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

Packages that use interaction

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

Uses of interaction in fr.curie.BiNoM.pathways

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

edu.rpi.cs.xgmml.GraphicNode

BioPAXToCytoscapeConverter.addInteractionNode(edu.rpi.cs.xgmml.GraphicGraph grf, interaction in, java.util.HashMap pathways, java.util.HashMap interactions, java.util.HashMap pathwaySteps, java.util.HashMap nodes) Adds a 'interaction' node to Pathway Structure interface

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

Subinterfaces of interaction 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	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	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	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	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 interaction

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	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	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	physicalInteractionImpl Implementation of physicalInteraction 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 interaction

interaction	pathwayImpl.addPATHWAY_DASH_COMPONENTS_asinteraction()
interaction	pathway.addPATHWAY_DASH_COMPONENTS_asinteraction() Adds an anonymous value for the 'PATHWAY_DASH_COMPONENTS' property
interaction	pathwayImpl.addPATHWAY_DASH_COMPONENTS_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource)
interaction	pathway.addPATHWAY_DASH_COMPONENTS_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'PATHWAY_DASH_COMPONENTS' property.
interaction	pathwayStepImpl.addSTEP_DASH_INTERACTIONS_asinteraction()
interaction	pathwayStep.addSTEP_DASH_INTERACTIONS_asinteraction() Adds an anonymous value for the 'STEP_DASH_INTERACTIONS' property
interaction	pathwayStepImpl.addSTEP_DASH_INTERACTIONS_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource)
interaction	pathwayStep.addSTEP_DASH_INTERACTIONS_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource) Adds a value for the 'STEP_DASH_INTERACTIONS' property.
static interaction	biopax_DASH_level2_DOT_owlFactory.createinteraction(com.hp.hpl.jena.rdf.model.Resource resource, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of interaction.
static interaction	biopax_DASH_level2_DOT_owlFactory.createinteraction(java.lang.String uri, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of interaction.
interaction	modulationImpl.getCONTROLLED_asinteraction()
interaction	controlImpl.getCONTROLLED_asinteraction()
interaction	control.getCONTROLLED_asinteraction() Gets the 'CONTROLLED' property value
interaction	catalysisImpl.getCONTROLLED_asinteraction()
static interaction	biopax_DASH_level2_DOT_owlFactory.getinteraction(com.hp.hpl.jena.rdf.model.Resource resource, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of interaction.
static interaction	biopax_DASH_level2_DOT_owlFactory.getinteraction(java.lang.String uri, com.hp.hpl.jena.rdf.model.Model model) Create a new instance of interaction.
interaction	modulationImpl.setCONTROLLED_asinteraction()
interaction	controlImpl.setCONTROLLED_asinteraction()
interaction	control.setCONTROLLED_asinteraction() Sets the 'CONTROLLED' property value to an anonymous node
interaction	catalysisImpl.setCONTROLLED_asinteraction()
interaction	modulationImpl.setCONTROLLED_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource)
interaction	controlImpl.setCONTROLLED_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource)
interaction	control.setCONTROLLED_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource) Sets the 'CONTROLLED' property value to the given resource, and add's rdf:type properties.
interaction	catalysisImpl.setCONTROLLED_asinteraction(com.hp.hpl.jena.rdf.model.Resource resource)

