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A

AboutBox - Class in fr.curie.BiNoM.cytoscape.utils
About BiNoM box.
AboutBox() - Constructor for class fr.curie.BiNoM.cytoscape.utils.AboutBox
 
absoluteRegionChanged(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when absoluteRegion has changed
absoluteRegionChanged(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when absoluteRegion has changed
absoluteRegionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
The Jena Property for absoluteRegion
absoluteRegionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
The Jena Property for absoluteRegion
AbstractBioPAXImportTaskFactory - Interface in fr.curie.BiNoM.biopax
 
AbstractClusterNetworksTaskFactory - Interface in fr.curie.BiNoM.analysis
 
AbstractExcludeIntermediateNodesTaskFactory - Interface in fr.curie.BiNoM.analysis
 
AbstractModularViewTaskFactory - Interface in fr.curie.BiNoM.analysis
 
AbstractTask - Interface in fr.curie.BiNoM.lib
 
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
 
ACSNProcedures - Class in fr.curie.BiNoM.pathways.utils.acsn
 
ACSNProcedures() - Constructor for class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.biopax.BioPAXImportDialog
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXToggleNamingService
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.ain.ImportFromSimpleTextInfluenceFile
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.CalcCentrality
 
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.ConvertReactionNetworkToEntityNetwork
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.ConvertToUndirectedGraph
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.createNeighborhoodSets
 
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.ExcludeIntermediateNodes
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetwork
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetwork
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.LinearizeNetwork
 
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.OptimalCutSetAnalyzer
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerDialog
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysis
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzer
 
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.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.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.celldesigner.checkCellDesignerFile
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.colorCellDesignerProteins
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CSMLImportFromFile
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotes
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.MergingMaps
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.modifyCellDesignerNotes
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesigner
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.ProduceNaviCellMapFiles
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.influence.FromToNodes
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.influence.InfluenceAreaInArray
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.influence.InfluenceAreaInAttribute
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.influence.InfluenceArrayAsGraphic
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.influence.InfluenceArrayAsText
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.influence.InfluenceByAttribute
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.influence.InfluenceFeatures
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.influence.InputReachParameter
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.influence.UpdateInfluenceAttrib
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ClusterByShortPath
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.CreateConnectionsBetweenNests
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.CreateNestNetwork
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.DestroyUnusedNetworksAsNest
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.FindCommonNodes
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InterOf2SelectedNests
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ListComponents
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ListNodesByNest
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.MergeSelectedNests
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.NestInNodeAttribute
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.PackInNestNode
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.RecreateLostConnectionsInsideNests
 
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.AboutBox
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.ComboBoxes
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.CopySelectedNodesAndEdges
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.CreateSetIntersectionGraph
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.ListAllNodes
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.ListAllReactions
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilter
 
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.SelectDownstreamNeighbours
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.SelectEdgesBetweenSelectedNodes
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.SelectNodesByAttributeSubstring
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.SelectUpstreamNeighbours
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContents
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.TextBox
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.TextBoxDialog
 
actionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 
activityAttribute - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
activityFromIn(double, double[]) - Method in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
ADD - Static variable in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyEditFrame
 
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_FIRST_NEIGHBOURS - Static variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
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)
addAddMethod(Method, Class) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto
 
addAssociatedReactionNetworkToGraphFromIndex(Graph, Graph) - Method in class fr.curie.BiNoM.pathways.utils.acsn.DatabaseComparison
 
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
addAttributeUniqueNameConcatenatedValues(GraphicNode, String, String, String, ObjectType.Enum) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
addAuthor(String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
Add a 'author' property value
addAuthor(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.DegradationImpl
 
addAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
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.GeneImpl
 
addAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
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.MolecularInteractionImpl
 
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.ProteinImpl
 
addAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
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
 
addBiopaxProperty(String, String, String, OntModel) - Static method in class fr.curie.BiNoM.pathways.test.TestBioPAX
 
addChild(BioPAXClassDesc) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
addCofactor(PhysicalEntity) - 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(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Catalysis
Adds a value for the 'cofactor' property.
addCofactor(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addCofactor() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addCofactor(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
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.CellularLocationVocabularyImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
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.ControlImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
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.EntityFeatureImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
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.ExperimentalFormVocabularyImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
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.PhenotypeVocabularyImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
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.RnaReferenceImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
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.SequenceModificationVocabularyImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
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.SmallMoleculeReferenceImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
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) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addComplex(String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
addComplex_(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addComplexBioPAX(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addComplexComponentConnections(Complex, HashMap<String, PhysicalEntity>, HashMap<String, PhysicalEntity>, HashMap, HashMap, GraphicGraph, GraphicNode) - Method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
 
addComplexesToNetworkAsClicks() - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
addComplexesToNetworksAsNodes() - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
addComplexNodes(Graph, Graph) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
addComplexNodes() - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
addComponent(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Adds a value for the 'component' property
addComponent() - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Adds an anonymous value for the 'component' property
addComponent(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Adds a value for the 'component' property.
addComponent(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addComponent() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addComponent(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addComponentStoichiometry(Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Adds a value for the 'componentStoichiometry' property
addComponentStoichiometry() - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Adds an anonymous value for the 'componentStoichiometry' property
addComponentStoichiometry(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Adds a value for the 'componentStoichiometry' property.
addComponentStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addComponentStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addComponentStoichiometry(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addConfidence(Score) - 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(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Adds a value for the 'confidence' property.
addConfidence(Score) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addConfidence() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addConfidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addConnections(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
addConnectionsAlongSequence(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
addControl(Control) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
 
addController(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addController(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addController(Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Adds a value for the 'controller' property
addController(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Adds a value for the 'controller' property
addController(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addController(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addController(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Modulation
Adds a value for the 'controller' property
addController(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addController(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addController(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation
Adds a value for the 'controller' property
addController(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addController(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addController_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addController_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addController_asPathway() - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Adds an anonymous value for the 'controller' property
addController_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Adds a value for the 'controller' property.
addController_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addController_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addController_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addController_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addController_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addController_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addController_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addController_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addController_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Adds an anonymous value for the 'controller' property
addController_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Adds a value for the 'controller' property.
addController_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addController_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addController_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.Modulation
Adds an anonymous value for the 'controller' property
addController_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Modulation
Adds a value for the 'controller' property.
addController_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addController_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addController_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation
Adds an anonymous value for the 'controller' property
addController_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation
Adds a value for the 'controller' property.
addController_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addController_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addConversionReaction(Conversion, ListOfReactionsDocument.ListOfReactions) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addDataSource(Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Adds a value for the 'dataSource' property
addDataSource() - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Adds an anonymous value for the 'dataSource' property
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Adds a value for the 'dataSource' property.
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addDataSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addDeltaG(DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Adds a value for the 'deltaG' property
addDeltaG() - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Adds an anonymous value for the 'deltaG' property
addDeltaG(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Adds a value for the 'deltaG' property.
addDeltaG(DeltaG) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addDeltaG() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addDeltaG(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addDeltaG(DeltaG) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addDeltaG() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addDeltaG(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addDeltaH(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Add a 'deltaH' property value
addDeltaH(Float) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addDeltaH(Float) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addDeltaS(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Add a 'deltaS' property value
addDeltaS(Float) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addDeltaS(Float) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addECNumber(String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Add a 'eCNumber' property value
addECNumber(String) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addECNumber(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(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ChemicalStructureImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceLocationImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.UtilityClassImpl
 
addedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
addElementaryReaction(String, String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addElementaryReaction(String, String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
addEntityBioPAX(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addEntityFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addEntityFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addEntityFeature(EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds a value for the 'entityFeature' property
addEntityFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds an anonymous value for the 'entityFeature' property
addEntityFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds a value for the 'entityFeature' property.
addEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addEntityFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addEntityFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addEntityFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addEntityFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addEntityFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.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(com.hp.hpl.jena.rdf.model.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(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.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(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addEvidence(Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Adds a value for the 'evidence' property
addEvidence() - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Adds an anonymous value for the 'evidence' property
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Adds a value for the 'evidence' property.
addEvidence(Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds a value for the 'evidence' property
addEvidence() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds an anonymous value for the 'evidence' property
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds a value for the 'evidence' property.
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
addEvidence(Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds a value for the 'evidence' property
addEvidence() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds an anonymous value for the 'evidence' property
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds a value for the 'evidence' property.
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addEvidence(Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds a value for the 'evidence' property
addEvidence() - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds an anonymous value for the 'evidence' property
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds a value for the 'evidence' property.
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addEvidence(com.hp.hpl.jena.rdf.model.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(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addEvidenceCode(EvidenceCodeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Adds a value for the 'evidenceCode' property
addEvidenceCode() - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Adds an anonymous value for the 'evidenceCode' property
addEvidenceCode(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Adds a value for the 'evidenceCode' property.
addEvidenceCode(EvidenceCodeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addEvidenceCode() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addEvidenceCode(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addExperimentalFeature(EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds a value for the 'experimentalFeature' property
addExperimentalFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds an anonymous value for the 'experimentalFeature' property
addExperimentalFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds a value for the 'experimentalFeature' property.
addExperimentalFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalForm(ExperimentalForm) - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Adds a value for the 'experimentalForm' property
addExperimentalForm() - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Adds an anonymous value for the 'experimentalForm' property
addExperimentalForm(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Adds a value for the 'experimentalForm' property.
addExperimentalForm(ExperimentalForm) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addExperimentalForm() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addExperimentalForm(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addExperimentalFormDescription(ExperimentalFormVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds a value for the 'experimentalFormDescription' property
addExperimentalFormDescription() - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds an anonymous value for the 'experimentalFormDescription' property
addExperimentalFormDescription(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds a value for the 'experimentalFormDescription' property.
addExperimentalFormDescription(ExperimentalFormVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalFormDescription() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalFormDescription(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalFormEntity(Gene) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds a value for the 'experimentalFormEntity' property
addExperimentalFormEntity(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds a value for the 'experimentalFormEntity' property
addExperimentalFormEntity(Gene) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalFormEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalFormEntity_asGene() - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds an anonymous value for the 'experimentalFormEntity' property
addExperimentalFormEntity_asGene(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds a value for the 'experimentalFormEntity' property.
addExperimentalFormEntity_asGene() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalFormEntity_asGene(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalFormEntity_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds an anonymous value for the 'experimentalFormEntity' property
addExperimentalFormEntity_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Adds a value for the 'experimentalFormEntity' property.
addExperimentalFormEntity_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addExperimentalFormEntity_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
addFamilies(Vector) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addFamily(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addFamily(String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
addFamily_(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addFeature(EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Adds a value for the 'feature' property
addFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Adds an anonymous value for the 'feature' property
addFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Adds a value for the 'feature' property.
addFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addFeature() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addFeature(BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Adds a value for the 'feature' property
addFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addFeature() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addFeature_asBindingFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Adds an anonymous value for the 'feature' property
addFeature_asBindingFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Adds a value for the 'feature' property.
addFeature_asBindingFeature() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addFeature_asBindingFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addFeatureLocation(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addFeatureLocation() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addFeatureLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addFeatureLocation(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addFeatureLocation() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addFeatureLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addFeatureLocation(SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds a value for the 'featureLocation' property
addFeatureLocation() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds an anonymous value for the 'featureLocation' property
addFeatureLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds a value for the 'featureLocation' property.
addFeatureLocation(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addFeatureLocation() - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addFeatureLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addFeatureLocation(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addFeatureLocation() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addFeatureLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addFeatureLocation(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addFeatureLocation() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addFeatureLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addFeatureLocationType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addFeatureLocationType() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addFeatureLocationType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addFeatureLocationType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addFeatureLocationType() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addFeatureLocationType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addFeatureLocationType(SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds a value for the 'featureLocationType' property
addFeatureLocationType() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds an anonymous value for the 'featureLocationType' property
addFeatureLocationType(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds a value for the 'featureLocationType' property.
addFeatureLocationType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addFeatureLocationType() - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addFeatureLocationType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addFeatureLocationType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addFeatureLocationType() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addFeatureLocationType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addFeatureLocationType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addFeatureLocationType() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addFeatureLocationType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addFirstNeighbours(Graph, Graph, boolean) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
addFirstNeighbours() - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
addGetMethod(Method, Class) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto
 
addGOTerm(String, String) - Method in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Adds to OWL model an openControlledVocabulary term
addGroupToPoint(CellDesignerPathwayStaining.ColorPoint, Vector<String>) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
addHPadPanel(Container, int, int, int) - Static method in class fr.curie.BiNoM.lib.GraphicUtils
 
addHSepPanel(Container, int, int, int, int) - Static method in class fr.curie.BiNoM.lib.GraphicUtils
 
addHSepPanel(Container, int, int, int) - Static method in class fr.curie.BiNoM.lib.GraphicUtils
 
addHypotheticalInfluences(SbmlDocument, boolean, boolean) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
addHypotheticalInfluences(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.testCellDesigner
 
addIncludedParticipant(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Adds included PhysicalEntity (such as the components of a complex)
addInteractionNode(GraphicGraph, Interaction, HashMap, HashMap, HashMap, HashMap) - Method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
Adds a 'interaction' node to Pathway Structure interface
addInteractionReaction(Interaction, ListOfReactionsDocument.ListOfReactions) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
 
addInteractionScore(Score) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Adds a value for the 'interactionScore' property
addInteractionScore() - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Adds an anonymous value for the 'interactionScore' property
addInteractionScore(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Adds a value for the 'interactionScore' property.
addInteractionScore(Score) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addInteractionScore() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addInteractionScore(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addIntersectingFamilies() - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
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(com.hp.hpl.jena.rdf.model.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(com.hp.hpl.jena.rdf.model.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(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addLeft() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addLeft(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addLeft() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addLeft(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addLeft(PhysicalEntity) - 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(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Adds a value for the 'left' property.
addLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addLeft() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addLeft(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addLeft() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addLeft(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addLeft() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addLeft(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addLeft() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addLeft(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addMap(String, int, int) - Method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
Add map data (filename, deltaX, deltaY) to the internal list of maps to be merged.
addMemberEntityReference(DnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Adds a value for the 'memberEntityReference' property
addMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addMemberEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addMemberEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addMemberEntityReference(EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds a value for the 'memberEntityReference' property
addMemberEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds an anonymous value for the 'memberEntityReference' property
addMemberEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds a value for the 'memberEntityReference' property.
addMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addMemberEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addMemberEntityReference(ProteinReference) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
Adds a value for the 'memberEntityReference' property
addMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addMemberEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addMemberEntityReference(RnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Adds a value for the 'memberEntityReference' property
addMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addMemberEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addMemberEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addMemberEntityReference(SmallMoleculeReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Adds a value for the 'memberEntityReference' property
addMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addMemberEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addMemberEntityReference_asDnaReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Adds an anonymous value for the 'memberEntityReference' property
addMemberEntityReference_asDnaReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Adds a value for the 'memberEntityReference' property.
addMemberEntityReference_asDnaReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addMemberEntityReference_asDnaReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addMemberEntityReference_asProteinReference() - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
Adds an anonymous value for the 'memberEntityReference' property
addMemberEntityReference_asProteinReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
Adds a value for the 'memberEntityReference' property.
addMemberEntityReference_asProteinReference() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addMemberEntityReference_asProteinReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addMemberEntityReference_asRnaReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Adds an anonymous value for the 'memberEntityReference' property
addMemberEntityReference_asRnaReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Adds a value for the 'memberEntityReference' property.
addMemberEntityReference_asRnaReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addMemberEntityReference_asRnaReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addMemberEntityReference_asSmallMoleculeReference() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Adds an anonymous value for the 'memberEntityReference' property
addMemberEntityReference_asSmallMoleculeReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Adds a value for the 'memberEntityReference' property.
addMemberEntityReference_asSmallMoleculeReference() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addMemberEntityReference_asSmallMoleculeReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addMemberFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addMemberFeature() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addMemberFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
addMemberFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addMemberFeature() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addMemberFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
addMemberFeature(EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds a value for the 'memberFeature' property
addMemberFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds an anonymous value for the 'memberFeature' property
addMemberFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Adds a value for the 'memberFeature' property.
addMemberFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addMemberFeature() - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addMemberFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
addMemberFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addMemberFeature() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addMemberFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
addMemberFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addMemberFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addMemberFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
addMemberPhysicalEntity(Complex) - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Adds a value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addMemberPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addMemberPhysicalEntity(Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Adds a value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addMemberPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addMemberPhysicalEntity(DnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Adds a value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addMemberPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addMemberPhysicalEntity(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Adds a value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Adds an anonymous value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Adds a value for the 'memberPhysicalEntity' property.
addMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addMemberPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addMemberPhysicalEntity(Protein) - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Adds a value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addMemberPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addMemberPhysicalEntity(Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Adds a value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addMemberPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addMemberPhysicalEntity(RnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Adds a value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addMemberPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addMemberPhysicalEntity(SmallMolecule) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Adds a value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addMemberPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addMemberPhysicalEntity_asComplex() - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Adds an anonymous value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity_asComplex(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Adds a value for the 'memberPhysicalEntity' property.
addMemberPhysicalEntity_asComplex() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addMemberPhysicalEntity_asComplex(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addMemberPhysicalEntity_asDna() - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Adds an anonymous value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity_asDna(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Adds a value for the 'memberPhysicalEntity' property.
addMemberPhysicalEntity_asDna() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addMemberPhysicalEntity_asDna(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addMemberPhysicalEntity_asDnaRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Adds an anonymous value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity_asDnaRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Adds a value for the 'memberPhysicalEntity' property.
addMemberPhysicalEntity_asDnaRegion() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addMemberPhysicalEntity_asDnaRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addMemberPhysicalEntity_asProtein() - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Adds an anonymous value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity_asProtein(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Adds a value for the 'memberPhysicalEntity' property.
addMemberPhysicalEntity_asProtein() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addMemberPhysicalEntity_asProtein(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addMemberPhysicalEntity_asRna() - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Adds an anonymous value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity_asRna(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Adds a value for the 'memberPhysicalEntity' property.
addMemberPhysicalEntity_asRna() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addMemberPhysicalEntity_asRna(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addMemberPhysicalEntity_asRnaRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Adds an anonymous value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity_asRnaRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Adds a value for the 'memberPhysicalEntity' property.
addMemberPhysicalEntity_asRnaRegion() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addMemberPhysicalEntity_asRnaRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addMemberPhysicalEntity_asSmallMolecule() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Adds an anonymous value for the 'memberPhysicalEntity' property
addMemberPhysicalEntity_asSmallMolecule(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Adds a value for the 'memberPhysicalEntity' property.
addMemberPhysicalEntity_asSmallMolecule() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addMemberPhysicalEntity_asSmallMolecule(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addMetanodeConnections(Graph, boolean, boolean) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
addModification(String, PhysicalEntity, CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
addModifierToReaction(String, BioPAXToSBMLConverter.BioPAXSpecies) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
 
addModuleNames(Vector<ModifyCellDesignerNotes.AnnotationSection>, String, String) - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
addMolecule(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addMolecule(String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
addMolecule_(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addMRNAs(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addName(String) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Add a 'name' property value
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addName(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Add a 'name' property value
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
addName(String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Add a 'name' property value
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addName(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Add a 'name' property value
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addName(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addNextStep(PathwayStep) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addNextStep() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addNextStep(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addNextStep(PathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds a value for the 'nextStep' property
addNextStep() - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds an anonymous value for the 'nextStep' property
addNextStep(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds a value for the 'nextStep' property.
addNextStep(PathwayStep) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addNextStep() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addNextStep(com.hp.hpl.jena.rdf.model.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
 
addNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addNotFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addNotFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addNotFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addNotFeature(EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Adds a value for the 'notFeature' property
addNotFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Adds an anonymous value for the 'notFeature' property
addNotFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Adds a value for the 'notFeature' property.
addNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addNotFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addNotFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addNotFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addNotFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addNotFeature(BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Adds a value for the 'notFeature' property
addNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addNotFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addNotFeature_asBindingFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Adds an anonymous value for the 'notFeature' property
addNotFeature_asBindingFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Adds a value for the 'notFeature' property.
addNotFeature_asBindingFeature() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addNotFeature_asBindingFeature(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addOnlyConnectingNeighbours - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addParticipant(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Adds a value for the 'participant' property
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addParticipant(Gene) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Adds a value for the 'participant' property
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addParticipant(Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.Interaction
Adds a value for the 'participant' property
addParticipant() - Method in interface fr.curie.BiNoM.pathways.biopax.Interaction
Adds an anonymous value for the 'participant' property
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Interaction
Adds a value for the 'participant' property.
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addParticipant(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteraction
Adds a value for the 'participant' property
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addParticipant(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds a value for the 'participant' property
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addParticipant(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addParticipant_asGene() - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Adds an anonymous value for the 'participant' property
addParticipant_asGene(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Adds a value for the 'participant' property.
addParticipant_asGene() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addParticipant_asGene(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addParticipant_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Adds an anonymous value for the 'participant' property
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Adds a value for the 'participant' property.
addParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addParticipant_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteraction
Adds an anonymous value for the 'participant' property
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteraction
Adds a value for the 'participant' property.
addParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addParticipant_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds an anonymous value for the 'participant' property
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds a value for the 'participant' property.
addParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addParticipant_asPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addParticipantStoichiometry(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addParticipantStoichiometry(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addParticipantStoichiometry(Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Adds a value for the 'participantStoichiometry' property
addParticipantStoichiometry() - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Adds an anonymous value for the 'participantStoichiometry' property
addParticipantStoichiometry(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Adds a value for the 'participantStoichiometry' property.
addParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addParticipantStoichiometry(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addParticipantStoichiometry(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addParticipantStoichiometry(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addParticipantStoichiometry(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addPathwayComponent(Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Adds a value for the 'pathwayComponent' property
addPathwayComponent(Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Adds a value for the 'pathwayComponent' property
addPathwayComponent(Interaction) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addPathwayComponent(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addPathwayComponent_asInteraction() - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Adds an anonymous value for the 'pathwayComponent' property
addPathwayComponent_asInteraction(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Adds a value for the 'pathwayComponent' property.
addPathwayComponent_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addPathwayComponent_asInteraction(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addPathwayComponent_asPathway() - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Adds an anonymous value for the 'pathwayComponent' property
addPathwayComponent_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Adds a value for the 'pathwayComponent' property.
addPathwayComponent_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addPathwayComponent_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addPathwayInfluence(String, String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addPathwayInfluence(String, String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
addPathwayInfluenceBioPAX(String, String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
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
addPathwayOrder(PathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Adds a value for the 'pathwayOrder' property
addPathwayOrder() - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Adds an anonymous value for the 'pathwayOrder' property
addPathwayOrder(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Adds a value for the 'pathwayOrder' property.
addPathwayOrder(PathwayStep) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addPathwayOrder() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addPathwayOrder(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
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
addPhenotype(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addPhenotype(String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
addPhenotype_(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addPhenotypeBioPAX(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addPluginMenu() - Method in class fr.curie.BiNoM.celldesigner.plugin.BiNoMPlugin
 
addPluginMenu() - Method in class fr.curie.BiNoM.celldesigner.plugin2.Plugin
 
addPluginMenu() - Method in class fr.curie.BiNoM.celldesigner.sample.SamplePlugin
 
addPrefixToIds(String, String) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
addProduct(Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds a value for the 'product' property
addProduct(Protein) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds a value for the 'product' property
addProduct(Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds a value for the 'product' property
addProduct(Dna) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addProduct(Protein) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addProduct(Rna) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addProduct_asDna() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds an anonymous value for the 'product' property
addProduct_asDna(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds a value for the 'product' property.
addProduct_asDna() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addProduct_asDna(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addProduct_asProtein() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds an anonymous value for the 'product' property
addProduct_asProtein(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds a value for the 'product' property.
addProduct_asProtein() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addProduct_asProtein(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addProduct_asRna() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds an anonymous value for the 'product' property
addProduct_asRna(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Adds a value for the 'product' property.
addProduct_asRna() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addProduct_asRna(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addPublication(BiochemicalReaction, String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addPublication(biochemicalReaction, String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
addPublicationBioPAX(BiochemicalReaction, String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addPublicationXrefsToEntity(Entity, Vector) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
addPublicationXrefsToEntityReference(EntityReference, Vector) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
addReaction(String, String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addReaction(String, String) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
addReactionBioPAX(String, String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
addRelationshipType(RelationshipTypeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXref
Adds a value for the 'relationshipType' property
addRelationshipType() - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXref
Adds an anonymous value for the 'relationshipType' property
addRelationshipType(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXref
Adds a value for the 'relationshipType' property.
addRelationshipType(RelationshipTypeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
addRelationshipType() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
addRelationshipType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
addRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addRight() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addRight(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addRight() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addRight(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addRight(PhysicalEntity) - 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(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Adds a value for the 'right' property.
addRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addRight() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addRight(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addRight() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addRight(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addRight() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addRight(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addRight() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addRight(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addRmvMethod(Method, Class) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto
 
addSetMethod(Method, Class) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto
 
