xref)
void	registerIdSpace(String idSpacePrefix, String iriPrefix)
void	setCurrentId(String currentId)
void	setDataVersionTagValue(String dataVersionTagValue) Sets the value of the data-version tag for the current ontology that is being parsed.
void	setDefaultNamespaceTagValue(String defaultNamespaceTagValue) Sets the value of the default-namespace tag for the current ontology being parsed.
void	setOntologyTagValue(String ontologyTagValue) Sets the value of the ontology tag for the current ontology that is being parsed.
void	startFrame(String name)
void	startHeader()
String	unescapeTagValue(String value)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OBOConsumer

public OBOConsumer(OWLOntology ontology,
           OWLOntologyLoaderConfiguration configuration,
           IRI baseIRI)

OBOConsumer

public OBOConsumer(OWLOntologyManager owlOntologyManager,
           OWLOntology ontology,
           OWLOntologyLoaderConfiguration configuration,
           IRI baseIRI)

Method Detail

getOWLOntologyManager

public OWLOntologyManager getOWLOntologyManager()

getOntology

public OWLOntology getOntology()

getCurrentId

public String getCurrentId()

addSymbolicIdMapping

public void addSymbolicIdMapping(String symbolicName,
                        IRI fullIRI)

setDefaultNamespaceTagValue

public void setDefaultNamespaceTagValue(String defaultNamespaceTagValue)

Sets the value of the default-namespace tag for the current ontology being parsed.

Parameters:

defaultNamespaceTagValue - The value of the default-namespace tag.

getDefaultNamespaceTagValue

public String getDefaultNamespaceTagValue()

Gets the default-namespace tag value for the current ontology. If not default-namespace tag value has been set explicitly then this method returns the default value which is equal to OBOVocabulary.OBO_IRI_BASE.

Returns:

The default-namespace tag value. Not null.

setOntologyTagValue

public void setOntologyTagValue(String ontologyTagValue)

Sets the value of the ontology tag for the current ontology that is being parsed. This is used to construct an OWLOntologyID for the current ontology once the ontology header has been parsed in its entirety.

Parameters:

ontologyTagValue - The ontology tag value. Ultimately, this will be translated to an IRI.

setDataVersionTagValue

public void setDataVersionTagValue(String dataVersionTagValue)

Sets the value of the data-version tag for the current ontology that is being parsed. This is used to construct an OWLOntologyID for the current ontology once the ontology header has been parsed in its entirety.

Parameters:

dataVersionTagValue - The data-version tag value. Ultimately, this will be translated to an IRI.

registerIdSpace

public void registerIdSpace(String idSpacePrefix,
                   String iriPrefix)

getIdSpaceManager

public IDSpaceManager getIdSpaceManager()

Gets a COPY of the IDSpaceManager held by this OBOConsumer.

Returns:

A copy of the IDSpaceManager held by this consumer.

setCurrentId

public void setCurrentId(String currentId)

addUnionOfOperand

public void addUnionOfOperand(OWLClassExpression classExpression)

addIntersectionOfOperand

public void addIntersectionOfOperand(OWLClassExpression classExpression)

getStanzaType

public String getStanzaType()

isTerm

public boolean isTerm()

isTypedef

public boolean isTypedef()

isInstanceType

public boolean isInstanceType()

startHeader

public void startHeader()

Specified by:

startHeader in interface OBOParserHandler

endHeader

public void endHeader()

Specified by:

endHeader in interface OBOParserHandler

startFrame

public void startFrame(String name)

Specified by:

startFrame in interface OBOParserHandler

endFrame

public void endFrame()

Specified by:

endFrame in interface OBOParserHandler

handleTagValue

public void handleTagValue(String tag,
                  String value,
                  String qualifierBlock,
                  String comment)

Specified by:

handleTagValue in interface OBOParserHandler

unescapeTagValue

public String unescapeTagValue(String value)

getCurrentClass

public OWLClass getCurrentClass()

getCurrentEntity

public OWLEntity getCurrentEntity()

getIRIFromTagName

public IRI getIRIFromTagName(String tagName)

Gets an IRI from a tag name.

Parameters:

tagName - The tag name.

Returns:

The IRI for the tag name. For built in tags this is obtained from the OBOVocabulary enum. Not null.

Throws:

NullPointerException - if tagName is null.

getIRIFromOBOId

public IRI getIRIFromOBOId(String oboId)

Gets an IRI from an OBO ID. The OBO ID may be a canonical OBO ID of the form idspace:sequence or it may be a non-canonical ID.

Parameters:

oboId - The OBO ID

Returns:

An IRI obtained from the translation of the OBO ID.

getRelationIRIFromSymbolicIdOrOBOId

public IRI getRelationIRIFromSymbolicIdOrOBOId(String symbolicIdOrOBOId)

parseXRef

public OWLAnnotation parseXRef(String xref)