A B C D E F G H I K L M N O P Q R S T U V W X Y

C

calcAllMaterialComponents(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils

For every protein name, creates a subgraph with all its modifications, complexes, locations

calcNodesInOut() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph

catalysis - Interface in fr.curie.BiNoM.pathways.biopax

Interface for catalysis ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

catalysisImpl - Class in fr.curie.BiNoM.pathways.biopax

Implementation of catalysis Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

catalysisListener - Interface in fr.curie.BiNoM.pathways.biopax

Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.catalysis to receive notification when properties changed, added or removed.

cd - Variable in class fr.curie.BiNoM.pathways.test.ProduceClickableMap

CDesigner2BioPAX - Class in fr.curie.BiNoM.pathways.test.examples

CDesigner2BioPAX() - Constructor for class fr.curie.BiNoM.pathways.test.examples.CDesigner2BioPAX

celldesigner - Variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

Auxilary BiNoM wrapper of CellDesigner

CellDesigner - Class in fr.curie.BiNoM.pathways.wrappers

Wrapper class for CellDesigner with some utilities implemented

CellDesigner() - Constructor for class fr.curie.BiNoM.pathways.wrappers.CellDesigner

CellDesigner2BioPAX - Class in fr.curie.BiNoM.pathways.converters

CellDesigner2BioPAX() - Constructor for class fr.curie.BiNoM.pathways.converters.CellDesigner2BioPAX

CellDesigner2Cytoscape - Class in fr.curie.BiNoM.pathways.converters

CellDesigner2Cytoscape() - Constructor for class fr.curie.BiNoM.pathways.converters.CellDesigner2Cytoscape

CellDesignerAssociateSource - Class in fr.curie.BiNoM.cytoscape.celldesigner

CellDesignerAssociateSourceTask - Class in fr.curie.BiNoM.cytoscape.celldesigner

CellDesignerAssociateSourceTask(File, String) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSourceTask

CellDesignerColorSpecies - Class in fr.curie.BiNoM.pathways

CellDesignerColorSpecies() - Constructor for class fr.curie.BiNoM.pathways.CellDesignerColorSpecies

CellDesignerExport - Class in fr.curie.BiNoM.cytoscape.celldesigner

CellDesignerExport(File) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExport

CellDesignerExportTask - Class in fr.curie.BiNoM.cytoscape.celldesigner

CellDesignerExportTask(File, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask

CellDesignerExportToFile - Class in fr.curie.BiNoM.cytoscape.celldesigner

CellDesignerExportToFile() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFile

CellDesignerImport - Class in fr.curie.BiNoM.cytoscape.celldesigner

CellDesignerImport(File) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImport

CellDesignerImportFromFile - Class in fr.curie.BiNoM.cytoscape.celldesigner

CellDesignerImportFromFile() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportFromFile

CellDesignerImportTask - Class in fr.curie.BiNoM.cytoscape.celldesigner

CellDesignerImportTask(File) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportTask

CellDesignerSourceDB - Class in fr.curie.BiNoM.cytoscape.celldesigner

cellDesignerTerms - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

Map from CellDesigner terms (strings) to OpenControlledVocabulary objects

CellDesignerToBioPAXConverter - Class in fr.curie.BiNoM.pathways

Implementation of converter from CellDesigner 3.* file to BioPAX

CellDesignerToBioPAXConverter() - Constructor for class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

CellDesignerToCytoscapeConverter - Class in fr.curie.BiNoM.pathways

Direct converter from CellDesigner to Cytoscape.

CellDesignerToCytoscapeConverter() - Constructor for class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

CellDesignerToCytoscapeConverter.Graph - Class in fr.curie.BiNoM.pathways

Simple container for GraphDocument and SbmlDocument objects

CellDesignerVisualStyleDefinition - Class in fr.curie.BiNoM.cytoscape.celldesigner

CELLTYPEChanged(bioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.bioSourceListener

Called when CELLTYPE has changed

CELLTYPEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.bioSource

The Jena Property for CELLTYPE

CELLULAR_DASH_LOCATIONChanged(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantListener

Called when CELLULAR_DASH_LOCATION has changed

CELLULAR_DASH_LOCATIONChanged(sequenceParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipantListener

Called when CELLULAR_DASH_LOCATION has changed

CELLULAR_DASH_LOCATIONProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant

The Jena Property for CELLULAR_DASH_LOCATION

checkAndModifyEntitiesIDs(SbmlDocument, SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

checkAndModifySpeciesIDs(SbmlDocument, SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

Utility function.

