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

The Class OBOConsumer.

Author:

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

Constructor Summary

Constructors

Constructor and Description
OBOConsumer(org.semanticweb.owlapi.model.OWLOntologyManager owlOntologyManager, org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration configuration, org.semanticweb.owlapi.model.IRI baseIRI) Deprecated.
OBOConsumer(org.semanticweb.owlapi.model.OWLOntology ontology, org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration configuration, org.semanticweb.owlapi.model.IRI baseIRI) Instantiates a new oBO consumer.

Method Summary

Modifier and Type	Method and Description
void	addIntersectionOfOperand(org.semanticweb.owlapi.model.OWLClassExpression classExpression) Adds the intersection of operand.
void	addSymbolicIdMapping(String symbolicName, org.semanticweb.owlapi.model.IRI fullIRI) Adds the symbolic id mapping.
void	addUnionOfOperand(org.semanticweb.owlapi.model.OWLClassExpression classExpression) Adds the union of operand.
void	endFrame() end frame
void	endHeader() end header
org.semanticweb.owlapi.model.OWLClass	getCurrentClass() Gets the current class.
org.semanticweb.owlapi.model.OWLEntity	getCurrentEntity() Gets the current entity.
String	getCurrentId() Gets the current id.
String	getDefaultNamespaceTagValue() Gets the default-namespace tag value for the current ontology.
IDSpaceManager	getIdSpaceManager() Gets a COPY of the IDSpaceManager held by this OBOConsumer.
org.semanticweb.owlapi.model.IRI	getIRIFromOBOId(String oboId) Gets an IRI from an OBO ID.
org.semanticweb.owlapi.model.IRI	getIRIFromTagName(String tagName) Gets an IRI from a tag name.
org.semanticweb.owlapi.model.OWLOntology	getOntology() Gets the ontology.
org.semanticweb.owlapi.model.OWLOntologyManager	getOWLOntologyManager() Gets the oWL ontology manager.
org.semanticweb.owlapi.model.IRI	getRelationIRIFromSymbolicIdOrOBOId(String symbolicIdOrOBOId) Gets the relation iri from symbolic id or obo id.
String	getStanzaType() Gets the stanza type.
void	handleTagValue(String tag, String value, String qualifierBlock, String comment)
boolean	isInstanceType() Checks if is instance type.
boolean	isTerm() Checks if is term.
boolean	isTypedef() Checks if is typedef.
org.semanticweb.owlapi.model.OWLAnnotation	parseXRef(String xref) Parses the x ref.
void	registerIdSpace(String idSpacePrefix, String iriPrefix) Register id space.
void	setCurrentId(String currentId) Sets the current id.
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() start header
String	unescapeTagValue(String value) Unescape tag value.

Methods inherited from class java.lang.Object

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

Constructor Detail

OBOConsumer

public OBOConsumer(org.semanticweb.owlapi.model.OWLOntology ontology,
                   org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration configuration,
                   org.semanticweb.owlapi.model.IRI baseIRI)

Instantiates a new oBO consumer.

Parameters:

ontology - the ontology

configuration - the configuration

baseIRI - the base iri

OBOConsumer

@Deprecated
public OBOConsumer(org.semanticweb.owlapi.model.OWLOntologyManager owlOntologyManager,
                               org.semanticweb.owlapi.model.OWLOntology ontology,
                               org.semanticweb.owlapi.model.OWLOntologyLoaderConfiguration configuration,
                               org.semanticweb.owlapi.model.IRI baseIRI)

Deprecated.

Instantiates a new oBO consumer.

Parameters:

owlOntologyManager - the owl ontology manager

ontology - the ontology

configuration - the configuration

baseIRI - the base iri

Method Detail

getOWLOntologyManager

public org.semanticweb.owlapi.model.OWLOntologyManager getOWLOntologyManager()

Gets the oWL ontology manager.

Returns:

the oWL ontology manager

getOntology

public org.semanticweb.owlapi.model.OWLOntology getOntology()

Gets the ontology.

Returns:

the ontology

getCurrentId

public String getCurrentId()

Gets the current id.

Returns:

the current id

addSymbolicIdMapping

public void addSymbolicIdMapping(String symbolicName,
                                 org.semanticweb.owlapi.model.IRI fullIRI)

Adds the symbolic id mapping.

Parameters:

symbolicName - the symbolic name

fullIRI - the full iri

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

Returns:

The default-namespace tag value. Not null. OBOVocabulary.OBO_IRI_BASE.

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

Parameters:

ontologyTagValue - The ontology tag value. Ultimately, this will be translated to an IRI. OWLOntologyID for the current ontology once the ontology header has been parsed in its entirety.

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

Parameters:

dataVersionTagValue - The data-version tag value. Ultimately, this will be translated to an IRI. OWLOntologyID for the current ontology once the ontology header has been parsed in its entirety.

registerIdSpace

public void registerIdSpace(String idSpacePrefix,
                            String iriPrefix)

Register id space.

Parameters:

idSpacePrefix - the id space prefix

iriPrefix - the iri prefix

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)

Sets the current id.

Parameters:

currentId - the new current id

addUnionOfOperand

public void addUnionOfOperand(org.semanticweb.owlapi.model.OWLClassExpression classExpression)

Adds the union of operand.

Parameters:

classExpression - the class expression

addIntersectionOfOperand

public void addIntersectionOfOperand(org.semanticweb.owlapi.model.OWLClassExpression classExpression)

Adds the intersection of operand.

Parameters:

classExpression - the class expression

getStanzaType

public String getStanzaType()

Gets the stanza type.

Returns:

the stanza type

isTerm

public boolean isTerm()

Checks if is term.

Returns:

true, if is term

isTypedef

public boolean isTypedef()

Checks if is typedef.

Returns:

true, if is typedef

isInstanceType

public boolean isInstanceType()

Checks if is instance type.

Returns:

true, if is instance type

startHeader

public void startHeader()

Description copied from interface: OBOParserHandler

start header

Specified by:

startHeader in interface OBOParserHandler

endHeader

public void endHeader()

Description copied from interface: OBOParserHandler

end header

Specified by:

endHeader in interface OBOParserHandler

startFrame

public void startFrame(String name)

Specified by:

startFrame in interface OBOParserHandler

Parameters:

name - name

endFrame

public void endFrame()

Description copied from interface: OBOParserHandler

end frame

Specified by:

endFrame in interface OBOParserHandler

handleTagValue

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

Specified by:

handleTagValue in interface OBOParserHandler

Parameters:

tag - tag

value - value

qualifierBlock - qualifierBlock

comment - comment

unescapeTagValue

public String unescapeTagValue(String value)

Unescape tag value.

Parameters:

value - the value

Returns:

the string

getCurrentClass

public org.semanticweb.owlapi.model.OWLClass getCurrentClass()

Gets the current class.

Returns:

the current class

getCurrentEntity

public org.semanticweb.owlapi.model.OWLEntity getCurrentEntity()

Gets the current entity.

Returns:

the current entity

getIRIFromTagName

public org.semanticweb.owlapi.model.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.

getIRIFromOBOId

public org.semanticweb.owlapi.model.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 org.semanticweb.owlapi.model.IRI getRelationIRIFromSymbolicIdOrOBOId(String symbolicIdOrOBOId)

Gets the relation iri from symbolic id or obo id.

Parameters:

symbolicIdOrOBOId - the symbolic id or obo id

Returns:

the relation iri from symbolic id or obo id

parseXRef

public org.semanticweb.owlapi.model.OWLAnnotation parseXRef(String xref)

Parses the x ref.

Parameters:

xref - the xref

Returns:

the oWL annotation