fr.curie.BiNoM.pathways.biopax
Interface conversion

All Superinterfaces:

entity, interaction, physicalInteraction, com.ibm.adtech.jastor.Thing

All Known Subinterfaces:

biochemicalReaction, complexAssembly, transport, transportWithBiochemicalReaction

All Known Implementing Classes:

biochemicalReactionImpl, complexAssemblyImpl, conversionImpl, transportImpl, transportWithBiochemicalReactionImpl

public interface conversion
extends physicalInteraction, com.ibm.adtech.jastor.Thing

Interface for conversion ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

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

RDF Schema Standard Properties
comment : Definition: An interaction in which one or more entities is physically transformed into one or more other entities. Comment: This class is designed to represent a simple, single-step transformation. Multi-step transformations, such as the conversion of glucose to pyruvate in the glycolysis pathway, should be represented as pathways, if known. Since it is a highly abstract class in the ontology, instances of the conversion class should never be created. Examples: A biochemical reaction converts substrates to products, the process of complex assembly converts single molecules to a complex, transport converts entities in one compartment to the same entities in another compartment.^^http://www.w3.org/2001/XMLSchema#string

Field Summary

static com.hp.hpl.jena.rdf.model.Property	LEFTProperty The Jena Property for LEFT
static com.hp.hpl.jena.rdf.model.Property	RIGHTProperty The Jena Property for RIGHT
static com.hp.hpl.jena.rdf.model.Property	SPONTANEOUSProperty The Jena Property for SPONTANEOUS
static com.hp.hpl.jena.rdf.model.Resource	TYPE The rdf:type for this ontology class

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

INTERACTION_DASH_TYPEProperty

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

EVIDENCEProperty, PARTICIPANTSProperty

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

AVAILABILITYProperty, COMMENTProperty, DATA_DASH_SOURCEProperty, NAMEProperty, SHORT_DASH_NAMEProperty, SYNONYMSProperty, XREFProperty

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

copyright

Method Summary

physicalEntityParticipant	addLEFT() Adds an anonymous value for the 'LEFT' property
void	addLEFT(physicalEntityParticipant LEFT) Adds a value for the 'LEFT' property
physicalEntityParticipant	addLEFT(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'LEFT' property.
physicalEntityParticipant	addPARTICIPANTS_asphysicalEntityParticipant() Adds an anonymous value for the 'PARTICIPANTS' property
physicalEntityParticipant	addPARTICIPANTS_asphysicalEntityParticipant(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'PARTICIPANTS' property.
void	addPARTICIPANTS(physicalEntityParticipant PARTICIPANTS) Adds a value for the 'PARTICIPANTS' property
physicalEntityParticipant	addRIGHT() Adds an anonymous value for the 'RIGHT' property
void	addRIGHT(physicalEntityParticipant RIGHT) Adds a value for the 'RIGHT' property
physicalEntityParticipant	addRIGHT(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'RIGHT' property.
java.util.Iterator	getLEFT() Get an Iterator the 'LEFT' property values.
java.util.Iterator	getPARTICIPANTS_asphysicalEntityParticipant() Get an Iterator the 'PARTICIPANTS' property values.
java.util.Iterator	getRIGHT() Get an Iterator the 'RIGHT' property values.
java.lang.String	getSPONTANEOUS() Gets the 'SPONTANEOUS' property value
void	removeLEFT(physicalEntityParticipant LEFT) Removes a value for the 'LEFT' property.
void	removePARTICIPANTS(physicalEntityParticipant PARTICIPANTS) Removes a value for the 'PARTICIPANTS' property.
void	removeRIGHT(physicalEntityParticipant RIGHT) Removes a value for the 'RIGHT' property.
void	setSPONTANEOUS(java.lang.String SPONTANEOUS) Sets the 'SPONTANEOUS' property value

Methods inherited from interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

addINTERACTION_DASH_TYPE, addINTERACTION_DASH_TYPE, addINTERACTION_DASH_TYPE, getINTERACTION_DASH_TYPE, removeINTERACTION_DASH_TYPE

Methods inherited from interface fr.curie.BiNoM.pathways.biopax.interaction

addEVIDENCE, addEVIDENCE, addEVIDENCE, addPARTICIPANTS_asentity, addPARTICIPANTS_asentity, addPARTICIPANTS, getEVIDENCE, getPARTICIPANTS_asentity, removeEVIDENCE, removePARTICIPANTS

Methods inherited from interface fr.curie.BiNoM.pathways.biopax.entity

addAVAILABILITY, addCOMMENT, addDATA_DASH_SOURCE, addDATA_DASH_SOURCE, addDATA_DASH_SOURCE, addSYNONYMS, addXREF, addXREF, addXREF, getAVAILABILITY, getCOMMENT, getDATA_DASH_SOURCE, getNAME, getSHORT_DASH_NAME, getSYNONYMS, getXREF, removeAVAILABILITY, removeCOMMENT, removeDATA_DASH_SOURCE, removeSYNONYMS, removeXREF, setNAME, setSHORT_DASH_NAME

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

clearCache, isRDFType, listStatements, model, registerListener, removeStatements, resource, unregisterListener, uri

Field Detail

TYPE

static final com.hp.hpl.jena.rdf.model.Resource TYPE

The rdf:type for this ontology class

LEFTProperty

static final com.hp.hpl.jena.rdf.model.Property LEFTProperty

The Jena Property for LEFT

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

RDF Schema Standard Properties
comment : The participants on the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the LEFT property may be either reactants or products. LEFT is a sub-property of PARTICIPANTS.^^http://www.w3.org/2001/XMLSchema#string

