Uses of Interface
fr.curie.BiNoM.pathways.biopax.entity

Packages that use entity

fr.curie.BiNoM.pathways	Set of converters for conversion of one systems biology format into an other.
fr.curie.BiNoM.pathways.biopax	Java mapping of BioPAX version 2 (generated by Jastor)
fr.curie.BiNoM.pathways.utils	Utility classes
fr.curie.BiNoM.pathways.wrappers	Auxilary containers representing different systems biology formats

Uses of entity in fr.curie.BiNoM.pathways

Methods in fr.curie.BiNoM.pathways with parameters of type entity

void	CellDesignerToBioPAXConverter.addPublicationXrefsToEntity(entity ent, java.util.Vector v)

Uses of entity in fr.curie.BiNoM.pathways.biopax

Subinterfaces of entity in fr.curie.BiNoM.pathways.biopax

interface	biochemicalReaction Interface for biochemicalReaction ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	catalysis Interface for catalysis ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	complex Interface for complex ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	complexAssembly Interface for complexAssembly ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	control Interface for control ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	conversion Interface for conversion ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	dna Interface for dna ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	interaction Interface for interaction ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	modulation Interface for modulation ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	pathway Interface for pathway ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	physicalEntity Interface for physicalEntity ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	physicalInteraction Interface for physicalInteraction ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	protein Interface for protein ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	rna Interface for rna ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	smallMolecule Interface for smallMolecule ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	transport Interface for transport ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.
interface	transportWithBiochemicalReaction Interface for transportWithBiochemicalReaction ontology class Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

Classes in fr.curie.BiNoM.pathways.biopax that implement entity

class	biochemicalReactionImpl Implementation of biochemicalReaction Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	catalysisImpl Implementation of catalysis Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	complexAssemblyImpl Implementation of complexAssembly Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	complexImpl Implementation of complex Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	controlImpl Implementation of control Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	conversionImpl Implementation of conversion Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	dnaImpl Implementation of dna Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	entityImpl Implementation of entity Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	interactionImpl Implementation of interaction Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	modulationImpl Implementation of modulation Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	pathwayImpl Implementation of pathway Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	physicalEntityImpl Implementation of physicalEntity Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	physicalInteractionImpl Implementation of physicalInteraction Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	proteinImpl Implementation of protein Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	rnaImpl Implementation of rna Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	smallMoleculeImpl Implementation of smallMolecule Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	transportImpl Implementation of transport Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.
class	transportWithBiochemicalReactionImpl Implementation of transportWithBiochemicalReaction Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

Methods in fr.curie.BiNoM.pathways.biopax that return entity

entity	transportWithBiochemicalReactionImpl.addPARTICIPANTS_asentity()
entity	transportImpl.addPARTICIPANTS_asentity()
entity	physicalInteractionImpl.addPARTICIPANTS_asentity()
entity	modulationImpl.addPARTICIPANTS_asentity()
entity	interactionImpl.addPARTICIPANTS_asentity()
entity	interaction.addPARTICIPANTS_asentity() Adds an anonymous value for the 'PARTICIPANTS' property
entity	conversionImpl.addPARTICIPANTS_asentity()
entity	controlImpl.addPARTICIPANTS_asentity()
entity	complexAssemblyImpl.addPARTICIPANTS_asentity()
entity	catalysisImpl.addPARTICIPANTS_asentity()
entity	biochemicalReactionImpl.addPARTICIPANTS_asentity()
entity	transportWithBiochemicalReactionImpl.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource)
entity	transportImpl.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource)
entity	physicalInteractionImpl.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource)
entity	modulationImpl.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource)
entity	interactionImpl.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource)
entity	interaction.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'PARTICIPANTS' property.
entity	conversionImpl.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource)
entity	controlImpl.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource)
entity	complexAssemblyImpl.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource)
entity	catalysisImpl.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource)
entity	biochemicalReactionImpl.addPARTICIPANTS_asentity(com.hp.hpl.jena.rdf.model.Resource resource)
static entity	biopax_DASH_level2_DOT_owlFactory.createentity(com.hp.hpl.jena.rdf.model.Resource resource, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of entity.
static entity	biopax_DASH_level2_DOT_owlFactory.createentity(java.lang.String uri, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of entity.
static entity	biopax_DASH_level2_DOT_owlFactory.getentity(com.hp.hpl.jena.rdf.model.Resource resource, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of entity.
static entity	biopax_DASH_level2_DOT_owlFactory.getentity(java.lang.String uri, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of entity.

