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generateMapFile(String, String) - Method in class fr.curie.BiNoM.pathways.test.ProduceClickableMap
generateMassActionLaw(Reaction, HashMap) - Static method in class fr.curie.BiNoM.pathways.utils.insertMassActionLaws
generateNames(BioPAX, boolean) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService: Function for generating names
generateUniqueID(String, HashMap) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService: Adds # symbols until the id will become unique
genericUtilityName - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService: Names of utilities
getAccessionNumberTable() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
getAccNumberFileName() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
getAddedEdgeCount() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
getAddedEdges() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
getAddedNodeCount() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
getAddedNodes() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
getAllbiochemicalReaction(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of biochemicalReaction for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#biochemicalReaction
getAllbioSource(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of bioSource for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#bioSource
getAllcatalysis(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of catalysis for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#catalysis
getAllchemicalStructure(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of chemicalStructure for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#chemicalStructure
getAllCompartments() - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
getAllcomplex(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of complex for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#complex
getAllcomplexAssembly(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of complexAssembly for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#complexAssembly
getAllconfidence(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of confidence for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#confidence
getAllcontrol(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of control for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#control
getAllconversion(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of conversion for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#conversion
getAlldataSource(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of dataSource for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#dataSource
getAlldeltaGprimeO(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of deltaGprimeO for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#deltaGprimeO
getAlldna(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of dna for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#dna
getAllentity(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of entity for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#entity
getAllevidence(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of evidence for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#evidence
getAllexperimentalForm(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of experimentalForm for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#experimentalForm
getAllexternalReferenceUtilityClass(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of externalReferenceUtilityClass for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#externalReferenceUtilityClass
getAllinteraction(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of interaction for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#interaction
getAllkPrime(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of kPrime for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#kPrime
getAllmodulation(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of modulation for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#modulation
getAllObjectsHash(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner
getAllopenControlledVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of openControlledVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#openControlledVocabulary
getAllpathway(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of pathway for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#pathway
getAllpathwayStep(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of pathwayStep for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#pathwayStep
getAllphysicalEntity(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of physicalEntity for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#physicalEntity
getAllphysicalEntityParticipant(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of physicalEntityParticipant for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#physicalEntityParticipant
getAllphysicalInteraction(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of physicalInteraction for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#physicalInteraction
getAllprotein(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of protein for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#protein
getAllpublicationXref(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of publicationXref for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#publicationXref
getAllrelationshipXref(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of relationshipXref for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#relationshipXref
getAllrna(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of rna for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#rna
getAllsequenceFeature(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of sequenceFeature for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#sequenceFeature
getAllsequenceInterval(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of sequenceInterval for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#sequenceInterval
getAllsequenceLocation(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of sequenceLocation for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#sequenceLocation
getAllsequenceParticipant(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of sequenceParticipant for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#sequenceParticipant
getAllsequenceSite(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of sequenceSite for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#sequenceSite
getAllsmallMolecule(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of smallMolecule for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#smallMolecule
getAlltransport(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of transport for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#transport
getAlltransportWithBiochemicalReaction(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of transportWithBiochemicalReaction for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#transportWithBiochemicalReaction
getAllunificationXref(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of unificationXref for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#unificationXref
getAllutilityClass(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of utilityClass for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#utilityClass
getAllxref(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Return an instance of xref for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level2.owl#xref
getAssociatedNetworks(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSourceDB
getAttrDescV() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc
getAttributesWithSubstringInName(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Element: Finds all attributes in whose name the substring is contained
getAttributeValue() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition.ObjectMapping
getAttributeValues(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Element: Returns all attributes attached with a given name
getAttValue(GraphicNode, String) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML
getAUTHORS() - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXref: Iterates through the 'AUTHORS' property values.
getAUTHORS() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl
getAVAILABILITY() - Method in interface fr.curie.BiNoM.pathways.biopax.entity: Iterates through the 'AVAILABILITY' property values.
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getAVAILABILITY() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
GetBiggestGraph(Vector) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
getbiochemicalReaction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of biochemicalReaction.
getbiochemicalReaction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of biochemicalReaction.
getBioPAX(CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImport
getBioPAX(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSourceDB
getBioPAX() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObject
getBioPAXGraphQuery() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask
getBioPAXGraphQueryEngine() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
getbioSource(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of bioSource.
getbioSource(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of bioSource.
getBrowseInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserFrame
getCanonName() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc
getcatalysis(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of catalysis.
getcatalysis(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of catalysis.