CHEMICAL_DASH_FORMULAChanged(smallMolecule) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMoleculeListener

Called when CHEMICAL_DASH_FORMULA has changed

CHEMICAL_DASH_FORMULAProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.smallMolecule

The Jena Property for CHEMICAL_DASH_FORMULA

chemicalStructure - Interface in fr.curie.BiNoM.pathways.biopax

Interface for chemicalStructure ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

chemicalStructureImpl - Class in fr.curie.BiNoM.pathways.biopax

Implementation of chemicalStructure Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

chemicalStructureListener - Interface in fr.curie.BiNoM.pathways.biopax

Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.chemicalStructure to receive notification when properties changed, added or removed.

ChemType - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork

CIRCLE - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge

clearAndCopy(CyNetwork, CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.chemicalStructureImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.confidenceImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.experimentalFormImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.externalReferenceUtilityClassImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayStepImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceIntervalImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceLocationImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceSiteImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.utilityClassImpl

clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl

clearNetwork(CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils

clearReport() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository

ClusterNetworks - Class in fr.curie.BiNoM.cytoscape.analysis

ClusterNetworks() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworks

ClusterNetworksDialog - Class in fr.curie.BiNoM.cytoscape.analysis

ClusterNetworksTask - Class in fr.curie.BiNoM.cytoscape.analysis

ClusterNetworksTask(Vector<GraphDocument>, StructureAnalysisUtils.Option, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTask

coefficientInConservationLaw - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node

Auxillary property for analysis of conservation laws

COFACTORAdded(catalysis, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of COFACTOR has been added

COFACTORProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.catalysis

The Jena Property for COFACTOR

COFACTORRemoved(catalysis, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of COFACTOR has been removed

colCount - Variable in class fr.curie.BiNoM.pathways.utils.SimpleTable

CollapseMetaNodes(Graph, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils

Calculates modular representation of graph global, using Graph.Metanodes list of subgraphs showIntersections - if true then all metanode intersections will be shown explicitly nodeIntersectionView - if true then all the edges connecting nodes in the intersection will not be shown, but instead for every common node there will be a 'INTERSECT' edge shown

CombineIncludedGraphsApprox(Vector<Graph>, float) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms

Clusters graphs with node overlap more than threshold

COMMENTAdded(biochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of COMMENT has been added

COMMENTAdded(bioSource, String) - Method in interface fr.curie.BiNoM.pathways.biopax.bioSourceListener

Called when a value of COMMENT has been added

COMMENTAdded(catalysis, String) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of COMMENT has been added

COMMENTAdded(chemicalStructure, String) - Method in interface fr.curie.BiNoM.pathways.biopax.chemicalStructureListener

Called when a value of COMMENT has been added

COMMENTAdded(complexAssembly, String) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of COMMENT has been added

COMMENTAdded(complex, String) - Method in interface fr.curie.BiNoM.pathways.biopax.complexListener

Called when a value of COMMENT has been added

COMMENTAdded(confidence, String) - Method in interface fr.curie.BiNoM.pathways.biopax.confidenceListener

Called when a value of COMMENT has been added

COMMENTAdded(control, String) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of COMMENT has been added

COMMENTAdded(conversion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of COMMENT has been added

COMMENTAdded(dataSource, String) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSourceListener

Called when a value of COMMENT has been added

COMMENTAdded(deltaGprimeO, String) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeOListener

Called when a value of COMMENT has been added

COMMENTAdded(dna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.dnaListener

Called when a value of COMMENT has been added

COMMENTAdded(entity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.entityListener

Called when a value of COMMENT has been added

COMMENTAdded(evidence, String) - Method in interface fr.curie.BiNoM.pathways.biopax.evidenceListener