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
 
addStepProcess(Control) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Adds a value for the 'stepProcess' property
addStepProcess(Control) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addStepProcess(Interaction) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addStepProcess(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addStepProcess(Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds a value for the 'stepProcess' property
addStepProcess(Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds a value for the 'stepProcess' property
addStepProcess(Interaction) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addStepProcess(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addStepProcess_asControl() - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Adds an anonymous value for the 'stepProcess' property
addStepProcess_asControl(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Adds a value for the 'stepProcess' property.
addStepProcess_asControl() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addStepProcess_asControl(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addStepProcess_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addStepProcess_asInteraction(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addStepProcess_asInteraction() - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds an anonymous value for the 'stepProcess' property
addStepProcess_asInteraction(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds a value for the 'stepProcess' property.
addStepProcess_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addStepProcess_asInteraction(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addStepProcess_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addStepProcess_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
addStepProcess_asPathway() - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds an anonymous value for the 'stepProcess' property
addStepProcess_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Adds a value for the 'stepProcess' property.
addStepProcess_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addStepProcess_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
addSubRegion(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Adds a value for the 'subRegion' property
addSubRegion(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Adds a value for the 'subRegion' property
addSubRegion(DnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addSubRegion(RnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addSubRegion(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Adds a value for the 'subRegion' property
addSubRegion(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Adds a value for the 'subRegion' property
addSubRegion(DnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addSubRegion(RnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addSubRegion(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Adds a value for the 'subRegion' property
addSubRegion(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Adds a value for the 'subRegion' property
addSubRegion(RnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addSubRegion(DnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addSubRegion(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Adds a value for the 'subRegion' property
addSubRegion(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Adds a value for the 'subRegion' property
addSubRegion(RnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addSubRegion(DnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addSubRegion_asDnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Adds an anonymous value for the 'subRegion' property
addSubRegion_asDnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Adds a value for the 'subRegion' property.
addSubRegion_asDnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addSubRegion_asDnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addSubRegion_asDnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Adds an anonymous value for the 'subRegion' property
addSubRegion_asDnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Adds a value for the 'subRegion' property.
addSubRegion_asDnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addSubRegion_asDnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addSubRegion_asDnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Adds an anonymous value for the 'subRegion' property
addSubRegion_asDnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Adds a value for the 'subRegion' property.
addSubRegion_asDnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addSubRegion_asDnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addSubRegion_asDnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Adds an anonymous value for the 'subRegion' property
addSubRegion_asDnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Adds a value for the 'subRegion' property.
addSubRegion_asDnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addSubRegion_asDnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addSubRegion_asRnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Adds an anonymous value for the 'subRegion' property
addSubRegion_asRnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Adds a value for the 'subRegion' property.
addSubRegion_asRnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addSubRegion_asRnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addSubRegion_asRnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Adds an anonymous value for the 'subRegion' property
addSubRegion_asRnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Adds a value for the 'subRegion' property.
addSubRegion_asRnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addSubRegion_asRnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addSubRegion_asRnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Adds an anonymous value for the 'subRegion' property
addSubRegion_asRnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Adds a value for the 'subRegion' property.
addSubRegion_asRnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addSubRegion_asRnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addSubRegion_asRnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Adds an anonymous value for the 'subRegion' property
addSubRegion_asRnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Adds a value for the 'subRegion' property.
addSubRegion_asRnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addSubRegion_asRnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addSuffixForMultipleAliases - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
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
addTabbedPane(BioPAXObject, BioPAX, boolean) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserFrame
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
addTerm(String) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Add a 'term' property value
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
addTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
addToReport(String) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
addTransition(SbmlDocument, String, String, String, String, String, String, String) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
addTransition(SbmlDocument, String, String, String, String, String, String, String) - Static method in class fr.curie.BiNoM.pathways.test.testCellDesigner
 
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.biopax.propedit.BioPAXAttrDesc
 
addValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
addValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringListAttrDesc
 
addVPadPanel(Container, int, int, int) - Static method in class fr.curie.BiNoM.lib.GraphicUtils
 
addWithConstraints(int, Component) - Method in class fr.curie.BiNoM.cytoscape.utils.GridBagDialog
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
addXref(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Adds a value for the 'xref' property
addXref() - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Adds an anonymous value for the 'xref' property
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Adds a value for the 'xref' property.
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
addXref(com.hp.hpl.jena.rdf.model.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(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
addXref(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Adds a value for the 'xref' property
addXref() - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Adds an anonymous value for the 'xref' property
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Adds a value for the 'xref' property.
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
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(com.hp.hpl.jena.rdf.model.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(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
addXref(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds a value for the 'xref' property
addXref() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds an anonymous value for the 'xref' property
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Adds a value for the 'xref' property.
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
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(com.hp.hpl.jena.rdf.model.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.EvidenceCodeVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
addXref(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Adds a value for the 'xref' property
addXref() - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Adds an anonymous value for the 'xref' property
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Adds a value for the 'xref' property.
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
addXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
addXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addXref() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
addXref(com.hp.hpl.jena.rdf.model.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(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
addXref_asPublicationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Adds an anonymous value for the 'xref' property
addXref_asPublicationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Adds a value for the 'xref' property.
addXref_asPublicationXref() - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
addXref_asPublicationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
addXref_asUnificationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Adds an anonymous value for the 'xref' property
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Adds a value for the 'xref' property.
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
addXref_asUnificationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Adds an anonymous value for the 'xref' property
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Adds a value for the 'xref' property.
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
addXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
addXref_asUnificationXref(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
adjacency - Variable in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
AgilentCGHMapping - Class in fr.curie.BiNoM.pathways.test
 
AgilentCGHMapping() - Constructor for class fr.curie.BiNoM.pathways.test.AgilentCGHMapping
 
aliasesToKeep - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
aliaspoints - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
ALL_PATHS - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
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
 
allActivity(double) - Method in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
allannotations - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask.extractingNotesOptions
 
allannotations - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
allGraphs - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
allInfluence(double) - Method in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
allnames - Variable in class fr.curie.BiNoM.pathways.utils.GMTFile
 
allNodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
all individual nodes from elementary paths (target nodes excepted)
AllNodesWithActivities - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
allproteins - Variable in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
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
 
analyzeGeneticInteractionBioGrid() - Static method in class fr.curie.BiNoM.pathways.utils.GeneticInteractionNetworks
 
analyzeHitFrequency(Vector<Vector<String>>) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
analyzer - Variable in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerDialog
 
analyzer - Variable in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerBootstrapDialog
 
analyzer - Variable in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerDialog
 
analyzer - Variable in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
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
 
applyCellDesignerOptions(SbmlDocument, CellDesignerExportToFileDialog.CellDesignerExportToFileOptions) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
applyLayout - Variable in class fr.curie.BiNoM.biopax.BioPAXImportBaseTask
 
asrnas - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
assignColors(SbmlDocument, GraphDocument) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter
 
assignColorsFromTableReactions(SbmlDocument, HashMap) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter
 
assignColorsFromTableSpecies(SbmlDocument, HashMap) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter
 
assignColorsToGroupsFromTable(String) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
assignColorsToPoints(Vector<CellDesignerPathwayStaining.ColorPoint>) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
assignColorToAllReactions(SbmlDocument, String) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
assignColorToGenes(SbmlDocument, String, Color) - Method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
assignColorToProteins(SbmlDocument, String, Color) - Method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
assignColorToProteins(SbmlDocument, String, Color) - Method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
assignColorToReactions(SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.test.testRemoveEditPoints
 
assignColorToSpecies(SbmlDocument, String, Color) - Method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies
 
assignCytoscapeColorsToReactions(SbmlDocument, CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
assignCytoscapeColorsToSpecies(SbmlDocument, CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
assignEdgeIds() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
assignEdgeWeightsByConnectivity(Graph, boolean) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
assignFontSizeToAllSpecies(SbmlDocument, float) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
assignFontSizeToAllSpecies(SbmlDocument, float) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
assignRandomColorsToGroups(boolean) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
ATTR_SEP - Static variable in class fr.curie.BiNoM.celldesigner.lib.NetworkFactory
 
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, int) - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Attribute
 
Attribute(String, String) - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Attribute
 
ATTRIBUTE_TYPE_REAL - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Attribute
 
ATTRIBUTE_TYPE_STRING - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Attribute
 
Attributes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Element
 
authorAdded(PublicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when a value of author has been added
authorProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
The Jena Property for author
authorRemoved(PublicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when a value of author has been removed
automaticallyProcessNotes() - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
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(Degradation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
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(DnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
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(Gene, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of availability has been added
availabilityAdded(GeneticInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
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(MolecularInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
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(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(RnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
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(TemplateReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of availability has been added
availabilityAdded(TemplateReactionRegulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
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(Degradation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
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(DnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
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(Gene, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of availability has been removed
availabilityRemoved(GeneticInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
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(MolecularInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
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(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(RnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
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(TemplateReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of availability has been removed
availabilityRemoved(TemplateReactionRegulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
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
averageSizeOfRandomBiggestComponent - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 

B

B - Static variable in class fr.curie.BiNoM.cytoscape.utils.GridBagDialog
 
backforwStates() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserFrame
 
BAR - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
 
baseString - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
 
BindingFeature - Interface in fr.curie.BiNoM.pathways.biopax
Interface for BindingFeature ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
BindingFeatureImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of BindingFeature Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
BindingFeatureListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.BindingFeature to receive notification when properties changed, added or removed.
bindsToChanged(BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when bindsTo has changed
bindsToChanged(CovalentBindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when bindsTo has changed
bindsToProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BindingFeature
The Jena Property for bindsTo
BiNoMPlugin - Class in fr.curie.BiNoM.celldesigner.plugin
 
BiNoMPlugin(boolean) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPlugin
 
BiNoMPlugin() - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPlugin
 
BiNoMPlugin - Class in fr.curie.BiNoM.cytoscape.plugin
 
BiNoMPlugin() - Constructor for class fr.curie.BiNoM.cytoscape.plugin.BiNoMPlugin
 
BiNoMPluginAction - Class in fr.curie.BiNoM.celldesigner.plugin
 
BiNoMPluginAction(BiNoMPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginAction
 
BiNoMPluginDialog - Class in fr.curie.BiNoM.celldesigner.plugin
 
BiNoMPluginDialog(BiNoMPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
This is the default constructor
BiNoMPluginDialog(Frame) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
BiNoMPluginDialog(Frame, boolean) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
BiNoMPluginDialog(Frame, String) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
BiNoMPluginDialog(Frame, String, boolean) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
BiNoMPluginDialog(Frame, String, boolean, GraphicsConfiguration) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
BiNoMPluginDialog(Dialog) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
BiNoMPluginDialog(Dialog, boolean) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
BiNoMPluginDialog(Dialog, String) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
BiNoMPluginDialog(Dialog, String, boolean) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
BiNoMPluginDialog(Dialog, String, boolean, GraphicsConfiguration) - Constructor for class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
BiochemicalPathwayStep - Interface in fr.curie.BiNoM.pathways.biopax
Interface for BiochemicalPathwayStep ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
BiochemicalPathwayStepImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of BiochemicalPathwayStep Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
BiochemicalPathwayStepListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep to receive notification when properties changed, added or removed.
BiochemicalReaction - Interface in fr.curie.BiNoM.pathways.biopax
Interface for BiochemicalReaction ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
BiochemicalReactionImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of BiochemicalReaction Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
BiochemicalReactionListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.BiochemicalReaction to receive notification when properties changed, added or removed.
BiographUtils - Class in fr.curie.BiNoM.pathways.analysis.structure
Set of functions using specific graph node semantics of BiNoM
BiographUtils() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
biopax - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
 
biopax - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Input for conversion
biopax - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
The result of the conversion
biopax - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
biopax - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
biopax - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
Input BioPAX object
BioPAX - Class in fr.curie.BiNoM.pathways.wrappers
 
BioPAX() - Constructor for class fr.curie.BiNoM.pathways.wrappers.BioPAX
 
BioPAX(String, String, String) - Constructor for class fr.curie.BiNoM.pathways.wrappers.BioPAX
Non-standard constructor with some prefixes
biopax - Variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
BioPAX2CellDesigner - Class in fr.curie.BiNoM.pathways.converters
 
BioPAX2CellDesigner() - Constructor for class fr.curie.BiNoM.pathways.converters.BioPAX2CellDesigner
 
BioPAX2Cytoscape - Class in fr.curie.BiNoM.pathways.converters
 
BioPAX2Cytoscape() - Constructor for class fr.curie.BiNoM.pathways.converters.BioPAX2Cytoscape
 
BioPAX2SBML - Class in fr.curie.BiNoM.pathways.converters
 
BioPAX2SBML() - Constructor for class fr.curie.BiNoM.pathways.converters.BioPAX2SBML
 
biopax_DASH_level3_DOT_owlFactory - Class in fr.curie.BiNoM.pathways.biopax
Factory for instantiating objects for ontology classes in the biopax-level3.owl ontology.
biopax_DASH_level3_DOT_owlFactory() - Constructor for class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
 
biopax_map - Static variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
A map from BioPAX file key to static set of BioPAX objects
bioPAXAlgos - Variable in class fr.curie.BiNoM.biopax.BioPAXImportBaseTask
 
BioPAXAssociateSource - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXAssociateSourceTask - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXAssociateSourceTask(File, String) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSourceTask
 
BioPAXAttrDesc - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXAttrDesc(BioPAXClassDesc, String) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
BioPAXAttrDescProto - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXAttrDescProto.SubType - Enum in fr.curie.BiNoM.biopax.propedit
 
BioPAXAttrDescProto.Type - Enum in fr.curie.BiNoM.biopax.propedit
 
BioPAXAttrDescProtoFactory - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXAttrDescProtoFactory(BioPAXClassDesc, BioPAXClassDescFactory) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProtoFactory
 
BioPAXClassDesc - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXClassDesc(BioPAX, Class) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
BioPAXClassDesc.HierarchyScanner - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXClassDesc.HierarchyScanner() - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc.HierarchyScanner
 
BioPAXClassDescFactory - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXClassTree - Class in fr.curie.BiNoM.celldesigner.biopax.propedit
 
BioPAXClassTree(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.biopax.propedit.BioPAXClassTree
 
BioPAXClassTree - Class in fr.curie.BiNoM.cytoscape.biopax.propedit
 
BioPAXClassTree() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassTree
 
BioPAXClassTreeFrame - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXConnectedComponents - Class in fr.curie.BiNoM.pathways.test
 
BioPAXConnectedComponents() - Constructor for class fr.curie.BiNoM.pathways.test.BioPAXConnectedComponents
 
BioPAXConnectedComponents - Class in fr.curie.BiNoM.pathways.test.examples
 
BioPAXConnectedComponents() - Constructor for class fr.curie.BiNoM.pathways.test.examples.BioPAXConnectedComponents
 
BioPAXDBRepository - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXDBRepository() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDBRepository
 
BioPAXDisplayIndexInfo - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXDisplayIndexInfo() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDisplayIndexInfo
 
BioPAXDisplayIndexInfoDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXDisplayIndexInfoDialog() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDisplayIndexInfoDialog
 
BioPAXDoubleAttrDesc - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXDoubleAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleAttrDesc
 
BioPAXDoubleListAttrDesc - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXDoubleListAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleListAttrDesc
 
BioPAXEntityReactionDistribution(Graph, String, boolean) - Method in class fr.curie.BiNoM.pathways.utils.acsn.DatabaseComparison
 
BioPAXExportTask - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXExportTask(File, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportTask
 
BioPAXExportToFile - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXExportToFile() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportToFile
 
biopaxFileString - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Standard BioPAX v.3 prefix
BioPAXGenerateIndex - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXGenerateIndex() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndex
 
BioPAXGenerateIndexDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXGenerateIndexTask - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXGenerateIndexTask(String, String) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexTask
 
BioPAXGraphMapper - Class in fr.curie.BiNoM.pathways.utils
Creates a BioPAX index - mapping of BioPAX content onto an attributed (di)graph
BioPAXGraphMapper() - Constructor for class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
 
BioPAXGraphMappingService - Class in fr.curie.BiNoM.pathways.utils
Service class performing creating BioPAX index
BioPAXGraphMappingService() - Constructor for class fr.curie.BiNoM.pathways.utils.BioPAXGraphMappingService
 
BioPAXGraphQuery - Class in fr.curie.BiNoM.pathways.utils
A simple container of the BioPAX standard query
BioPAXGraphQuery() - Constructor for class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
 
BioPAXGraphQueryEngine - Class in fr.curie.BiNoM.pathways.utils
The actual implementation of the standard query
BioPAXGraphQueryEngine() - Constructor for class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
 
BioPAXImportBaseTask - Class in fr.curie.BiNoM.biopax
 
BioPAXImportBaseTask(File, URL, String, int[], BioPAXToCytoscapeConverter.Option, boolean) - Constructor for class fr.curie.BiNoM.biopax.BioPAXImportBaseTask
 
BioPAXImportDialog - Class in fr.curie.BiNoM.biopax
 
BioPAXImportFromFile - Class in fr.curie.BiNoM.celldesigner.biopax
 
BioPAXImportFromFile(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.biopax.BioPAXImportFromFile
 
BioPAXImportFromFile - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXImportFromFile() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportFromFile
 
BioPAXImportFromURL - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXImportFromURL() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportFromURL
 
BioPAXImportTask - Class in fr.curie.BiNoM.celldesigner.biopax
 
BioPAXImportTask(CellDesignerPlugin, File, URL, String, int[], BioPAXToCytoscapeConverter.Option, boolean) - Constructor for class fr.curie.BiNoM.celldesigner.biopax.BioPAXImportTask
 
BioPAXImportTask - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXImportTask(File, URL, String, int[], BioPAXToCytoscapeConverter.Option, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTask
 
BioPAXImportTaskFactory - Class in fr.curie.BiNoM.celldesigner.biopax
 
BioPAXImportTaskFactory(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.biopax.BioPAXImportTaskFactory
 
BioPAXImportTaskFactory - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXImportTaskFactory() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTaskFactory
 
BioPAXIndex2Tables - Class in fr.curie.BiNoM.pathways.converters
 
BioPAXIndex2Tables() - Constructor for class fr.curie.BiNoM.pathways.converters.BioPAXIndex2Tables
 
BioPAXIndexPathAnalysis - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXIndexPathAnalysis() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexPathAnalysis
 
BioPAXIndexRepository - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXIndexRepository() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
BioPAXIntegerAttrDesc - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXIntegerAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerAttrDesc
 
BioPAXIntegerListAttrDesc - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXIntegerListAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerListAttrDesc
 
BioPAXLoadIndex - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXLoadIndex() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndex
 
BioPAXLoadIndexDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXLoadIndexTask - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXLoadIndexTask(String, String) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexTask
 
BioPAXMerge - Class in fr.curie.BiNoM.pathways.utils
Utilities for merging BioPAX objects
BioPAXMerge() - Constructor for class fr.curie.BiNoM.pathways.utils.BioPAXMerge
 
biopaxmodel - Variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
BioPAX OWL as com.hp.hpl.jena.ontology.OntModel
bioPAXName - Variable in class fr.curie.BiNoM.biopax.BioPAXImportBaseTask
 
biopaxNaming - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
Naming service used for the mapping
BioPAXNamingService - Class in fr.curie.BiNoM.pathways.utils
BioPAX Naming Service.
BioPAXNamingService() - Constructor for class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Empty constructor
BioPAXNamingService(BioPAX, boolean) - Constructor for class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Constructor calling the generateNames function.
BioPAXNamingService(BioPAX) - Constructor for class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Constructor calling the constructor above (?!??), calling generateNames without printing anything.
BioPAXNamingServiceManager - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXNamingServiceManager() - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXNamingServiceManager
 
BioPAXObject - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXObject(BioPAXClassDesc, Object, BioPAX) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXObject
 
BioPAXObjectAttrDesc - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXObjectAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
BioPAXObjectFactory - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXObjectListAttrDesc - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXObjectListAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
bioPAXOption - Variable in class fr.curie.BiNoM.biopax.BioPAXImportBaseTask
 
BioPAXPathAnalysis - Class in fr.curie.BiNoM.pathways.test.examples
 
BioPAXPathAnalysis() - Constructor for class fr.curie.BiNoM.pathways.test.examples.BioPAXPathAnalysis
 
BioPAXPropertyBrowser - Class in fr.curie.BiNoM.celldesigner.biopax.propedit
 
BioPAXPropertyBrowser(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.biopax.propedit.BioPAXPropertyBrowser
 
BioPAXPropertyBrowser - Class in fr.curie.BiNoM.cytoscape.biopax.propedit
 
BioPAXPropertyBrowser() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowser
 
BioPAXPropertyBrowserFrame - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXPropertyBrowserPanel - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXPropertyBrowserPanel(BioPAXObject, BioPAX, boolean, boolean, BioPAXPropertyBrowserFrame) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserPanel
Constructor for a panel used to display BioPAX object information.
BioPAXPropertyEditFrame - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXPropertyManager - Class in fr.curie.BiNoM.celldesigner.biopax.propedit
 
BioPAXPropertyManager - Class in fr.curie.BiNoM.cytoscape.biopax.propedit
 
BioPAXPropertyUtils - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXPropertyUtils() - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
BioPAXPropertyUtils.ObjectLabel - Class in fr.curie.BiNoM.biopax.propedit
 
bioPAXreactions - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cutted uris (after # separator) to BioPAX 'conversion' objects
BioPAXRepository - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXRepository() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXRepository
 
BioPAXSaveAssociated - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXSaveAssociated() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXSaveAssociated
 
BioPAXSelectEntities - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXSelectEntities() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntities
 
BioPAXSelectEntitiesDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXSelectEntitiesDialog() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesDialog
 
BioPAXSelectEntitiesTask - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXSelectEntitiesTask(BioPAXGraphQuery, int, int) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask
 
BioPAXSourceDB - Class in fr.curie.BiNoM.biopax
 
BioPAXStandardQuery - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXStandardQuery() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQuery
 
BioPAXStandardQuery - Class in fr.curie.BiNoM.pathways.test.examples
 
BioPAXStandardQuery() - Constructor for class fr.curie.BiNoM.pathways.test.examples.BioPAXStandardQuery
 
BioPAXStandardQueryDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXStandardQueryTask - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXStandardQueryTask(BioPAXStandardQueryTask.StandardQueryOptions, BioPAXGraphQuery, Vector, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask
 
BioPAXStandardQueryTask() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask
 
BioPAXStandardQueryTask.StandardQueryOptions - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXStandardQueryTask.StandardQueryOptions() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions
 
biopaxString - Static variable in class fr.curie.BiNoM.pathways.test.TestBioPAX
 
biopaxString - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Standard BioPAX v.3 prefix
BioPAXStringAttrDesc - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXStringAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
BioPAXStringListAttrDesc - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXStringListAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXStringListAttrDesc
 
BioPAXSyncNetworks - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXSyncNetworks() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXSyncNetworks
 
BioPAXSyncNetworksDialog - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioPAXToCellDesignerConverter - Class in fr.curie.BiNoM.pathways
 
BioPAXToCellDesignerConverter() - Constructor for class fr.curie.BiNoM.pathways.BioPAXToCellDesignerConverter
 
BioPAXToCytoscapeConverter - Class in fr.curie.BiNoM.pathways
Converts BioPAX (represented by BioPAX object) to XGMML (represented by GraphDocument object)
BioPAXToCytoscapeConverter() - Constructor for class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
 
BioPAXToCytoscapeConverter.Graph - Class in fr.curie.BiNoM.pathways
Little auxiliary container for BioPAX and GraphDocument object
BioPAXToCytoscapeConverter.Option - Class in fr.curie.BiNoM.pathways
Set of conversion options
BioPAXToCytoscapeConverter.Option() - Constructor for class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option
 
BioPAXToggleNamingService - Class in fr.curie.BiNoM.biopax.propedit
 
BioPAXToggleNamingService() - Constructor for class fr.curie.BiNoM.biopax.propedit.BioPAXToggleNamingService
 
BioPAXToSBMLConverter - Class in fr.curie.BiNoM.pathways
Converts BioPAX (represented by BioPAX object) to SBML (represented by org.sbml.x2001.ns.celldesigner.SbmlDocument object)
BioPAXToSBMLConverter() - Constructor for class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
 
BioPAXToSBMLConverter.BioPAXSpecies - Class in fr.curie.BiNoM.pathways
Represents BioPAX physicalEntityParticipants grouped into distinctive chemical species (entity, characterized by a definite location and a definite modification).
BioPAXToSBMLConverter.BioPAXSpecies() - Constructor for class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter.BioPAXSpecies
 
BioPAXUtilities - Class in fr.curie.BiNoM.pathways.utils
Set of utilities for manipulating com.hp.hpl.jena.rdf.model.Model objects
BioPAXUtilities() - Constructor for class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
 
BioPAXViewQueryLog - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXViewQueryLog() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXViewQueryLog
 
BioPAXViewQueryLogDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
BioPAXVisualStyleDefinition - Class in fr.curie.BiNoM.cytoscape.biopax
 
BioSource - Interface in fr.curie.BiNoM.pathways.biopax
Interface for BioSource ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
BioSourceImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of BioSource Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
BioSourceListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.BioSource to receive notification when properties changed, added or removed.
BipartiteGraph - Class in fr.curie.BiNoM.pathways.analysis.structure
Was supposed to deal with Bi-partite graphs specifically but has not been used yet
BipartiteGraph() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.BipartiteGraph
 
BlogCreator - Class in fr.curie.BiNoM.pathways.navicell
 
BlogCreator() - Constructor for class fr.curie.BiNoM.pathways.navicell.BlogCreator
 
booleanOption(String, String) - Method in class fr.curie.BiNoM.pathways.utils.OptionParser
 
bpnm - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
BioPAX Naming service used for conversion
bsc - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
BioPAXToSBML Converter is needed to created the Reaction Network part of the index

C

calcAllMaterialComponents(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
For every protein name, creates a subgraph with all its modifications, complexes, locations
calcAllToAllInfluences() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
calcAveragePair(Vector<Pair>) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
calcAveragePair(Vector<Pair>) - Static method in class fr.curie.BiNoM.pathways.test.testRemoveEditPoints
 
calcAveragePairwiseDistance(double[][]) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
calcAveragePathLength(Vector<Path>) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
CalcCentrality - Class in fr.curie.BiNoM.cytoscape.analysis
 