getCellDesigner(CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImport
getCellDesigner(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerSourceDB
getCelldesignerSpeciesName(SbmlDocument.Sbml, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getCELLTYPE() - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource: Gets the 'CELLTYPE' property value
getCELLTYPE() - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl
getCELLULAR_DASH_LOCATION() - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant: Gets the 'CELLULAR_DASH_LOCATION' property value
getCELLULAR_DASH_LOCATION() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl
getCELLULAR_DASH_LOCATION() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl
getCHEMICAL_DASH_FORMULA() - Method in interface fr.curie.BiNoM.pathways.biopax.smallMolecule: Gets the 'CHEMICAL_DASH_FORMULA' property value
getCHEMICAL_DASH_FORMULA() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl
getchemicalStructure(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of chemicalStructure.
getchemicalStructure(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of chemicalStructure.
getChildrenClassDescV() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc
getClassDesc() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc
getClassDesc(String) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDescFactory
getClassDesc(Class) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDescFactory
getClassDesc() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObject
getClusteredNetworks(Vector<GraphDocument>, float) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
getCOFACTOR() - Method in interface fr.curie.BiNoM.pathways.biopax.catalysis: Get an Iterator the 'COFACTOR' property values.
getCOFACTOR() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getColorCode(CellDesignerColorSpecies.SimpleTable, int, boolean) - Method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.chemicalStructureImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.confidenceImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl
getCOMMENT() - Method in interface fr.curie.BiNoM.pathways.biopax.entity: Iterates through the 'COMMENT' property values.
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.experimentalFormImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.externalReferenceUtilityClassImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayStepImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceIntervalImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceLocationImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceSiteImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl
getCOMMENT() - Method in interface fr.curie.BiNoM.pathways.biopax.utilityClass: Iterates through the 'COMMENT' property values.
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.utilityClassImpl
getCOMMENT() - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl
getCompartment(String) - Method in class fr.curie.BiNoM.pathways.wrappers.BioPAX
getCompartmentHash(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter: Creates the map of compartments
getCompartmentHash(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
getcomplex(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of complex.
getcomplex(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of complex.
getcomplexAssembly(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of complexAssembly.
getcomplexAssembly(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of complexAssembly.
getComplexById(Vector, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
getComplexes(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter: Creates the list of complexes
getCOMPONENTS() - Method in interface fr.curie.BiNoM.pathways.biopax.complex: Get an Iterator the 'COMPONENTS' property values.
getCOMPONENTS() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl
getconfidence(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of confidence.
getconfidence(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of confidence.
getCONFIDENCE() - Method in interface fr.curie.BiNoM.pathways.biopax.evidence: Get an Iterator the 'CONFIDENCE' property values.
getCONFIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl
getCONFIDENCE_DASH_VALUE() - Method in interface fr.curie.BiNoM.pathways.biopax.confidence: Gets the 'CONFIDENCE_DASH_VALUE' property value
getCONFIDENCE_DASH_VALUE() - Method in class fr.curie.BiNoM.pathways.biopax.confidenceImpl
GetConnectedComponent(Graph, Node) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
getConnectedComponents(GraphDocument) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
getcontrol(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of control.
getcontrol(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of control.
getCONTROL_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getCONTROL_DASH_TYPE() - Method in interface fr.curie.BiNoM.pathways.biopax.control: Gets the 'CONTROL_DASH_TYPE' property value
getCONTROL_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getCONTROL_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getCONTROLLED_ascatalysis() - Method in interface fr.curie.BiNoM.pathways.biopax.modulation: Gets the 'CONTROLLED' property value
getCONTROLLED_ascatalysis() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getCONTROLLED_asconversion() - Method in interface fr.curie.BiNoM.pathways.biopax.catalysis: Gets the 'CONTROLLED' property value
getCONTROLLED_asconversion() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getCONTROLLED_asinteraction() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getCONTROLLED_asinteraction() - Method in interface fr.curie.BiNoM.pathways.biopax.control: Gets the 'CONTROLLED' property value
getCONTROLLED_asinteraction() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getCONTROLLED_asinteraction() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getCONTROLLED_aspathway() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getCONTROLLED_aspathway() - Method in interface fr.curie.BiNoM.pathways.biopax.control: Gets the 'CONTROLLED' property value
getCONTROLLED_aspathway() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getCONTROLLED_aspathway() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getControlledURI(control) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter
getCONTROLLER() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getCONTROLLER() - Method in interface fr.curie.BiNoM.pathways.biopax.control: Gets the 'CONTROLLER' property value
getCONTROLLER() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getCONTROLLER() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getconversion(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of conversion.
getconversion(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of conversion.
getCreateEdge(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getCreateNode(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getCyclicComponents(GraphDocument, StructureAnalysisUtils.Option) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponentsTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.CycleDecompositionTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetworkTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.MaterialComponentsTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.ModularViewTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.MonoMolecularReactionsAsEdgesTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.PruneGraphTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.StronglyConnectedComponentsTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSourceTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExport
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImport
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSourceTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExport
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImport
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateTask
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExport
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExportTask
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl
getDATA_DASH_SOURCE() - Method in interface fr.curie.BiNoM.pathways.biopax.entity: Get an Iterator the 'DATA_DASH_SOURCE' property values.