SPONTANEOUSProperty

static final com.hp.hpl.jena.rdf.model.Property SPONTANEOUSProperty

The Jena Property for SPONTANEOUS

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

RDF Schema Standard Properties
comment : Specifies whether a conversion occurs spontaneously (i.e. uncatalyzed, under biological conditions) left-to-right, right-to-left, or not at all. If the spontaneity is not known, the SPONTANEOUS property should be left empty.^^http://www.w3.org/2001/XMLSchema#string

RIGHTProperty

static final com.hp.hpl.jena.rdf.model.Property RIGHTProperty

The Jena Property for RIGHT

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

RDF Schema Standard Properties
comment : The participants on the right side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the RIGHT property may be either reactants or products. RIGHT is a sub-property of PARTICIPANTS.^^http://www.w3.org/2001/XMLSchema#string

Method Detail

getPARTICIPANTS_asphysicalEntityParticipant

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

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

Specified by:

getPARTICIPANTS_asphysicalEntityParticipant in interface interaction

Specified by:

getPARTICIPANTS_asphysicalEntityParticipant in interface physicalInteraction

Returns:

Iterator of physicalEntityParticipant

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

interaction.PARTICIPANTSProperty

addPARTICIPANTS

void addPARTICIPANTS(physicalEntityParticipant PARTICIPANTS)
                     throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'PARTICIPANTS' property

Specified by:

addPARTICIPANTS in interface interaction

Specified by:

addPARTICIPANTS in interface physicalInteraction

Parameters:

The - physicalEntityParticipant to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

interaction.PARTICIPANTSProperty

addPARTICIPANTS_asphysicalEntityParticipant

physicalEntityParticipant addPARTICIPANTS_asphysicalEntityParticipant()
                                                                      throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'PARTICIPANTS' property

Specified by:

addPARTICIPANTS_asphysicalEntityParticipant in interface interaction

Specified by:

addPARTICIPANTS_asphysicalEntityParticipant in interface physicalInteraction

Returns:

The anoymous physicalEntityParticipant created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

interaction.PARTICIPANTSProperty

addPARTICIPANTS_asphysicalEntityParticipant

physicalEntityParticipant addPARTICIPANTS_asphysicalEntityParticipant(com.hp.hpl.jena.rdf.model.Resource resource)
                                                                      throws com.ibm.adtech.jastor.JastorException

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

Specified by:

addPARTICIPANTS_asphysicalEntityParticipant in interface interaction

Specified by:

addPARTICIPANTS_asphysicalEntityParticipant in interface physicalInteraction

Parameters:

The - om.hp.hpl.jena.rdf.model.Resource to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

interaction.PARTICIPANTSProperty

removePARTICIPANTS

void removePARTICIPANTS(physicalEntityParticipant PARTICIPANTS)
                        throws com.ibm.adtech.jastor.JastorException

Removes a value for the 'PARTICIPANTS' 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:

removePARTICIPANTS in interface interaction

Specified by:

removePARTICIPANTS in interface physicalInteraction

Parameters:

The - physicalEntityParticipant to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

interaction.PARTICIPANTSProperty

getLEFT

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

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

Returns:

Iterator of physicalEntityParticipant

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

LEFTProperty

addLEFT

void addLEFT(physicalEntityParticipant LEFT)
             throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'LEFT' property

Parameters:

The - physicalEntityParticipant to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

LEFTProperty

addLEFT

physicalEntityParticipant addLEFT()
                                  throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'LEFT' property

Returns:

The anoymous physicalEntityParticipant created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

LEFTProperty

addLEFT

physicalEntityParticipant addLEFT(com.hp.hpl.jena.rdf.model.Resource resource)
                                  throws com.ibm.adtech.jastor.JastorException

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

Parameters:

The - om.hp.hpl.jena.rdf.model.Resource to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

LEFTProperty

removeLEFT

void removeLEFT(physicalEntityParticipant LEFT)
                throws com.ibm.adtech.jastor.JastorException

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

Parameters:

The - physicalEntityParticipant to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

LEFTProperty

getSPONTANEOUS

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

Gets the 'SPONTANEOUS' property value

Returns:

String

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SPONTANEOUSProperty

setSPONTANEOUS

void setSPONTANEOUS(java.lang.String SPONTANEOUS)
                    throws com.ibm.adtech.jastor.JastorException

Sets the 'SPONTANEOUS' property value

Parameters:

{@link - java.lang.String}

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

SPONTANEOUSProperty

getRIGHT

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

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

Returns:

Iterator of physicalEntityParticipant

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

RIGHTProperty

addRIGHT

void addRIGHT(physicalEntityParticipant RIGHT)
              throws com.ibm.adtech.jastor.JastorException

Adds a value for the 'RIGHT' property

Parameters:

The - physicalEntityParticipant to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

RIGHTProperty

addRIGHT

physicalEntityParticipant addRIGHT()
                                   throws com.ibm.adtech.jastor.JastorException

Adds an anonymous value for the 'RIGHT' property

Returns:

The anoymous physicalEntityParticipant created

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

RIGHTProperty

addRIGHT

physicalEntityParticipant addRIGHT(com.hp.hpl.jena.rdf.model.Resource resource)
                                   throws com.ibm.adtech.jastor.JastorException

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

Parameters:

The - om.hp.hpl.jena.rdf.model.Resource to add

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

RIGHTProperty

removeRIGHT

void removeRIGHT(physicalEntityParticipant RIGHT)
                 throws com.ibm.adtech.jastor.JastorException

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

Parameters:

The - physicalEntityParticipant to remove

Throws:

com.ibm.adtech.jastor.JastorException

See Also:

RIGHTProperty