fr.curie.BiNoM.pathways.biopax
Class proteinImpl

java.lang.Object
  com.hp.hpl.jena.rdf.listeners.StatementListener
      com.ibm.adtech.jastor.ThingImpl
          fr.curie.BiNoM.pathways.biopax.proteinImpl

All Implemented Interfaces:

com.hp.hpl.jena.rdf.model.ModelChangedListener, com.ibm.adtech.jastor.Thing, entity, physicalEntity, protein

public class proteinImpl
extends com.ibm.adtech.jastor.ThingImpl
implements protein

Implementation of protein Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

(URI: http://www.biopax.org/release/biopax-level2.owl#protein)

Field Summary

Fields inherited from class com.ibm.adtech.jastor.ThingImpl

copyright

Fields inherited from interface fr.curie.BiNoM.pathways.biopax.protein

TYPE

Fields inherited from interface com.ibm.adtech.jastor.Thing

copyright

Method Summary

void	addAVAILABILITY(java.lang.String AVAILABILITY) Add a 'AVAILABILITY' property value
void	addCOMMENT(java.lang.String COMMENT) Add a 'COMMENT' property value
dataSource	addDATA_DASH_SOURCE() Adds an anonymous value for the 'DATA_DASH_SOURCE' property
void	addDATA_DASH_SOURCE(dataSource DATA_DASH_SOURCE) Adds a value for the 'DATA_DASH_SOURCE' property
dataSource	addDATA_DASH_SOURCE(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'DATA_DASH_SOURCE' property.
void	addedStatement(com.hp.hpl.jena.rdf.model.Statement stmt)
void	addSYNONYMS(java.lang.String SYNONYMS) Add a 'SYNONYMS' property value
xref	addXREF() Adds an anonymous value for the 'XREF' property
xref	addXREF(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'XREF' property.
void	addXREF(xref XREF) Adds a value for the 'XREF' property
void	clearCache()
java.util.Iterator	getAVAILABILITY() Iterates through the 'AVAILABILITY' property values.
java.util.Iterator	getCOMMENT() Iterates through the 'COMMENT' property values.
java.util.Iterator	getDATA_DASH_SOURCE() Get an Iterator the 'DATA_DASH_SOURCE' property values.
java.lang.String	getNAME() Gets the 'NAME' property value
bioSource	getORGANISM() Gets the 'ORGANISM' property value
java.lang.String	getSEQUENCE() Gets the 'SEQUENCE' property value
java.lang.String	getSHORT_DASH_NAME() Gets the 'SHORT_DASH_NAME' property value
java.util.Iterator	getSYNONYMS() Iterates through the 'SYNONYMS' property values.
java.util.Iterator	getXREF() Get an Iterator the 'XREF' property values.
java.util.List	listStatements()
void	registerListener(com.ibm.adtech.jastor.ThingListener listener)
void	removeAVAILABILITY(java.lang.String AVAILABILITY) Remove a 'AVAILABILITY' property value.
void	removeCOMMENT(java.lang.String COMMENT) Remove a 'COMMENT' property value.
void	removeDATA_DASH_SOURCE(dataSource DATA_DASH_SOURCE) Removes a value for the 'DATA_DASH_SOURCE' property.
void	removedStatement(com.hp.hpl.jena.rdf.model.Statement stmt)
void	removeSYNONYMS(java.lang.String SYNONYMS) Remove a 'SYNONYMS' property value.
void	removeXREF(xref XREF) Removes a value for the 'XREF' property.
void	setNAME(java.lang.String NAME) Sets the 'NAME' property value
bioSource	setORGANISM() Sets the 'ORGANISM' property value to an anonymous node
void	setORGANISM(bioSource ORGANISM) Sets the 'ORGANISM' property value
bioSource	setORGANISM(com.hp.hpl.jena.rdf.model.Resource resource) Sets the 'ORGANISM' property value to the given resource, and add's rdf:type properties.
void	setSEQUENCE(java.lang.String SEQUENCE) Sets the 'SEQUENCE' property value
void	setSHORT_DASH_NAME(java.lang.String SHORT_DASH_NAME) Sets the 'SHORT_DASH_NAME' property value
void	unregisterListener(com.ibm.adtech.jastor.ThingListener listener)

Methods inherited from class com.ibm.adtech.jastor.ThingImpl

equals, isRDFType, model, removeStatements, resource, toString, uri

Methods inherited from class com.hp.hpl.jena.rdf.listeners.StatementListener

addedStatements, addedStatements, addedStatements, addedStatements, notifyEvent, removedStatements, removedStatements, removedStatements, removedStatements

Methods inherited from class java.lang.Object

getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface com.ibm.adtech.jastor.Thing

isRDFType, model, removeStatements, resource, uri

Method Detail

listStatements

public java.util.List listStatements()

Specified by:

listStatements in interface com.ibm.adtech.jastor.Thing

Overrides:

listStatements in class com.ibm.adtech.jastor.ThingImpl

clearCache

public void clearCache()

Specified by:

clearCache in interface com.ibm.adtech.jastor.Thing

Overrides:

clearCache in class com.ibm.adtech.jastor.ThingImpl

getDATA_DASH_SOURCE

public java.util.Iterator getDATA_DASH_SOURCE()
                                       throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Get an Iterator the 'DATA_DASH_SOURCE' property values. This Iteartor may be used to remove all such values.