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getDATA_DASH_SOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getDatabaseFileName() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
getdataSource(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of dataSource.
getdataSource(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of dataSource.
getDB() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl
getDB() - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl
getDB() - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl
getDB() - Method in interface fr.curie.BiNoM.pathways.biopax.xref: Gets the 'DB' property value
getDB() - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl
getDB_DASH_VERSION() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl
getDB_DASH_VERSION() - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl
getDB_DASH_VERSION() - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl
getDB_DASH_VERSION() - Method in interface fr.curie.BiNoM.pathways.biopax.xref: Gets the 'DB_DASH_VERSION' property value
getDB_DASH_VERSION() - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl
getDefaultEdgeLineColor() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getDefaultEdgeLineType() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getDefaultEdgeSourceArrow() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getDefaultEdgeTargetArrow() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getDefaultNodeBorderColor() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getDefaultNodeBorderLineType() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getDefaultNodeColor() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getDefaultNodeShape() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getDefaultNodeSize() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getDefaultNsPrefix(Model) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
getDELTA_DASH_G() - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction: Get an Iterator the 'DELTA_DASH_G' property values.
getDELTA_DASH_G() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getDELTA_DASH_G() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getDELTA_DASH_G_DASH_PRIME_DASH_O() - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO: Gets the 'DELTA_DASH_G_DASH_PRIME_DASH_O' property value
getDELTA_DASH_G_DASH_PRIME_DASH_O() - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl
getDELTA_DASH_H() - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction: Iterates through the 'DELTA_DASH_H' property values.
getDELTA_DASH_H() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getDELTA_DASH_H() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getDELTA_DASH_S() - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction: Iterates through the 'DELTA_DASH_S' property values.
getDELTA_DASH_S() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getDELTA_DASH_S() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getdeltaGprimeO(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of deltaGprimeO.
getdeltaGprimeO(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of deltaGprimeO.
getDescription() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.OWLExtensionFilter
getDescription() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.XGMMLExtensionFilter
getDIRECTION() - Method in interface fr.curie.BiNoM.pathways.biopax.catalysis: Gets the 'DIRECTION' property value
getDIRECTION() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getdna(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of dna.
getdna(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of dna.
getEC_DASH_NUMBER() - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction: Iterates through the 'EC_DASH_NUMBER' property values.
getEC_DASH_NUMBER() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getEC_DASH_NUMBER() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getEdge(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getEdge(Node, Node, boolean) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getEdgeAttribute() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getEdgeByLabel(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getEdgeIndex(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getEdgeLineColorMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getEdgeLineTypeMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getEdgeNodes() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
getEdges() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
getEdgeSourceArrowMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getEdgeTargetArrowMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getEditInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserFrame
getEditPanelAction(boolean) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc
getElementType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc
getElementType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleAttrDesc
getElementType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleListAttrDesc
getElementType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerAttrDesc
getElementType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerListAttrDesc
getElementType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc
getElementType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc
getElementType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringAttrDesc
getElementType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringListAttrDesc
getEntities(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner: Fills entities map
getentity(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of entity.
getentity(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of entity.
getEntityId(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getEntityName(String, CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity, SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getEntityName(String, CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity, SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getevidence(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of evidence.
getevidence(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of evidence.
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getEVIDENCE() - Method in interface fr.curie.BiNoM.pathways.biopax.interaction: Get an Iterator the 'EVIDENCE' property values.
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getEVIDENCE() - Method in interface fr.curie.BiNoM.pathways.biopax.pathway: Get an Iterator the 'EVIDENCE' property values.
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getEVIDENCE() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getEVIDENCE_DASH_CODE() - Method in interface fr.curie.BiNoM.pathways.biopax.evidence: Get an Iterator the 'EVIDENCE_DASH_CODE' property values.
getEVIDENCE_DASH_CODE() - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl
getEXPERIMENTAL_DASH_FORM() - Method in interface fr.curie.BiNoM.pathways.biopax.evidence: Get an Iterator the 'EXPERIMENTAL_DASH_FORM' property values.
getEXPERIMENTAL_DASH_FORM() - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl
getEXPERIMENTAL_DASH_FORM_DASH_TYPE() - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalForm: Get an Iterator the 'EXPERIMENTAL_DASH_FORM_DASH_TYPE' property values.
getEXPERIMENTAL_DASH_FORM_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.experimentalFormImpl
getexperimentalForm(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of experimentalForm.
getexperimentalForm(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of experimentalForm.
getexternalReferenceUtilityClass(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of externalReferenceUtilityClass.
getexternalReferenceUtilityClass(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of externalReferenceUtilityClass.
getFEATURE_DASH_LOCATION() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature: Get an Iterator the 'FEATURE_DASH_LOCATION' property values.