CalcCentrality() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.CalcCentrality
 
CalcCentralityTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
CalcCentralityTask(GraphDocument, Vector<String>, boolean, StructureAnalysisUtils.Option, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.CalcCentralityTask
 
calcCombinations(int, int) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Calculate the number of combinations of k size for a set of n elements.
calcDegreeDistribution(Graph, HashMap<Integer, Vector<Node>>, Vector<Integer>, boolean) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
calcDistributionOfConnectedComponentSizes(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
calcIntersectionOfSets(HashSet<String>, HashSet<String>) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
calcMean(float[]) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
calcNodeBetweenness(Graph, Vector<String>, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
calcNodeInfluence(Node, Vector<Path>, boolean) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
calcNodeInfluence(float, Vector<Path>) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
calcNodesInOut() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
calcPathInfluence(Path) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
calcPathProperties(Path) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
calcPathwayInfluence(Vector<Vector<Path>>) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
calcPercolationThreshold(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
calcPValues(float[], float[][]) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
calcRandomPathwayInfluence(Vector<Vector<Path>>, float[]) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
calcSignificanceVsNumberOfGenes(Graph, Vector<String>, int, int[]) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
calcSpecialPValue(float[], float[][]) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
calcStandardDeviation(float[]) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
calcSubnetworkComplexProfile() - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
calcUnionOfSets() - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
Catalysis - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Catalysis ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
catalysisDirectionChanged(Catalysis) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when catalysisDirection has changed
catalysisDirectionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Catalysis
The Jena Property for catalysisDirection
CatalysisImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Catalysis Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
CatalysisListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Catalysis to receive notification when properties changed, added or removed.
cd - Variable in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
cd - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
CDesigner2BioPAX - Class in fr.curie.BiNoM.pathways.test.examples
 
CDesigner2BioPAX() - Constructor for class fr.curie.BiNoM.pathways.test.examples.CDesigner2BioPAX
 
celldesigner - Variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Auxiliary BiNoM wrapper of CellDesigner
CellDesigner - Class in fr.curie.BiNoM.pathways.wrappers
Wrapper class for CellDesigner with some utilities implemented
CellDesigner() - Constructor for class fr.curie.BiNoM.pathways.wrappers.CellDesigner
 
CellDesigner2BioPAX - Class in fr.curie.BiNoM.pathways.converters
 
CellDesigner2BioPAX() - Constructor for class fr.curie.BiNoM.pathways.converters.CellDesigner2BioPAX
 
CellDesigner2Cytoscape - Class in fr.curie.BiNoM.pathways.converters
 
CellDesigner2Cytoscape() - Constructor for class fr.curie.BiNoM.pathways.converters.CellDesigner2Cytoscape
 
CellDesignerAssociateSource - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
CellDesignerAssociateSourceTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
CellDesignerAssociateSourceTask(File, String) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSourceTask
 
CellDesignerColorProteins - Class in fr.curie.BiNoM.pathways
 
CellDesignerColorProteins() - Constructor for class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
CellDesignerColorSpecies - Class in fr.curie.BiNoM.pathways
 
CellDesignerColorSpecies() - Constructor for class fr.curie.BiNoM.pathways.CellDesignerColorSpecies
 
CellDesignerExportTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
CellDesignerExportTask(File, CellDesignerExportToFileDialog.CellDesignerExportToFileOptions) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
CellDesignerExportToFile - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
CellDesignerExportToFile() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFile
 
CellDesignerExportToFileDialog - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
CellDesignerExportToFileDialog.CellDesignerExportToFileOptions - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
CellDesignerExportToFileDialog.CellDesignerExportToFileOptions() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
CellDesignerGenerator - Class in fr.curie.BiNoM.pathways.utils
 
CellDesignerGenerator() - Constructor for class fr.curie.BiNoM.pathways.utils.CellDesignerGenerator
 
CellDesignerImportFromFile - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
CellDesignerImportFromFile() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportFromFile
 
CellDesignerImportTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
CellDesignerImportTask(File) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportTask
 
CellDesignerPathwayStaining - Class in fr.curie.BiNoM.pathways.coloring
 
CellDesignerPathwayStaining() - Constructor for class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
CellDesignerPathwayStaining.ColorPoint - Class in fr.curie.BiNoM.pathways.coloring
 
CellDesignerPathwayStaining.ColorPoint() - Constructor for class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining.ColorPoint
 
CellDesignerSourceDB - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
cellDesignerTerms - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Map from CellDesigner terms (strings) to OpenControlledVocabulary objects
CellDesignerToBioPAXConverter - Class in fr.curie.BiNoM.pathways
Implementation of converter from CellDesigner 3.* file to BioPAX
CellDesignerToBioPAXConverter() - Constructor for class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
CellDesignerToCytoscapeConverter - Class in fr.curie.BiNoM.pathways
Direct converter from CellDesigner to Cytoscape.
CellDesignerToCytoscapeConverter() - Constructor for class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
CellDesignerToCytoscapeConverter.Graph - Class in fr.curie.BiNoM.pathways
Simple container for GraphDocument and SbmlDocument objects
CellDesignerVisualStyleDefinition - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
cellTypeChanged(BioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSourceListener
Called when cellType has changed
cellTypeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BioSource
The Jena Property for cellType
cellularLocationChanged(Complex) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when cellularLocation has changed
cellularLocationChanged(Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when cellularLocation has changed
cellularLocationChanged(DnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when cellularLocation has changed
cellularLocationChanged(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when cellularLocation has changed
cellularLocationChanged(Protein) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when cellularLocation has changed
cellularLocationChanged(Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when cellularLocation has changed
cellularLocationChanged(RnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when cellularLocation has changed
cellularLocationChanged(SmallMolecule) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when cellularLocation has changed
cellularLocationProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
The Jena Property for cellularLocation
CellularLocationVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for CellularLocationVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
cellularLocationVocabularyHash - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
CellularLocationVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of CellularLocationVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
CellularLocationVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.CellularLocationVocabulary to receive notification when properties changed, added or removed.
CellVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for CellVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
CellVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of CellVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
CellVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.CellVocabulary to receive notification when properties changed, added or removed.
cf - Static variable in class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
cf - Static variable in class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 
ch - Static variable in class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
ch - Static variable in class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 
changeClassesOfSpecies() - Method in class fr.curie.BiNoM.pathways.BioPAXToCellDesignerConverter
 
changeFontSize - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
changeModelName(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
changeModelNotes(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
changeSpeciesCoordinates - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
checkAliases(ReactionDocument.Reaction, String, Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
checkAllTranslations(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
checkAndModifyEntitiesIDs(SbmlDocument, SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
checkAndModifySpeciesIDs(SbmlDocument, SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Utility function.
checkBoxes - Variable in class fr.curie.BiNoM.analysis.ExcludeIntermediateNodesDialog
 
checkBoxes - Variable in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogConstitutiveReactions
 
checkCellDesignerFile - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
checkCellDesignerFile() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.checkCellDesignerFile
 
CheckCellDesignerFile - Class in fr.curie.BiNoM.pathways.utils
 
CheckCellDesignerFile() - Constructor for class fr.curie.BiNoM.pathways.utils.CheckCellDesignerFile
 
checkCellDesignerFileDialog - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
checkCellDesignerFileTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
checkCellDesignerFileTask(String) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.checkCellDesignerFileTask
 
checkComponentSignificance - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
checkedForConsistency - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
checkEdgeInfluence() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Convert every edge with no influence attribute to "activation".
checkIfReactionConnectedToIncludedSpecies() - Method in class fr.curie.BiNoM.pathways.utils.CheckCellDesignerFile
 
checkInconsistenciesInNames(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.testCellDesigner
 
checkRows() - Method in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Check for rows having a single 1, these are exceptions, i.e.
checkSpecies(ReactionDocument.Reaction, String, Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
checkSpeciesAliases(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
checkUserFamiliesForConsistency() - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
chemicalFormulaChanged(SmallMoleculeReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when chemicalFormula has changed
chemicalFormulaProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
The Jena Property for chemicalFormula
ChemicalStructure - Interface in fr.curie.BiNoM.pathways.biopax
Interface for ChemicalStructure ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ChemicalStructureImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of ChemicalStructure Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ChemicalStructureListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.ChemicalStructure to receive notification when properties changed, added or removed.
ChemType - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
ChemType - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
CIRCLE - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
 
className(String) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
clearAndCopy(CyNetwork, CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ChemicalStructureImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceLocationImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.UtilityClassImpl
 
clearCache() - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
clearNetwork(CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
 
clearReport() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
ClusterByShortPath - Class in fr.curie.BiNoM.cytoscape.nestmanager
Dialog of function clustering by oriented shortest paths Launch the task of creating clusters
ClusterByShortPath() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ClusterByShortPath
 
ClusterByShortPathTask - Class in fr.curie.BiNoM.cytoscape.nestmanager
Task of creating networks from clusters by copy of nodes and edges from the current network
ClusterByShortPathTask(ClusterByShortPath) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ClusterByShortPathTask
 
clustering(int, int) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering
 
ClusterNetworks - Class in fr.curie.BiNoM.celldesigner.analysis
 
ClusterNetworks(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.ClusterNetworks
 
ClusterNetworks - Class in fr.curie.BiNoM.cytoscape.analysis
 
ClusterNetworks() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworks
 
ClusterNetworksDialog - Class in fr.curie.BiNoM.analysis
 
ClusterNetworksDialog(AbstractClusterNetworksTaskFactory) - Constructor for class fr.curie.BiNoM.analysis.ClusterNetworksDialog
 
ClusterNetworksTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
ClusterNetworksTask(PluginModel, CellDesignerPlugin, int[], StructureAnalysisUtils.Option) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.ClusterNetworksTask
 
ClusterNetworksTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
ClusterNetworksTask(int[], StructureAnalysisUtils.Option, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTask
 
ClusterNetworksTaskFactory - Class in fr.curie.BiNoM.celldesigner.analysis
 
ClusterNetworksTaskFactory - Class in fr.curie.BiNoM.cytoscape.analysis
 
ClusterNetworksTaskFactory() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTaskFactory
 
coefficientInConservationLaw - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
Auxiliary property for analysis of conservation laws
cofactorAdded(Catalysis, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of cofactor has been added
cofactorProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Catalysis
The Jena Property for cofactor
cofactorRemoved(Catalysis, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of cofactor has been removed
colCount - Variable in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
CollapseMetaNodes(Graph, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
Calculates modular representation of graph global, using Graph.Metanodes list of subgraphs showIntersections - if true then all metanode intersections will be shown explicitly nodeIntersectionView - if true then all the edges connecting nodes in the intersection will not be shown, but instead for every common node there will be a 'INTERSECT' edge shown
colorCellDesignerProteins - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
colorCellDesignerProteins() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.colorCellDesignerProteins
 
colorCellDesignerProteinsDialog - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
colorCellDesignerProteinsTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
colorCellDesignerProteinsTask(String, String) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.colorCellDesignerProteinsTask
 
colorForNumber(float, float, float) - Static method in class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
colorProteins(String, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
colorProteins(String, String) - Static method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
CombinationGenerator - Class in fr.curie.BiNoM.pathways.utils
The CombinationGenerator Java class systematically generates all combinations of n elements, taken r at a time.
CombinationGenerator(int, int) - Constructor for class fr.curie.BiNoM.pathways.utils.CombinationGenerator
Constructor.
CombineIncludedGraphsApprox(Vector<Graph>, float) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
Clusters graphs with node overlap more than threshold
ComboBoxes - Class in fr.curie.BiNoM.cytoscape.utils
A dialog box to select values of different list of strings Fields displays in comboboxes values to be selected Field index corresponds to datas index datas contains lists of values The result got by launch is at index 0 the selected field and at index 1 to n (label size - 1) the values selected in comboboxes selected is the field selected when launching dialog
ComboBoxes(JFrame, String, String[], ArrayList<String>, String, ArrayList<ArrayList<String>>) - Constructor for class fr.curie.BiNoM.cytoscape.utils.ComboBoxes
 
commentAdded(BindingFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when a value of comment has been added
commentAdded(BiochemicalPathwayStep, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of comment has been added
commentAdded(BiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of comment has been added
commentAdded(BioSource, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSourceListener
Called when a value of comment has been added
commentAdded(Catalysis, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of comment has been added
commentAdded(CellularLocationVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyListener
Called when a value of comment has been added
commentAdded(CellVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CellVocabularyListener
Called when a value of comment has been added
commentAdded(ChemicalStructure, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructureListener
Called when a value of comment has been added
commentAdded(ComplexAssembly, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of comment has been added
commentAdded(Complex, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of comment has been added
commentAdded(ControlledVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabularyListener
Called when a value of comment has been added
commentAdded(Control, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of comment has been added
commentAdded(Conversion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of comment has been added
commentAdded(CovalentBindingFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when a value of comment has been added
commentAdded(Degradation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of comment has been added
commentAdded(DeltaG, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaGListener
Called when a value of comment has been added
commentAdded(Dna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of comment has been added
commentAdded(DnaReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of comment has been added
commentAdded(DnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of comment has been added
commentAdded(DnaRegionReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of comment has been added
commentAdded(EntityFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeatureListener
Called when a value of comment has been added
commentAdded(Entity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityListener
Called when a value of comment has been added
commentAdded(EntityReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of comment has been added
commentAdded(EntityReferenceTypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyListener
Called when a value of comment has been added
commentAdded(EvidenceCodeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyListener
Called when a value of comment has been added
commentAdded(Evidence, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceListener
Called when a value of comment has been added
commentAdded(ExperimentalForm, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormListener
Called when a value of comment has been added
commentAdded(ExperimentalFormVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyListener
Called when a value of comment has been added
commentAdded(FragmentFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.FragmentFeatureListener
Called when a value of comment has been added
commentAdded(Gene, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of comment has been added
commentAdded(GeneticInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of comment has been added
commentAdded(Interaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of comment has been added
commentAdded(InteractionVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionVocabularyListener
Called when a value of comment has been added
commentAdded(KPrime, String) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrimeListener
Called when a value of comment has been added
commentAdded(ModificationFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when a value of comment has been added
commentAdded(Modulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of comment has been added
commentAdded(MolecularInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of comment has been added
commentAdded(Pathway, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of comment has been added
commentAdded(PathwayStep, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStepListener
Called when a value of comment has been added
commentAdded(PhenotypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyListener
Called when a value of comment has been added
commentAdded(PhysicalEntity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of comment has been added
commentAdded(Protein, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of comment has been added
commentAdded(ProteinReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of comment has been added
commentAdded(Provenance, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProvenanceListener
Called when a value of comment has been added
commentAdded(PublicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when a value of comment has been added
commentAdded(RelationshipTypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyListener
Called when a value of comment has been added
commentAdded(RelationshipXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXrefListener
Called when a value of comment has been added
commentAdded(Rna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of comment has been added
commentAdded(RnaReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of comment has been added
commentAdded(RnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of comment has been added
commentAdded(RnaRegionReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of comment has been added
commentAdded(Score, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ScoreListener
Called when a value of comment has been added
commentAdded(SequenceInterval, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceIntervalListener
Called when a value of comment has been added
commentAdded(SequenceLocation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceLocationListener
Called when a value of comment has been added
commentAdded(SequenceModificationVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyListener
Called when a value of comment has been added
commentAdded(SequenceRegionVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyListener
Called when a value of comment has been added
commentAdded(SequenceSite, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceSiteListener
Called when a value of comment has been added
commentAdded(SmallMolecule, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of comment has been added
commentAdded(SmallMoleculeReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of comment has been added
commentAdded(Stoichiometry, String) - Method in interface fr.curie.BiNoM.pathways.biopax.StoichiometryListener
Called when a value of comment has been added
commentAdded(TemplateReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of comment has been added
commentAdded(TemplateReactionRegulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of comment has been added
commentAdded(TissueVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TissueVocabularyListener
Called when a value of comment has been added
commentAdded(Transport, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of comment has been added
commentAdded(TransportWithBiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of comment has been added
commentAdded(UnificationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.UnificationXrefListener
Called when a value of comment has been added
commentAdded(UtilityClass, String) - Method in interface fr.curie.BiNoM.pathways.biopax.UtilityClassListener
Called when a value of comment has been added
commentAdded(Xref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.XrefListener
Called when a value of comment has been added
commentProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Entity
The Jena Property for comment
commentProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.UtilityClass
The Jena Property for comment
commentRemoved(BindingFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when a value of comment has been removed
commentRemoved(BiochemicalPathwayStep, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of comment has been removed
commentRemoved(BiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of comment has been removed
commentRemoved(BioSource, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSourceListener
Called when a value of comment has been removed
commentRemoved(Catalysis, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of comment has been removed
commentRemoved(CellularLocationVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyListener
Called when a value of comment has been removed
commentRemoved(CellVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CellVocabularyListener
Called when a value of comment has been removed
commentRemoved(ChemicalStructure, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructureListener
Called when a value of comment has been removed
commentRemoved(ComplexAssembly, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of comment has been removed
commentRemoved(Complex, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of comment has been removed
commentRemoved(ControlledVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabularyListener
Called when a value of comment has been removed
commentRemoved(Control, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of comment has been removed
commentRemoved(Conversion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of comment has been removed
commentRemoved(CovalentBindingFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when a value of comment has been removed
commentRemoved(Degradation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of comment has been removed
commentRemoved(DeltaG, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaGListener
Called when a value of comment has been removed
commentRemoved(Dna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of comment has been removed
commentRemoved(DnaReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of comment has been removed
commentRemoved(DnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of comment has been removed
commentRemoved(DnaRegionReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of comment has been removed
commentRemoved(EntityFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeatureListener
Called when a value of comment has been removed
commentRemoved(Entity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityListener
Called when a value of comment has been removed
commentRemoved(EntityReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of comment has been removed
commentRemoved(EntityReferenceTypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyListener
Called when a value of comment has been removed
commentRemoved(EvidenceCodeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyListener
Called when a value of comment has been removed
commentRemoved(Evidence, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceListener
Called when a value of comment has been removed
commentRemoved(ExperimentalForm, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormListener
Called when a value of comment has been removed
commentRemoved(ExperimentalFormVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyListener
Called when a value of comment has been removed
commentRemoved(FragmentFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.FragmentFeatureListener
Called when a value of comment has been removed
commentRemoved(Gene, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of comment has been removed
commentRemoved(GeneticInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of comment has been removed
commentRemoved(Interaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of comment has been removed
commentRemoved(InteractionVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionVocabularyListener
Called when a value of comment has been removed
commentRemoved(KPrime, String) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrimeListener
Called when a value of comment has been removed
commentRemoved(ModificationFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when a value of comment has been removed
commentRemoved(Modulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of comment has been removed
commentRemoved(MolecularInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of comment has been removed
commentRemoved(Pathway, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of comment has been removed
commentRemoved(PathwayStep, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStepListener
Called when a value of comment has been removed
commentRemoved(PhenotypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyListener
Called when a value of comment has been removed
commentRemoved(PhysicalEntity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of comment has been removed
commentRemoved(Protein, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of comment has been removed
commentRemoved(ProteinReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of comment has been removed
commentRemoved(Provenance, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProvenanceListener
Called when a value of comment has been removed
commentRemoved(PublicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when a value of comment has been removed
commentRemoved(RelationshipTypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyListener
Called when a value of comment has been removed
commentRemoved(RelationshipXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXrefListener
Called when a value of comment has been removed
commentRemoved(Rna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of comment has been removed
commentRemoved(RnaReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of comment has been removed
commentRemoved(RnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of comment has been removed
commentRemoved(RnaRegionReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of comment has been removed
commentRemoved(Score, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ScoreListener
Called when a value of comment has been removed
commentRemoved(SequenceInterval, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceIntervalListener
Called when a value of comment has been removed
commentRemoved(SequenceLocation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceLocationListener
Called when a value of comment has been removed
commentRemoved(SequenceModificationVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyListener
Called when a value of comment has been removed
commentRemoved(SequenceRegionVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyListener
Called when a value of comment has been removed
commentRemoved(SequenceSite, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceSiteListener
Called when a value of comment has been removed
commentRemoved(SmallMolecule, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of comment has been removed
commentRemoved(SmallMoleculeReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of comment has been removed
commentRemoved(Stoichiometry, String) - Method in interface fr.curie.BiNoM.pathways.biopax.StoichiometryListener
Called when a value of comment has been removed
commentRemoved(TemplateReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of comment has been removed
commentRemoved(TemplateReactionRegulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of comment has been removed
commentRemoved(TissueVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TissueVocabularyListener
Called when a value of comment has been removed
commentRemoved(Transport, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of comment has been removed
commentRemoved(TransportWithBiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of comment has been removed
commentRemoved(UnificationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.UnificationXrefListener
Called when a value of comment has been removed
commentRemoved(UtilityClass, String) - Method in interface fr.curie.BiNoM.pathways.biopax.UtilityClassListener
Called when a value of comment has been removed
commentRemoved(Xref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.XrefListener
Called when a value of comment has been removed
Comments - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
Comments - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
comments - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
comp_ids - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
comp_ids_n - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
compare(InteractionGraph.NodeDegree) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph.NodeDegree
 
compareIn(InteractionGraph.NodeDegree) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph.NodeDegree
 
compareOut(InteractionGraph.NodeDegree) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph.NodeDegree
 
compareTo(ShortPathClustering.Distance) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Distance
 
compareTo(Object) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer.optCutSetData
 
compareTo(OmegaScoreData) - Method in class fr.curie.BiNoM.pathways.analysis.structure.OmegaScoreData
 
compareTwoSets(Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
compartment - Variable in class fr.curie.BiNoM.pathways.utils.SpeciesStructure
 
compartmentHash - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Map from compartment ids to CompartmentDocument.Compartment objects
compartments - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
List of compartments (represented as openControlledVocabulary objects)
compile() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
 
COMPLETE_REACTIONS - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
For all reactions, attaches all connected nodes from the index (species, publications, pathway steps, etc.)
Complex - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Complex ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ComplexAssembly - Interface in fr.curie.BiNoM.pathways.biopax
Interface for ComplexAssembly ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ComplexAssemblyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of ComplexAssembly Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ComplexAssemblyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.ComplexAssembly to receive notification when properties changed, added or removed.
complexes - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Map of CellDesigner CelldesignerComplexSpeciesAliasDocument.CelldesignerComplexSpeciesAlias objects
complexExpand - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions
 
ComplexImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Complex Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
complexList - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cut uris (after # separator) to 'complex' entities
ComplexListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Complex to receive notification when properties changed, added or removed.
complexMap - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
complexNoExpand - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions
 
complexSpeciesAliasIdMap - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
complexSpeciesAliasMap - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
complexSpeciesMap - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
componentAdded(Complex, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of component has been added
componentProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Complex
The Jena Property for component
componentRemoved(Complex, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of component has been removed
components - Variable in class fr.curie.BiNoM.pathways.utils.SpeciesStructure
 
componentStoichiometryAdded(Complex, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of componentStoichiometry has been added
componentStoichiometryProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Complex
The Jena Property for componentStoichiometry
componentStoichiometryRemoved(Complex, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of componentStoichiometry has been removed
computeDegrees() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph
 
computeDepth(int) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
ComputeNaviCellMaps - Class in fr.curie.BiNoM.pathways.utils
 
ComputeNaviCellMaps() - Constructor for class fr.curie.BiNoM.pathways.utils.ComputeNaviCellMaps
 
ComputingByBFS - Class in fr.curie.BiNoM.cytoscape.utils
Put the graph from Cytoscape network in practical data structure: arrays of nodes, edges, sources, targets and adjacency Use breadth first search to iterate class for computing list of edges between nodes Influence by a simple recurrent model the shortest path matrix used in clustering Reverse breadth first search is used by extract edges between nodes Influence Area by the same model but without weights
ComputingByBFS() - Constructor for class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
ComputingByBFS(GraphPerspective, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
Confidence - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
Confidence - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
confidenceAdded(Evidence, Score) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceListener
Called when a value of confidence has been added
confidenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Evidence
The Jena Property for confidence
confidenceRemoved(Evidence, Score) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceListener
Called when a value of confidence has been removed
CONNECT_BY_SHORTEST_PATHS - Static variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
connectByShortestPaths(Graph, Graph) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
connectByShortestPaths() - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
ConnectedComponents - Class in fr.curie.BiNoM.celldesigner.analysis
 
ConnectedComponents(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.ConnectedComponents
 
ConnectedComponents - Class in fr.curie.BiNoM.cytoscape.analysis
 
ConnectedComponents() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponents
 
ConnectedComponents(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
ConnectedComponentsTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
ConnectedComponentsTask(CellDesignerPlugin, GraphDocument) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.ConnectedComponentsTask
 
ConnectedComponentsTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
ConnectedComponentsTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponentsTask
 
ConnectionToDatabases - Class in fr.curie.BiNoM.pathways.utils.acsn
 
ConnectionToDatabases() - Constructor for class fr.curie.BiNoM.pathways.utils.acsn.ConnectionToDatabases
 
considerCompartmentNameRatherThanId - Static variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Check off if you want to use compartment id and not name
consistency - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
constitutiveReactions - Variable in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogConstitutiveReactions
 
constitutiveReactions() - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
containsEdge(CyNetwork, CyEdge) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkIntersection
 
containsNode(CyNetwork, CyNode) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkIntersection
 
content - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes.AnnotationSection
 