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

void	pathwayImpl.addPATHWAY_DASH_COMPONENTS(interaction PATHWAY_DASH_COMPONENTS)
void	pathway.addPATHWAY_DASH_COMPONENTS(interaction PATHWAY_DASH_COMPONENTS) Adds a value for the 'PATHWAY_DASH_COMPONENTS' property
void	pathwayStepImpl.addSTEP_DASH_INTERACTIONS(interaction STEP_DASH_INTERACTIONS)
void	pathwayStep.addSTEP_DASH_INTERACTIONS(interaction STEP_DASH_INTERACTIONS) Adds a value for the 'STEP_DASH_INTERACTIONS' property
void	interactionListener.AVAILABILITYAdded(interaction source, java.lang.String newValue) Called when a value of AVAILABILITY has been added
void	interactionListener.AVAILABILITYRemoved(interaction source, java.lang.String oldValue) Called when a value of AVAILABILITY has been removed
void	interactionListener.COMMENTAdded(interaction source, java.lang.String newValue) Called when a value of COMMENT has been added
void	interactionListener.COMMENTRemoved(interaction source, java.lang.String oldValue) Called when a value of COMMENT has been removed
void	interactionListener.DATA_DASH_SOURCEAdded(interaction source, dataSource newValue) Called when a value of DATA_DASH_SOURCE has been added
void	interactionListener.DATA_DASH_SOURCERemoved(interaction source, dataSource oldValue) Called when a value of DATA_DASH_SOURCE has been removed
void	interactionListener.EVIDENCEAdded(interaction source, evidence newValue) Called when a value of EVIDENCE has been added
void	interactionListener.EVIDENCERemoved(interaction source, evidence oldValue) Called when a value of EVIDENCE has been removed
void	interactionListener.NAMEChanged(interaction source) Called when NAME has changed
void	interactionListener.PARTICIPANTSAdded(interaction source, entity newValue) Called when a value of PARTICIPANTS has been added
void	interactionListener.PARTICIPANTSAdded(interaction source, physicalEntityParticipant newValue) Called when a value of PARTICIPANTS has been added
void	interactionListener.PARTICIPANTSRemoved(interaction source, entity oldValue) Called when a value of PARTICIPANTS has been removed
void	interactionListener.PARTICIPANTSRemoved(interaction source, physicalEntityParticipant oldValue) Called when a value of PARTICIPANTS has been removed
void	pathwayListener.PATHWAY_DASH_COMPONENTSAdded(pathway source, interaction newValue) Called when a value of PATHWAY_DASH_COMPONENTS has been added
void	pathwayListener.PATHWAY_DASH_COMPONENTSRemoved(pathway source, interaction oldValue) Called when a value of PATHWAY_DASH_COMPONENTS has been removed
void	pathwayImpl.removePATHWAY_DASH_COMPONENTS(interaction PATHWAY_DASH_COMPONENTS)
void	pathway.removePATHWAY_DASH_COMPONENTS(interaction PATHWAY_DASH_COMPONENTS) Removes a value for the 'PATHWAY_DASH_COMPONENTS' property.
void	pathwayStepImpl.removeSTEP_DASH_INTERACTIONS(interaction STEP_DASH_INTERACTIONS)
void	pathwayStep.removeSTEP_DASH_INTERACTIONS(interaction STEP_DASH_INTERACTIONS) Removes a value for the 'STEP_DASH_INTERACTIONS' property.
void	modulationImpl.setCONTROLLED(interaction CONTROLLED)
void	controlImpl.setCONTROLLED(interaction CONTROLLED)
void	control.setCONTROLLED(interaction CONTROLLED) Sets the 'CONTROLLED' property value
void	catalysisImpl.setCONTROLLED(interaction CONTROLLED)
void	interactionListener.SHORT_DASH_NAMEChanged(interaction source) Called when SHORT_DASH_NAME has changed
void	pathwayStepListener.STEP_DASH_INTERACTIONSAdded(pathwayStep source, interaction newValue) Called when a value of STEP_DASH_INTERACTIONS has been added
void	pathwayStepListener.STEP_DASH_INTERACTIONSRemoved(pathwayStep source, interaction oldValue) Called when a value of STEP_DASH_INTERACTIONS has been removed
void	interactionListener.SYNONYMSAdded(interaction source, java.lang.String newValue) Called when a value of SYNONYMS has been added
void	interactionListener.SYNONYMSRemoved(interaction source, java.lang.String oldValue) Called when a value of SYNONYMS has been removed
void	interactionListener.XREFAdded(interaction source, xref newValue) Called when a value of XREF has been added
void	interactionListener.XREFRemoved(interaction source, xref oldValue) Called when a value of XREF has been removed

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

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

static void

BioPAXGraphMapper.setReactionEffectAttribute(interaction in, edu.rpi.cs.xgmml.GraphicNode node, java.lang.String substring) If there is a comment with which contains substring+":", this comment is added as a value of an attribute named substring