getFEATURE_DASH_LOCATION() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl
getFEATURE_DASH_TYPE() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature: Gets the 'FEATURE_DASH_TYPE' property value
getFEATURE_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl
getFileKey(String) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter: key could be based on: filename + date + size or md5(filecontents);
getFirstAttribute(GraphicNode, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils: Get first attribute in the list with name
getFirstAttribute(GraphicEdge, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils: Get first attribute in the list with name
getFirstAttributeValue(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Element: Finds first in the list attribute with a given name
getGenes(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter: Creates the list of genes
getGridBagLayoutMaxRows() - Static method in class fr.curie.BiNoM.cytoscape.lib.Utils
getHangingNodes() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getID() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl
getID() - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl
getID() - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl
getID() - Method in interface fr.curie.BiNoM.pathways.biopax.xref: Gets the 'ID' property value
getID() - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl
getID_DASH_VERSION() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl
getID_DASH_VERSION() - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl
getID_DASH_VERSION() - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl
getID_DASH_VERSION() - Method in interface fr.curie.BiNoM.pathways.biopax.xref: Gets the 'ID_DASH_VERSION' property value
getID_DASH_VERSION() - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl
getIdByUri(String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService: Used to get id of the thing with uri
getIDList(Vector) - Method in class fr.curie.BiNoM.pathways.utils.AccessionNumberTable
getIncludedSpeciesInComplex(SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getIncludedSpeciesInComplex(SbmlDocument.Sbml, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.analysis.ModularViewDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSource
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSourceDB
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSyncNetworksDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
getInstance(BioPAX) - Static method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDescFactory
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassTreeFrame
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectFactory
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDisplayIndexInfoDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXViewQueryLogDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSource
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerSourceDB
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleFactory
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.netwop.DoubleNetworkDifferenceDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateConfirmDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContentsDialog
getinteraction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of interaction.
getinteraction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of interaction.
getINTERACTION_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getINTERACTION_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getINTERACTION_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getINTERACTION_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getINTERACTION_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getINTERACTION_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getINTERACTION_DASH_TYPE() - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction: Get an Iterator the 'INTERACTION_DASH_TYPE' property values.
getINTERACTION_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getINTERACTION_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getINTERACTION_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getIONIC_DASH_STRENGTH() - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO: Iterates through the 'IONIC_DASH_STRENGTH' property values.
getIONIC_DASH_STRENGTH() - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl
getIONIC_DASH_STRENGTH() - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime: Iterates through the 'IONIC_DASH_STRENGTH' property values.
getIONIC_DASH_STRENGTH() - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl
getJavaRelease() - Static method in class fr.curie.BiNoM.cytoscape.lib.Utils
getJClass() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc
getK_DASH_PRIME() - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime: Gets the 'K_DASH_PRIME' property value
getK_DASH_PRIME() - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl
getKEQ() - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction: Get an Iterator the 'KEQ' property values.
getKEQ() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getKEQ() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getkPrime(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of kPrime.
getkPrime(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of kPrime.
getLEFT() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getLEFT() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getLEFT() - Method in interface fr.curie.BiNoM.pathways.biopax.conversion: Get an Iterator the 'LEFT' property values.
getLEFT() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getLEFT() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getLEFT() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getMappingValue() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition.ObjectMapping
getMaterialComponents(GraphDocument) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
getMetaType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc
getMetaType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc
getMetaType() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc
getModularView(GraphDocument, Vector<GraphDocument>, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
getmodulation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of modulation.
getmodulation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of modulation.
getMOLECULAR_DASH_WEIGHT() - Method in interface fr.curie.BiNoM.pathways.biopax.smallMolecule: Gets the 'MOLECULAR_DASH_WEIGHT' property value
getMOLECULAR_DASH_WEIGHT() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl
getName() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc
getName() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc
getName() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getName() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getNAME() - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource: Gets the 'NAME' property value
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getNAME() - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource: Iterates through the 'NAME' property values.
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl
getNAME() - Method in interface fr.curie.BiNoM.pathways.biopax.entity: Gets the 'NAME' property value
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl
getNAME() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature: Gets the 'NAME' property value
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getNAME() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getNameByUri(String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService: Used to get name of the thing with uri
getNameOfIncludedSpecies(SbmlDocument, CelldesignerSpeciesDocument.CelldesignerSpecies) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getNameOfIncludedSpecies(SbmlDocument.Sbml, CelldesignerSpeciesDocument.CelldesignerSpecies) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getNameOfModificationResidue(SbmlDocument, CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getNameOfModificationResidue(SbmlDocument.Sbml, CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getNamingServiceMode() - Static method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXToggleNamingService
getNetwork(String) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
getNetwork(int) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
getNetwork() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
getNetworkNames() - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
getNetworkNames(String) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
getNetworks(int[]) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
getNEXT_DASH_STEP() - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep: Get an Iterator the 'NEXT_DASH_STEP' property values.