Methods in fr.curie.BiNoM.pathways.biopax with parameters of type entity

void	transportWithBiochemicalReactionImpl.addPARTICIPANTS(entity PARTICIPANTS)
void	transportImpl.addPARTICIPANTS(entity PARTICIPANTS)
void	physicalInteractionImpl.addPARTICIPANTS(entity PARTICIPANTS)
void	modulationImpl.addPARTICIPANTS(entity PARTICIPANTS)
void	interactionImpl.addPARTICIPANTS(entity PARTICIPANTS)
void	interaction.addPARTICIPANTS(entity PARTICIPANTS) Adds a value for the 'PARTICIPANTS' property
void	conversionImpl.addPARTICIPANTS(entity PARTICIPANTS)
void	controlImpl.addPARTICIPANTS(entity PARTICIPANTS)
void	complexAssemblyImpl.addPARTICIPANTS(entity PARTICIPANTS)
void	catalysisImpl.addPARTICIPANTS(entity PARTICIPANTS)
void	biochemicalReactionImpl.addPARTICIPANTS(entity PARTICIPANTS)
void	entityListener.AVAILABILITYAdded(entity source, java.lang.String newValue) Called when a value of AVAILABILITY has been added
void	entityListener.AVAILABILITYRemoved(entity source, java.lang.String oldValue) Called when a value of AVAILABILITY has been removed
void	entityListener.COMMENTAdded(entity source, java.lang.String newValue) Called when a value of COMMENT has been added
void	entityListener.COMMENTRemoved(entity source, java.lang.String oldValue) Called when a value of COMMENT has been removed
void	entityListener.DATA_DASH_SOURCEAdded(entity source, dataSource newValue) Called when a value of DATA_DASH_SOURCE has been added
void	entityListener.DATA_DASH_SOURCERemoved(entity source, dataSource oldValue) Called when a value of DATA_DASH_SOURCE has been removed
void	entityListener.NAMEChanged(entity source) Called when NAME has changed
void	biochemicalReactionListener.PARTICIPANTSAdded(biochemicalReaction source, entity newValue) Called when a value of PARTICIPANTS has been added
void	catalysisListener.PARTICIPANTSAdded(catalysis source, entity newValue) Called when a value of PARTICIPANTS has been added
void	complexAssemblyListener.PARTICIPANTSAdded(complexAssembly source, entity newValue) Called when a value of PARTICIPANTS has been added
void	controlListener.PARTICIPANTSAdded(control source, entity newValue) Called when a value of PARTICIPANTS has been added
void	conversionListener.PARTICIPANTSAdded(conversion source, entity newValue) Called when a value of PARTICIPANTS has been added
void	interactionListener.PARTICIPANTSAdded(interaction source, entity newValue) Called when a value of PARTICIPANTS has been added
void	modulationListener.PARTICIPANTSAdded(modulation source, entity newValue) Called when a value of PARTICIPANTS has been added
void	physicalInteractionListener.PARTICIPANTSAdded(physicalInteraction source, entity newValue) Called when a value of PARTICIPANTS has been added
void	transportListener.PARTICIPANTSAdded(transport source, entity newValue) Called when a value of PARTICIPANTS has been added
void	transportWithBiochemicalReactionListener.PARTICIPANTSAdded(transportWithBiochemicalReaction source, entity newValue) Called when a value of PARTICIPANTS has been added
void	biochemicalReactionListener.PARTICIPANTSRemoved(biochemicalReaction source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	catalysisListener.PARTICIPANTSRemoved(catalysis source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	complexAssemblyListener.PARTICIPANTSRemoved(complexAssembly source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	controlListener.PARTICIPANTSRemoved(control source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	conversionListener.PARTICIPANTSRemoved(conversion source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	interactionListener.PARTICIPANTSRemoved(interaction source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	modulationListener.PARTICIPANTSRemoved(modulation source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	physicalInteractionListener.PARTICIPANTSRemoved(physicalInteraction source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	transportListener.PARTICIPANTSRemoved(transport source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	transportWithBiochemicalReactionListener.PARTICIPANTSRemoved(transportWithBiochemicalReaction source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	transportWithBiochemicalReactionImpl.removePARTICIPANTS(entity PARTICIPANTS)
void	transportImpl.removePARTICIPANTS(entity PARTICIPANTS)
void	physicalInteractionImpl.removePARTICIPANTS(entity PARTICIPANTS)
void	modulationImpl.removePARTICIPANTS(entity PARTICIPANTS)
void	interactionImpl.removePARTICIPANTS(entity PARTICIPANTS)
void	interaction.removePARTICIPANTS(entity PARTICIPANTS) Removes a value for the 'PARTICIPANTS' property.
void	conversionImpl.removePARTICIPANTS(entity PARTICIPANTS)
void	controlImpl.removePARTICIPANTS(entity PARTICIPANTS)
void	complexAssemblyImpl.removePARTICIPANTS(entity PARTICIPANTS)
void	catalysisImpl.removePARTICIPANTS(entity PARTICIPANTS)
void	biochemicalReactionImpl.removePARTICIPANTS(entity PARTICIPANTS)
void	entityListener.SHORT_DASH_NAMEChanged(entity source) Called when SHORT_DASH_NAME has changed
void	entityListener.SYNONYMSAdded(entity source, java.lang.String newValue) Called when a value of SYNONYMS has been added
void	entityListener.SYNONYMSRemoved(entity source, java.lang.String oldValue) Called when a value of SYNONYMS has been removed
void	entityListener.XREFAdded(entity source, xref newValue) Called when a value of XREF has been added
void	entityListener.XREFRemoved(entity source, xref oldValue) Called when a value of XREF has been removed

Uses of entity in fr.curie.BiNoM.pathways.utils

Methods in fr.curie.BiNoM.pathways.utils with parameters of type entity

java.lang.String	BioPAXNamingService.createEntityId(entity e) Creates entity id
java.lang.String	BioPAXNamingService.createEntityName(entity pe) Creates a name for entity pe
static java.lang.String	Utils.getPropertyURI(entity res, java.lang.String pname)
static java.util.Vector	Utils.getPropertyURIs(entity res, java.lang.String pname)
void	BioPAXNamingService.printEntityName(entity e)
static void	Utils.printPropertyURIs(entity res) Simply prints all statement uris in the entity res
void	BioPAXNamingService.putEntity(entity e) Adds an entity for naming

Uses of entity in fr.curie.BiNoM.pathways.wrappers

Methods in fr.curie.BiNoM.pathways.wrappers with parameters of type entity

void	Transpath.addAccno(entity ent, java.lang.String accno)
void	Transpath.addAccnoAnnotate(entity ent, java.lang.String accno)
void	Transpath.addPublication(entity ent, com.biobaseInternational.ItemDocument.Item it)
void	Transpath.addSynonym(entity ent, java.lang.String syn)