Specified by:

getDATA_DASH_SOURCE in interface entity

Returns:

Iterator of dataSource

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.DATA_DASH_SOURCEProperty

addDATA_DASH_SOURCE

public void addDATA_DASH_SOURCE(dataSource DATA_DASH_SOURCE)
                         throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Adds a value for the 'DATA_DASH_SOURCE' property

Specified by:

addDATA_DASH_SOURCE in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.DATA_DASH_SOURCEProperty

addDATA_DASH_SOURCE

public dataSource addDATA_DASH_SOURCE()
                               throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Adds an anonymous value for the 'DATA_DASH_SOURCE' property

Specified by:

addDATA_DASH_SOURCE in interface entity

Returns:

The anoymous dataSource created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.DATA_DASH_SOURCEProperty

addDATA_DASH_SOURCE

public dataSource addDATA_DASH_SOURCE(com.hp.hpl.jena.rdf.model.Resource resource)
                               throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Adds a value for the 'DATA_DASH_SOURCE' property. This method is equivalent constructing a new instance of dataSource with the factory and calling addDATA_DASH_SOURCE(fr.curie.BiNoM.pathways.biopax.dataSource DATA_DASH_SOURCE) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#dataSource. That is, this method should not be used as a shortcut for creating new objects in the model.

Specified by:

addDATA_DASH_SOURCE in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.DATA_DASH_SOURCEProperty

removeDATA_DASH_SOURCE

public void removeDATA_DASH_SOURCE(dataSource DATA_DASH_SOURCE)
                            throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Removes a value for the 'DATA_DASH_SOURCE' property. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Specified by:

removeDATA_DASH_SOURCE in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.DATA_DASH_SOURCEProperty

getAVAILABILITY

public java.util.Iterator getAVAILABILITY()
                                   throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Iterates through the 'AVAILABILITY' property values. This Iteartor may be used to remove all such values.

Specified by:

getAVAILABILITY in interface entity

Returns:

Iterator of String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.AVAILABILITYProperty

addAVAILABILITY

public void addAVAILABILITY(java.lang.String AVAILABILITY)
                     throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Add a 'AVAILABILITY' property value

Specified by:

addAVAILABILITY in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.AVAILABILITYProperty

removeAVAILABILITY

public void removeAVAILABILITY(java.lang.String AVAILABILITY)
                        throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Remove a 'AVAILABILITY' property value. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Specified by:

removeAVAILABILITY in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.AVAILABILITYProperty

getCOMMENT

public java.util.Iterator getCOMMENT()
                              throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Iterates through the 'COMMENT' property values. This Iteartor may be used to remove all such values.

Specified by:

getCOMMENT in interface entity

Returns:

Iterator of String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.COMMENTProperty

addCOMMENT

public void addCOMMENT(java.lang.String COMMENT)
                throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Add a 'COMMENT' property value

Specified by:

addCOMMENT in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.COMMENTProperty

removeCOMMENT

public void removeCOMMENT(java.lang.String COMMENT)
                   throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Remove a 'COMMENT' property value. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Specified by:

removeCOMMENT in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.COMMENTProperty

getSHORT_DASH_NAME

public java.lang.String getSHORT_DASH_NAME()
                                    throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Gets the 'SHORT_DASH_NAME' property value

Specified by:

getSHORT_DASH_NAME in interface entity

Returns:

String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.SHORT_DASH_NAMEProperty

setSHORT_DASH_NAME

public void setSHORT_DASH_NAME(java.lang.String SHORT_DASH_NAME)
                        throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Sets the 'SHORT_DASH_NAME' property value

Specified by:

setSHORT_DASH_NAME in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.SHORT_DASH_NAMEProperty

getSYNONYMS

public java.util.Iterator getSYNONYMS()
                               throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Iterates through the 'SYNONYMS' property values. This Iteartor may be used to remove all such values.

Specified by:

getSYNONYMS in interface entity

Returns:

Iterator of String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.SYNONYMSProperty

addSYNONYMS

public void addSYNONYMS(java.lang.String SYNONYMS)
                 throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Add a 'SYNONYMS' property value

Specified by:

addSYNONYMS in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.SYNONYMSProperty

removeSYNONYMS

public void removeSYNONYMS(java.lang.String SYNONYMS)
                    throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Remove a 'SYNONYMS' property value. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Specified by:

removeSYNONYMS in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.SYNONYMSProperty

getNAME

public java.lang.String getNAME()
                         throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Gets the 'NAME' property value

Specified by:

getNAME in interface entity

Returns:

String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.NAMEProperty

setNAME

public void setNAME(java.lang.String NAME)
             throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Sets the 'NAME' property value

Specified by:

setNAME in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.NAMEProperty

getXREF

public java.util.Iterator getXREF()
                           throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Get an Iterator the 'XREF' property values. This Iteartor may be used to remove all such values.