getNEXT_DASH_STEP() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayStepImpl
getNode(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getNodeAttribute() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getNodeBorderColorMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getNodeBorderLineTypeMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getNodeByLabel(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getNodeColorMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getNodeImageMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getNodeIndex(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getNodes() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
getNodesByLabelInclusion(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getNodeShapeMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getNodeSizeMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
getNullEmptyNetwork() - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkFactory
getObject() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObject
getObject(String, BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectFactory
getObject(Thing, BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectFactory
getObjectClassDesc() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc
getObjectClassDesc() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleAttrDesc
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleListAttrDesc
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerAttrDesc
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerListAttrDesc
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringAttrDesc
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringListAttrDesc
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleAttrDesc
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleListAttrDesc
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerAttrDesc
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerListAttrDesc
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringAttrDesc
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringListAttrDesc
getopenControlledVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of openControlledVocabulary.
getopenControlledVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of openControlledVocabulary.
getORGANISM() - Method in interface fr.curie.BiNoM.pathways.biopax.complex: Get an Iterator the 'ORGANISM' property values.
getORGANISM() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl
getORGANISM() - Method in interface fr.curie.BiNoM.pathways.biopax.dna: Get an Iterator the 'ORGANISM' property values.
getORGANISM() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl
getORGANISM() - Method in interface fr.curie.BiNoM.pathways.biopax.pathway: Gets the 'ORGANISM' property value
getORGANISM() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getORGANISM() - Method in interface fr.curie.BiNoM.pathways.biopax.protein: Gets the 'ORGANISM' property value
getORGANISM() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl
getORGANISM() - Method in interface fr.curie.BiNoM.pathways.biopax.rna: Gets the 'ORGANISM' property value
getORGANISM() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl
getParentClassDescV() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc
getParentClassDescV(Class) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDescFactory
getPARTICIPANT() - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalForm: Gets the 'PARTICIPANT' property value
getPARTICIPANT() - Method in class fr.curie.BiNoM.pathways.biopax.experimentalFormImpl
getPARTICIPANTS_asentity() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getPARTICIPANTS_asentity() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getPARTICIPANTS_asentity() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getPARTICIPANTS_asentity() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getPARTICIPANTS_asentity() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getPARTICIPANTS_asentity() - Method in interface fr.curie.BiNoM.pathways.biopax.interaction: Get an Iterator the 'PARTICIPANTS' property values.
getPARTICIPANTS_asentity() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl
getPARTICIPANTS_asentity() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getPARTICIPANTS_asentity() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getPARTICIPANTS_asentity() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getPARTICIPANTS_asentity() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getPARTICIPANTS_asphysicalEntityParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getPARTICIPANTS_asphysicalEntityParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getPARTICIPANTS_asphysicalEntityParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getPARTICIPANTS_asphysicalEntityParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getPARTICIPANTS_asphysicalEntityParticipant() - Method in interface fr.curie.BiNoM.pathways.biopax.conversion: Get an Iterator the 'PARTICIPANTS' property values.
getPARTICIPANTS_asphysicalEntityParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getPARTICIPANTS_asphysicalEntityParticipant() - Method in interface fr.curie.BiNoM.pathways.biopax.interaction: Get an Iterator the 'PARTICIPANTS' property values.
getPARTICIPANTS_asphysicalEntityParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl
getPARTICIPANTS_asphysicalEntityParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getPARTICIPANTS_asphysicalEntityParticipant() - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction: Get an Iterator the 'PARTICIPANTS' property values.
getPARTICIPANTS_asphysicalEntityParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getPARTICIPANTS_asphysicalEntityParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getPARTICIPANTS_asphysicalEntityParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getpathway(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of pathway.
getpathway(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of pathway.
getPATHWAY_DASH_COMPONENTS_asinteraction() - Method in interface fr.curie.BiNoM.pathways.biopax.pathway: Get an Iterator the 'PATHWAY_DASH_COMPONENTS' property values.
getPATHWAY_DASH_COMPONENTS_asinteraction() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getPATHWAY_DASH_COMPONENTS_aspathway() - Method in interface fr.curie.BiNoM.pathways.biopax.pathway: Get an Iterator the 'PATHWAY_DASH_COMPONENTS' property values.
getPATHWAY_DASH_COMPONENTS_aspathway() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getPATHWAY_DASH_COMPONENTS_aspathwayStep() - Method in interface fr.curie.BiNoM.pathways.biopax.pathway: Get an Iterator the 'PATHWAY_DASH_COMPONENTS' property values.
getPATHWAY_DASH_COMPONENTS_aspathwayStep() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getpathwayStep(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of pathwayStep.
getpathwayStep(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of pathwayStep.
