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

A

accept(File) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.OWLExtensionFilter

accept(File) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.XGMMLExtensionFilter

AccessionNumberTable - Class in fr.curie.BiNoM.pathways.utils

Class for conversion from some accession numbers and names to the id- and namespace used by a database

AccessionNumberTable() - Constructor for class fr.curie.BiNoM.pathways.utils.AccessionNumberTable

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworks

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponents

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.CycleDecomposition

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetwork

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetwork

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.MaterialComponents

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.ModularView

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.MonoMolecularReactionsAsEdges

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysis

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.PruneGraph

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.StronglyConnectedComponents

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSource

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportToFile

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportDialog

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportFromFile

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportFromURL

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSaveAssociated

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSyncNetworks

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassTree

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowser

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyEditor

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXToggleNamingService

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDisplayIndexInfo

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndex

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexPathAnalysis

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndex

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntities

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQuery

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXViewQueryLog

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSource

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFile

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportFromFile

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.netwop.DoubleNetworkDifference

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.netwop.DoubleNetworkDifferenceDialog

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdate

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.netwop.TestNetworkOP

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExportToFile

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.CopySelectedNodesAndEdges

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdges

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.SelectEdgesBetweenSelectedNodes

actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContents

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

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

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

For all species adds all reactions in which they participate

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

For a set of entities in the input adds all complexes in which at list one participates

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

For a set of entities in the input adds all their complexes

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

For all chemical species adds reactions in which at least one of the species participates as reactants and another one as product

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

Simply connects all publicationXrefs to the entities

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

For all entities adds all their forms (chemical species)

addAccno(entity, String) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath

addAccnoAnnotate(entity, String) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath

addAttribute(GraphicNode, String, String, String, ObjectType.Enum) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Add an attribute to GraphicNode

addAttribute(GraphicEdge, String, String, String, ObjectType.Enum) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Add an attribute to GraphicEdge

addAUTHORS(String) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXref

Add a 'AUTHORS' property value

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

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

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

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

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

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

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

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

addAVAILABILITY(String) - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Add a 'AVAILABILITY' property value

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

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

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

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

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

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

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

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

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

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

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

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

addBiopaxModelOntology - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX

not used

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

addChild(BioPAXClassDesc) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc

addCOFACTOR(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysis

Adds a value for the 'COFACTOR' property

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

Adds an anonymous value for the 'COFACTOR' property

addCOFACTOR(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysis

Adds a value for the 'COFACTOR' property.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

addCOMMENT(String) - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Add a 'COMMENT' property value

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

addCOMMENT(String) - Method in interface fr.curie.BiNoM.pathways.biopax.utilityClass

Add a 'COMMENT' property value

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

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

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

Adds to gr all connecting reactions, found in grglobal

addComplex(String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork

addCOMPONENTS(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.complex

Adds a value for the 'COMPONENTS' property

addCOMPONENTS() - Method in interface fr.curie.BiNoM.pathways.biopax.complex

Adds an anonymous value for the 'COMPONENTS' property

addCOMPONENTS(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.complex

Adds a value for the 'COMPONENTS' property.

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

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

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

addCONFIDENCE(confidence) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds a value for the 'CONFIDENCE' property

addCONFIDENCE() - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds an anonymous value for the 'CONFIDENCE' property

addCONFIDENCE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds a value for the 'CONFIDENCE' property.

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

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

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

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

addControl(control) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

addConversionReaction(conversion, ListOfReactionsDocument.ListOfReactions) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

addDATA_DASH_SOURCE(dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Adds a value for the 'DATA_DASH_SOURCE' property

addDATA_DASH_SOURCE() - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Adds an anonymous value for the 'DATA_DASH_SOURCE' property

addDATA_DASH_SOURCE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Adds a value for the 'DATA_DASH_SOURCE' property.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

addDELTA_DASH_G(deltaGprimeO) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Adds a value for the 'DELTA_DASH_G' property

addDELTA_DASH_G() - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Adds an anonymous value for the 'DELTA_DASH_G' property

addDELTA_DASH_G(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Adds a value for the 'DELTA_DASH_G' property.