Called when a value of COMMENT has been added

COMMENTAdded(experimentalForm, String) - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalFormListener

Called when a value of COMMENT has been added

COMMENTAdded(externalReferenceUtilityClass, String) - Method in interface fr.curie.BiNoM.pathways.biopax.externalReferenceUtilityClassListener

Called when a value of COMMENT has been added

COMMENTAdded(interaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.interactionListener

Called when a value of COMMENT has been added

COMMENTAdded(kPrime, String) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrimeListener

Called when a value of COMMENT has been added

COMMENTAdded(modulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of COMMENT has been added

COMMENTAdded(openControlledVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabularyListener

Called when a value of COMMENT has been added

COMMENTAdded(pathway, String) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayListener

Called when a value of COMMENT has been added

COMMENTAdded(pathwayStep, String) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStepListener

Called when a value of COMMENT has been added

COMMENTAdded(physicalEntity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityListener

Called when a value of COMMENT has been added

COMMENTAdded(physicalEntityParticipant, String) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantListener

Called when a value of COMMENT has been added

COMMENTAdded(physicalInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of COMMENT has been added

COMMENTAdded(protein, String) - Method in interface fr.curie.BiNoM.pathways.biopax.proteinListener

Called when a value of COMMENT has been added

COMMENTAdded(publicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXrefListener

Called when a value of COMMENT has been added

COMMENTAdded(relationshipXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.relationshipXrefListener

Called when a value of COMMENT has been added

COMMENTAdded(rna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.rnaListener

Called when a value of COMMENT has been added

COMMENTAdded(sequenceFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeatureListener

Called when a value of COMMENT has been added

COMMENTAdded(sequenceInterval, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceIntervalListener

Called when a value of COMMENT has been added

COMMENTAdded(sequenceLocation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceLocationListener

Called when a value of COMMENT has been added

COMMENTAdded(sequenceParticipant, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipantListener

Called when a value of COMMENT has been added

COMMENTAdded(sequenceSite, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceSiteListener

Called when a value of COMMENT has been added

COMMENTAdded(smallMolecule, String) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMoleculeListener

Called when a value of COMMENT has been added

COMMENTAdded(transport, String) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of COMMENT has been added

COMMENTAdded(transportWithBiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of COMMENT has been added

COMMENTAdded(unificationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.unificationXrefListener

Called when a value of COMMENT has been added

COMMENTAdded(utilityClass, String) - Method in interface fr.curie.BiNoM.pathways.biopax.utilityClassListener

Called when a value of COMMENT has been added

COMMENTAdded(xref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.xrefListener

Called when a value of COMMENT has been added

COMMENTProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.entity

The Jena Property for COMMENT

COMMENTProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.utilityClass

The Jena Property for COMMENT

COMMENTRemoved(biochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of COMMENT has been removed

COMMENTRemoved(bioSource, String) - Method in interface fr.curie.BiNoM.pathways.biopax.bioSourceListener

Called when a value of COMMENT has been removed

COMMENTRemoved(catalysis, String) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of COMMENT has been removed

COMMENTRemoved(chemicalStructure, String) - Method in interface fr.curie.BiNoM.pathways.biopax.chemicalStructureListener

Called when a value of COMMENT has been removed

COMMENTRemoved(complexAssembly, String) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of COMMENT has been removed

COMMENTRemoved(complex, String) - Method in interface fr.curie.BiNoM.pathways.biopax.complexListener

Called when a value of COMMENT has been removed

COMMENTRemoved(confidence, String) - Method in interface fr.curie.BiNoM.pathways.biopax.confidenceListener

Called when a value of COMMENT has been removed

COMMENTRemoved(control, String) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of COMMENT has been removed

COMMENTRemoved(conversion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of COMMENT has been removed

COMMENTRemoved(dataSource, String) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSourceListener

Called when a value of COMMENT has been removed

COMMENTRemoved(deltaGprimeO, String) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeOListener

Called when a value of COMMENT has been removed

COMMENTRemoved(dna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.dnaListener

Called when a value of COMMENT has been removed

COMMENTRemoved(entity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.entityListener