getPH() - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO: Iterates through the 'PH' property values.
getPH() - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl
getPH() - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime: Iterates through the 'PH' property values.
getPH() - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl
getPHYSICAL_DASH_ENTITY() - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant: Gets the 'PHYSICAL_DASH_ENTITY' property value
getPHYSICAL_DASH_ENTITY() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl
getPHYSICAL_DASH_ENTITY() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl
getphysicalEntity(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of physicalEntity.
getphysicalEntity(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of physicalEntity.
getphysicalEntityParticipant(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of physicalEntityParticipant.
getphysicalEntityParticipant(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of physicalEntityParticipant.
getphysicalInteraction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of physicalInteraction.
getphysicalInteraction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of physicalInteraction.
getPMG() - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO: Iterates through the 'PMG' property values.
getPMG() - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl
getPMG() - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime: Iterates through the 'PMG' property values.
getPMG() - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl
getPOSITION_DASH_STATUS() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceSite: Gets the 'POSITION_DASH_STATUS' property value
getPOSITION_DASH_STATUS() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceSiteImpl
getPropertyURI(entity, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
getPropertyURIs(entity, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
getPropertyURIs(utilityClass, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
getprotein(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of protein.
getprotein(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of protein.
getProteinById(Vector, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
getProteins(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter: Creates the list of proteins
getPrunedGraph(GraphDocument, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
getpublicationXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of publicationXref.
getpublicationXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of publicationXref.
getReactionById(Vector, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
getReactions(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter: Creates the list of reactions
getReactionString(ReactionDocument.Reaction, SbmlDocument, boolean) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter: Function for printing the CellDesigner reactions
getRELATIONSHIP_DASH_TYPE() - Method in interface fr.curie.BiNoM.pathways.biopax.relationshipXref: Gets the 'RELATIONSHIP_DASH_TYPE' property value
getRELATIONSHIP_DASH_TYPE() - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl
getrelationshipXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of relationshipXref.
getrelationshipXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of relationshipXref.
getReport() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
getRIGHT() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getRIGHT() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getRIGHT() - Method in interface fr.curie.BiNoM.pathways.biopax.conversion: Get an Iterator the 'RIGHT' property values.
getRIGHT() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getRIGHT() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getRIGHT() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getrna(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of rna.
getrna(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of rna.
getSelectedNodes() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
getSEQUENCE() - Method in interface fr.curie.BiNoM.pathways.biopax.dna: Iterates through the 'SEQUENCE' property values.
getSEQUENCE() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl
getSEQUENCE() - Method in interface fr.curie.BiNoM.pathways.biopax.protein: Gets the 'SEQUENCE' property value
getSEQUENCE() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl
getSEQUENCE() - Method in interface fr.curie.BiNoM.pathways.biopax.rna: Gets the 'SEQUENCE' property value
getSEQUENCE() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl
getSEQUENCE_DASH_FEATURE_DASH_LIST() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipant: Get an Iterator the 'SEQUENCE_DASH_FEATURE_DASH_LIST' property values.
getSEQUENCE_DASH_FEATURE_DASH_LIST() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl
getSEQUENCE_DASH_INTERVAL_DASH_BEGIN() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceInterval: Gets the 'SEQUENCE_DASH_INTERVAL_DASH_BEGIN' property value
getSEQUENCE_DASH_INTERVAL_DASH_BEGIN() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceIntervalImpl
getSEQUENCE_DASH_INTERVAL_DASH_END() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceInterval: Gets the 'SEQUENCE_DASH_INTERVAL_DASH_END' property value
getSEQUENCE_DASH_INTERVAL_DASH_END() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceIntervalImpl
getSEQUENCE_DASH_POSITION() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceSite: Gets the 'SEQUENCE_DASH_POSITION' property value
getSEQUENCE_DASH_POSITION() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceSiteImpl
getsequenceFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of sequenceFeature.
getsequenceFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of sequenceFeature.
getsequenceInterval(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of sequenceInterval.
getsequenceInterval(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of sequenceInterval.
getsequenceLocation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of sequenceLocation.
getsequenceLocation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of sequenceLocation.
getsequenceParticipant(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of sequenceParticipant.
getsequenceParticipant(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of sequenceParticipant.
getsequenceSite(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of sequenceSite.
getsequenceSite(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of sequenceSite.