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

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

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

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

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

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

addDELTA_DASH_H(Double) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Add a 'DELTA_DASH_H' property value

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

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

addDELTA_DASH_S(Double) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Add a 'DELTA_DASH_S' property value

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

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

addEC_DASH_NUMBER(String) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Add a 'EC_DASH_NUMBER' property value

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

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

addedEdge(CyEdge) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator

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

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

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

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

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

addedNode(CyNode) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

addElementaryReaction(String, String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

addEVIDENCE(evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Adds a value for the 'EVIDENCE' property

addEVIDENCE() - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Adds an anonymous value for the 'EVIDENCE' property

addEVIDENCE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Adds a value for the 'EVIDENCE' property.

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

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

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

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

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

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

addEVIDENCE(evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds a value for the 'EVIDENCE' property

addEVIDENCE() - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds an anonymous value for the 'EVIDENCE' property

addEVIDENCE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds a value for the 'EVIDENCE' property.

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

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

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

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

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

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

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

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

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

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

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

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

addEVIDENCE_DASH_CODE(openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds a value for the 'EVIDENCE_DASH_CODE' property

addEVIDENCE_DASH_CODE() - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds an anonymous value for the 'EVIDENCE_DASH_CODE' property

addEVIDENCE_DASH_CODE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds a value for the 'EVIDENCE_DASH_CODE' property.

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

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

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

addEXPERIMENTAL_DASH_FORM(experimentalForm) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds a value for the 'EXPERIMENTAL_DASH_FORM' property

addEXPERIMENTAL_DASH_FORM() - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds an anonymous value for the 'EXPERIMENTAL_DASH_FORM' property

addEXPERIMENTAL_DASH_FORM(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds a value for the 'EXPERIMENTAL_DASH_FORM' property.

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

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

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

addEXPERIMENTAL_DASH_FORM_DASH_TYPE(openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalForm

Adds a value for the 'EXPERIMENTAL_DASH_FORM_DASH_TYPE' property

addEXPERIMENTAL_DASH_FORM_DASH_TYPE() - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalForm

Adds an anonymous value for the 'EXPERIMENTAL_DASH_FORM_DASH_TYPE' property

addEXPERIMENTAL_DASH_FORM_DASH_TYPE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalForm

Adds a value for the 'EXPERIMENTAL_DASH_FORM_DASH_TYPE' property.

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

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

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

addFamily(String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork

addFEATURE_DASH_LOCATION(sequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Adds a value for the 'FEATURE_DASH_LOCATION' property

addFEATURE_DASH_LOCATION() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Adds an anonymous value for the 'FEATURE_DASH_LOCATION' property

addFEATURE_DASH_LOCATION(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Adds a value for the 'FEATURE_DASH_LOCATION' property.

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

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

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

addGOTerm(String, String) - Method in class fr.curie.BiNoM.pathways.wrappers.BioPAX

Adds to OWL model an openControlledVocabulary term

addHPadPanel(Container, int, int, int) - Static method in class fr.curie.BiNoM.cytoscape.lib.GraphicUtils

addHSepPanel(Container, int, int, int, int) - Static method in class fr.curie.BiNoM.cytoscape.lib.GraphicUtils

addHSepPanel(Container, int, int, int) - Static method in class fr.curie.BiNoM.cytoscape.lib.GraphicUtils

addIncludedParticipant(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

Adds included physicalEntityParticipant (such as complex components)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

addINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

Adds a value for the 'INTERACTION_DASH_TYPE' property

addINTERACTION_DASH_TYPE() - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

Adds an anonymous value for the 'INTERACTION_DASH_TYPE' property

addINTERACTION_DASH_TYPE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

Adds a value for the 'INTERACTION_DASH_TYPE' property.

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

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

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

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

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

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

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

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

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

addInteractionNode(GraphicGraph, interaction, HashMap, HashMap, HashMap, HashMap) - Method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter

Adds a 'interaction' node to Pathway Structure interface

addIONIC_DASH_STRENGTH(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO

Add a 'IONIC_DASH_STRENGTH' property value

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

addIONIC_DASH_STRENGTH(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime

Add a 'IONIC_DASH_STRENGTH' property value

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

addKEQ(kPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Adds a value for the 'KEQ' property

addKEQ() - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Adds an anonymous value for the 'KEQ' property

addKEQ(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Adds a value for the 'KEQ' property.