Control - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Control ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ControlImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Control Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
controlledChanged(Catalysis) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when controlled has changed
controlledChanged(Control) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when controlled has changed
controlledChanged(Modulation) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when controlled has changed
controlledChanged(TemplateReactionRegulation) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when controlled has changed
controlledProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Control
The Jena Property for controlled
ControlledVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for ControlledVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ControlledVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of ControlledVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ControlledVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.ControlledVocabulary to receive notification when properties changed, added or removed.
controllerAdded(Catalysis, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of controller has been added
controllerAdded(Catalysis, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of controller has been added
controllerAdded(Control, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of controller has been added
controllerAdded(Control, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of controller has been added
controllerAdded(Modulation, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of controller has been added
controllerAdded(Modulation, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of controller has been added
controllerAdded(TemplateReactionRegulation, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of controller has been added
controllerAdded(TemplateReactionRegulation, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of controller has been added
controllerProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Control
The Jena Property for controller
controllerRemoved(Catalysis, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of controller has been removed
controllerRemoved(Catalysis, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of controller has been removed
controllerRemoved(Control, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of controller has been removed
controllerRemoved(Control, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of controller has been removed
controllerRemoved(Modulation, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of controller has been removed
controllerRemoved(Modulation, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of controller has been removed
controllerRemoved(TemplateReactionRegulation, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of controller has been removed
controllerRemoved(TemplateReactionRegulation, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of controller has been removed
ControlListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Control to receive notification when properties changed, added or removed.
controls - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cutted uris (after # separator) to BioPAX 'control' objects
controlTypeChanged(Catalysis) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when controlType has changed
controlTypeChanged(Control) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when controlType has changed
controlTypeChanged(Modulation) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when controlType has changed
controlTypeChanged(TemplateReactionRegulation) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when controlType has changed
controlTypeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Control
The Jena Property for controlType
Conversion - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Conversion ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
conversionDirectionChanged(BiochemicalReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when conversionDirection has changed
conversionDirectionChanged(ComplexAssembly) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when conversionDirection has changed
conversionDirectionChanged(Conversion) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when conversionDirection has changed
conversionDirectionChanged(Degradation) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when conversionDirection has changed
conversionDirectionChanged(Transport) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when conversionDirection has changed
conversionDirectionChanged(TransportWithBiochemicalReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when conversionDirection has changed
conversionDirectionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Conversion
The Jena Property for conversionDirection
ConversionImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Conversion Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ConversionListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Conversion to receive notification when properties changed, added or removed.
convert(com.ibm.adtech.jastor.Thing, BioPAX) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectFactory
 
convert(Object, BioPAX) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectFactory
 
convert(int, InputStream, String, BioPAXToCytoscapeConverter.Option) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
Convert from InputStream and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
convert(int, BioPAXToCytoscapeConverter, String, BioPAXToCytoscapeConverter.Option) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
Convert using BioPAXToCytoscapeConverter and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
convert(int, String, String, BioPAXToCytoscapeConverter.Option) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
Convert using file name and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
convert(int, String, BioPAXToCytoscapeConverter.Option) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
Convert from file (specified by path) and return fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph
convert() - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
The main conversion function to be used from outside
convert(String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Principal conversion function used from outside
convert(GraphDocument, BioPAX) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter
 
convertExprTreeToMathMLString(ExprTree) - Static method in class fr.curie.BiNoM.pathways.utils.InsertCellDesignerParameters
 
convertExprTreeToMathMLString(ExprTree) - Static method in class fr.curie.BiNoM.pathways.utils.insertMassActionLaws
 
convertFromListOfReactionsToSBML(Vector) - Static method in class fr.curie.BiNoM.pathways.utils.GraphUtils
 
convertGraphToXGMML(Graph) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML
Converts internal BiNoM graph representation to GraphDocument
convertHGNC2HUGOthrowInternet(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
convertListOfNamesToQuery(Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Utility converting vector of names and ids to a BioPAXGraphQuery object
convertPaintToColor(Paint) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
convertPathMatrixColToBinary() - Method in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Convert the path matrix columns (nodes) to a list of binary (BitSet) objects.
convertPathMatrixRowToBinary() - Method in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
convert path matrix rows to BitSet objects
convertReactionNetworkIntoEntityNetwork(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
ConvertReactionNetworkToEntityNetwork - Class in fr.curie.BiNoM.cytoscape.analysis
 
ConvertReactionNetworkToEntityNetwork() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ConvertReactionNetworkToEntityNetwork
 
ConvertReactionNetworkToEntityNetworkTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
ConvertReactionNetworkToEntityNetworkTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ConvertReactionNetworkToEntityNetworkTask
 
convertSetofGMTsToTable(Vector<String>) - Static method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
convertSetToVector(HashSet<String>) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
convertSpeciesToName(SbmlDocument, String, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Generates a unique name for a species speciesID
convertSpeciesToName(SbmlDocument.Sbml, String, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
convertSpeciesToName(SbmlDocument.Sbml, String, boolean, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Generates a unique name for a species speciesID
convertSpeciesToName(SbmlDocument, String, boolean, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
convertSpeciesToName(SbmlDocument.Sbml, String, boolean, boolean, boolean, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Generates a name for a species speciesID
convertTableSetToGMT(String, String, int) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
convertToCellDesigner() - Method in class fr.curie.BiNoM.pathways.BioPAXToCellDesignerConverter
 
ConvertToUndirectedGraph - Class in fr.curie.BiNoM.cytoscape.analysis
 
ConvertToUndirectedGraph() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ConvertToUndirectedGraph
 
ConvertToUndirectedGraphTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
ConvertToUndirectedGraphTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ConvertToUndirectedGraphTask
 
convertXGMMLtoGMT(String, String, boolean) - Static method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
convertXGMMLToGraph(GraphDocument) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML
Converts GraphDocument to internal BiNoM graph representation (fr.curie.BiNoM.pathways.analysis.structure.Graph)
copy(String, CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
 
copy(CyNetwork, CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
 
copy(ArrayList<HashSet<Integer>>) - Method in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
copy() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Edge
 
copyLayout(SbmlDocument, GraphDocument) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter
 
copyModelNotesToFile(File, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
copyModelNotesToFile(File, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
copyModelNotesToFile(String, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
copyModelNotesToFile(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
copyResourceRecursive(String, Model, Model, com.ibm.adtech.jastor.Thing, HashMap) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAX1
 
CopySelectedNodesAndEdges - Class in fr.curie.BiNoM.cytoscape.utils
 
CopySelectedNodesAndEdges(boolean) - Constructor for class fr.curie.BiNoM.cytoscape.utils.CopySelectedNodesAndEdges
 
copyURIwithAllLinks(String, String, Model, Model) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAX1
 
copyURIwithAllLinks(String, String, Model, Model) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
Extract a part of model which is necessary to define a things with uri
correct(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
CorrectCytoscapeEdgeIds(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
CorrectCytoscapeNodeIds(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
After reading XGMML files saved by Cytoscape, this function is used to recover the original Node Ids (Cytoscape will put negative numbers for it).
correctHtml(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
correctId(String) - Static method in class fr.curie.BiNoM.pathways.utils.GraphUtils
 
correctKineticLaw(String, Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.utils.InsertCellDesignerParameters
 
correctName(String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Eliminates spaces, stars, dashes from the string
correctName(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Substitutes strings ' ','*','-','[',']','__',':' to underscore symbol
countAll(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
countEntities(Vector, Vector) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
 
countGraphs - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
countOccurenciesInSets(Vector<String>, Vector<Float>) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
countTokens() - Method in class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer
Total number of tokens present in the input string
CovalentBindingFeature - Interface in fr.curie.BiNoM.pathways.biopax
Interface for CovalentBindingFeature ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
CovalentBindingFeatureImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of CovalentBindingFeature Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
CovalentBindingFeatureListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.CovalentBindingFeature to receive notification when properties changed, added or removed.
create(VisualStyleDefinition) - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleFactory
 
create() - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.ModuleVisualStyle
 
createAttributeTable(CellDesignerColorProteins.SimpleTable, SbmlDocument, String, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
createAttributeTable(RemoveNonExpressedProteins.SimpleTable, SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
createBindingFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BindingFeature.
createBindingFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BindingFeature.
createBiochemicalPathwayStep(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BiochemicalPathwayStep.
createBiochemicalPathwayStep(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BiochemicalPathwayStep.
createBiochemicalReaction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BiochemicalReaction.
createBiochemicalReaction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BiochemicalReaction.
createBiopaxIndividual(String, String, OntModel) - Static method in class fr.curie.BiNoM.pathways.test.TestBioPAX
 
createBioSource(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BioSource.
createBioSource(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BioSource.
createCatalysis(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Catalysis.
createCatalysis(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Catalysis.
createCelldesignerSpecies(String, String, String, String, String) - Method in class fr.curie.BiNoM.pathways.utils.CellDesignerGenerator
 
createCellDesignerTerms() - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Encodes a list of standard terms (protein modification types (GOs) and influence types) by controlledVocabulary terms
createCellularLocationVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CellularLocationVocabulary.
createCellularLocationVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CellularLocationVocabulary.
createCellVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CellVocabulary.
createCellVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CellVocabulary.
createCGHTableFromDir(String) - Method in class fr.curie.BiNoM.pathways.test.AgilentCGHMapping
 
createChemicalStructure(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ChemicalStructure.
createChemicalStructure(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ChemicalStructure.
createCompartments(HashMap<String, Integer>, PluginModel, CellDesignerPlugin) - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkFactory
 
createCompartments() - Method in class fr.curie.BiNoM.pathways.BioPAXToCellDesignerConverter
 
createComplex(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Complex.
createComplex(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Complex.
createComplexAssembly(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ComplexAssembly.
createComplexAssembly(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ComplexAssembly.
createComplexSpecies(String, String) - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkFactory
 
createComplexSpeciesAlias(String, String, SpeciesStructure, int, int) - Method in class fr.curie.BiNoM.pathways.utils.CellDesignerGenerator
 
CreateConnectionsBetweenNests - Class in fr.curie.BiNoM.cytoscape.nestmanager
Create edges between nests from a reference network Delete all old edges between nests Search if every edge of reference network belongs to different network nest Several edges having same interaction type become one edge (left and right are got as same)
CreateConnectionsBetweenNests() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.CreateConnectionsBetweenNests
 
createControl(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Control.
createControl(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Control.
createControlledVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ControlledVocabulary.
createControlledVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ControlledVocabulary.
createConversion(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Conversion.
createConversion(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Conversion.
createCovalentBindingFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CovalentBindingFeature.
createCovalentBindingFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CovalentBindingFeature.
createDegradation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Degradation.
createDegradation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Degradation.
createDeltaG(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DeltaG.
createDeltaG(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DeltaG.
createDna(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Dna.
createDna(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Dna.
createDnaReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaReference.
createDnaReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaReference.
createDnaRegion(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaRegion.
createDnaRegion(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaRegion.
createDnaRegionReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaRegionReference.
createDnaRegionReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaRegionReference.
createEntity(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Entity.
createEntity(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Entity.
createEntityFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityFeature.
createEntityFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityFeature.
createEntityForHomodimer(String, HashMap<String, SpeciesDocument.Species>, Vector, HashMap<String, PhysicalEntity>, HashMap<String, EntityReference>, SbmlDocument.Sbml, BioPAX, String) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
createEntityForSpecies(String, SbmlDocument.Sbml, BioPAX) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Makes a physical entity from CellDesigner species
createEntityForSpecies(String, SbmlDocument.Sbml, BioPAX, boolean) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
createEntityForSpecies(String, HashMap<String, SpeciesDocument.Species>, Vector, HashMap<String, PhysicalEntity>, HashMap<String, EntityReference>, SbmlDocument.Sbml, BioPAX, String) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
createEntityId(Entity) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Creates entity id
createEntityName(Entity) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Creates a name for entity pe
createEntityReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityReference.
createEntityReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityReference.
createEntityReferenceMap() - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
 
createEntityReferenceTypeVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityReferenceTypeVocabulary.
createEntityReferenceTypeVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityReferenceTypeVocabulary.
createEvidence(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Evidence.
createEvidence(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Evidence.
createEvidenceCodeVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EvidenceCodeVocabulary.
createEvidenceCodeVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EvidenceCodeVocabulary.
createExperimentalForm(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ExperimentalForm.
createExperimentalForm(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ExperimentalForm.
createExperimentalFormVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ExperimentalFormVocabulary.
createExperimentalFormVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ExperimentalFormVocabulary.
createFragmentFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of FragmentFeature.
createFragmentFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of FragmentFeature.
createGene(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Gene.
createGene(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Gene.
createGeneticInteraction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of GeneticInteraction.
createGeneticInteraction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of GeneticInteraction.
createGMTFromOCSANAOutput(String) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
createGraph() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph
 
createGraphDocument(Object) - Method in class fr.curie.BiNoM.celldesigner.lib.GraphDocumentFactory
 
createGraphDocument(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.lib.GraphDocumentFactory
 
createIndex(String) - Method in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
createIndexForBioPAX(BioPAX) - Method in class fr.curie.BiNoM.pathways.utils.acsn.DatabaseComparison
 
createIndexNodeHash() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
createInteraction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Interaction.
createInteraction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Interaction.
createInteractionVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of InteractionVocabulary.
createInteractionVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of InteractionVocabulary.
createKineticLawXML(String) - Static method in class fr.curie.BiNoM.pathways.utils.InsertCellDesignerParameters
 
createKPrime(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of KPrime.
createKPrime(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of KPrime.
createModificationFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ModificationFeature.
createModificationFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ModificationFeature.
createModulation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Modulation.
createModulation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Modulation.
createMolecularInteraction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of MolecularInteraction.
createMolecularInteraction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of MolecularInteraction.
createNameForComplex(Complex) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Create a name for a Complex.
createNeighborhoodSets - Class in fr.curie.BiNoM.cytoscape.analysis
 
createNeighborhoodSets() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.createNeighborhoodSets
 
createNeighborhoodSetsDialog - Class in fr.curie.BiNoM.cytoscape.analysis
 
CreateNestNetwork - Class in fr.curie.BiNoM.cytoscape.nestmanager
Create a new network composed of nests from networks selected in a list by NestUtils.selectNetworks
CreateNestNetwork() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.CreateNestNetwork
 
createNestNetwork(ArrayList<String>, TreeMap<String, CyNetwork>) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
createNetwork(PluginModel, CellDesignerPlugin, GraphDocument) - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkFactory
 
createNetwork(String, GraphDocument, VisualStyle, boolean, TaskMonitor) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkFactory
 
createNetwork(String, GraphDocument, VisualStyleDefinition, boolean, TaskMonitor) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkFactory
 
createNewCellDesignerFile(String, int, int) - Method in class fr.curie.BiNoM.pathways.utils.CellDesignerGenerator
 
createNewCompartment(String, String) - Method in class fr.curie.BiNoM.pathways.utils.CellDesignerGenerator
 
createNewProtein(String, String) - Method in class fr.curie.BiNoM.pathways.utils.CellDesignerGenerator
 
createNewSpecies(String, String) - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkFactory
 
createObject(String, String, BioPAX) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectFactory
 
createPathway(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Pathway.
createPathway(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Pathway.
createPathwayStep(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PathwayStep.
createPathwayStep(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PathwayStep.
createPhenotypeVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PhenotypeVocabulary.
createPhenotypeVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PhenotypeVocabulary.
createPhysicalEntity(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PhysicalEntity.
createPhysicalEntity(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PhysicalEntity.
createPoints() - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
createProtein(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Protein.
createProtein(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Protein.
createProteinReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ProteinReference.
createProteinReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ProteinReference.
createProteins(edu.rpi.cs.xgmml.GraphicNode[]) - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkFactory
 
createProvenance(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Provenance.
createProvenance(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Provenance.
createPublicationXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PublicationXref.
createPublicationXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PublicationXref.
createRelationshipTypeVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RelationshipTypeVocabulary.
createRelationshipTypeVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RelationshipTypeVocabulary.
createRelationshipXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RelationshipXref.
createRelationshipXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RelationshipXref.
createRna(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Rna.
createRna(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Rna.
createRnaReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaReference.
createRnaReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaReference.
createRnaRegion(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaRegion.
createRnaRegion(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaRegion.
createRnaRegionReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaRegionReference.
createRnaRegionReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaRegionReference.
createScore(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Score.
createScore(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Score.
createSecondaryIndex(String) - Method in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
createSequenceInterval(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceInterval.
createSequenceInterval(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceInterval.
createSequenceLocation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceLocation.
createSequenceLocation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceLocation.
createSequenceModificationVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceModificationVocabulary.
createSequenceModificationVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceModificationVocabulary.
createSequenceRegionVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceRegionVocabulary.
createSequenceRegionVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceRegionVocabulary.
createSequenceSite(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceSite.
createSequenceSite(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceSite.
createSetAttributes - Variable in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetVisuDialog
 
CreateSetIntersectionGraph - Class in fr.curie.BiNoM.cytoscape.utils
 
CreateSetIntersectionGraph() - Constructor for class fr.curie.BiNoM.cytoscape.utils.CreateSetIntersectionGraph
 
createSimpleSpecies(String, String) - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkFactory
 
createSmallMolecule(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SmallMolecule.
createSmallMolecule(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SmallMolecule.
createSmallMoleculeReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SmallMoleculeReference.
createSmallMoleculeReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SmallMoleculeReference.
createSpeciesAlias(String, String, float, float) - Method in class fr.curie.BiNoM.pathways.utils.CellDesignerGenerator
 
createSpeciesFromString(String, String, String, int, int) - Method in class fr.curie.BiNoM.pathways.utils.CellDesignerGenerator
 
createSpeciesMap(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
createStoichiometry(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Stoichiometry.
createStoichiometry(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Stoichiometry.
createTask(int[], StructureAnalysisUtils.Option) - Method in interface fr.curie.BiNoM.analysis.AbstractClusterNetworksTaskFactory
 
createTask(Graph, Vector) - Method in interface fr.curie.BiNoM.analysis.AbstractExcludeIntermediateNodesTaskFactory
 
createTask(int, int[], boolean, boolean) - Method in interface fr.curie.BiNoM.analysis.AbstractModularViewTaskFactory
 
createTask(File, URL, String, int[], BioPAXToCytoscapeConverter.Option, boolean) - Method in interface fr.curie.BiNoM.biopax.AbstractBioPAXImportTaskFactory
 
createTask(int[], StructureAnalysisUtils.Option) - Method in class fr.curie.BiNoM.celldesigner.analysis.ClusterNetworksTaskFactory
 
createTask(Graph, Vector) - Method in class fr.curie.BiNoM.celldesigner.analysis.ExcludeIntermediateNodesTaskFactory
 
createTask(int, int[], boolean, boolean) - Method in class fr.curie.BiNoM.celldesigner.analysis.ModularViewTaskFactory
 
createTask(File, URL, String, int[], BioPAXToCytoscapeConverter.Option, boolean) - Method in class fr.curie.BiNoM.celldesigner.biopax.BioPAXImportTaskFactory
 
createTask(int[], StructureAnalysisUtils.Option) - Method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTaskFactory
 
createTask(Graph, Vector) - Method in class fr.curie.BiNoM.cytoscape.analysis.ExcludeIntermediateNodesTaskFactory
 
createTask(int, int[], boolean, boolean) - Method in class fr.curie.BiNoM.cytoscape.analysis.ModularViewTaskFactory
 
createTask(File, URL, String, int[], BioPAXToCytoscapeConverter.Option, boolean) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTaskFactory
 
createTask(int[], StructureAnalysisUtils.Option) - Method in class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilterTaskFactory
 
createTempDirectory() - Static method in class fr.curie.BiNoM.pathways.navicell.WordPressBlogCreator
 
createTemplateReaction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TemplateReaction.
createTemplateReaction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TemplateReaction.
createTemplateReactionRegulation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TemplateReactionRegulation.
createTemplateReactionRegulation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TemplateReactionRegulation.
createTissueVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TissueVocabulary.
createTissueVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TissueVocabulary.
createTransport(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Transport.
createTransport(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Transport.
createTransportWithBiochemicalReaction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TransportWithBiochemicalReaction.
createTransportWithBiochemicalReaction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TransportWithBiochemicalReaction.
createUnificationXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of UnificationXref.
createUnificationXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of UnificationXref.
createUtilityClass(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of UtilityClass.
createUtilityClass(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of UtilityClass.
createUtilityId(UtilityClass) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Creates an id for utilityClass
createUtilityName(UtilityClass) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Creates a name for utilityClass object
createXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Xref.
createXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Xref.
CSML - Class in fr.curie.BiNoM.pathways.wrappers
 
CSML() - Constructor for class fr.curie.BiNoM.pathways.wrappers.CSML
 
CSMLImportFromFile - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
CSMLImportFromFile() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CSMLImportFromFile
 
CSMLImportTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
CSMLImportTask(File) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.CSMLImportTask
 
CSMLToCytoscapeConverter - Class in fr.curie.BiNoM.pathways
 
CSMLToCytoscapeConverter() - Constructor for class fr.curie.BiNoM.pathways.CSMLToCytoscapeConverter
 
cutFinalAmpersand(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
cutFirstLastNonVisibleSymbols(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
cutFirstNonVisibleSymbols(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
cutNameSpace(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
cutQuotes(String) - Static method in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
cutUri(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Convert string from the form # to simply
cw - Static variable in class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
cw - Static variable in class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 
cx - Static variable in class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
cx - Static variable in class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 
cy - Static variable in class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
cy - Static variable in class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 
CycleDecomposition - Class in fr.curie.BiNoM.celldesigner.analysis
 
CycleDecomposition(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.CycleDecomposition
 
CycleDecomposition - Class in fr.curie.BiNoM.cytoscape.analysis
 
CycleDecomposition() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.CycleDecomposition
 
CycleDecomposition(Graph, int) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
CycleDecompositionTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
CycleDecompositionTask(CellDesignerPlugin, GraphDocument) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.CycleDecompositionTask
 
CycleDecompositionTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
CycleDecompositionTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.CycleDecompositionTask
 
Cytoscape2BioPAX - Class in fr.curie.BiNoM.pathways.converters
 
Cytoscape2BioPAX() - Constructor for class fr.curie.BiNoM.pathways.converters.Cytoscape2BioPAX
 
Cytoscape2CellDesigner - Class in fr.curie.BiNoM.pathways.converters
 
Cytoscape2CellDesigner() - Constructor for class fr.curie.BiNoM.pathways.converters.Cytoscape2CellDesigner
 
Cytoscape2SBML - Class in fr.curie.BiNoM.pathways.converters
 
Cytoscape2SBML() - Constructor for class fr.curie.BiNoM.pathways.converters.Cytoscape2SBML
 
CytoscapeToBioPAXConverter - Class in fr.curie.BiNoM.pathways
Deprecated class.
CytoscapeToBioPAXConverter() - Constructor for class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter
 
CytoscapeToCellDesignerConverter - Class in fr.curie.BiNoM.pathways
Class used to export a part of CellDesigner file, using only species and reactions visualized in the current Cytoscape network
CytoscapeToCellDesignerConverter() - Constructor for class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter
 

D

database - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
The index with which the query is performed
DatabaseComparison - Class in fr.curie.BiNoM.pathways.utils.acsn
 
DatabaseComparison() - Constructor for class fr.curie.BiNoM.pathways.utils.acsn.DatabaseComparison
 
databaseCopyForPathAnalysis - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
Copy of the database to perform index path analysis
DataPathConsistencyAnalyzer - Class in fr.curie.BiNoM.pathways.analysis.structure
 
DataPathConsistencyAnalyzer() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
DataPathConsistencyAnalyzer.optCutSetData - Class in fr.curie.BiNoM.pathways.analysis.structure
Simple data structure to store optimal intervention sets data
DataPathConsistencyAnalyzer.optCutSetData(HashSet<String>, double) - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer.optCutSetData
 
DataPathConsistencyAnalyzer.optCutSetData(HashSet<String>, double, double, double) - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer.optCutSetData
 
dataSourceAdded(BiochemicalReaction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of dataSource has been added
dataSourceAdded(Catalysis, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of dataSource has been added
dataSourceAdded(ComplexAssembly, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of dataSource has been added
dataSourceAdded(Complex, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of dataSource has been added
dataSourceAdded(Control, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of dataSource has been added
dataSourceAdded(Conversion, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of dataSource has been added
dataSourceAdded(Degradation, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of dataSource has been added
dataSourceAdded(Dna, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of dataSource has been added
dataSourceAdded(DnaRegion, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of dataSource has been added
dataSourceAdded(Entity, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityListener
Called when a value of dataSource has been added
dataSourceAdded(Gene, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of dataSource has been added
dataSourceAdded(GeneticInteraction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of dataSource has been added
dataSourceAdded(Interaction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of dataSource has been added
dataSourceAdded(Modulation, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of dataSource has been added
dataSourceAdded(MolecularInteraction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of dataSource has been added
dataSourceAdded(Pathway, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of dataSource has been added
dataSourceAdded(PhysicalEntity, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of dataSource has been added
dataSourceAdded(Protein, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of dataSource has been added
dataSourceAdded(Rna, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of dataSource has been added
dataSourceAdded(RnaRegion, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of dataSource has been added
dataSourceAdded(SmallMolecule, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of dataSource has been added
dataSourceAdded(TemplateReaction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of dataSource has been added
dataSourceAdded(TemplateReactionRegulation, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of dataSource has been added
dataSourceAdded(Transport, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of dataSource has been added
dataSourceAdded(TransportWithBiochemicalReaction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of dataSource has been added
dataSourceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Entity
The Jena Property for dataSource
dataSourceRemoved(BiochemicalReaction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of dataSource has been removed
dataSourceRemoved(Catalysis, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of dataSource has been removed
dataSourceRemoved(ComplexAssembly, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of dataSource has been removed
dataSourceRemoved(Complex, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of dataSource has been removed
dataSourceRemoved(Control, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of dataSource has been removed
dataSourceRemoved(Conversion, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of dataSource has been removed
dataSourceRemoved(Degradation, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of dataSource has been removed
dataSourceRemoved(Dna, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of dataSource has been removed
dataSourceRemoved(DnaRegion, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of dataSource has been removed
dataSourceRemoved(Entity, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityListener
Called when a value of dataSource has been removed
dataSourceRemoved(Gene, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of dataSource has been removed
dataSourceRemoved(GeneticInteraction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of dataSource has been removed
dataSourceRemoved(Interaction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of dataSource has been removed
dataSourceRemoved(Modulation, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of dataSource has been removed
dataSourceRemoved(MolecularInteraction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of dataSource has been removed
dataSourceRemoved(Pathway, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of dataSource has been removed
dataSourceRemoved(PhysicalEntity, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of dataSource has been removed
dataSourceRemoved(Protein, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of dataSource has been removed
dataSourceRemoved(Rna, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of dataSource has been removed
dataSourceRemoved(RnaRegion, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of dataSource has been removed
dataSourceRemoved(SmallMolecule, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of dataSource has been removed
dataSourceRemoved(TemplateReaction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of dataSource has been removed
dataSourceRemoved(TemplateReactionRegulation, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of dataSource has been removed
dataSourceRemoved(Transport, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of dataSource has been removed
dataSourceRemoved(TransportWithBiochemicalReaction, Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of dataSource has been removed
dbChanged(PublicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when db has changed
dbChanged(RelationshipXref) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXrefListener
Called when db has changed
dbChanged(UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.UnificationXrefListener
Called when db has changed
dbChanged(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.XrefListener
Called when db has changed
dbProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Xref
The Jena Property for db
dbVersionChanged(PublicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when dbVersion has changed
dbVersionChanged(RelationshipXref) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXrefListener
Called when dbVersion has changed
dbVersionChanged(UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.UnificationXrefListener
Called when dbVersion has changed
dbVersionChanged(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.XrefListener
Called when dbVersion has changed
dbVersionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Xref
The Jena Property for dbVersion
decodeStructuredString(String) - Static method in class fr.curie.BiNoM.pathways.utils.SpeciesStructure
 
defaultActivityThreshold - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
defaultEdgeLineColor - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
defaultEdgeLineType - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
defaultEdgeSourceArrow - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
defaultEdgeTargetArrow - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
defaultNodeBorderColor - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
defaultNodeBorderLineStyle - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
defaultNodeBorderLineWidth - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
defaultNodeColor - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
defaultNodeShape - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
defaultNodeSize - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
defcomp_id - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
Degradation - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Degradation ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
DegradationImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Degradation Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
DegradationListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Degradation to receive notification when properties changed, added or removed.
degreeDistribution - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
degrees - Variable in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph
 
degrees - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
Delay - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
Delay - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
deleteInstance() - Static method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
deleteNestEdges(CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
DeltaG - Interface in fr.curie.BiNoM.pathways.biopax
Interface for DeltaG ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
deltaGAdded(BiochemicalReaction, DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of deltaG has been added
deltaGAdded(TransportWithBiochemicalReaction, DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of deltaG has been added
DeltaGImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of DeltaG Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
DeltaGListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.DeltaG to receive notification when properties changed, added or removed.
deltaGPrime0Changed(DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaGListener
Called when deltaGPrime0 has changed
deltaGPrime0Property - Static variable in interface fr.curie.BiNoM.pathways.biopax.DeltaG
The Jena Property for deltaGPrime0
deltaGProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
The Jena Property for deltaG
deltaGRemoved(BiochemicalReaction, DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of deltaG has been removed
deltaGRemoved(TransportWithBiochemicalReaction, DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of deltaG has been removed
deltaHAdded(BiochemicalReaction, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of deltaH has been added
deltaHAdded(TransportWithBiochemicalReaction, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of deltaH has been added
deltaHProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
The Jena Property for deltaH
deltaHRemoved(BiochemicalReaction, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of deltaH has been removed
deltaHRemoved(TransportWithBiochemicalReaction, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of deltaH has been removed
deltaSAdded(BiochemicalReaction, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of deltaS has been added
deltaSAdded(TransportWithBiochemicalReaction, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of deltaS has been added
deltaSProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
The Jena Property for deltaS
deltaSRemoved(BiochemicalReaction, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of deltaS has been removed
deltaSRemoved(TransportWithBiochemicalReaction, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of deltaS has been removed
describe() - Method in class fr.curie.BiNoM.cytoscape.plugin.BiNoMPlugin
Gives a description of this plugin.
DeselectInactivePaths() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
DeselectInconsistentNodes() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
DeselectInconsistentPaths() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
DestroyUnusedNetworksAsNest - Class in fr.curie.BiNoM.cytoscape.nestmanager
Propose a list of unused networks by the active nest network After selecting networks to be destroyed, ask confirmation
DestroyUnusedNetworksAsNest() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.DestroyUnusedNetworksAsNest
 
DestroyUnusedNetworksAsNestTask - Class in fr.curie.BiNoM.cytoscape.nestmanager
Destroy networks of the list
DestroyUnusedNetworksAsNestTask(ArrayList<String>) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.DestroyUnusedNetworksAsNestTask
 
detectSimpleSpeciesFromGeneList() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
determineRealValuedAttributes(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.GraphUtils
 
determineSizeOftheMap() - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
dialog - Static variable in class fr.curie.BiNoM.cytoscape.ain.ImportFromSimpleTextInfluenceFile
 
dialog - Static variable in class fr.curie.BiNoM.pathways.converters.SimpleTextInfluence2BioPAX
 
dialog1 - Static variable in class fr.curie.BiNoM.pathways.converters.SimpleTextInfluence2BioPAX
 
dialogCR - Static variable in class fr.curie.BiNoM.cytoscape.ain.ImportFromSimpleTextInfluenceFile
 
DIAMOND - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
Dijkstra(Graph, Node, Node, boolean, boolean, double) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
DijkstraAlgorithm(Graph, Node, Node, boolean, double) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
DijkstraAlgorithm(Graph, Node, Vector<Node>, boolean, double) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
DijkstraAlgorithmReturnIndexReverseOrder(Graph, Node, Vector<Node>, boolean, double) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
returns list of paths (as Vector) for each target separately
DijkstraProcedure(Graph, int, Vector<Integer>, double[], Vector<Vector<Integer>>, boolean, double) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
Principal Dijkstra procedure 2 for each vertex v in V[G] // Initializations 3 d[v] := infinity // Unknown distance function from s to v 4 previous[v] := undefined 5 d[s] := 0 // Distance from s to s 6 S := empty set // Set of all visited vertices 7 Q := V[G] // Set of all unvisited vertices 8 while Q is not an empty set // The algorithm itself 9 u := Extract_Min(Q) // Remove best vertex from priority queue 10 S := S union {u} // Mark it 'visited' 11 for each edge (u,v) outgoing from u 12 if d[u] + w(u,v) < d[v] // Relax (u,v) 13 d[v] := d[u] + w(u,v) 14 previous[v] := u
directed - Variable in class fr.curie.BiNoM.cytoscape.analysis.CalcCentrality
 
directedGraph - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
distance(ShortPathClustering.Cluster, ShortPathClustering.Cluster) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering
 
distances - Variable in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering
 
distinguishCompartments - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option
 
distinguishModifications - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option
 
distributionOfConnectedComponentSizes - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
divideInSections(String) - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
Dna - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Dna ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
DnaImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Dna Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
dnaList - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cut uris (after # separator) to 'dna' entities
DnaListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Dna to receive notification when properties changed, added or removed.
DnaReference - Interface in fr.curie.BiNoM.pathways.biopax
Interface for DnaReference ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
DnaReferenceImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of DnaReference Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
DnaReferenceListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.DnaReference to receive notification when properties changed, added or removed.
DnaRegion - Interface in fr.curie.BiNoM.pathways.biopax
Interface for DnaRegion ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
DnaRegionImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of DnaRegion Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
dnaRegionList - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cut uris (after # separator) to 'dnaRegion' entities
DnaRegionListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.DnaRegion to receive notification when properties changed, added or removed.
DnaRegionReference - Interface in fr.curie.BiNoM.pathways.biopax
Interface for DnaRegionReference ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
DnaRegionReferenceImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of DnaRegionReference Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
DnaRegionReferenceListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.DnaRegionReference to receive notification when properties changed, added or removed.
doMakeHiddenLevel2(String, String, int) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
doMergePngs(String, float, String, float, String, float, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
done() - Method in class fr.curie.BiNoM.pathways.utils.OptionParser
 
doQuery(BioPAXGraphQuery, int) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
Performs a query of queryType
doRemoveReactions(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
doScalePng(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
DoubleNetworkDifference - Class in fr.curie.BiNoM.cytoscape.netwop
 
DoubleNetworkDifference() - Constructor for class fr.curie.BiNoM.cytoscape.netwop.DoubleNetworkDifference
 
DoubleNetworkDifferenceDialog - Class in fr.curie.BiNoM.cytoscape.netwop
 
downloadToFile(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
downloadURL(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 

E

eclipseError(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
eclipseErrorln(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
eclipseParentErrorln(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
eclipseParentPrintln(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
eclipsePrint(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
eclipsePrintln(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
eCNumberAdded(BiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of eCNumber has been added
eCNumberAdded(TransportWithBiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of eCNumber has been added
eCNumberProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
The Jena Property for eCNumber
eCNumberRemoved(BiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of eCNumber has been removed
eCNumberRemoved(TransportWithBiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of eCNumber has been removed
Edge - Class in fr.curie.BiNoM.pathways.analysis.structure
Simple internal BiNoM implementation of Edge object.
Edge() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Edge
 
EDGE_ACTIVATION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_ATTR - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_ATTR - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_CATALYSIS - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_CATALYSIS_ACTIVATION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_CATALYSIS_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_CATALYSIS_UNKNOWN - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_CATALYSIS_UNKNOWN - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_CONTAINS - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_CONTROL_ACTIVATION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_CONTROL_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_CONTROL_UNKNOWN - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_geneticInteraction - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_INTERSECTION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_INTERSECTION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_LEFT - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_LEFT - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_MODIFIES - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_MODULATION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_MODULATION_ACTIVATION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_MODULATION_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_MODULATION_UNKNOWN - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_NEGATIVE_INFLUENCE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_NEXT - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_PHYSICAL_STIMULATION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_physicalInteraction - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_POSITIVE_INFLUENCE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_REFERENCE - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_RIGHT - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_RIGHT - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_SPECIESOF - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_STEP - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_TEMPLATEREACTIONREGULATION_ACTIVATION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_TEMPLATEREACTIONREGULATION_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_TEMPLATEREACTIONREGULATION_UNKNOWN - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
EDGE_TRANSCRIPTIONAL_ACTIVATION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_TRANSCRIPTIONAL_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_TRIGGER - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_UNKNOWN_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_UNKNOWN_NEGATIVE_INFLUENCE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_UNKNOWN_POSITIVE_INFLUENCE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EDGE_UNKNOWN_TRANSITION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
EdgeArrowType - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
Type of edge arrow (not used yet)
edgeAttr - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
EdgeHash - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
EdgeInfo - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
Some edge information
EdgeLabel - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
Edge label
edgeLineColorMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
edgeLineTypeMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
edges - Variable in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
Edges - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
edges - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
Map from edge ids to Edge objects
edgesConnectingSubGraphs(Graph, Graph, Graph, boolean) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
EdgesFromOtherNetwork - Class in fr.curie.BiNoM.cytoscape.analysis
 
EdgesFromOtherNetwork() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetwork
 
EdgesFromOtherNetworkDialog - Class in fr.curie.BiNoM.cytoscape.analysis
 
EdgesFromOtherNetworkTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
EdgesFromOtherNetworkTask(CyNetwork[], CyNetwork) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkTask
 
edgesLinkingNodes(GraphPerspective, HashSet<CyNode>) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
edgeSourceArrowMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
edgeTargetArrowMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
Element - Class in fr.curie.BiNoM.pathways.analysis.structure
Abstract class for attributed graph elements (Nodes, Edges, HyperEdges, etc.)
Element() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Element
 
elemNodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
set of unique nodes from elementary paths
elemPaths - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
elementary paths, set of paths sinking to target nodes
ELLIPSE - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
EnrichedNodePaths - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
EnrichedNodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
entities - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
entities - Static variable in class fr.curie.BiNoM.pathways.wrappers.CellDesigner
Map from Species Ids to all CellDesigner objects
entities - Variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
entitiesForToken(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
Entity - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Entity ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
EntityFeature - Interface in fr.curie.BiNoM.pathways.biopax
Interface for EntityFeature ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
entityFeatureAdded(DnaReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of entityFeature has been added
entityFeatureAdded(DnaRegionReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of entityFeature has been added
entityFeatureAdded(EntityReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of entityFeature has been added
entityFeatureAdded(ProteinReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of entityFeature has been added
entityFeatureAdded(RnaReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of entityFeature has been added
entityFeatureAdded(RnaRegionReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of entityFeature has been added
entityFeatureAdded(SmallMoleculeReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of entityFeature has been added
EntityFeatureImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of EntityFeature Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
EntityFeatureListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.EntityFeature to receive notification when properties changed, added or removed.
entityFeatureProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityReference
The Jena Property for entityFeature
entityFeatureRemoved(DnaReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of entityFeature has been removed
entityFeatureRemoved(DnaRegionReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of entityFeature has been removed
entityFeatureRemoved(EntityReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of entityFeature has been removed
entityFeatureRemoved(ProteinReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of entityFeature has been removed
entityFeatureRemoved(RnaReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of entityFeature has been removed
entityFeatureRemoved(RnaRegionReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of entityFeature has been removed
entityFeatureRemoved(SmallMoleculeReference, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of entityFeature has been removed
EntityImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Entity Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
EntityListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Entity to receive notification when properties changed, added or removed.
EntityReference - Interface in fr.curie.BiNoM.pathways.biopax
Interface for EntityReference ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
entityReferenceChanged(Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when entityReference has changed
entityReferenceChanged(DnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when entityReference has changed
entityReferenceChanged(Protein) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when entityReference has changed
entityReferenceChanged(Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when entityReference has changed
entityReferenceChanged(RnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when entityReference has changed
entityReferenceChanged(SmallMolecule) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when entityReference has changed
EntityReferenceImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of EntityReference Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
EntityReferenceListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.EntityReference to receive notification when properties changed, added or removed.
entityReferenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Dna
The Jena Property for entityReference
entityReferenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
The Jena Property for entityReference
entityReferenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Protein
The Jena Property for entityReference
entityReferenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Rna
The Jena Property for entityReference
entityReferenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
The Jena Property for entityReference
entityReferenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
The Jena Property for entityReference
entityReferences - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
entityReferenceTypeChanged(DnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when entityReferenceType has changed
entityReferenceTypeChanged(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when entityReferenceType has changed
entityReferenceTypeChanged(EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when entityReferenceType has changed
entityReferenceTypeChanged(ProteinReference) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when entityReferenceType has changed
entityReferenceTypeChanged(RnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when entityReferenceType has changed
entityReferenceTypeChanged(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when entityReferenceType has changed
entityReferenceTypeChanged(SmallMoleculeReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when entityReferenceType has changed
entityReferenceTypeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityReference
The Jena Property for entityReferenceType
EntityReferenceTypeVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for EntityReferenceTypeVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
EntityReferenceTypeVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of EntityReferenceTypeVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
EntityReferenceTypeVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabulary to receive notification when properties changed, added or removed.
entitySynonym - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
Map from node names and synonyms to the Vector of Node objects
entityToReferenceUris - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
Map from entity uris to reference uris
entityXREF - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
Map from node xrefs to the Vector of Node objects
epilogue() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
epilogue() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserFrame
 
equals(Object) - Method in class fr.curie.BiNoM.pathways.utils.Pair
 
errorWeigth - Static variable in class fr.curie.BiNoM.cytoscape.influence.FromToNodes
 
estimate(CyNetwork, NetworkOperation.Estimator) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkDifference
 
estimate(CyNetwork, NetworkOperation.Estimator) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkIntersection
 
estimate(CyNetwork, NetworkOperation.Estimator) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation
 
estimate(CyNetwork, NetworkOperation.Estimator) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkUnion
 
eval(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkDifference
 
eval(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkIntersection
 
eval(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation
 
eval(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkUnion
 
Evidence - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Evidence ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
evidenceAdded(BindingFeature, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when a value of evidence has been added
evidenceAdded(BiochemicalPathwayStep, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of evidence has been added
evidenceAdded(BiochemicalReaction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of evidence has been added
evidenceAdded(Catalysis, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of evidence has been added
evidenceAdded(ComplexAssembly, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of evidence has been added
evidenceAdded(Complex, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of evidence has been added
evidenceAdded(Control, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of evidence has been added
evidenceAdded(Conversion, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of evidence has been added
evidenceAdded(CovalentBindingFeature, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when a value of evidence has been added
evidenceAdded(Degradation, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of evidence has been added
evidenceAdded(Dna, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of evidence has been added
evidenceAdded(DnaReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of evidence has been added
evidenceAdded(DnaRegion, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of evidence has been added
evidenceAdded(DnaRegionReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of evidence has been added
evidenceAdded(EntityFeature, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeatureListener
Called when a value of evidence has been added
evidenceAdded(Entity, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityListener
Called when a value of evidence has been added
evidenceAdded(EntityReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of evidence has been added
evidenceAdded(FragmentFeature, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.FragmentFeatureListener
Called when a value of evidence has been added
evidenceAdded(Gene, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of evidence has been added
evidenceAdded(GeneticInteraction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of evidence has been added
evidenceAdded(Interaction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of evidence has been added
evidenceAdded(ModificationFeature, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when a value of evidence has been added
evidenceAdded(Modulation, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of evidence has been added
evidenceAdded(MolecularInteraction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of evidence has been added
evidenceAdded(Pathway, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of evidence has been added
evidenceAdded(PathwayStep, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStepListener
Called when a value of evidence has been added
evidenceAdded(PhysicalEntity, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of evidence has been added
evidenceAdded(Protein, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of evidence has been added
evidenceAdded(ProteinReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of evidence has been added
evidenceAdded(Rna, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of evidence has been added
evidenceAdded(RnaReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of evidence has been added
evidenceAdded(RnaRegion, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of evidence has been added
evidenceAdded(RnaRegionReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of evidence has been added
evidenceAdded(SmallMolecule, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of evidence has been added
evidenceAdded(SmallMoleculeReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of evidence has been added
evidenceAdded(TemplateReaction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of evidence has been added
evidenceAdded(TemplateReactionRegulation, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of evidence has been added
evidenceAdded(Transport, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of evidence has been added
evidenceAdded(TransportWithBiochemicalReaction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of evidence has been added
evidenceCodeAdded(Evidence, EvidenceCodeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceListener
Called when a value of evidenceCode has been added
evidenceCodeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Evidence
The Jena Property for evidenceCode
evidenceCodeRemoved(Evidence, EvidenceCodeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceListener
Called when a value of evidenceCode has been removed
EvidenceCodeVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for EvidenceCodeVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
EvidenceCodeVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of EvidenceCodeVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
EvidenceCodeVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabulary to receive notification when properties changed, added or removed.
EvidenceImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Evidence Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
EvidenceListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Evidence to receive notification when properties changed, added or removed.
evidenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Entity
The Jena Property for evidence
evidenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
The Jena Property for evidence
evidenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityReference
The Jena Property for evidence
evidenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
The Jena Property for evidence
evidenceRemoved(BindingFeature, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when a value of evidence has been removed
evidenceRemoved(BiochemicalPathwayStep, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of evidence has been removed
evidenceRemoved(BiochemicalReaction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of evidence has been removed
evidenceRemoved(Catalysis, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of evidence has been removed
evidenceRemoved(ComplexAssembly, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of evidence has been removed
evidenceRemoved(Complex, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of evidence has been removed
evidenceRemoved(Control, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of evidence has been removed
evidenceRemoved(Conversion, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of evidence has been removed
evidenceRemoved(CovalentBindingFeature, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when a value of evidence has been removed
evidenceRemoved(Degradation, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of evidence has been removed
evidenceRemoved(Dna, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of evidence has been removed
evidenceRemoved(DnaReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of evidence has been removed
evidenceRemoved(DnaRegion, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of evidence has been removed
evidenceRemoved(DnaRegionReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of evidence has been removed
evidenceRemoved(EntityFeature, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeatureListener
Called when a value of evidence has been removed
evidenceRemoved(Entity, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityListener
Called when a value of evidence has been removed
evidenceRemoved(EntityReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of evidence has been removed
evidenceRemoved(FragmentFeature, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.FragmentFeatureListener
Called when a value of evidence has been removed
evidenceRemoved(Gene, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of evidence has been removed
evidenceRemoved(GeneticInteraction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of evidence has been removed
evidenceRemoved(Interaction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of evidence has been removed
evidenceRemoved(ModificationFeature, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when a value of evidence has been removed
evidenceRemoved(Modulation, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of evidence has been removed
evidenceRemoved(MolecularInteraction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of evidence has been removed
evidenceRemoved(Pathway, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of evidence has been removed
evidenceRemoved(PathwayStep, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStepListener
Called when a value of evidence has been removed
evidenceRemoved(PhysicalEntity, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of evidence has been removed
evidenceRemoved(Protein, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of evidence has been removed
evidenceRemoved(ProteinReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of evidence has been removed
evidenceRemoved(Rna, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of evidence has been removed
evidenceRemoved(RnaReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of evidence has been removed
evidenceRemoved(RnaRegion, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of evidence has been removed
evidenceRemoved(RnaRegionReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of evidence has been removed
evidenceRemoved(SmallMolecule, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of evidence has been removed
evidenceRemoved(SmallMoleculeReference, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of evidence has been removed
evidenceRemoved(TemplateReaction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of evidence has been removed
evidenceRemoved(TemplateReactionRegulation, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of evidence has been removed
evidenceRemoved(Transport, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of evidence has been removed
evidenceRemoved(TransportWithBiochemicalReaction, Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of evidence has been removed
exceptionNode - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Exception node list: correspond to rows of the original matrix having a single '1' value.
ExcludeIntermediateNodes - Class in fr.curie.BiNoM.celldesigner.analysis
 
ExcludeIntermediateNodes(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.ExcludeIntermediateNodes
 
ExcludeIntermediateNodes - Class in fr.curie.BiNoM.cytoscape.analysis
 
ExcludeIntermediateNodes() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ExcludeIntermediateNodes
 
ExcludeIntermediateNodes(Graph, Vector, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
ExcludeIntermediateNodesDialog - Class in fr.curie.BiNoM.analysis
 
ExcludeIntermediateNodesTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
ExcludeIntermediateNodesTask(PluginModel, CellDesignerPlugin, Graph, Vector) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.ExcludeIntermediateNodesTask
 
ExcludeIntermediateNodesTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
ExcludeIntermediateNodesTask(Graph, Vector) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ExcludeIntermediateNodesTask
 
ExcludeIntermediateNodesTaskFactory - Class in fr.curie.BiNoM.celldesigner.analysis
 
ExcludeIntermediateNodesTaskFactory - Class in fr.curie.BiNoM.cytoscape.analysis
 
ExcludeIntermediateNodesTaskFactory() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ExcludeIntermediateNodesTaskFactory
 
excludeSmallMolecules - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
If false, all smallMolecules are excluded in queries
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.ClusterNetworksTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.ConnectedComponentsTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.CycleDecompositionTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.ExcludeIntermediateNodesTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.ExtractReactionNetworkTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.LinearizeNetworkTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.MaterialComponentsTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.ModularViewTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.MonoMolecularReactionsAsEdgesTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.PruneGraphTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.analysis.StronglyConnectedComponentsTask
 
execute() - Method in class fr.curie.BiNoM.celldesigner.biopax.BioPAXImportTask
 
execute() - Method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTask
 
execute() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExcludeIntermediateNodesTask
 
execute() - Method in class fr.curie.BiNoM.cytoscape.analysis.ModularViewTask
 
execute() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTask
 
execute() - Method in class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilterTask
 
execute() - Method in interface fr.curie.BiNoM.lib.AbstractTask
 
executeTask(Task) - Static method in class fr.curie.BiNoM.cytoscape.lib.TaskManager
 
expandSetsOfLists_ExpandSets(String, String, String) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
expandSetsOfLists_SplitSets(String, String, String) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
experimentalFeatureAdded(ExperimentalForm, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormListener
Called when a value of experimentalFeature has been added
experimentalFeatureProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
The Jena Property for experimentalFeature
experimentalFeatureRemoved(ExperimentalForm, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormListener
Called when a value of experimentalFeature has been removed
ExperimentalForm - Interface in fr.curie.BiNoM.pathways.biopax
Interface for ExperimentalForm ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
experimentalFormAdded(Evidence, ExperimentalForm) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceListener
Called when a value of experimentalForm has been added
experimentalFormDescriptionAdded(ExperimentalForm, ExperimentalFormVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormListener
Called when a value of experimentalFormDescription has been added
experimentalFormDescriptionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
The Jena Property for experimentalFormDescription
experimentalFormDescriptionRemoved(ExperimentalForm, ExperimentalFormVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormListener
Called when a value of experimentalFormDescription has been removed
experimentalFormEntityAdded(ExperimentalForm, Gene) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormListener
Called when a value of experimentalFormEntity has been added
experimentalFormEntityAdded(ExperimentalForm, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormListener
Called when a value of experimentalFormEntity has been added
experimentalFormEntityProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
The Jena Property for experimentalFormEntity
experimentalFormEntityRemoved(ExperimentalForm, Gene) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormListener
Called when a value of experimentalFormEntity has been removed
experimentalFormEntityRemoved(ExperimentalForm, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormListener
Called when a value of experimentalFormEntity has been removed
ExperimentalFormImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of ExperimentalForm Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ExperimentalFormListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.ExperimentalForm to receive notification when properties changed, added or removed.
experimentalFormProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Evidence
The Jena Property for experimentalForm
experimentalFormRemoved(Evidence, ExperimentalForm) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceListener
Called when a value of experimentalForm has been removed
ExperimentalFormVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for ExperimentalFormVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ExperimentalFormVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of ExperimentalFormVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ExperimentalFormVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabulary to receive notification when properties changed, added or removed.
exportCellDesignerNotes() - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
extractAllStringBetween(String, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
extractAttributesFromNotes(String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
extractAttributesFromNotes(Notes) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
extractAttributesFromNotes(CelldesignerNotes) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
extractAttributesFromNotes(String) - Static method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
extractBioGridMammalianNetwork() - Static method in class fr.curie.BiNoM.pathways.utils.GeneticInteractionNetworks
 
extractCellDesignerNotes - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
extractCellDesignerNotes() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotes
 
extractCellDesignerNotesDialog - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
extractCellDesignerNotesDialog() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesDialog
 
extractCellDesignerNotesTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
extractCellDesignerNotesTask(String, extractCellDesignerNotesTask.extractingNotesOptions) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask
 
extractCellDesignerNotesTask.extractingNotesOptions - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
extractCellDesignerNotesTask.extractingNotesOptions() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask.extractingNotesOptions
 
extractClosestNodes(Set, double[], HashSet<Integer>, Vector, double) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
Sub-routine for Dijkstra algorithm search for an items with minimum d[item] and removes from Q
extractDistanceSubMatrix(int[][], Vector<Integer>) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
extractedNetwork - Variable in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
extractFolderName(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
extractFromModel(Model, Graph, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
From all elements in graph BIOPAX_URI attribute values are used to extract a part of the source
extractFromModel(Model, Graph) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
 
extractFromModel(Model, Vector, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
 
extractFromModel(Model, GraphDocument, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
 
extractFromModel(Model, GraphDocument) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
 
extractGenomePosition(String) - Static method in class fr.curie.BiNoM.pathways.test.AgilentCGHMapping
 
extractGlobalModifier(String, Vector<String>) - Static method in class fr.curie.BiNoM.pathways.utils.SpeciesStructure
 
extractGMTFromCellDesigner(String) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
ExtractGMTFromCellDesigner - Class in fr.curie.BiNoM.pathways.utils
 
ExtractGMTFromCellDesigner() - Constructor for class fr.curie.BiNoM.pathways.utils.ExtractGMTFromCellDesigner
 
extractGMTFromCellDesigner(SbmlDocument, String) - Method in class fr.curie.BiNoM.pathways.utils.ExtractGMTFromCellDesigner
 
extractHUGO(String) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
extractNodes(ArrayList<Integer>, ArrayList<Integer>) - Method in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
extractProteinNamesFromNodeName(String) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
extractProteinNamesFromNodeNames(Vector<Node>) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
extractPubMedIds(Graph) - Method in class fr.curie.BiNoM.pathways.utils.acsn.DatabaseComparison
 
extractPubMedReferenceFromComment(String) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Extracts pubmed ids from a string in the form PMID: xxxxxx and creates publicationXref list
ExtractReactionNetwork - Class in fr.curie.BiNoM.celldesigner.analysis
 
ExtractReactionNetwork(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.ExtractReactionNetwork
 
ExtractReactionNetwork - Class in fr.curie.BiNoM.cytoscape.analysis
 
ExtractReactionNetwork() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetwork
 
ExtractReactionNetwork(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
From arbitrary interface extract standard Reaction Network interface
ExtractReactionNetworkTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
ExtractReactionNetworkTask(CellDesignerPlugin, GraphDocument) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.ExtractReactionNetworkTask
 
ExtractReactionNetworkTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
ExtractReactionNetworkTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetworkTask
 
extractReactionParts(String, StringBuffer, StringBuffer, StringBuffer) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
extractReactionParts(String, StringBuffer, StringBuffer, StringBuffer) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
extractReactionParts_(String, StringBuffer, StringBuffer, StringBuffer) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
ExtractSubnetwork - Class in fr.curie.BiNoM.cytoscape.analysis
 
ExtractSubnetwork() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetwork
 
extractSubnetwork(int) - Method in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
ExtractSubnetworkDialog - Class in fr.curie.BiNoM.cytoscape.analysis
 
ExtractSubnetworkTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
ExtractSubnetworkTask(GraphDocument, Vector<String>, StructureAnalysisUtils.Option, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetworkTask
 
extractURIwithAllLinks(Model, Vector, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
Extract a part of model which is necessary to define all things with uris

F

factorial(int) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Calculate the factorial of a given number
families - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
families - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
featureAdded(Complex, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of feature has been added
featureAdded(Dna, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of feature has been added
featureAdded(DnaRegion, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of feature has been added
featureAdded(PhysicalEntity, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of feature has been added
featureAdded(Protein, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of feature has been added
featureAdded(Rna, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of feature has been added
featureAdded(RnaRegion, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of feature has been added
featureAdded(SmallMolecule, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of feature has been added
featureAdded(SmallMolecule, BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of feature has been added
featureLocationAdded(BindingFeature, SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when a value of featureLocation has been added
featureLocationAdded(CovalentBindingFeature, SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when a value of featureLocation has been added
featureLocationAdded(EntityFeature, SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeatureListener
Called when a value of featureLocation has been added
featureLocationAdded(FragmentFeature, SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.FragmentFeatureListener
Called when a value of featureLocation has been added
featureLocationAdded(ModificationFeature, SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when a value of featureLocation has been added
featureLocationProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
The Jena Property for featureLocation
featureLocationRemoved(BindingFeature, SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when a value of featureLocation has been removed
featureLocationRemoved(CovalentBindingFeature, SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when a value of featureLocation has been removed
featureLocationRemoved(EntityFeature, SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeatureListener
Called when a value of featureLocation has been removed
featureLocationRemoved(FragmentFeature, SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.FragmentFeatureListener
Called when a value of featureLocation has been removed
featureLocationRemoved(ModificationFeature, SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when a value of featureLocation has been removed
featureLocationTypeAdded(BindingFeature, SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when a value of featureLocationType has been added
featureLocationTypeAdded(CovalentBindingFeature, SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when a value of featureLocationType has been added
featureLocationTypeAdded(EntityFeature, SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeatureListener
Called when a value of featureLocationType has been added
featureLocationTypeAdded(FragmentFeature, SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.FragmentFeatureListener
Called when a value of featureLocationType has been added
featureLocationTypeAdded(ModificationFeature, SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when a value of featureLocationType has been added
featureLocationTypeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
The Jena Property for featureLocationType
featureLocationTypeRemoved(BindingFeature, SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when a value of featureLocationType has been removed
featureLocationTypeRemoved(CovalentBindingFeature, SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when a value of featureLocationType has been removed
featureLocationTypeRemoved(EntityFeature, SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeatureListener
Called when a value of featureLocationType has been removed
featureLocationTypeRemoved(FragmentFeature, SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.FragmentFeatureListener
Called when a value of featureLocationType has been removed
featureLocationTypeRemoved(ModificationFeature, SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when a value of featureLocationType has been removed
featureProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
The Jena Property for feature
featureRemoved(Complex, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of feature has been removed
featureRemoved(Dna, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of feature has been removed
featureRemoved(DnaRegion, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of feature has been removed
featureRemoved(PhysicalEntity, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of feature has been removed
featureRemoved(Protein, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of feature has been removed
featureRemoved(Rna, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of feature has been removed
featureRemoved(RnaRegion, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of feature has been removed
featureRemoved(SmallMolecule, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of feature has been removed
featureRemoved(SmallMolecule, BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of feature has been removed
fieldNames - Variable in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
fieldNumByName(String) - Method in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
file - Variable in class fr.curie.BiNoM.biopax.BioPAXImportBaseTask
 
filename - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Name of CellDesigner file
fileName - Variable in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
filename - Variable in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
fileNameGeneList - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
fileNameIn - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
fileNameOut - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
fileNameReactionsToKeep - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
fileNameReferenceGraph - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
fileNameSpeciesToKeep - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
fileOption(String, String) - Method in class fr.curie.BiNoM.pathways.utils.OptionParser
 
fileRequiredOption(String, String) - Method in class fr.curie.BiNoM.pathways.utils.OptionParser
 
fillActiveNodesList() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
fillContent() - Method in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogFamily
 
fillIdentifiers(ModifyCellDesignerNotes.AnnotationSection, String) - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
fillPathList() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
fillPathMatrix(ArrayList<Path>) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Fill a matrix of integers with elementary paths data.
fillTheData() - Method in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerDialog
Fill the data for the different elements of the interface.
fillTheData() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerBootstrapDialog
 
fillTheData() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerDialog
 
fillTheData() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
filterIDs(BioPAX, GraphDocument) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter
 
filterIDs(BioPAX, Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter
 
filterIDs(SbmlDocument, GraphDocument) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter
 
filterIDs(SbmlDocument, Vector, Vector, Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter
 
filterIDsCompleteReactions(SbmlDocument, Vector, Vector, Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter
 
filterPathwaySteps(BioPAX, HashMap, HashMap, HashMap) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter
 
findAllAliasesForSpecies(SbmlDocument.Sbml, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Finds all CellDesigner species aliases
findAllMembers(String, Vector) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
findAllMembers(String, Vector) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
findAllMembers_(String, Vector) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
FindAllPaths(Graph, Node, Set<Node>, boolean, double) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
Note: searchRadius here is the number of edges from source (edge weights are not considered)
FindAllPaths(Graph, Node, Set<Node>, boolean, double, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
findBioPAXSpeciesAndReactions(Vector, Vector) - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportTask
 
FindCommonNodes - Class in fr.curie.BiNoM.cytoscape.nestmanager
Create an belonging matrix for every node in module Complete it by node size and frequency in modules Delete and create intersection edges containing number of common nodes Put number of nodes in node attribute Put number of common nodes in edge attributes
FindCommonNodes() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.FindCommonNodes
 
findIndependentSpecies() - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Procedure of grouping physicalEntityParticipants into BioPAXSpecies (chemical species)
findKeggLinks(String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ConnectionToDatabases
 
findLinksReactome(String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ConnectionToDatabases
 
findLinksToAtlasOfOncology(String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ConnectionToDatabases
 
findMinimalHittingSet(int, String) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
findPaths() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
findPaths(GraphDocument, Vector<String>, Vector<String>, StructureAnalysisUtils.Option) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
 
findReactionRegulators(Graph, String, String[]) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
findReactionRegulators(Graph, Set<String>, String[]) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
findSBMLSpeciesAndReactions(SbmlDocument, Vector, Vector, Vector, Vector) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
findSet(String) - Method in class fr.curie.BiNoM.pathways.utils.GMTFile
 
findStringInVectorBySubstring(Vector<String>, String) - Static method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
fixedNodeList - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
flipDiagram(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
flipPosition(CelldesignerLinkAnchorDocument.CelldesignerLinkAnchor.Position.Enum) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
fontSize - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
fontSize - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
formatAnnotation - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask.extractingNotesOptions
 
formatAnnotation - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
formatHitSetSB() - Method in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Final format for hit set list.
FormatProteinNotes - Class in fr.curie.BiNoM.pathways.navicell
 
FormatProteinNotes(Set<String>, ProduceClickableMap.AtlasInfo, String[][], String) - Constructor for class fr.curie.BiNoM.pathways.navicell.FormatProteinNotes
 
forwardEnabled() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserFrame
 
foundEntities - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
foundGenes - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
fr.curie.BiNoM.analysis - package fr.curie.BiNoM.analysis
 
fr.curie.BiNoM.biopax - package fr.curie.BiNoM.biopax
 
fr.curie.BiNoM.biopax.propedit - package fr.curie.BiNoM.biopax.propedit
 
fr.curie.BiNoM.celldesigner.analysis - package fr.curie.BiNoM.celldesigner.analysis
 
fr.curie.BiNoM.celldesigner.biopax - package fr.curie.BiNoM.celldesigner.biopax
 
fr.curie.BiNoM.celldesigner.biopax.propedit - package fr.curie.BiNoM.celldesigner.biopax.propedit
 
fr.curie.BiNoM.celldesigner.lib - package fr.curie.BiNoM.celldesigner.lib
 
fr.curie.BiNoM.celldesigner.plugin - package fr.curie.BiNoM.celldesigner.plugin
 
fr.curie.BiNoM.celldesigner.plugin2 - package fr.curie.BiNoM.celldesigner.plugin2
 
fr.curie.BiNoM.celldesigner.sample - package fr.curie.BiNoM.celldesigner.sample
 
fr.curie.BiNoM.cytoscape.ain - package fr.curie.BiNoM.cytoscape.ain
 
fr.curie.BiNoM.cytoscape.analysis - package fr.curie.BiNoM.cytoscape.analysis
 
fr.curie.BiNoM.cytoscape.biopax - package fr.curie.BiNoM.cytoscape.biopax
 
fr.curie.BiNoM.cytoscape.biopax.propedit - package fr.curie.BiNoM.cytoscape.biopax.propedit
 
fr.curie.BiNoM.cytoscape.biopax.query - package fr.curie.BiNoM.cytoscape.biopax.query
 
fr.curie.BiNoM.cytoscape.celldesigner - package fr.curie.BiNoM.cytoscape.celldesigner
 
fr.curie.BiNoM.cytoscape.influence - package fr.curie.BiNoM.cytoscape.influence
 
fr.curie.BiNoM.cytoscape.lib - package fr.curie.BiNoM.cytoscape.lib
 
fr.curie.BiNoM.cytoscape.nestmanager - package fr.curie.BiNoM.cytoscape.nestmanager
 
fr.curie.BiNoM.cytoscape.netwop - package fr.curie.BiNoM.cytoscape.netwop
 
fr.curie.BiNoM.cytoscape.plugin - package fr.curie.BiNoM.cytoscape.plugin
Cytoscape plugins
fr.curie.BiNoM.cytoscape.sbml - package fr.curie.BiNoM.cytoscape.sbml
 
fr.curie.BiNoM.cytoscape.utils - package fr.curie.BiNoM.cytoscape.utils
 
fr.curie.BiNoM.lib - package fr.curie.BiNoM.lib
 
fr.curie.BiNoM.pathways - package fr.curie.BiNoM.pathways
 
fr.curie.BiNoM.pathways.analysis.structure - package fr.curie.BiNoM.pathways.analysis.structure
Tools for structural analysis of biological graphs
fr.curie.BiNoM.pathways.biopax - package fr.curie.BiNoM.pathways.biopax
 
fr.curie.BiNoM.pathways.coloring - package fr.curie.BiNoM.pathways.coloring
 
fr.curie.BiNoM.pathways.converters - package fr.curie.BiNoM.pathways.converters
 
fr.curie.BiNoM.pathways.navicell - package fr.curie.BiNoM.pathways.navicell
 
fr.curie.BiNoM.pathways.test - package fr.curie.BiNoM.pathways.test
 
fr.curie.BiNoM.pathways.test.examples - package fr.curie.BiNoM.pathways.test.examples
 
fr.curie.BiNoM.pathways.utils - package fr.curie.BiNoM.pathways.utils
 
fr.curie.BiNoM.pathways.utils.acsn - package fr.curie.BiNoM.pathways.utils.acsn
 
fr.curie.BiNoM.pathways.wrappers - package fr.curie.BiNoM.pathways.wrappers
 
FragmentFeature - Interface in fr.curie.BiNoM.pathways.biopax
Interface for FragmentFeature ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
FragmentFeatureImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of FragmentFeature Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
FragmentFeatureListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.FragmentFeature to receive notification when properties changed, added or removed.
FromToNodes - Class in fr.curie.BiNoM.cytoscape.influence
In menu, this class selects nodes and edges between 2 lists of nodes by intersection of 2 sets made get by descending and ascending the graph This class is also used as up class for other menu classes providing input of reach parameter,formatted output of arrays and two lists node dialog
FromToNodes() - Constructor for class fr.curie.BiNoM.cytoscape.influence.FromToNodes
 
FULL_INDEX_CONVERSION - Static variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
Mode of conversion: from BioPAX to full index (see BiNoM documentation)

G

Gene - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Gene ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
GeneImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Gene Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
geneList - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
GeneListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Gene to receive notification when properties changed, added or removed.
generateAllCombinations(Vector<String>, Vector<Vector<String>>, Vector<String>, Vector<HashSet<String>>, String, int) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
generateAllPairwiseGMT(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
generateMassActionLaw(Reaction, HashMap) - Static method in class fr.curie.BiNoM.pathways.utils.InsertCellDesignerParameters
 
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 for BioPAX objects from a file.
generatePathActivitiesReport() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
generateReadableNamesForReactionsAndSpecies - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
generateReport() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
generateSample(Vector<Integer>, boolean, Vector<String>, Vector<Integer>) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
generateSampling(int) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
generateSamplingConserveDegreeDistribution(int) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
generateSetsFromRankedLists(int) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
generateTags() - Method in class fr.curie.BiNoM.pathways.BioPAXToCellDesignerConverter
 
generateUniqueID(String, HashMap) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Adds # symbols until the id is unique
genericUtilityName - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Names of utilities
genes - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
GeneticInteraction - Interface in fr.curie.BiNoM.pathways.biopax
Interface for GeneticInteraction ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
GeneticInteractionImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of GeneticInteraction Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
GeneticInteractionListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.GeneticInteraction to receive notification when properties changed, added or removed.
GeneticInteractionNetworks - Class in fr.curie.BiNoM.pathways.utils
 
GeneticInteractionNetworks() - Constructor for class fr.curie.BiNoM.pathways.utils.GeneticInteractionNetworks
 
geneTypes - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
get(String, String, BioPAXAttrDescProto.Type) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProtoFactory
 
get(String, String, BioPAXAttrDescProto.Type, BioPAXAttrDescProto.SubType) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProtoFactory
 
getAbsoluteRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Gets the 'absoluteRegion' property value
getAbsoluteRegion() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getAbsoluteRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Gets the 'absoluteRegion' property value
getAbsoluteRegion() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getAccessionNumberTable() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
getAccNumberFileName() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
getActivityDistribution() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
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
 
getAlias(SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
getAllAttributeNames(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.GraphUtils
 
getAllBindingFeature(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of BindingFeature for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#BindingFeature
getAllBiochemicalPathwayStep(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of BiochemicalPathwayStep for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#BiochemicalPathwayStep
getAllBiochemicalReaction(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of BiochemicalReaction for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#BiochemicalReaction
getAllBioSource(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of BioSource for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#BioSource
getAllCatalysis(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Catalysis for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Catalysis
getAllCellularLocationVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of CellularLocationVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#CellularLocationVocabulary
getAllCellVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of CellVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#CellVocabulary
getAllChemicalStructure(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of ChemicalStructure for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#ChemicalStructure
getAllCompartments() - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
 
getAllComplex(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Complex for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Complex
getAllComplexAssembly(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of ComplexAssembly for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#ComplexAssembly
getAllComplexes(Vector) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
getAllControl(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Control for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Control
getAllControlledVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of ControlledVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#ControlledVocabulary
getAllConversion(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Conversion for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Conversion
getAllCovalentBindingFeature(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of CovalentBindingFeature for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#CovalentBindingFeature
getAllDegradation(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Degradation for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Degradation
getAllDeltaG(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of DeltaG for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#DeltaG
getAllDna(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Dna for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Dna
getAllDnaReference(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of DnaReference for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#DnaReference
getAllDnaRegion(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of DnaRegion for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#DnaRegion
getAllDnaRegionReference(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of DnaRegionReference for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#DnaRegionReference
getAllEntity(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Entity for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Entity
getAllEntityFeature(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of EntityFeature for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#EntityFeature
getAllEntityReference(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of EntityReference for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#EntityReference
getAllEntityReferenceTypeVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of EntityReferenceTypeVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#EntityReferenceTypeVocabulary
getAllEvidence(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Evidence for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Evidence
getAllEvidenceCodeVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of EvidenceCodeVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#EvidenceCodeVocabulary
getAllExperimentalForm(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of ExperimentalForm for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#ExperimentalForm
getAllExperimentalFormVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of ExperimentalFormVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#ExperimentalFormVocabulary
getAllFragmentFeature(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of FragmentFeature for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#FragmentFeature
getAllGene(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Gene for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Gene
getAllGeneticInteraction(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of GeneticInteraction for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#GeneticInteraction
getAllInteraction(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Interaction for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Interaction
getAllInteractionVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of InteractionVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#InteractionVocabulary
getAllKPrime(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of KPrime for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#KPrime
getAllModificationFeature(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of ModificationFeature for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#ModificationFeature
getAllModulation(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Modulation for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Modulation
getAllMolecularInteraction(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of MolecularInteraction for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#MolecularInteraction
getAllObjectsHash(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner
 
getAllPathway(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Pathway for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Pathway
getAllPathwayStep(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of PathwayStep for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#PathwayStep
getAllPhenotypeVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of PhenotypeVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#PhenotypeVocabulary
getAllPhysicalEntity(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of PhysicalEntity for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#PhysicalEntity
getAllProtein(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Protein for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Protein
getAllProteinReference(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of ProteinReference for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#ProteinReference
getAllProvenance(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Provenance for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Provenance
getAllPublicationXref(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of PublicationXref for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#PublicationXref
getAllRelationshipTypeVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of RelationshipTypeVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#RelationshipTypeVocabulary
getAllRelationshipXref(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of RelationshipXref for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#RelationshipXref
getAllRna(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Rna for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Rna
getAllRnaReference(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of RnaReference for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#RnaReference
getAllRnaRegion(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of RnaRegion for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#RnaRegion
getAllRnaRegionReference(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of RnaRegionReference for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#RnaRegionReference
getAllScore(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Score for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Score
getAllSequenceInterval(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of SequenceInterval for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#SequenceInterval
getAllSequenceLocation(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of SequenceLocation for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#SequenceLocation
getAllSequenceModificationVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of SequenceModificationVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#SequenceModificationVocabulary
getAllSequenceRegionVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of SequenceRegionVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#SequenceRegionVocabulary
getAllSequenceSite(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of SequenceSite for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#SequenceSite
getAllSmallMolecule(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of SmallMolecule for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#SmallMolecule
getAllSmallMoleculeReference(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of SmallMoleculeReference for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#SmallMoleculeReference
getAllStoichiometry(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Stoichiometry for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Stoichiometry
getAllTemplateReaction(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of TemplateReaction for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#TemplateReaction
getAllTemplateReactionRegulation(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of TemplateReactionRegulation for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#TemplateReactionRegulation
getAllTissueVocabulary(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of TissueVocabulary for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#TissueVocabulary
getAllTransport(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Transport for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Transport
getAllTransportWithBiochemicalReaction(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of TransportWithBiochemicalReaction for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#TransportWithBiochemicalReaction
getAllUnificationXref(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of UnificationXref for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#UnificationXref
getAllUtilityClass(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of UtilityClass for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#UtilityClass
getAllXref(Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return an instance of Xref for every resource in the model with rdf:Type http://www.biopax.org/release/biopax-level3.owl#Xref
getAntisenseRNAById(String) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
getAntisenseRNAs(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
getAsEdgeVector() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
getAssociatedNetworks(BioPAX) - Method in class fr.curie.BiNoM.biopax.BioPAXSourceDB
 
getAttrDescV() - Method in class fr.curie.BiNoM.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
 
getAuthor() - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
Iterates through the 'author' property values.
getAuthor() - 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.DegradationImpl
 
getAvailability() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getAvailability() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
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.GeneImpl
 
getAvailability() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
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.MolecularInteractionImpl
 
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.ProteinImpl
 
getAvailability() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getAvailability() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getAvailability() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getAvailability() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getAvailability() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getAvailability() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
getAvailability() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getAverageConnectivities() - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
getAverageConnectivity(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
GetBiggestGraph(Vector) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
getBindingFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BindingFeature.
getBindingFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BindingFeature.
getBindsTo() - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeature
Gets the 'bindsTo' property value
getBindsTo() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
getBindsTo() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
getBiochemicalPathwayStep(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BiochemicalPathwayStep.
getBiochemicalPathwayStep(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BiochemicalPathwayStep.
getBiochemicalReaction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BiochemicalReaction.
getBiochemicalReaction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BiochemicalReaction.
getBioPAX(Object) - Method in class fr.curie.BiNoM.biopax.BioPAXSourceDB
 
getBioPAX() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
getBioPAX() - Method in class fr.curie.BiNoM.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_level3_DOT_owlFactory
Create a new instance of BioSource.
getBioSource(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of BioSource.
getBiPartiteSetConnectionGraph(String, String, int) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
getBlogLinker() - Method in class fr.curie.BiNoM.pathways.navicell.WordPressBlogCreator
 
getBrowseInstance() - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserFrame
 
getCanonName() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
getCatalysis(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Catalysis.
getCatalysis(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Catalysis.
getCatalysisDirection() - Method in interface fr.curie.BiNoM.pathways.biopax.Catalysis
Gets the 'catalysisDirection' property value
getCatalysisDirection() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
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
 
getCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
getCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getCellularLocation() - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Gets the 'cellularLocation' property value
getCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
getCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getCellularLocationVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CellularLocationVocabulary.
getCellularLocationVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CellularLocationVocabulary.
getCellVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CellVocabulary.
getCellVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CellVocabulary.
getChemicalFormula() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Gets the 'chemicalFormula' property value
getChemicalFormula() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
getChemicalStructure(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ChemicalStructure.
getChemicalStructure(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ChemicalStructure.
getChildrenClassDescV() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
getClass(Object) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
getClass(Class) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
getClassDesc() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getClassDesc(String) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDescFactory
 
getClassDesc(Class) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDescFactory
 
getClassDesc() - Method in class fr.curie.BiNoM.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
 
getColor() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
getColorCode(CellDesignerColorProteins.SimpleTable, int, boolean, boolean) - Method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
getColorCode(CellDesignerColorSpecies.SimpleTable, int, boolean, boolean) - Method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies
 
getColorCode(RemoveNonExpressedProteins.SimpleTable, int, boolean, boolean) - Method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
getColorFromString(String) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
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.CellularLocationVocabularyImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
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.ControlImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
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.EntityFeatureImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
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.ExperimentalFormVocabularyImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
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.PhenotypeVocabularyImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
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.RnaReferenceImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
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.SequenceModificationVocabularyImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
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.SmallMoleculeReferenceImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getComment() - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
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
 
getCompartmentNames(edu.rpi.cs.xgmml.GraphicNode[]) - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkFactory
 
getComplex(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Complex.
getComplex(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Complex.
getComplexAssembly(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ComplexAssembly.
getComplexAssembly(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ComplexAssembly.
getComplexById(String) - 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
getComponent() - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Get an Iterator the 'component' property values.
getComponent() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
getComponentStoichiometry() - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Get an Iterator the 'componentStoichiometry' property values.
getComponentStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
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
 
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
 
getConnectionGraphCoverageScore(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
getControl(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Control.
getControl(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Control.
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_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
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
 
getControlled_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getControlled_asTemplateReaction() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation
Gets the 'controlled' property value
getControlled_asTemplateReaction() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getControlledURI(Control) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter
 
getControlledVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ControlledVocabulary.
getControlledVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ControlledVocabulary.
getController_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
getController_asPathway() - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Get an Iterator the 'controller' property values.
getController_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
getController_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
getController_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getController_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
getController_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Get an Iterator the 'controller' property values.
getController_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
getController_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.Modulation
Get an Iterator the 'controller' property values.
getController_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
getController_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation
Get an Iterator the 'controller' property values.
getController_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getControlType() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
getControlType() - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Gets the 'controlType' property value
getControlType() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
getControlType() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
getControlType() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getConversion(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Conversion.
getConversion(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Conversion.
getConversionDirection() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getConversionDirection() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
getConversionDirection() - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Gets the 'conversionDirection' property value
getConversionDirection() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
getConversionDirection() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
getConversionDirection() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
getConversionDirection() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getCovalentBindingFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CovalentBindingFeature.
getCovalentBindingFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of CovalentBindingFeature.
getCreateDistance() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Cluster
 
getCreateEdge(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
getCreateNode(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
getCURI(com.ibm.adtech.jastor.Thing, BioPAX) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
getCurrentModelSize() - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkUtils
 
getCyclicComponents(GraphDocument, StructureAnalysisUtils.Option) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.CalcCentralityTask
 
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.ConvertReactionNetworkToEntityNetworkTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.ConvertToUndirectedGraphTask
 
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.ExcludeIntermediateNodesTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetworkTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetworkTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.LinearizeNetworkTask
 
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.BioPAXExportTask
 
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.CellDesignerExportTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CSMLImportTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExportTask
 
getCyNetwork() - Method in class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilterTask
 
getDatabaseFileName() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getDataSource() - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Get an Iterator the 'dataSource' property values.
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
getDataSource() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
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
 
getDbVersion() - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
getDbVersion() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
getDbVersion() - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
getDbVersion() - Method in interface fr.curie.BiNoM.pathways.biopax.Xref
Gets the 'dbVersion' property value
getDbVersion() - 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
 
getDefaultNodeBorderLineStyle() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
getDefaultNodeBorderLineWidth() - 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
 
getDegradation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Degradation.
getDegradation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Degradation.
getDeltaG() - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Get an Iterator the 'deltaG' property values.
getDeltaG() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getDeltaG(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DeltaG.
getDeltaG(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DeltaG.
getDeltaG() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getDeltaGPrime0() - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaG
Gets the 'deltaGPrime0' property value
getDeltaGPrime0() - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
getDeltaH() - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Iterates through the 'deltaH' property values.
getDeltaH() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getDeltaH() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getDeltaS() - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Iterates through the 'deltaS' property values.
getDeltaS() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getDeltaS() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getDescription() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.OWLExtensionFilter
 
getDescription() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.XGMMLExtensionFilter
 
getDna(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Dna.
getDna(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Dna.
getDnaReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaReference.
getDnaReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaReference.
getDnaRegion(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaRegion.
getDnaRegion(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaRegion.
getDnaRegionReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaRegionReference.
getDnaRegionReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of DnaRegionReference.
getECNumber() - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Iterates through the 'eCNumber' property values.
getECNumber() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getECNumber() - 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
 
getEdgeList(GraphPerspective) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
getEdgeNodes() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
 
getEdges() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
 
getEdgeSet(GraphPerspective) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
getEdgeSign(Edge) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
getEdgeSourceArrowMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
getEdgeTargetArrowMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
getEdgeType(Edge) - Static method in class fr.curie.BiNoM.pathways.utils.GraphUtils
 
getEditInstance() - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserFrame
 
getEditPanelAction(boolean) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getElementType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getElementType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleAttrDesc
 
getElementType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleListAttrDesc
 
getElementType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerAttrDesc
 
getElementType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerListAttrDesc
 
getElementType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
getElementType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
getElementType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
getElementType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringListAttrDesc
 
getEntities(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner
Fills entities map
getEntitiesNames(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner
 
getEntity(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Entity.
getEntity(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Entity.
getEntityFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityFeature.
getEntityFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityFeature.
getEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getEntityFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Get an Iterator the 'entityFeature' property values.
getEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
getEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
getEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getEntityFeature() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
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
 
getEntityReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityReference.
getEntityReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityReference.
getEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Gets the 'entityReference' property value
getEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Gets the 'entityReference' property value
getEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Gets the 'entityReference' property value
getEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Gets the 'entityReference' property value
getEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Gets the 'entityReference' property value
getEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Gets the 'entityReference' property value
getEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getEntityReference_asDnaReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Gets the 'entityReference' property value
getEntityReference_asDnaReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getEntityReference_asDnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Gets the 'entityReference' property value
getEntityReference_asDnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getEntityReference_asProteinReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Gets the 'entityReference' property value
getEntityReference_asProteinReference() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getEntityReference_asRnaReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Gets the 'entityReference' property value
getEntityReference_asRnaReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getEntityReference_asRnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Gets the 'entityReference' property value
getEntityReference_asRnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getEntityReference_asSmallMoleculeReference() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Gets the 'entityReference' property value
getEntityReference_asSmallMoleculeReference() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getEntityReferenceType() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Gets the 'entityReferenceType' property value
getEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
getEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
getEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
getEntityReferenceTypeVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityReferenceTypeVocabulary.
getEntityReferenceTypeVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EntityReferenceTypeVocabulary.
getEntityType(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
 
getErrorMessage() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProtoFactory
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getEvidence(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Evidence.
getEvidence(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_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.ComplexImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getEvidence() - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Get an Iterator the 'evidence' property values.
getEvidence() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Get an Iterator the 'evidence' property values.
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
getEvidence() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Get an Iterator the 'evidence' property values.
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
getEvidence() - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Get an Iterator the 'evidence' property values.
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
getEvidence() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getEvidenceCode() - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Get an Iterator the 'evidenceCode' property values.
getEvidenceCode() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
getEvidenceCodeVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EvidenceCodeVocabulary.
getEvidenceCodeVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of EvidenceCodeVocabulary.
getExperimentalFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Get an Iterator the 'experimentalFeature' property values.
getExperimentalFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
getExperimentalForm(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ExperimentalForm.
getExperimentalForm(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ExperimentalForm.
getExperimentalForm() - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Get an Iterator the 'experimentalForm' property values.
getExperimentalForm() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
getExperimentalFormDescription() - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Get an Iterator the 'experimentalFormDescription' property values.
getExperimentalFormDescription() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
getExperimentalFormEntity_asGene() - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Get an Iterator the 'experimentalFormEntity' property values.
getExperimentalFormEntity_asGene() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
getExperimentalFormEntity_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Get an Iterator the 'experimentalFormEntity' property values.
getExperimentalFormEntity_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
getExperimentalFormVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ExperimentalFormVocabulary.
getExperimentalFormVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ExperimentalFormVocabulary.
getFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
getFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Get an Iterator the 'feature' property values.
getFeature() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
getFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getFeature() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getFeature_asBindingFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Get an Iterator the 'feature' property values.
getFeature_asBindingFeature() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getFeatureLocation() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
getFeatureLocation() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
getFeatureLocation() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Get an Iterator the 'featureLocation' property values.
getFeatureLocation() - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
getFeatureLocation() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
getFeatureLocation() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
getFeatureLocationType() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
getFeatureLocationType() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
getFeatureLocationType() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Get an Iterator the 'featureLocationType' property values.
getFeatureLocationType() - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
getFeatureLocationType() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
getFeatureLocationType() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
getFileKey(String) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
key could be based on: filename + date + size or md5(filecontents);
getFirstAttribute(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Element
 
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
getFirstAttributeValueWithSubstringInName(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Element
 
getFragmentFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of FragmentFeature.
getFragmentFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of FragmentFeature.
getGene(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Gene.
getGene(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Gene.
getGene(SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
getGenes(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Creates the list of genes
getGenesFromKEGGPathway(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.KEGGAccess
 
getGeneticInteraction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of GeneticInteraction.
getGeneticInteraction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of GeneticInteraction.
getGraph(ProjectDocument) - Method in class fr.curie.BiNoM.pathways.CSMLToCytoscapeConverter
 
getGridBagLayoutMaxRows() - Static method in class fr.curie.BiNoM.lib.Utils
 
getHangingNodes() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
getHugosFromCellDesignerIdentity(CelldesignerSpeciesIdentity) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
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
 
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
 
getIdVersion() - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
getIdVersion() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
getIdVersion() - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
getIdVersion() - Method in interface fr.curie.BiNoM.pathways.biopax.Xref
Gets the 'idVersion' property value
getIdVersion() - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
getIncidenceMatrix() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
getIncludedSpecies(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
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(AbstractClusterNetworksTaskFactory) - Static method in class fr.curie.BiNoM.analysis.ClusterNetworksDialog
 
getInstance() - Static method in class fr.curie.BiNoM.analysis.ExcludeIntermediateNodesDialog
 
getInstance() - Static method in class fr.curie.BiNoM.analysis.ModularViewDialog
 
getInstance() - Static method in class fr.curie.BiNoM.biopax.BioPAXImportDialog
 
getInstance() - Static method in class fr.curie.BiNoM.biopax.BioPAXSourceDB
 
getInstance(BioPAX) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDescFactory
 
getInstance() - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassTreeFrame
 
getInstance() - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectFactory
 
getInstance() - Static method in class fr.curie.BiNoM.celldesigner.lib.GraphDocumentFactory
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.analysis.createNeighborhoodSetsDialog
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkDialog
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetworkDialog
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisDialog
 
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.BioPAXSyncNetworksDialog
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
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.CellDesignerExportToFileDialog
 
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.celldesigner.checkCellDesignerFileDialog
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.colorCellDesignerProteinsDialog
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesDialog
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.modifyCellDesignerNotesDialog
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerDialog
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.ProduceNaviCellMapFilesDialog
 
getInstance() - Static method in class fr.curie.BiNoM.cytoscape.lib.GraphDocumentFactory
 
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
 
getInstance() - Static method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
getInstanceList(boolean) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
getInteraction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Interaction.
getInteraction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Interaction.
getInteractionScore() - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Get an Iterator the 'interactionScore' property values.
getInteractionScore() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
getInteractionType() - Method in interface fr.curie.BiNoM.pathways.biopax.Interaction
Gets the 'interactionType' property value
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
getInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getInteractionVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of InteractionVocabulary.
getInteractionVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of InteractionVocabulary.
getIntraMolecular() - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeature
Gets the 'intraMolecular' property value
getIntraMolecular() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
getIntraMolecular() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
getIonicStrength() - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaG
Gets the 'ionicStrength' property value
getIonicStrength() - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
getIonicStrength() - Method in interface fr.curie.BiNoM.pathways.biopax.KPrime
Gets the 'ionicStrength' property value
getIonicStrength() - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
getJavaRelease() - Static method in class fr.curie.BiNoM.lib.Utils
 
getJClass() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
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_level3_DOT_owlFactory
Create a new instance of KPrime.
getKPrime(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of KPrime.
getKPrime() - Method in interface fr.curie.BiNoM.pathways.biopax.KPrime
Gets the 'kPrime' property value
getKPrime() - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
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.DegradationImpl
 
getLeft() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
getLeft() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getListOfEntityNamesFromId(String) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
getListOfReactionsTable(Graph, BioPAX, org.sbml.x2001.ns.celldesigner.SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.GraphUtils
 
getListOfSets(String) - Method in class fr.curie.BiNoM.pathways.utils.GMTFile
 
getListOfSets(String) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
getMapIconURL() - Method in class fr.curie.BiNoM.pathways.navicell.WordPressBlogCreator
 
getMappingValue() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition.ObjectMapping
 
getMaterialComponentForEntityName(Graph, String) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
Extract a material component subgraph
getMaterialComponents(GraphDocument) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
 
getMaximumSetSize() - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
getMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getMemberEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Get an Iterator the 'memberEntityReference' property values.
getMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
getMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
getMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getMemberEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
getMemberEntityReference_asDnaReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Get an Iterator the 'memberEntityReference' property values.
getMemberEntityReference_asDnaReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getMemberEntityReference_asProteinReference() - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
Get an Iterator the 'memberEntityReference' property values.
getMemberEntityReference_asProteinReference() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
getMemberEntityReference_asRnaReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Get an Iterator the 'memberEntityReference' property values.
getMemberEntityReference_asRnaReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getMemberEntityReference_asSmallMoleculeReference() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Get an Iterator the 'memberEntityReference' property values.
getMemberEntityReference_asSmallMoleculeReference() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
getMemberFeature() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
getMemberFeature() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
getMemberFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Get an Iterator the 'memberFeature' property values.
getMemberFeature() - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
getMemberFeature() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
getMemberFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
getMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
getMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getMemberPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Get an Iterator the 'memberPhysicalEntity' property values.
getMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
getMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getMemberPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getMemberPhysicalEntity_asComplex() - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Get an Iterator the 'memberPhysicalEntity' property values.
getMemberPhysicalEntity_asComplex() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
getMemberPhysicalEntity_asDna() - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Get an Iterator the 'memberPhysicalEntity' property values.
getMemberPhysicalEntity_asDna() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getMemberPhysicalEntity_asDnaRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Get an Iterator the 'memberPhysicalEntity' property values.
getMemberPhysicalEntity_asDnaRegion() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getMemberPhysicalEntity_asProtein() - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Get an Iterator the 'memberPhysicalEntity' property values.
getMemberPhysicalEntity_asProtein() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getMemberPhysicalEntity_asRna() - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Get an Iterator the 'memberPhysicalEntity' property values.
getMemberPhysicalEntity_asRna() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getMemberPhysicalEntity_asRnaRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Get an Iterator the 'memberPhysicalEntity' property values.
getMemberPhysicalEntity_asRnaRegion() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getMemberPhysicalEntity_asSmallMolecule() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Get an Iterator the 'memberPhysicalEntity' property values.
getMemberPhysicalEntity_asSmallMolecule() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getMessage() - Method in exception fr.curie.BiNoM.pathways.navicell.ProduceClickableMap.NaviCellException
 
getMetaType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getMetaType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
getMetaType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
getModificationFeature(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ModificationFeature.
getModificationFeature(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ModificationFeature.
getModificationType() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
getModificationType() - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeature
Gets the 'modificationType' property value
getModificationType() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
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_level3_DOT_owlFactory
Create a new instance of Modulation.
getModulation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Modulation.
getMolecularInteraction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of MolecularInteraction.
getMolecularInteraction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of MolecularInteraction.
getMolecularWeight() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Gets the 'molecularWeight' property value
getMolecularWeight() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
getName() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getName() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
getName() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
getName() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Cluster
 
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
Iterates through the 'name' property values.
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 class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getName() - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Iterates through the 'name' property values.
getName() - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
getName() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Iterates through the 'name' property values.
getName() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
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.MolecularInteractionImpl
 
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.ProteinImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
getName() - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Iterates through the 'name' property values.
getName() - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getName() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
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, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
getNameOfIncludedSpecies(SbmlDocument.Sbml, CelldesignerSpeciesDocument.CelldesignerSpecies, String) - 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
 
getNamesOfGivenOccurence(int) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
getNamingService(BioPAX) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXNamingServiceManager
 
getNamingServiceMode() - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
getNamingServiceMode() - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXToggleNamingService
 
getNegativeThreshold(float[][]) - Static method in class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
getNegativeThreshold(float[]) - Static method in class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
getNeighborhoodSets(Graph, Vector<String>, boolean, boolean, int, int, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
getNeighbours(Graph, Node) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
getNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.CalcCentralityTask
 
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(jp.sbi.celldesigner.plugin.CellDesignerPlugin) - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkUtils
 
getNetworkNames(jp.sbi.celldesigner.plugin.CellDesignerPlugin, String) - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkUtils
 
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
 
getNetworksMap() - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
getNext() - Method in class fr.curie.BiNoM.pathways.utils.CombinationGenerator
 
getNextStep() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
getNextStep() - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Get an Iterator the 'nextStep' property values.
getNextStep() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
getNode() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph.NodeDegree
 
getNode(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
getNodeActivity(Node) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
getNodeArray(GraphPerspective) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
getNodeAttribute() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
getNodeBorderColorMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
getNodeBorderLineStyleMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
getNodeBorderLineWidthMapping() - 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
 
getNodeFirstNeighbors(Graph, Node, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
getNodeImageMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
getNodeIndex(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
getNodeList(GraphPerspective) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
getNodeNamesFromAnAttribute(Vector<Node>, String) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
getNodeNeighbors(Graph, Node, boolean, boolean, int) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
getNodes() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
 
getNodesByLabelInclusion(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
getNodeSet(GraphPerspective) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
getNodeSet() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Cluster
 
getNodeShapeMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
getNodeSizeMapping() - Method in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
getNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
getNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getNotFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Get an Iterator the 'notFeature' property values.
getNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
getNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getNotFeature() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getNotFeature_asBindingFeature() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Get an Iterator the 'notFeature' property values.
getNotFeature_asBindingFeature() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getNullEmptyNetwork() - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkFactory
 
getNumLeft() - Method in class fr.curie.BiNoM.pathways.utils.CombinationGenerator
 
getObject() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObject
 
getObject(String, BioPAX) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectFactory
 
getObject(com.ibm.adtech.jastor.Thing, BioPAX) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectFactory
 
getObjectClassDesc() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
getObjectClassDesc() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleAttrDesc
 
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleListAttrDesc
 
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerAttrDesc
 
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerListAttrDesc
 
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
getObjectIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringListAttrDesc
 
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleAttrDesc
 
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleListAttrDesc
 
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerAttrDesc
 
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerListAttrDesc
 
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
getObjectValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringListAttrDesc
 
getOne(Vector<BioPAXAttrDesc.CMethod>, String, String) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Gets the 'organism' property value
getOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Gets the 'organism' property value
getOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.Gene
Gets the 'organism' property value
getOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
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.ProteinReference
Gets the 'organism' property value
getOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
getOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Gets the 'organism' property value
getOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Gets the 'organism' property value
getOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getParentClassDescV() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
getParentClassDescV(Class) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDescFactory
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
getParticipant() - Method in interface fr.curie.BiNoM.pathways.biopax.Interaction
Get an Iterator the 'participant' property values.
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
getParticipant() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getParticipant_asGene() - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Get an Iterator the 'participant' property values.
getParticipant_asGene() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
getParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
getParticipant_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Get an Iterator the 'participant' property values.
getParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
getParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
getParticipant_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteraction
Get an Iterator the 'participant' property values.
getParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
getParticipant_asPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Get an Iterator the 'participant' property values.
getParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
getParticipant_asPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
getParticipantStoichiometry() - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Get an Iterator the 'participantStoichiometry' property values.
getParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
getParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
getParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
getParticipantStoichiometry() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getPathConsistencyAndSummaryActivity(Path) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
getPathConsistencyAndSummaryActivity(Path, float[]) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
getPathSign(Path) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
getPathSign(Graph, String) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
getPathSign(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.SignsOfPaths
 
getPathway(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Pathway.
getPathway(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Pathway.
getPathwayComponent_asInteraction() - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Get an Iterator the 'pathwayComponent' property values.
getPathwayComponent_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
getPathwayComponent_asPathway() - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Get an Iterator the 'pathwayComponent' property values.
getPathwayComponent_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
getPathwayNodes() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
getPathwayOrder() - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Get an Iterator the 'pathwayOrder' property values.
getPathwayOrder() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
getPathwayStep(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PathwayStep.
getPathwayStep(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PathwayStep.
getPatoData() - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabulary
Gets the 'patoData' property value
getPatoData() - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
getPh() - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaG
Gets the 'ph' property value
getPh() - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
getPh() - Method in interface fr.curie.BiNoM.pathways.biopax.KPrime
Gets the 'ph' property value
getPh() - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
getPhenotype() - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Gets the 'phenotype' property value
getPhenotype() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
getPhenotypeVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PhenotypeVocabulary.
getPhenotypeVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PhenotypeVocabulary.
getPhysicalEntity(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PhysicalEntity.
getPhysicalEntity(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PhysicalEntity.
getPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.Stoichiometry
Gets the 'physicalEntity' property value
getPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
getPhysicalEntityType(PhysicalEntity) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
 
getPMg() - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaG
Gets the 'pMg' property value
getPMg() - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
getPMg() - Method in interface fr.curie.BiNoM.pathways.biopax.KPrime
Gets the 'pMg' property value
getPMg() - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
getPositionStatus() - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceSite
Gets the 'positionStatus' property value
getPositionStatus() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
getPositiveThreshold(float[][]) - Static method in class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
getPositiveThreshold(float[]) - Static method in class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
getProduct_asDna() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Get an Iterator the 'product' property values.
getProduct_asDna() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getProduct_asProtein() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Get an Iterator the 'product' property values.
getProduct_asProtein() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getProduct_asRna() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Get an Iterator the 'product' property values.
getProduct_asRna() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getPropertyURI(Entity, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
getPropertyURI(Resource, 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_level3_DOT_owlFactory
Create a new instance of Protein.
getProtein(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Protein.
getProtein(SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
getProteinById(String) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
getProteinReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ProteinReference.
getProteinReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of ProteinReference.
getProteins(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Creates the list of proteins
getProteinsInComplex(org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
getProvenance(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Provenance.
getProvenance(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Provenance.
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_level3_DOT_owlFactory
Create a new instance of PublicationXref.
getPublicationXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of PublicationXref.
getPValue(float, float[], boolean) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
getReactionById(String) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
getReactionCenter(ReactionDocument.Reaction, HashMap<String, Pair>) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
getReactionCenter(ReactionDocument.Reaction, HashMap<String, Pair>) - Static method in class fr.curie.BiNoM.pathways.test.testRemoveEditPoints
 
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
getReactionString(ReactionDocument.Reaction, SbmlDocument, boolean, boolean) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
getRegionType() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Gets the 'regionType' property value
getRegionType() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getRegionType() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Gets the 'regionType' property value
getRegionType() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getRelationshipType() - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXref
Get an Iterator the 'relationshipType' property values.
getRelationshipType() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
getRelationshipTypeVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RelationshipTypeVocabulary.
getRelationshipTypeVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RelationshipTypeVocabulary.
getRelationshipXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RelationshipXref.
getRelationshipXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RelationshipXref.
getReport() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
getResourceType(Resource) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
 
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.DegradationImpl
 
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_level3_DOT_owlFactory
Create a new instance of Rna.
getRna(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Rna.
getRNA(SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
getRNAAliasBySpeciesId(SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
getRNAById(String) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
getRnaReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaReference.
getRnaReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaReference.
getRnaRegion(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaRegion.
getRnaRegion(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaRegion.
getRnaRegionReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaRegionReference.
getRnaRegionReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of RnaRegionReference.
getRNAs(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
getSamplingSizes() - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
getScaledImage(BufferedImage, int, int) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
getScaledImageSlow(BufferedImage, int, int) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
getScore(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Score.
getScore(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Score.
getScoreSource() - Method in interface fr.curie.BiNoM.pathways.biopax.Score
Gets the 'scoreSource' property value
getScoreSource() - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
getSectionByName(Vector<ModifyCellDesignerNotes.AnnotationSection>, String) - Static method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
getSelectedNodes(CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
getSelectedNodes() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
getSequence() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Gets the 'sequence' property value
getSequence() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getSequence() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Gets the 'sequence' property value
getSequence() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getSequence() - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
Gets the 'sequence' property value
getSequence() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
getSequence() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Gets the 'sequence' property value
getSequence() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getSequence() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Gets the 'sequence' property value
getSequence() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getSequenceInterval(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceInterval.
getSequenceInterval(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceInterval.
getSequenceIntervalBegin() - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
Gets the 'sequenceIntervalBegin' property value
getSequenceIntervalBegin() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
getSequenceIntervalEnd() - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
Gets the 'sequenceIntervalEnd' property value
getSequenceIntervalEnd() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
getSequenceLocation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceLocation.
getSequenceLocation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceLocation.
getSequenceModificationVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceModificationVocabulary.
getSequenceModificationVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceModificationVocabulary.
getSequencePosition() - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceSite
Gets the 'sequencePosition' property value
getSequencePosition() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
getSequenceRegionVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceRegionVocabulary.
getSequenceRegionVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceRegionVocabulary.
getSequenceSite(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceSite.
getSequenceSite(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SequenceSite.
getSet() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Cluster
 
getSmallMolecule(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SmallMolecule.
getSmallMolecule(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SmallMolecule.
getSmallMoleculeReference(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SmallMoleculeReference.
getSmallMoleculeReference(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of SmallMoleculeReference.
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, String) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
getSpecies(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.InsertCellDesignerParameters
 