Specified by:

getXREF in interface entity

Returns:

Iterator of xref

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.XREFProperty

addXREF

public void addXREF(xref XREF)
             throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Adds a value for the 'XREF' property

Specified by:

addXREF in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.XREFProperty

addXREF

public xref addXREF()
             throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Adds an anonymous value for the 'XREF' property

Specified by:

addXREF in interface entity

Returns:

The anoymous xref created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.XREFProperty

addXREF

public xref addXREF(com.hp.hpl.jena.rdf.model.Resource resource)
             throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Adds a value for the 'XREF' property. This method is equivalent constructing a new instance of xref with the factory and calling addXREF(fr.curie.BiNoM.pathways.biopax.xref XREF) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#xref. That is, this method should not be used as a shortcut for creating new objects in the model.

Specified by:

addXREF in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.XREFProperty

removeXREF

public void removeXREF(xref XREF)
                throws com.ibm.adtech.jastor.JastorException

Description copied from interface: entity

Removes a value for the 'XREF' property. This method should not be invoked while iterator through values. In that case, the remove() method of the Iterator itself should be used.

Specified by:

removeXREF in interface entity

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

entity.XREFProperty

getSEQUENCE

public java.lang.String getSEQUENCE()
                             throws com.ibm.adtech.jastor.JastorException

Description copied from interface: protein

Gets the 'SEQUENCE' property value

Specified by:

getSEQUENCE in interface protein

Returns:

String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

protein.SEQUENCEProperty

setSEQUENCE

public void setSEQUENCE(java.lang.String SEQUENCE)
                 throws com.ibm.adtech.jastor.JastorException

Description copied from interface: protein

Sets the 'SEQUENCE' property value

Specified by:

setSEQUENCE in interface protein

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

protein.SEQUENCEProperty

getORGANISM

public bioSource getORGANISM()
                      throws com.ibm.adtech.jastor.JastorException

Description copied from interface: protein

Gets the 'ORGANISM' property value

Specified by:

getORGANISM in interface protein

Returns:

bioSource

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

protein.ORGANISMProperty

setORGANISM

public void setORGANISM(bioSource ORGANISM)
                 throws com.ibm.adtech.jastor.JastorException

Description copied from interface: protein

Sets the 'ORGANISM' property value

Specified by:

setORGANISM in interface protein

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

protein.ORGANISMProperty

setORGANISM

public bioSource setORGANISM()
                      throws com.ibm.adtech.jastor.JastorException

Description copied from interface: protein

Sets the 'ORGANISM' property value to an anonymous node

Specified by:

setORGANISM in interface protein

Returns:

bioSource, the created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

protein.ORGANISMProperty

setORGANISM

public bioSource setORGANISM(com.hp.hpl.jena.rdf.model.Resource resource)
                      throws com.ibm.adtech.jastor.JastorException

Description copied from interface: protein

Sets the 'ORGANISM' property value to the given resource, and add's rdf:type properties. This method is equivalent constructing a new instance of bioSource with the factory. and calling setORGANISM(fr.curie.BiNoM.pathways.biopax.bioSource ORGANISM) The resource argument have rdf:type http://www.biopax.org/release/biopax-level2.owl#bioSource. That is, this method should not be used as a shortcut for creating new objects in the model.

Specified by:

setORGANISM in interface protein

Returns:

bioSource, the newly created value

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

protein.ORGANISMProperty

registerListener

public void registerListener(com.ibm.adtech.jastor.ThingListener listener)

Specified by:

registerListener in interface com.ibm.adtech.jastor.Thing

Overrides:

registerListener in class com.ibm.adtech.jastor.ThingImpl

unregisterListener

public void unregisterListener(com.ibm.adtech.jastor.ThingListener listener)

Specified by:

unregisterListener in interface com.ibm.adtech.jastor.Thing

Overrides:

unregisterListener in class com.ibm.adtech.jastor.ThingImpl

addedStatement

public void addedStatement(com.hp.hpl.jena.rdf.model.Statement stmt)

Specified by:

addedStatement in interface com.hp.hpl.jena.rdf.model.ModelChangedListener

Overrides:

addedStatement in class com.hp.hpl.jena.rdf.listeners.StatementListener

removedStatement

public void removedStatement(com.hp.hpl.jena.rdf.model.Statement stmt)

Specified by:

removedStatement in interface com.hp.hpl.jena.rdf.model.ModelChangedListener

Overrides:

removedStatement in class com.hp.hpl.jena.rdf.listeners.StatementListener