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl
getSHORT_DASH_NAME() - Method in interface fr.curie.BiNoM.pathways.biopax.entity: Gets the 'SHORT_DASH_NAME' property value
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl
getSHORT_DASH_NAME() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature: Gets the 'SHORT_DASH_NAME' property value
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getSHORT_DASH_NAME() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getsmallMolecule(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of smallMolecule.
getsmallMolecule(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of smallMolecule.
getSOURCE() - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXref: Iterates through the 'SOURCE' property values.
getSOURCE() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl
getSpecies(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter: Creates the list of species
getSpecies(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter: Creates the map from species id to SpeciesDocument.Species
getSpecies(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.insertMassActionLaws
getSpeciesAliasInReaction(ReactionDocument.Reaction, String, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter: Finds CellDesigner alias of species 'id' in the reation r
getSpeciesById(Vector, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
getSpeciesName(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity, String, String, String, boolean, boolean, String, SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getSpeciesName(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity, String, String, String, boolean, boolean, String, SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
getSpektrumGR(float) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies
getSPONTANEOUS() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getSPONTANEOUS() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getSPONTANEOUS() - Method in interface fr.curie.BiNoM.pathways.biopax.conversion: Gets the 'SPONTANEOUS' property value
getSPONTANEOUS() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getSPONTANEOUS() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getSPONTANEOUS() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getSTEP_DASH_INTERACTIONS_asinteraction() - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep: Get an Iterator the 'STEP_DASH_INTERACTIONS' property values.
getSTEP_DASH_INTERACTIONS_asinteraction() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayStepImpl
getSTEP_DASH_INTERACTIONS_aspathway() - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep: Get an Iterator the 'STEP_DASH_INTERACTIONS' property values.
getSTEP_DASH_INTERACTIONS_aspathway() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayStepImpl
getSTOICHIOMETRIC_DASH_COEFFICIENT() - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant: Gets the 'STOICHIOMETRIC_DASH_COEFFICIENT' property value
getSTOICHIOMETRIC_DASH_COEFFICIENT() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl
getSTOICHIOMETRIC_DASH_COEFFICIENT() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleAttrDesc
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleListAttrDesc
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerAttrDesc
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerListAttrDesc
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringAttrDesc
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringListAttrDesc
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleAttrDesc
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleListAttrDesc
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerAttrDesc
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerListAttrDesc
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringAttrDesc
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringListAttrDesc
getStronglyConnectedComponents(GraphDocument) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
getSTRUCTURE() - Method in interface fr.curie.BiNoM.pathways.biopax.smallMolecule: Get an Iterator the 'STRUCTURE' property values.
getSTRUCTURE() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl
getSTRUCTURE_DASH_DATA() - Method in interface fr.curie.BiNoM.pathways.biopax.chemicalStructure: Gets the 'STRUCTURE_DASH_DATA' property value
getSTRUCTURE_DASH_DATA() - Method in class fr.curie.BiNoM.pathways.biopax.chemicalStructureImpl
getSTRUCTURE_DASH_FORMAT() - Method in interface fr.curie.BiNoM.pathways.biopax.chemicalStructure: Gets the 'STRUCTURE_DASH_FORMAT' property value
getSTRUCTURE_DASH_FORMAT() - Method in class fr.curie.BiNoM.pathways.biopax.chemicalStructureImpl
getSubGraphByLabelInclusions(Graph, String) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils: Simply extraxts a subgraph with nodes whose name have label as a substring
getSuffixForMultipleAliases(SbmlDocument.Sbml, String, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter: Axillary function, adds ' (prime) to Cytoscape node name to distinguish multiple CellDesigner species aliases
getSuppressedEdgeCount() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
getSuppressedEdges() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
getSuppressedNodeCount() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
getSuppressedNodes() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
getSymbol() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl
getSYNONYMS() - Method in interface fr.curie.BiNoM.pathways.biopax.entity: Iterates through the 'SYNONYMS' property values.
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl
getSYNONYMS() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature: Iterates through the 'SYNONYMS' property values.
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getSYNONYMS() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getTAXON_DASH_XREF() - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource: Gets the 'TAXON_DASH_XREF' property value
getTAXON_DASH_XREF() - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl
getTEMPERATURE() - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO: Iterates through the 'TEMPERATURE' property values.
getTEMPERATURE() - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl
getTEMPERATURE() - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime: Iterates through the 'TEMPERATURE' property values.
getTEMPERATURE() - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl
getTERM() - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary: Iterates through the 'TERM' property values.
getTERM() - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl
getText() - Method in class fr.curie.BiNoM.cytoscape.lib.MLLabel
getText(XmlObject) - Static method in class fr.curie.BiNoM.pathways.utils.Utils: Read the text of XmlObject
getThing(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Returns an instance of an interface for the given Resource.
getThing(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Returns an instance of an interface for the given Resource URI.
getTISSUE() - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource: Gets the 'TISSUE' property value
getTISSUE() - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponentsTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.CycleDecompositionTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetworkTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.MaterialComponentsTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.ModularViewTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.MonoMolecularReactionsAsEdgesTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.PruneGraphTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.StronglyConnectedComponentsTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSourceTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExport
getTitle() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImport
getTitle() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSourceTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExport
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImport
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateTask
getTitle() - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExport
getTitle() - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExportTask
getTITLE() - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXref: Gets the 'TITLE' property value
getTITLE() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl
gettransport(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of transport.