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

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

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

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

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

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

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

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

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

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

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

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

addLEFT(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Adds a value for the 'LEFT' property

addLEFT() - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Adds an anonymous value for the 'LEFT' property

addLEFT(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Adds a value for the 'LEFT' property.

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

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

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

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

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

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

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

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

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

addMetanodeConnections(Graph, boolean, boolean) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph

AddModificationToComplexComponent(sequenceParticipant, MoleculeDocument.Molecule, MoleculeDocument.Molecule) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath

AddModificationToParticipant(sequenceParticipant, MoleculeDocument.Molecule) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath

addMolecule(String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork

addNAME(String) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Add a 'NAME' property value

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

addNEXT_DASH_STEP(pathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Adds a value for the 'NEXT_DASH_STEP' property

addNEXT_DASH_STEP() - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Adds an anonymous value for the 'NEXT_DASH_STEP' property

addNEXT_DASH_STEP(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Adds a value for the 'NEXT_DASH_STEP' property.

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

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

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

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

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

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

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

addORGANISM(bioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.complex

Adds a value for the 'ORGANISM' property

addORGANISM() - Method in interface fr.curie.BiNoM.pathways.biopax.complex

Adds an anonymous value for the 'ORGANISM' property

addORGANISM(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.complex

Adds a value for the 'ORGANISM' property.

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

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

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

addORGANISM(bioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.dna

Adds a value for the 'ORGANISM' property

addORGANISM() - Method in interface fr.curie.BiNoM.pathways.biopax.dna

Adds an anonymous value for the 'ORGANISM' property

addORGANISM(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.dna

Adds a value for the 'ORGANISM' property.

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

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

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

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

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

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

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

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

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

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

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

addPARTICIPANTS(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Adds a value for the 'PARTICIPANTS' property

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

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

addPARTICIPANTS(entity) - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Adds a value for the 'PARTICIPANTS' property

addPARTICIPANTS(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Adds a value for the 'PARTICIPANTS' property

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

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

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

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

addPARTICIPANTS(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

Adds a value for the 'PARTICIPANTS' property

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

addPARTICIPANTS_asentity() - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Adds an anonymous value for the 'PARTICIPANTS' property

addPARTICIPANTS_asentity(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Adds a value for the 'PARTICIPANTS' property.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

addPARTICIPANTS_asphysicalEntityParticipant() - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Adds an anonymous value for the 'PARTICIPANTS' property

addPARTICIPANTS_asphysicalEntityParticipant(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Adds a value for the 'PARTICIPANTS' property.

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

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

addPARTICIPANTS_asphysicalEntityParticipant() - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Adds an anonymous value for the 'PARTICIPANTS' property

addPARTICIPANTS_asphysicalEntityParticipant(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Adds a value for the 'PARTICIPANTS' property.

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

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

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

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

addPARTICIPANTS_asphysicalEntityParticipant() - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

Adds an anonymous value for the 'PARTICIPANTS' property

addPARTICIPANTS_asphysicalEntityParticipant(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

Adds a value for the 'PARTICIPANTS' property.

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

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

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

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

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

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

addPATHWAY_DASH_COMPONENTS(interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds a value for the 'PATHWAY_DASH_COMPONENTS' property

addPATHWAY_DASH_COMPONENTS(pathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds a value for the 'PATHWAY_DASH_COMPONENTS' property

addPATHWAY_DASH_COMPONENTS(pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds a value for the 'PATHWAY_DASH_COMPONENTS' property

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

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

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

addPATHWAY_DASH_COMPONENTS_asinteraction() - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds an anonymous value for the 'PATHWAY_DASH_COMPONENTS' property

addPATHWAY_DASH_COMPONENTS_asinteraction(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds a value for the 'PATHWAY_DASH_COMPONENTS' property.

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

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

addPATHWAY_DASH_COMPONENTS_aspathway() - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds an anonymous value for the 'PATHWAY_DASH_COMPONENTS' property

addPATHWAY_DASH_COMPONENTS_aspathway(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds a value for the 'PATHWAY_DASH_COMPONENTS' property.

