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

Packages that use physicalEntity

fr.curie.BiNoM.pathways.biopax	Java mapping of BioPAX version 2 (generated by Jastor)
fr.curie.BiNoM.pathways.wrappers	Auxilary containers representing different systems biology formats

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

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

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	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	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.

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

class	complexImpl Implementation of complex 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	physicalEntityImpl Implementation of physicalEntity 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.

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

static physicalEntity	biopax_DASH_level2_DOT_owlFactory.createphysicalEntity(com.hp.hpl.jena.rdf.model.Resource resource, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of physicalEntity.
static physicalEntity	biopax_DASH_level2_DOT_owlFactory.createphysicalEntity(java.lang.String uri, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of physicalEntity.
physicalEntity	sequenceParticipantImpl.getPHYSICAL_DASH_ENTITY()
physicalEntity	physicalEntityParticipantImpl.getPHYSICAL_DASH_ENTITY()
physicalEntity	physicalEntityParticipant.getPHYSICAL_DASH_ENTITY() Gets the 'PHYSICAL_DASH_ENTITY' property value
static physicalEntity	biopax_DASH_level2_DOT_owlFactory.getphysicalEntity(com.hp.hpl.jena.rdf.model.Resource resource, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of physicalEntity.
static physicalEntity	biopax_DASH_level2_DOT_owlFactory.getphysicalEntity(java.lang.String uri, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of physicalEntity.
physicalEntity	sequenceParticipantImpl.setPHYSICAL_DASH_ENTITY()
physicalEntity	physicalEntityParticipantImpl.setPHYSICAL_DASH_ENTITY()
physicalEntity	physicalEntityParticipant.setPHYSICAL_DASH_ENTITY() Sets the 'PHYSICAL_DASH_ENTITY' property value to an anonymous node
physicalEntity	sequenceParticipantImpl.setPHYSICAL_DASH_ENTITY(com.hp.hpl.jena.rdf.model.Resource resource)
physicalEntity	physicalEntityParticipantImpl.setPHYSICAL_DASH_ENTITY(com.hp.hpl.jena.rdf.model.Resource resource)
physicalEntity	physicalEntityParticipant.setPHYSICAL_DASH_ENTITY(com.hp.hpl.jena.rdf.model.Resource resource) Sets the 'PHYSICAL_DASH_ENTITY' property value to the given resource, and add's rdf:type properties.

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

void	physicalEntityListener.AVAILABILITYAdded(physicalEntity source, java.lang.String newValue) Called when a value of AVAILABILITY has been added
void	physicalEntityListener.AVAILABILITYRemoved(physicalEntity source, java.lang.String oldValue) Called when a value of AVAILABILITY has been removed
void	physicalEntityListener.COMMENTAdded(physicalEntity source, java.lang.String newValue) Called when a value of COMMENT has been added
void	physicalEntityListener.COMMENTRemoved(physicalEntity source, java.lang.String oldValue) Called when a value of COMMENT has been removed
void	physicalEntityListener.DATA_DASH_SOURCEAdded(physicalEntity source, dataSource newValue) Called when a value of DATA_DASH_SOURCE has been added
void	physicalEntityListener.DATA_DASH_SOURCERemoved(physicalEntity source, dataSource oldValue) Called when a value of DATA_DASH_SOURCE has been removed
void	physicalEntityListener.NAMEChanged(physicalEntity source) Called when NAME has changed
void	sequenceParticipantImpl.setPHYSICAL_DASH_ENTITY(physicalEntity PHYSICAL_DASH_ENTITY)
void	physicalEntityParticipantImpl.setPHYSICAL_DASH_ENTITY(physicalEntity PHYSICAL_DASH_ENTITY)
void	physicalEntityParticipant.setPHYSICAL_DASH_ENTITY(physicalEntity PHYSICAL_DASH_ENTITY) Sets the 'PHYSICAL_DASH_ENTITY' property value
void	physicalEntityListener.SHORT_DASH_NAMEChanged(physicalEntity source) Called when SHORT_DASH_NAME has changed
void	physicalEntityListener.SYNONYMSAdded(physicalEntity source, java.lang.String newValue) Called when a value of SYNONYMS has been added
void	physicalEntityListener.SYNONYMSRemoved(physicalEntity source, java.lang.String oldValue) Called when a value of SYNONYMS has been removed
void	physicalEntityListener.XREFAdded(physicalEntity source, xref newValue) Called when a value of XREF has been added
void	physicalEntityListener.XREFRemoved(physicalEntity source, xref oldValue) Called when a value of XREF has been removed

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

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

void	Transpath.associateWithSpecies(physicalEntity ent, java.lang.String species)