Called when a value of COMMENT has been removed

COMMENTRemoved(evidence, String) - Method in interface fr.curie.BiNoM.pathways.biopax.evidenceListener

Called when a value of COMMENT has been removed

COMMENTRemoved(experimentalForm, String) - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalFormListener

Called when a value of COMMENT has been removed

COMMENTRemoved(externalReferenceUtilityClass, String) - Method in interface fr.curie.BiNoM.pathways.biopax.externalReferenceUtilityClassListener

Called when a value of COMMENT has been removed

COMMENTRemoved(interaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.interactionListener

Called when a value of COMMENT has been removed

COMMENTRemoved(kPrime, String) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrimeListener

Called when a value of COMMENT has been removed

COMMENTRemoved(modulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of COMMENT has been removed

COMMENTRemoved(openControlledVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabularyListener

Called when a value of COMMENT has been removed

COMMENTRemoved(pathway, String) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayListener

Called when a value of COMMENT has been removed

COMMENTRemoved(pathwayStep, String) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStepListener

Called when a value of COMMENT has been removed

COMMENTRemoved(physicalEntity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityListener

Called when a value of COMMENT has been removed

COMMENTRemoved(physicalEntityParticipant, String) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantListener

Called when a value of COMMENT has been removed

COMMENTRemoved(physicalInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of COMMENT has been removed

COMMENTRemoved(protein, String) - Method in interface fr.curie.BiNoM.pathways.biopax.proteinListener

Called when a value of COMMENT has been removed

COMMENTRemoved(publicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXrefListener

Called when a value of COMMENT has been removed

COMMENTRemoved(relationshipXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.relationshipXrefListener

Called when a value of COMMENT has been removed

COMMENTRemoved(rna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.rnaListener

Called when a value of COMMENT has been removed

COMMENTRemoved(sequenceFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeatureListener

Called when a value of COMMENT has been removed

COMMENTRemoved(sequenceInterval, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceIntervalListener

Called when a value of COMMENT has been removed

COMMENTRemoved(sequenceLocation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceLocationListener

Called when a value of COMMENT has been removed

COMMENTRemoved(sequenceParticipant, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipantListener

Called when a value of COMMENT has been removed

COMMENTRemoved(sequenceSite, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceSiteListener

Called when a value of COMMENT has been removed

COMMENTRemoved(smallMolecule, String) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMoleculeListener

Called when a value of COMMENT has been removed

COMMENTRemoved(transport, String) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of COMMENT has been removed

COMMENTRemoved(transportWithBiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of COMMENT has been removed

COMMENTRemoved(unificationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.unificationXrefListener

Called when a value of COMMENT has been removed

COMMENTRemoved(utilityClass, String) - Method in interface fr.curie.BiNoM.pathways.biopax.utilityClassListener

Called when a value of COMMENT has been removed

COMMENTRemoved(xref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.xrefListener

Called when a value of COMMENT has been removed

Comments - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork

compareTwoSets(Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

compartmentHash - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

Map from compartment ids to CompartmentDocument.Compartment objects

compartments - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

List of compartments (represented as openControlledVocabulary objects)

compile() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard

COMPLETE_REACTIONS - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

For all reactions, attaches all connected nodes from the index (species, publications, pathway steps, etc.)

complex - Interface in fr.curie.BiNoM.pathways.biopax

Interface for complex ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

complexAssembly - Interface in fr.curie.BiNoM.pathways.biopax

Interface for complexAssembly ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

complexAssemblyImpl - Class in fr.curie.BiNoM.pathways.biopax

Implementation of complexAssembly Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

complexAssemblyListener - Interface in fr.curie.BiNoM.pathways.biopax

Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.complexAssembly to receive notification when properties changed, added or removed.

complexes_list - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

List of CellDesigner CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias objects

complexExpand - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions

complexImpl - Class in fr.curie.BiNoM.pathways.biopax

Implementation of complex Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

complexList - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

Map from cutted uris (after # separator) to 'complex' entities

complexListener - Interface in fr.curie.BiNoM.pathways.biopax

Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.complex to receive notification when properties changed, added or removed.