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

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

addPATHWAY_DASH_COMPONENTS_aspathwayStep() - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds an anonymous value for the 'PATHWAY_DASH_COMPONENTS' property

addPATHWAY_DASH_COMPONENTS_aspathwayStep(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Adds a value for the 'PATHWAY_DASH_COMPONENTS' property.

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

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

addPathwayInfluence(String, String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork

addPathwayNode(GraphicGraph, pathway, HashMap, HashMap, HashMap, HashMap, HashMap, BioPAXToCytoscapeConverter.Option) - Method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter

Adds a pathway node to Pathway Structure interface

addPathwayStepNode(GraphicGraph, pathwayStep, HashMap, HashMap, HashMap, HashMap, HashMap, BioPAXToCytoscapeConverter.Option) - Method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter

Adds a 'pathway step' node to Pathway Structure interface

addPH(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO

Add a 'PH' property value

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

addPH(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime

Add a 'PH' property value

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

addPhenotype(String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork

addPMG(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO

Add a 'PMG' property value

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

addPMG(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime

Add a 'PMG' property value

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

addPublication(biochemicalReaction, String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork

addPublication(entity, ItemDocument.Item) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath

addPublicationXrefsToEntity(entity, Vector) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

addReaction(String, String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork

addReferencesToReaction(ReactionDocument.Reaction, biochemicalReaction) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath

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

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

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

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

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

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

addRIGHT(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Adds a value for the 'RIGHT' property

addRIGHT() - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Adds an anonymous value for the 'RIGHT' property

addRIGHT(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Adds a value for the 'RIGHT' property.

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

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

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

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

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

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

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

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

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

addSEQUENCE(String) - Method in interface fr.curie.BiNoM.pathways.biopax.dna

Add a 'SEQUENCE' property value

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

addSEQUENCE_DASH_FEATURE_DASH_LIST(sequenceFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipant

Adds a value for the 'SEQUENCE_DASH_FEATURE_DASH_LIST' property

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

Adds an anonymous value for the 'SEQUENCE_DASH_FEATURE_DASH_LIST' property

addSEQUENCE_DASH_FEATURE_DASH_LIST(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipant

Adds a value for the 'SEQUENCE_DASH_FEATURE_DASH_LIST' property.

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

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

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

addSOURCE(String) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXref

Add a 'SOURCE' property value

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

addSTEP_DASH_INTERACTIONS(interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Adds a value for the 'STEP_DASH_INTERACTIONS' property

addSTEP_DASH_INTERACTIONS(pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Adds a value for the 'STEP_DASH_INTERACTIONS' property

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

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

addSTEP_DASH_INTERACTIONS_asinteraction() - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Adds an anonymous value for the 'STEP_DASH_INTERACTIONS' property

addSTEP_DASH_INTERACTIONS_asinteraction(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Adds a value for the 'STEP_DASH_INTERACTIONS' property.

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

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

addSTEP_DASH_INTERACTIONS_aspathway() - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Adds an anonymous value for the 'STEP_DASH_INTERACTIONS' property

addSTEP_DASH_INTERACTIONS_aspathway(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Adds a value for the 'STEP_DASH_INTERACTIONS' property.

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

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

addSTRUCTURE(chemicalStructure) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMolecule

Adds a value for the 'STRUCTURE' property

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

Adds an anonymous value for the 'STRUCTURE' property

addSTRUCTURE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMolecule

Adds a value for the 'STRUCTURE' property.

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

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

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

addSynonym(entity, String) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath

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

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

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

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

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

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

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

addSYNONYMS(String) - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Add a 'SYNONYMS' property value

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

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

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

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

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

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

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

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

addSYNONYMS(String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Add a 'SYNONYMS' property value

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

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

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

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

addSynonyms(BioPAXGraphQuery) - Method in class fr.curie.BiNoM.pathways.utils.AccessionNumberTable

To every node of query adds BIOPAX_NODE_SYNONYM attribute accordingly to found ids connected to the Node.Id

addTEMPERATURE(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO

Add a 'TEMPERATURE' property value

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

addTEMPERATURE(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime

Add a 'TEMPERATURE' property value

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

addTERM(String) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

Add a 'TERM' property value

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

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

addURL(String) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXref

Add a 'URL' property value

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

addValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXAttrDesc

addValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc

addValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringListAttrDesc

addVPadPanel(Container, int, int, int) - Static method in class fr.curie.BiNoM.cytoscape.lib.GraphicUtils