gettransport(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of transport.
gettransportWithBiochemicalReaction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of transportWithBiochemicalReaction.
gettransportWithBiochemicalReaction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of transportWithBiochemicalReaction.
getTypeForParticipant(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
getunificationXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of unificationXref.
getunificationXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of unificationXref.
getUriById(String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
getUriByName(String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
getURIs(CyNode) - Static method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyManager
getURIs(CyEdge) - Static method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyManager
getURL() - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXref: Iterates through the 'URL' property values.
getURL() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl
getUsedMemorySinceLastTime() - Static method in class fr.curie.BiNoM.pathways.utils.Utils: Returns a difference in used memory since last call of printUsedMemory,printUsedMemorySinceLastTime, getUsedMemorySinceLastTime,printUsedMemorySinceLastTimeByte functions
getutilityClass(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of utilityClass.
getutilityClass(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of utilityClass.
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleAttrDesc
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleListAttrDesc
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerAttrDesc
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerListAttrDesc
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringAttrDesc
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringListAttrDesc
getValue(XmlObject) - Static method in class fr.curie.BiNoM.pathways.utils.Utils: read XmlObject value
getVocabularyTerm(Iterator) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
getVocabularyTerm(Iterator) - Static method in class fr.curie.BiNoM.pathways.utils.Utils: Returns first in the alphabetic order string from iterator it
getXGMMLGraph(String, SbmlDocument) - Method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter: Implementation of extracting Reaction Network interface (requires first conversion from BioPAX to SBML, from which the interface is converted).
getXGMMLGraph(String, SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter: The converter itself
getXGMMLPathwayGraph(String, BioPAX, BioPAXToCytoscapeConverter.Option) - Method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter: Implementation of extracting Pathway Structure interface (requires first conversion from BioPAX to SBML, from which the interface is converted).
getXGMMLProteinGraph(String, BioPAX, BioPAXToCytoscapeConverter.Option) - Method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter: Implementation of extracting Protein Interaction interface (requires first conversion from BioPAX to SBML, from which the interface is converted).
getXLink(ItemDocument.Item, String) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl
getxref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of xref.
getxref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory: Create a new instance of xref.
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl
getXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.confidence: Get an Iterator the 'XREF' property values.
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.confidenceImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl
getXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource: Get an Iterator the 'XREF' property values.
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl
getXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.entity: Get an Iterator the 'XREF' property values.
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl
getXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.evidence: Get an Iterator the 'XREF' property values.
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl
getXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary: Get an Iterator the 'XREF' property values.
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl
getXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature: Get an Iterator the 'XREF' property values.
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl
getXREF() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl
getXREF_aspublicationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.confidence: Get an Iterator the 'XREF' property values.
getXREF_aspublicationXref() - Method in class fr.curie.BiNoM.pathways.biopax.confidenceImpl
getXREF_aspublicationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource: Get an Iterator the 'XREF' property values.
getXREF_aspublicationXref() - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl
getXREF_asunificationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource: Get an Iterator the 'XREF' property values.
getXREF_asunificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl
getXREF_asunificationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary: Get an Iterator the 'XREF' property values.
getXREF_asunificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl
getYEAR() - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXref: Gets the 'YEAR' property value
getYEAR() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl
globalComment - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
globalGraph - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMappingService: Output of the conversion
Graph - Class in fr.curie.BiNoM.pathways.analysis.structure
Graph() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Graph
graph - Variable in class fr.curie.BiNoM.pathways.test.ProduceClickableMap
graph - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper: Resulting GraphDocument object
graph - Variable in class fr.curie.BiNoM.pathways.utils.GraphXGMMLParser
GraphAlgorithms - Class in fr.curie.BiNoM.pathways.analysis.structure: Implementation of graph algorithms without use of any node or edge semantics
GraphAlgorithms() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
graphDoc - Variable in class fr.curie.BiNoM.pathways.wrappers.XGMML: The GraphDocument object (XMLBeans mapping of XGMML)
graphDocument - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
graphDocument - Variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter.Graph
GraphDocumentFactory - Class in fr.curie.BiNoM.cytoscape.lib
GraphDocumentFactory() - Constructor for class fr.curie.BiNoM.cytoscape.lib.GraphDocumentFactory
GraphicUtils - Class in fr.curie.BiNoM.cytoscape.lib
GraphicUtils() - Constructor for class fr.curie.BiNoM.cytoscape.lib.GraphicUtils
GraphXGMMLParser - Class in fr.curie.BiNoM.pathways.utils: Simple XGMML parser
GraphXGMMLParser() - Constructor for class fr.curie.BiNoM.pathways.utils.GraphXGMMLParser

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