complexNoExpand - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions

COMPONENTSAdded(complex, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.complexListener

Called when a value of COMPONENTS has been added

COMPONENTSProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.complex

The Jena Property for COMPONENTS

COMPONENTSRemoved(complex, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.complexListener

Called when a value of COMPONENTS has been removed

confidence - Interface in fr.curie.BiNoM.pathways.biopax

Interface for confidence ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

Confidence - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork

CONFIDENCE_DASH_VALUEChanged(confidence) - Method in interface fr.curie.BiNoM.pathways.biopax.confidenceListener

Called when CONFIDENCE_DASH_VALUE has changed

CONFIDENCE_DASH_VALUEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.confidence

The Jena Property for CONFIDENCE_DASH_VALUE

CONFIDENCEAdded(evidence, confidence) - Method in interface fr.curie.BiNoM.pathways.biopax.evidenceListener

Called when a value of CONFIDENCE has been added

confidenceImpl - Class in fr.curie.BiNoM.pathways.biopax

Implementation of confidence Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

confidenceListener - Interface in fr.curie.BiNoM.pathways.biopax

Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.confidence to receive notification when properties changed, added or removed.

CONFIDENCEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.evidence

The Jena Property for CONFIDENCE

CONFIDENCERemoved(evidence, confidence) - Method in interface fr.curie.BiNoM.pathways.biopax.evidenceListener

Called when a value of CONFIDENCE has been removed

ConnectedComponents - Class in fr.curie.BiNoM.cytoscape.analysis

ConnectedComponents() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponents

ConnectedComponents(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms

ConnectedComponentsTask - Class in fr.curie.BiNoM.cytoscape.analysis

ConnectedComponentsTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponentsTask

considerCompartmentNameRatherThanId - Static variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

Check off if you want to use compartment id and not name

containsEdge(CyNetwork, CyEdge) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkIntersection

containsNode(CyNetwork, CyNode) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkIntersection

control - Interface in fr.curie.BiNoM.pathways.biopax

Interface for control ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

CONTROL_DASH_TYPEChanged(catalysis) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when CONTROL_DASH_TYPE has changed

CONTROL_DASH_TYPEChanged(control) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when CONTROL_DASH_TYPE has changed

CONTROL_DASH_TYPEChanged(modulation) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when CONTROL_DASH_TYPE has changed

CONTROL_DASH_TYPEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.control

The Jena Property for CONTROL_DASH_TYPE

controlImpl - Class in fr.curie.BiNoM.pathways.biopax

Implementation of control Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

CONTROLLEDChanged(catalysis) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when CONTROLLED has changed

CONTROLLEDChanged(control) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when CONTROLLED has changed

CONTROLLEDChanged(modulation) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when CONTROLLED has changed

CONTROLLEDProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.control

The Jena Property for CONTROLLED

CONTROLLERChanged(catalysis) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when CONTROLLER has changed

CONTROLLERChanged(control) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when CONTROLLER has changed

CONTROLLERChanged(modulation) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when CONTROLLER has changed

CONTROLLERProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.control

The Jena Property for CONTROLLER

controlListener - Interface in fr.curie.BiNoM.pathways.biopax

Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.control to receive notification when properties changed, added or removed.

controls - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

Map from cutted uris (after # separator) to BioPAX 'control' objects

conversion - Interface in fr.curie.BiNoM.pathways.biopax

Interface for conversion ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

conversionImpl - Class in fr.curie.BiNoM.pathways.biopax

Implementation of conversion Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

conversionListener - Interface in fr.curie.BiNoM.pathways.biopax

Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.conversion to receive notification when properties changed, added or removed.

convert(Thing, BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectFactory

convert(Object, BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectFactory

convert(int, InputStream, String, BioPAXToCytoscapeConverter.Option) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter

Convert from InputStream and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph

convert(int, BioPAXToCytoscapeConverter, String, BioPAXToCytoscapeConverter.Option) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter

Convert using BioPAXToCytoscapeConverter and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph

convert(int, String, String, BioPAXToCytoscapeConverter.Option) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter

Convert using file name and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph

convert(int, String, BioPAXToCytoscapeConverter.Option) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter

Convert from file (specified by path) and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph

convert() - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

The main conversion function to be used from outside

convert(String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

Principal conversion function used from outside

convert(GraphDocument, BioPAX) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter

convertExprTreeToMathMLString(ExprTree) - Static method in class fr.curie.BiNoM.pathways.utils.insertMassActionLaws

convertGraphToXGMML(Graph) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML

Converts internal BiNoM graph representation to GraphDocument

convertListOfNamesToQuery(Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

Utility converting vector of names and ids to a BioPAXGraphQuery object

convertSpeciesToName(SbmlDocument, String, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

Generates a unique name for a species speciesID

convertSpeciesToName(SbmlDocument.Sbml, String, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

Generates a unique name for a species speciesID

convertSpeciesToName(SbmlDocument.Sbml, String, boolean, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

Generates a name for a species speciesID

convertXGMMLToGraph(GraphDocument) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML

Converts GraphDocument to internal BiNoM graph representation (fr.curie.BiNoM.pathways.analysis.structure.Graph)

copy(String, CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils

copy(CyNetwork, CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils

copy() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Edge

copyLayout(SbmlDocument, GraphDocument) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter

copyResourceRecursive(String, Model, Model, Thing, HashMap) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAX1

CopySelectedNodesAndEdges - Class in fr.curie.BiNoM.cytoscape.utils

CopySelectedNodesAndEdges(boolean) - Constructor for class fr.curie.BiNoM.cytoscape.utils.CopySelectedNodesAndEdges

copyURIwithAllLinks(String, String, Model, Model) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAX1

copyURIwithAllLinks(String, String, Model, Model) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities

Extract a part of model which is necessary to define a things with uri

CorrectCytoscapeNodeIds(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

After reading XGMML files saved by Cytoscape, this function is used to recover the original Node Ids (Cytoscape will put negative numbers for it).

correctName(String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

Eliminates spaces, stars, dashes from the string

correctName(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Substitutes strings ' ','*','-','[',']','__',':' to underscore symbol

countEntities(Vector, Vector) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine

countGraphs - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph

countTokens() - Method in class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer

Total number of tokens present in the input string

create(VisualStyleDefinition) - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleFactory

createAccessionTable(String) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath

createbiochemicalReaction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of biochemicalReaction.

createbiochemicalReaction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of biochemicalReaction.

createBiopaxIndividual(String, String, OntModel) - Static method in class fr.curie.BiNoM.pathways.test.TestBioPAX

createbioSource(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of bioSource.

createbioSource(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of bioSource.

createcatalysis(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of catalysis.

createcatalysis(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of catalysis.

createCellDesignerTerms() - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

Encodes a list of standard terms (protein modification types (GOs) and influence types) by controlledVocabulary terms

createchemicalStructure(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of chemicalStructure.

createchemicalStructure(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of chemicalStructure.

createcomplex(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of complex.

createcomplex(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of complex.

createcomplexAssembly(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of complexAssembly.

createcomplexAssembly(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of complexAssembly.

createconfidence(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of confidence.

createconfidence(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of confidence.

createcontrol(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of control.

createcontrol(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of control.

createconversion(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of conversion.

createconversion(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of conversion.

createdataSource(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of dataSource.

createdataSource(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of dataSource.

createdeltaGprimeO(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of deltaGprimeO.

createdeltaGprimeO(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of deltaGprimeO.

createdna(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of dna.

createdna(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of dna.

createentity(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of entity.

createentity(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of entity.

createEntityId(entity) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

Creates entity id

createEntityName(entity) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

Creates a name for entity pe

createEntityParticipantForSpecies(String, Vector, Vector, HashMap, SbmlDocument.Sbml, BioPAX, String) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

Converts physicalEntity participant for a reaction rId

createevidence(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of evidence.

createevidence(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of evidence.

createexperimentalForm(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of experimentalForm.

createexperimentalForm(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of experimentalForm.

createexternalReferenceUtilityClass(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of externalReferenceUtilityClass.