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

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

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

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

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

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

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

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

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

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

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

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

addXREF(xref) - Method in interface fr.curie.BiNoM.pathways.biopax.confidence

Adds a value for the 'XREF' property

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

Adds an anonymous value for the 'XREF' property

addXREF(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.confidence

Adds a value for the 'XREF' property.

addXREF(publicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.confidence

Adds a value for the 'XREF' property

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

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

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

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

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

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

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

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

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

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

addXREF(xref) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Adds a value for the 'XREF' property

addXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Adds an anonymous value for the 'XREF' property

addXREF(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Adds a value for the 'XREF' property.

addXREF(publicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Adds a value for the 'XREF' property

addXREF(unificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Adds a value for the 'XREF' property

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

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

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

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

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

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

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

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

addXREF(xref) - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Adds a value for the 'XREF' property

addXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Adds an anonymous value for the 'XREF' property

addXREF(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Adds a value for the 'XREF' property.

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

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

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

addXREF(xref) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds a value for the 'XREF' property

addXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds an anonymous value for the 'XREF' property

addXREF(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Adds a value for the 'XREF' property.

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

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

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

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

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

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

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

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

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

addXREF(xref) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

Adds a value for the 'XREF' property

addXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

Adds an anonymous value for the 'XREF' property

addXREF(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

Adds a value for the 'XREF' property.

addXREF(unificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

Adds a value for the 'XREF' property

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

addXREF(xref) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Adds a value for the 'XREF' property

addXREF() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Adds an anonymous value for the 'XREF' property

addXREF(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Adds a value for the 'XREF' property.

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

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

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

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

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

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

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

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

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

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

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

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

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

Adds an anonymous value for the 'XREF' property

addXREF_aspublicationXref(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.confidence

Adds a value for the 'XREF' property.

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

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

addXREF_aspublicationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Adds an anonymous value for the 'XREF' property

addXREF_aspublicationXref(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Adds a value for the 'XREF' property.

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

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

addXREF_asunificationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Adds an anonymous value for the 'XREF' property

addXREF_asunificationXref(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Adds a value for the 'XREF' property.

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

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

addXREF_asunificationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

Adds an anonymous value for the 'XREF' property

addXREF_asunificationXref(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

Adds a value for the 'XREF' property.

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

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

ALL_PATHS - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option

ALL_SHORTEST_PATHS - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option

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

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

Check to show compartment information in species names

alwaysMentionCompartment - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

Check to include compartment label in the name

alwaysMentionCompartment - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

If checked, the compartment name will appear in all species names, otherwide the compartment name will be omited for that compartment containing majority of the species

analyseInstallSpyLog - Class in fr.curie.BiNoM.pathways.utils

analyseInstallSpyLog() - Constructor for class fr.curie.BiNoM.pathways.utils.analyseInstallSpyLog

analyzeSBMLFile - Class in fr.curie.BiNoM.pathways.test

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

annotationHash - Variable in class fr.curie.BiNoM.pathways.wrappers.Transpath

annotations - Variable in class fr.curie.BiNoM.pathways.wrappers.Transpath

apply(VisualStyleDefinition, CyNetworkView) - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleFactory

assignColorToSpecies(SbmlDocument, String, Color) - Method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies

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

associateWithSpecies(physicalEntity, String) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath

ATTR_SEP - Static variable in class fr.curie.BiNoM.cytoscape.lib.NetworkFactory

Attribute - Class in fr.curie.BiNoM.pathways.analysis.structure

Simple internal for BiNoM implementation of node and edge attribute

Attribute(String, String) - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Attribute

Attributes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Element

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

Called when a value of AUTHORS has been added

AUTHORSProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.publicationXref

The Jena Property for AUTHORS

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

Called when a value of AUTHORS has been removed

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

Called when a value of AVAILABILITY has been added

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

The Jena Property for AVAILABILITY

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed

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

Called when a value of AVAILABILITY has been removed