Uses of Class
fr.curie.BiNoM.pathways.wrappers.BioPAX

Packages that use BioPAX

fr.curie.BiNoM.cytoscape.biopax	Cytoscape interface for working with BioPAX files
fr.curie.BiNoM.cytoscape.biopax.propedit	BiNoM property editor implementation
fr.curie.BiNoM.cytoscape.biopax.query	Cytoscape interface to BioPAX query engine
fr.curie.BiNoM.pathways	Set of converters for conversion of one systems biology format into an other.
fr.curie.BiNoM.pathways.test	Diverse scripts (used internally, but you can find some examples of use there)
fr.curie.BiNoM.pathways.utils	Utility classes
fr.curie.BiNoM.pathways.wrappers	Auxilary containers representing different systems biology formats

Uses of BioPAX in fr.curie.BiNoM.cytoscape.biopax

Methods in fr.curie.BiNoM.cytoscape.biopax that return BioPAX

BioPAX	BioPAXSourceDB.getBioPAX(cytoscape.CyNetwork cyNetwork)
static BioPAX	BioPAXImport.getBioPAX(cytoscape.CyNetwork cyNetwork)

Methods in fr.curie.BiNoM.cytoscape.biopax with parameters of type BioPAX

java.util.Vector<cytoscape.CyNetwork>	BioPAXSourceDB.getAssociatedNetworks(BioPAX biopax)
void	BioPAXSyncNetworksDialog.raise(BioPAX biopax)
void	BioPAXSourceDB.setBioPAX(cytoscape.CyNetwork cyNetwork, BioPAX biopax)

Uses of BioPAX in fr.curie.BiNoM.cytoscape.biopax.propedit

Methods in fr.curie.BiNoM.cytoscape.biopax.propedit that return BioPAX

BioPAX

BioPAXObject.getBioPAX()

Methods in fr.curie.BiNoM.cytoscape.biopax.propedit with parameters of type BioPAX

com.ibm.adtech.jastor.Thing	BioPAXObjectFactory.convert(java.lang.Object obj, BioPAX biopax)
com.ibm.adtech.jastor.Thing	BioPAXObjectFactory.convert(com.ibm.adtech.jastor.Thing obj, BioPAX biopax)
BioPAXObject	BioPAXObjectFactory.createObject(java.lang.String type, java.lang.String uri, BioPAX biopax)
static BioPAXClassDescFactory	BioPAXClassDescFactory.getInstance(BioPAX biopax)
BioPAXObject	BioPAXObjectFactory.getObject(java.lang.String uri, BioPAX biopax)
BioPAXObject	BioPAXObjectFactory.getObject(com.ibm.adtech.jastor.Thing robj, BioPAX biopax)
void	BioPAXClassDescFactory.makeClassesDesc(BioPAX biopax)

Constructors in fr.curie.BiNoM.cytoscape.biopax.propedit with parameters of type BioPAX

BioPAXClassDesc(BioPAX biopax, java.lang.Class cls)

BioPAXObject(BioPAXClassDesc clsDesc, java.lang.Object obj, BioPAX biopax)

BioPAXPropertyBrowserPanel(BioPAXObject bobj, BioPAX biopax, boolean display_all, boolean edit_mode, BioPAXPropertyBrowserFrame browser_frame)

Uses of BioPAX in fr.curie.BiNoM.cytoscape.biopax.query

Methods in fr.curie.BiNoM.cytoscape.biopax.query with parameters of type BioPAX

void	BioPAXStandardQueryDialog.raise(BioPAX biopax)
void	BioPAXSelectEntitiesDialog.raise(BioPAX biopax)
void	BioPAXLoadIndexDialog.raise(BioPAX biopax)
void	BioPAXGenerateIndexDialog.raise(BioPAX biopax)
void	BioPAXDisplayIndexInfoDialog.raise(BioPAX biopax)

Uses of BioPAX in fr.curie.BiNoM.pathways

Fields in fr.curie.BiNoM.pathways declared as BioPAX

BioPAX	CellDesignerToBioPAXConverter.biopax The result of the conversion
BioPAX	BioPAXToSBMLConverter.biopax Input for conversion
BioPAX	BioPAXToCytoscapeConverter.Graph.biopax

Fields in fr.curie.BiNoM.pathways with type parameters of type BioPAX

static java.util.HashMap<java.lang.String,BioPAX>

BioPAXToCytoscapeConverter.biopax_map A map from BioPAX file key to static set of BioPAX objects

Methods in fr.curie.BiNoM.pathways that return BioPAX

BioPAX	CellDesignerToBioPAXConverter.convert() The main conversion function to be used from outside
static BioPAX	CytoscapeToBioPAXConverter.convert(edu.rpi.cs.xgmml.GraphDocument graph, BioPAX biopax)
BioPAX	CellDesignerToBioPAXConverter.populateModel() The converter itself

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

static BioPAX	CytoscapeToBioPAXConverter.convert(edu.rpi.cs.xgmml.GraphDocument graph, BioPAX biopax)
physicalEntityParticipant	CellDesignerToBioPAXConverter.createEntityParticipantForSpecies(java.lang.String id, java.util.Vector species, java.util.Vector complexes_list, java.util.HashMap physEntities, org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml sbml, BioPAX biopax, java.lang.String rId) Converts physicalEntity participant for a reaction rId
static void	CytoscapeToBioPAXConverter.filterIDs(BioPAX biopax, edu.rpi.cs.xgmml.GraphDocument gr)
static void	CytoscapeToBioPAXConverter.filterIDs(BioPAX biopax, java.util.Vector species, java.util.Vector reactions)
static void	CytoscapeToBioPAXConverter.filterPathwaySteps(BioPAX biopax, java.util.HashMap interactions, java.util.HashMap pathwaySteps, java.util.HashMap pathwayStepsRemove)
edu.rpi.cs.xgmml.GraphDocument	BioPAXToCytoscapeConverter.getXGMMLPathwayGraph(java.lang.String name, BioPAX biopax, BioPAXToCytoscapeConverter.Option option) Implementation of extracting Pathway Structure interface (requires first conversion from BioPAX to SBML, from which the interface is converted).
edu.rpi.cs.xgmml.GraphDocument	BioPAXToCytoscapeConverter.getXGMMLProteinGraph(java.lang.String name, BioPAX biopax, BioPAXToCytoscapeConverter.Option option) Implementation of extracting Protein Interaction interface (requires first conversion from BioPAX to SBML, from which the interface is converted).

Uses of BioPAX in fr.curie.BiNoM.pathways.test

Fields in fr.curie.BiNoM.pathways.test declared as BioPAX

static BioPAX

testEwingNetwork.biopax

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

Fields in fr.curie.BiNoM.pathways.utils declared as BioPAX

BioPAX

BioPAXGraphMapper.biopax Input BioPAX object

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

void	BioPAXNamingService.generateNames(BioPAX biopax, boolean verbose) Function for generating names
edu.rpi.cs.xgmml.GraphDocument	BioPAXGraphMappingService.mapBioPAXToGraph(BioPAX biopax) Creates BioPAX index as XGMML file from BioPAX object

Constructors in fr.curie.BiNoM.pathways.utils with parameters of type BioPAX

BioPAXNamingService(BioPAX biopax)

BioPAXNamingService(BioPAX biopax, boolean verbose)

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

Fields in fr.curie.BiNoM.pathways.wrappers declared as BioPAX

BioPAX

Transpath.biopax