createexternalReferenceUtilityClass(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of externalReferenceUtilityClass.

createGraphDocument(CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.GraphDocumentFactory

createIndexNodeHash() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph

createinteraction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of interaction.

createinteraction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of interaction.

createkPrime(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of kPrime.

createkPrime(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of kPrime.

createmodulation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of modulation.

createmodulation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of modulation.

createNameForComplex(complex) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

Generates a name for complex object

createNameForParticipant(physicalEntityParticipant, boolean) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

Creates a name for physicalEntityParticipant

createNetwork(String, GraphDocument, VisualStyle, boolean, TaskMonitor) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkFactory

createNetwork(String, GraphDocument, VisualStyleDefinition, boolean, TaskMonitor) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkFactory

createObject(String, String, BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectFactory

createopenControlledVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of openControlledVocabulary.

createopenControlledVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of openControlledVocabulary.

createpathway(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of pathway.

createpathway(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of pathway.

createpathwayStep(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of pathwayStep.

createpathwayStep(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of pathwayStep.

createphysicalEntity(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of physicalEntity.

createphysicalEntity(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of physicalEntity.

createphysicalEntityParticipant(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of physicalEntityParticipant.

createphysicalEntityParticipant(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of physicalEntityParticipant.

createphysicalInteraction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of physicalInteraction.

createphysicalInteraction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of physicalInteraction.

createprotein(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of protein.

createprotein(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of protein.

createpublicationXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of publicationXref.

createpublicationXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of publicationXref.

createrelationshipXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of relationshipXref.

createrelationshipXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of relationshipXref.

createrna(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of rna.

createrna(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of rna.

createsequenceFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of sequenceFeature.

createsequenceFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of sequenceFeature.

createsequenceInterval(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of sequenceInterval.

createsequenceInterval(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of sequenceInterval.

createsequenceLocation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of sequenceLocation.

createsequenceLocation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of sequenceLocation.

createsequenceParticipant(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of sequenceParticipant.

createsequenceParticipant(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of sequenceParticipant.

createsequenceSite(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of sequenceSite.

createsequenceSite(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of sequenceSite.

createsmallMolecule(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of smallMolecule.

createsmallMolecule(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of smallMolecule.

createtransport(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of transport.

createtransport(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of transport.

createtransportWithBiochemicalReaction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of transportWithBiochemicalReaction.

createtransportWithBiochemicalReaction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of transportWithBiochemicalReaction.

createunificationXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of unificationXref.

createunificationXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of unificationXref.

createutilityClass(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of utilityClass.

createutilityClass(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of utilityClass.

createUtilityId(utilityClass) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

Creates an id for utilityClass

createUtilityName(utilityClass) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

Creates a name for utilityClass object

createxref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of xref.

createxref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Create a new instance of xref.

cutQuotes(String) - Static method in class fr.curie.BiNoM.pathways.utils.SimpleTable

cutUri(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Convert string from the form # to simply

CycleDecomposition - Class in fr.curie.BiNoM.cytoscape.analysis

CycleDecomposition() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.CycleDecomposition

CycleDecomposition(Graph, int) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms

CycleDecompositionTask - Class in fr.curie.BiNoM.cytoscape.analysis

CycleDecompositionTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.CycleDecompositionTask

Cytoscape2BioPAX - Class in fr.curie.BiNoM.pathways.converters

Cytoscape2BioPAX() - Constructor for class fr.curie.BiNoM.pathways.converters.Cytoscape2BioPAX

Cytoscape2CellDesigner - Class in fr.curie.BiNoM.pathways.converters

Cytoscape2CellDesigner() - Constructor for class fr.curie.BiNoM.pathways.converters.Cytoscape2CellDesigner

CytoscapeToBioPAXConverter - Class in fr.curie.BiNoM.pathways

Deprecated class.

CytoscapeToBioPAXConverter() - Constructor for class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter

CytoscapeToCellDesignerConverter - Class in fr.curie.BiNoM.pathways

Class used to export a part of CellDesigner file, using only species and reactions visualized in the current Cytoscape network

CytoscapeToCellDesignerConverter() - Constructor for class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter