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

Packages that use pathway

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)

Uses of pathway in fr.curie.BiNoM.pathways

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

edu.rpi.cs.xgmml.GraphicNode

BioPAXToCytoscapeConverter.addPathwayNode(edu.rpi.cs.xgmml.GraphicGraph grf, pathway p, java.util.HashMap pathways, java.util.HashMap interactions, java.util.HashMap pathwaySteps, java.util.HashMap nodes, java.util.HashMap edges, BioPAXToCytoscapeConverter.Option option) Adds a pathway node to Pathway Structure interface

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

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

class

pathwayImpl Implementation of pathway 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 pathway

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

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

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