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(String) - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
getSpeciesHugos(CelldesignerSpeciesAlias) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
getSpeciesHugos(CelldesignerComplexSpeciesAlias) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
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
 
getSpeciesName(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity, String, String, String, boolean, boolean, String, SbmlDocument.Sbml, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
getSpektrumGR(float) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
getSpektrumGR(float) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies
 
getSpektrumGR(float) - Static method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
getSpektrumGRB(float) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
getSpektrumGRB(float) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies
 
getSpektrumGRB(float) - Static method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
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.DegradationImpl
 
getSpontaneous() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
getSpontaneous() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
getStepConversion() - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Gets the 'stepConversion' property value
getStepConversion() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
getStepDirection() - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Gets the 'stepDirection' property value
getStepDirection() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
getStepProcess_asControl() - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Get an Iterator the 'stepProcess' property values.
getStepProcess_asControl() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
getStepProcess_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
getStepProcess_asInteraction() - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Get an Iterator the 'stepProcess' property values.
getStepProcess_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
getStepProcess_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
getStepProcess_asPathway() - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Get an Iterator the 'stepProcess' property values.
getStepProcess_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
getStoichiometricCoefficient() - Method in interface fr.curie.BiNoM.pathways.biopax.Stoichiometry
Gets the 'stoichiometricCoefficient' property value
getStoichiometricCoefficient() - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
getStoichiometry(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Stoichiometry.
getStoichiometry(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Stoichiometry.
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleAttrDesc
 
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleListAttrDesc
 
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerAttrDesc
 
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerListAttrDesc
 
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
getStringIterator(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringListAttrDesc
 
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleAttrDesc
 
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleListAttrDesc
 
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerAttrDesc
 
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerListAttrDesc
 
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
getStringValue(BioPAXObject) - Method in class fr.curie.BiNoM.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.SmallMoleculeReference
Gets the 'structure' property value
getStructure() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
getStructureData() - Method in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructure
Gets the 'structureData' property value
getStructureData() - Method in class fr.curie.BiNoM.pathways.biopax.ChemicalStructureImpl
 
getStructureFormat() - Method in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructure
Gets the 'structureFormat' property value
getStructureFormat() - 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
getSubRegion_asDnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Get an Iterator the 'subRegion' property values.
getSubRegion_asDnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getSubRegion_asDnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Get an Iterator the 'subRegion' property values.
getSubRegion_asDnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getSubRegion_asDnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Get an Iterator the 'subRegion' property values.
getSubRegion_asDnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getSubRegion_asDnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Get an Iterator the 'subRegion' property values.
getSubRegion_asDnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getSubRegion_asRnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Get an Iterator the 'subRegion' property values.
getSubRegion_asRnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getSubRegion_asRnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Get an Iterator the 'subRegion' property values.
getSubRegion_asRnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
getSubRegion_asRnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Get an Iterator the 'subRegion' property values.
getSubRegion_asRnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getSubRegion_asRnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Get an Iterator the 'subRegion' property values.
getSubRegion_asRnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getSubType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto
 
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
 
getSystematicallyInconsistentNodes() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
getTagValues(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
getTemperature() - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaG
Gets the 'temperature' property value
getTemperature() - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
getTemperature() - Method in interface fr.curie.BiNoM.pathways.biopax.KPrime
Gets the 'temperature' property value
getTemperature() - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
getTemplate_asDna() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Gets the 'template' property value
getTemplate_asDna() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getTemplate_asDnaRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Gets the 'template' property value
getTemplate_asDnaRegion() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getTemplate_asRna() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Gets the 'template' property value
getTemplate_asRna() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getTemplate_asRnaRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Gets the 'template' property value
getTemplate_asRnaRegion() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getTemplateDirection() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Gets the 'templateDirection' property value
getTemplateDirection() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getTemplateReaction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TemplateReaction.
getTemplateReaction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TemplateReaction.
getTemplateReactionRegulation(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TemplateReactionRegulation.
getTemplateReactionRegulation(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TemplateReactionRegulation.
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
getTerm() - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Iterates through the 'term' property values.
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
getTerm() - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
getText() - Method in class fr.curie.BiNoM.cytoscape.analysis.CalcCentralityTask
 
getText() - Method in class fr.curie.BiNoM.lib.MLLabel
 
getText(XmlObject) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Read the text of XmlObject
getThing(com.hp.hpl.jena.rdf.model.Resource, com.hp.hpl.jena.rdf.model.Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Returns an instance of an interface for the given Resource.
getThing(String, com.hp.hpl.jena.rdf.model.Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_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
 
getTissueVocabulary(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TissueVocabulary.
getTissueVocabulary(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TissueVocabulary.
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.ClusterNetworksTask
 
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.ConnectedComponentsTask
 
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.CycleDecompositionTask
 
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.ExcludeIntermediateNodesTask
 
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.ExtractReactionNetworkTask
 
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.LinearizeNetworkTask
 
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.MaterialComponentsTask
 
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.ModularViewTask
 
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.MonoMolecularReactionsAsEdgesTask
 
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.PruneGraphTask
 
getTitle() - Method in class fr.curie.BiNoM.celldesigner.analysis.StronglyConnectedComponentsTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.CalcCentralityTask
 
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.ConvertReactionNetworkToEntityNetworkTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.ConvertToUndirectedGraphTask
 
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.ExcludeIntermediateNodesTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetworkTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetworkTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.LinearizeNetworkTask
 
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.OptimalCutSetAnalyzerTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerBootstrapTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerTask
 
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.BioPAXExportTask
 
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.CellDesignerExportTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.checkCellDesignerFileTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.colorCellDesignerProteinsTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CSMLImportTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.MergingMapsTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.modifyCellDesignerNotesTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.ProduceNaviCellMapFilesTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ClusterByShortPathTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.DestroyUnusedNetworksAsNestTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.RecreateLostConnectionsInsideNestsTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExportTask
 
getTitle() - Method in class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilterTask
 
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
 
getTotal() - Method in class fr.curie.BiNoM.pathways.utils.CombinationGenerator
 
getTransport(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Transport.
getTransport(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Transport.
getTransportWithBiochemicalReaction(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TransportWithBiochemicalReaction.
getTransportWithBiochemicalReaction(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of TransportWithBiochemicalReaction.
getType() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto
 
getTypeForParticipant(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Determine the type (Complex, Protein, Dna, etc.) of a given Physical Entity
getUnificationXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of UnificationXref.
getUnificationXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of UnificationXref.
getURI(Object) - Method in class fr.curie.BiNoM.biopax.BioPAXSourceDB
 
getURI() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils.ObjectLabel
 
getUriById(String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Return the URI given an ID
getUriByName(String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Return the URI for a given name
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
 
getUsedMemory() - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
getUsedMemoryMb() - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
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_level3_DOT_owlFactory
Create a new instance of UtilityClass.
getUtilityClass(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of UtilityClass.
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleAttrDesc
 
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleListAttrDesc
 
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerAttrDesc
 
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerListAttrDesc
 
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
getValue(BioPAXObject) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringListAttrDesc
 
getValue() - Method in interface fr.curie.BiNoM.pathways.biopax.Score
Gets the 'value' property value
getValue() - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
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
Return the first occurrence of a sorted Controlled Vocabulary list
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, org.sbml.x2001.ns.celldesigner.SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
The converter itself
getXGMMLInteractionGraph(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).
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).
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
getXref(String, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Xref.
getXref(Resource, Model) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Create a new instance of Xref.
getXref() - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Get an Iterator the 'xref' property values.
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
getXref() - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Get an Iterator the 'xref' property values.
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
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.EntityReference
Get an Iterator the 'xref' property values.
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
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.EvidenceCodeVocabularyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
getXref() - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Get an Iterator the 'xref' property values.
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
getXref() - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
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.Provenance
Get an Iterator the 'xref' property values.
getXref_asPublicationXref() - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
getXref_asUnificationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Get an Iterator the 'xref' property values.
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
getXref_asUnificationXref() - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Get an Iterator the 'xref' property values.
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
getXref_asUnificationXref() - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
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
 
getYN() - Method in class fr.curie.BiNoM.cytoscape.utils.TextBoxDialog
 
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
globalModifier - Variable in class fr.curie.BiNoM.pathways.utils.SpeciesStructure
 
gmtFile - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
GMTFile - Class in fr.curie.BiNoM.pathways.utils
 
GMTFile() - Constructor for class fr.curie.BiNoM.pathways.utils.GMTFile
 
graph - Variable in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph
 
graph - Variable in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
graph - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
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.analysis.structure.Path
 
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.celldesigner.lib
 
GraphDocumentFactory() - Constructor for class fr.curie.BiNoM.celldesigner.lib.GraphDocumentFactory
 
GraphDocumentFactory - Class in fr.curie.BiNoM.cytoscape.lib
 
GraphDocumentFactory() - Constructor for class fr.curie.BiNoM.cytoscape.lib.GraphDocumentFactory
 
GraphicUtils - Class in fr.curie.BiNoM.lib
 
GraphicUtils() - Constructor for class fr.curie.BiNoM.lib.GraphicUtils
 
graphTest() - Static method in class fr.curie.BiNoM.pathways.test.TestOPtCutSet
 
GraphUtils - Class in fr.curie.BiNoM.pathways.utils
 
GraphUtils() - Constructor for class fr.curie.BiNoM.pathways.utils.GraphUtils
 
GraphXGMMLParser - Class in fr.curie.BiNoM.pathways.utils
Simple XGMML parser
GraphXGMMLParser() - Constructor for class fr.curie.BiNoM.pathways.utils.GraphXGMMLParser
 
GridBagDialog - Class in fr.curie.BiNoM.cytoscape.utils
Parent of dialog classes using parameters of GridBagDialog
gridSizeX - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask.stainingOptions
 
gridSizeY - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask.stainingOptions
 
gridStepX - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
gridStepY - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
guessIdentifiers - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask.extractingNotesOptions
 
guessIdentifiers - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
guessPMIDIds(String) - Static method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
guessProteinIdentifiers(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 

H

H - Static variable in class fr.curie.BiNoM.cytoscape.utils.GridBagDialog
 
h - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
Node height
halt() - Method in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.CalcCentralityTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponentsTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.ConvertReactionNetworkToEntityNetworkTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.ConvertToUndirectedGraphTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.CycleDecompositionTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExcludeIntermediateNodesTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetworkTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetworkTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.LinearizeNetworkTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.MaterialComponentsTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.ModularViewTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.MonoMolecularReactionsAsEdgesTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerBootstrapTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.PruneGraphTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.analysis.StronglyConnectedComponentsTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSourceTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSourceTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.checkCellDesignerFileTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.colorCellDesignerProteinsTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CSMLImportTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.MergingMapsTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.modifyCellDesignerNotesTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.ProduceNaviCellMapFilesTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ClusterByShortPathTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.DestroyUnusedNetworksAsNestTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.RecreateLostConnectionsInsideNestsTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExportTask
 
halt() - Method in class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilterTask
 
hasError() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProtoFactory
 
hasMore() - Method in class fr.curie.BiNoM.pathways.utils.CombinationGenerator
 
hasMoreElements() - Method in class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer
Checks whether any token is left in the input string
hasMoreTokens() - Method in class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer
Checks whether any token is left in the input string
height - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
HEXAGON - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
hitSetSB - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Hitting sets encoded as a set of BitSet objects.
hitSetSizeOne - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
List of hitting sets of size one.
HittingSetHighestDegreeFirst(Graph, ArrayList<Node>, ArrayList<Node>) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
Find miminum hitting set for a graph with heuristic algorithm.
hprd - Variable in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 

I

Id - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
Edge unique id
Id - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
Node unique id
id - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter.BioPAXSpecies
 
idChanged(PublicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when id has changed
idChanged(RelationshipXref) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXrefListener
Called when id has changed
idChanged(UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.UnificationXrefListener
Called when id has changed
idChanged(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.XrefListener
Called when id has changed
identicalEdges(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
identicalNodes(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
identicalTo(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
idname - Variable in class fr.curie.BiNoM.pathways.utils.AccessionNumberTable
Map from id used by a database to the Vector of names in the table (id - is database identifier, name - some common name or accession number)
idName - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Some identifier for this BioPAX
idProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Xref
The Jena Property for id
idVersionChanged(PublicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when idVersion has changed
idVersionChanged(RelationshipXref) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXrefListener
Called when idVersion has changed
idVersionChanged(UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.UnificationXrefListener
Called when idVersion has changed
idVersionChanged(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.XrefListener
Called when idVersion has changed
idVersionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Xref
The Jena Property for idVersion
img - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition.ImageDefinition
 
ImportFromAINDialogConstitutiveReactions - Class in fr.curie.BiNoM.cytoscape.ain
 
ImportFromAINDialogConstitutiveReactions(JFrame, String, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogConstitutiveReactions
 
ImportFromAINDialogFamily - Class in fr.curie.BiNoM.cytoscape.ain
 
ImportFromAINDialogFamily(JFrame, String, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogFamily
 
ImportFromAINTask - Class in fr.curie.BiNoM.cytoscape.ain
 
ImportFromAINTask(File, String, Vector) - Constructor for class fr.curie.BiNoM.cytoscape.ain.ImportFromAINTask
 
ImportFromSimpleTextInfluenceFile - Class in fr.curie.BiNoM.cytoscape.ain
 
ImportFromSimpleTextInfluenceFile() - Constructor for class fr.curie.BiNoM.cytoscape.ain.ImportFromSimpleTextInfluenceFile
 
importString - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Standard BioPAX v.3 prefix
includedInConservationLaw - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
Auxiliary property for analysis of conservation laws
includedSpecies - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cut uris (after # separator) to BioPAXSpecies included into entities (these species group complex components, for example)
includedSpecies - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
includedSpeciesMap - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
includeInteractions - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option
 
includeNextLinks - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option
 
includePathways - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option
 
includesEdges(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
includesNodes(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
includesNodesPercentage(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
inclusionGraph(Vector) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
Creates a new graph where nodes represent other graphs and edges represent intersections in nodes between these graphs.
incomingEdges - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
List of all in-going edges.
independentSpecies - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Auxiliary map
independentSpeciesIds - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cut uris (after # separator) to BioPAXSpecies
index - Variable in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
indexOfS(String[], String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
IndexPathAnalysisDialog - Class in fr.curie.BiNoM.cytoscape.analysis
 
IndexPathAnalysisTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
IndexPathAnalysisTask(Vector<String>, Vector<String>, StructureAnalysisUtils.Option, VisualStyle, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask
 
influence - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
InfluenceAreaInArray - Class in fr.curie.BiNoM.cytoscape.influence
Display Influence Area from start nodes in text box
InfluenceAreaInArray() - Constructor for class fr.curie.BiNoM.cytoscape.influence.InfluenceAreaInArray
 
InfluenceAreaInAttribute - Class in fr.curie.BiNoM.cytoscape.influence
Empty attribute with influence computed as in influence area Avoid to crash attribute of previous computing
InfluenceAreaInAttribute() - Constructor for class fr.curie.BiNoM.cytoscape.influence.InfluenceAreaInAttribute
 
InfluenceArrayAsGraphic - Class in fr.curie.BiNoM.cytoscape.influence
Display Influence Array as Paved Window using paving window dialog
InfluenceArrayAsGraphic(boolean) - Constructor for class fr.curie.BiNoM.cytoscape.influence.InfluenceArrayAsGraphic
 
InfluenceArrayAsText - Class in fr.curie.BiNoM.cytoscape.influence
Display Influence Array for Visualizing 2 options 1: as text, not connected: nc, 3 digits after point 2: for computing, non connected=0, all possible digits
InfluenceArrayAsText(String) - Constructor for class fr.curie.BiNoM.cytoscape.influence.InfluenceArrayAsText
 
InfluenceByAttribute - Class in fr.curie.BiNoM.cytoscape.influence
Influence by Active Nodes from ACTIV_IN to Attribute result in ACTIV_OUT
InfluenceByAttribute() - Constructor for class fr.curie.BiNoM.cytoscape.influence.InfluenceByAttribute
 
InfluenceFeatures - Class in fr.curie.BiNoM.cytoscape.influence
Display the Network size and Parameter Features as min and max influence
InfluenceFeatures() - Constructor for class fr.curie.BiNoM.cytoscape.influence.InfluenceFeatures
 
influenceRadius - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask.stainingOptions
 
infradius - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
init(boolean, boolean) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserPanel
Initialization of the panel.
initializeModel() - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
initializeSignificanceAnalysis() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
initOrderedNodesList() - Method in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Initialize the ordered list of nodes by omega score.
initStructure(GraphPerspective, boolean) - Method in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
initWeigths() - Method in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
input - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Input for the query
INPUT_CURRENT_NETWORK - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask
 
INPUT_LISTOF_NAMES - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask
 
inputReach() - Method in class fr.curie.BiNoM.cytoscape.influence.FromToNodes
 
InputReachParameter - Class in fr.curie.BiNoM.cytoscape.influence
Action to input reach parameter, methods in FromToNodes
InputReachParameter() - Constructor for class fr.curie.BiNoM.cytoscape.influence.InputReachParameter
 
InsertCellDesignerParameters - Class in fr.curie.BiNoM.pathways.utils
 
InsertCellDesignerParameters() - Constructor for class fr.curie.BiNoM.pathways.utils.InsertCellDesignerParameters
 
insertHypotheticalInfluences_complexMutualInhibition - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
insertHypotheticalInfluences_inhCatalysisReactant - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
insertMapsTagBeforeModules - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask.extractingNotesOptions
 
insertMapsTagBeforeModules - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
insertMapsTagBeforeModuleTag(Vector<ModifyCellDesignerNotes.AnnotationSection>) - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
insertMassActionLaws(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.InsertCellDesignerParameters
 
insertMassActionLaws - Class in fr.curie.BiNoM.pathways.utils
 
insertMassActionLaws() - Constructor for class fr.curie.BiNoM.pathways.utils.insertMassActionLaws
 
insertMassActionLaws(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.insertMassActionLaws
 
instance - Static variable in class fr.curie.BiNoM.analysis.ClusterNetworksDialog
 
instance - Static variable in class fr.curie.BiNoM.analysis.ModularViewDialog
 
instance - Static variable in class fr.curie.BiNoM.biopax.BioPAXImportDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.createNeighborhoodSetsDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetworkDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSyncNetworksDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDisplayIndexInfoDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXViewQueryLogDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.checkCellDesignerFileDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.colorCellDesignerProteinsDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.modifyCellDesignerNotesDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.ProduceNaviCellMapFilesDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.netwop.DoubleNetworkDifferenceDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateConfirmDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog
 
instance - Static variable in class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContentsDialog
 
interaction - Variable in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph
 
Interaction - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Interaction ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
INTERACTION_CONVERSION - Static variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
Mode of conversion: from BioPAX to Protein-protein interaction BioPAX interface
InteractionGraph - Class in fr.curie.BiNoM.cytoscape.nestmanager
Put the graph from Cytoscape network in practical data structure Compute degrees and put them in a structure which can be sorted by several ways Compute the shortest path matrix used in clustering by breadth first search
InteractionGraph.IntEdge - Class in fr.curie.BiNoM.cytoscape.nestmanager
 
InteractionGraph.IntEdge(int, int) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph.IntEdge
 
InteractionGraph.IntEdge(int, int, int) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph.IntEdge
 
InteractionGraph.NodeDegree - Class in fr.curie.BiNoM.cytoscape.nestmanager
 
InteractionGraph.NodeDegree(int) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph.NodeDegree
 
InteractionImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Interaction Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
InteractionListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Interaction to receive notification when properties changed, added or removed.
interactions - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
Map from complete uris to interaction objects
interactionScoreAdded(GeneticInteraction, Score) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of interactionScore has been added
interactionScoreProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
The Jena Property for interactionScore
interactionScoreRemoved(GeneticInteraction, Score) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of interactionScore has been removed
interactionTypeChanged(BiochemicalReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when interactionType has changed
interactionTypeChanged(Catalysis) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when interactionType has changed
interactionTypeChanged(ComplexAssembly) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when interactionType has changed
interactionTypeChanged(Control) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when interactionType has changed
interactionTypeChanged(Conversion) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when interactionType has changed
interactionTypeChanged(Degradation) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when interactionType has changed
interactionTypeChanged(GeneticInteraction) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when interactionType has changed
interactionTypeChanged(Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when interactionType has changed
interactionTypeChanged(Modulation) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when interactionType has changed
interactionTypeChanged(MolecularInteraction) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when interactionType has changed
interactionTypeChanged(TemplateReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when interactionType has changed
interactionTypeChanged(TemplateReactionRegulation) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when interactionType has changed
interactionTypeChanged(Transport) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when interactionType has changed
interactionTypeChanged(TransportWithBiochemicalReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when interactionType has changed
interactionTypeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Interaction
The Jena Property for interactionType
InteractionVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for InteractionVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
InteractionVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of InteractionVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
InteractionVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.InteractionVocabulary to receive notification when properties changed, added or removed.
InterOf2SelectedNests - Class in fr.curie.BiNoM.cytoscape.nestmanager
Create networks from intersection of 2 nest networks (nodes and edges) Delete edges and nodes of intersection in 2 networks Dialog of confirmation displaying nodes to bet deleted Transfer positions to created intersection network
InterOf2SelectedNests() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.InterOf2SelectedNests
 
intersect2ListsOfSets(String, String) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
intersect2ListsOfSets(String, String, int, int) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
intersect2ListsOfSets(SetOverlapAnalysis, SetOverlapAnalysis) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
intersectGraphs(Vector<Graph>) - Method in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
intersection(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
intersectionThreshold - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
intraMolecularChanged(BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when intraMolecular has changed
intraMolecularChanged(CovalentBindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when intraMolecular has changed
intraMolecularProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BindingFeature
The Jena Property for intraMolecular
ionicStrengthChanged(DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaGListener
Called when ionicStrength has changed
ionicStrengthChanged(KPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrimeListener
Called when ionicStrength has changed
ionicStrengthProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DeltaG
The Jena Property for ionicStrength
ionicStrengthProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.KPrime
The Jena Property for ionicStrength
isBioPAXNetwork(Object) - Method in class fr.curie.BiNoM.biopax.BioPAXSourceDB
 
isCellDesignerNetwork(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerSourceDB
 
isColorChanged(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
isComplexSpecies() - Method in class fr.curie.BiNoM.pathways.utils.SpeciesStructure
 
isEmpty() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
 
isIntegerNumber(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
isNumber(String) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
isRealReaction(ReactionDocument.Reaction, SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Returns true if the reaction r describes real interaction (not influence on a phenotype, for example)
isSymlink(File) - Static method in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
isWordPress() - Method in class fr.curie.BiNoM.pathways.navicell.WordPressBlogCreator
 
itemStateChanged(ItemEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.ComboBoxes
 

K

KEGGAccess - Class in fr.curie.BiNoM.pathways.utils
 
KEGGAccess() - Constructor for class fr.curie.BiNoM.pathways.utils.KEGGAccess
 
KEGGgenesPrefix - Static variable in class fr.curie.BiNoM.pathways.utils.KEGGAccess
 
kEQAdded(BiochemicalReaction, KPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of kEQ has been added
kEQAdded(TransportWithBiochemicalReaction, KPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of kEQ has been added
kEQProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
The Jena Property for kEQ
kEQRemoved(BiochemicalReaction, KPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of kEQ has been removed
kEQRemoved(TransportWithBiochemicalReaction, KPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of kEQ has been removed
KPrime - Interface in fr.curie.BiNoM.pathways.biopax
Interface for KPrime ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
kPrimeChanged(KPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrimeListener
Called when kPrime has changed
KPrimeImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of KPrime Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
KPrimeListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.KPrime to receive notification when properties changed, added or removed.
kPrimeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.KPrime
The Jena Property for kPrime

L

label - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
labelNodeInfo - Variable in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
labelPathInfo - Variable in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
labelTargetInfo - Variable in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
LaplaceMatToSif - Class in fr.curie.BiNoM.pathways.utils
 
LaplaceMatToSif() - Constructor for class fr.curie.BiNoM.pathways.utils.LaplaceMatToSif
 
lastUsedMemory - Static variable in class fr.curie.BiNoM.pathways.utils.Utils
 
launchDialog(ArrayList<String>) - Method in class fr.curie.BiNoM.cytoscape.utils.ComboBoxes
 
launchDialog(ArrayList<String>) - Method in class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
launchDialog(int[], int[], ArrayList<String>, ArrayList<String>) - Method in class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 
leftAdded(BiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of left has been added
leftAdded(ComplexAssembly, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of left has been added
leftAdded(Conversion, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of left has been added
leftAdded(Degradation, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of left has been added
leftAdded(Transport, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of left has been added
leftAdded(TransportWithBiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of left has been added
leftProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Conversion
The Jena Property for left
leftRemoved(BiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of left has been removed
leftRemoved(ComplexAssembly, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of left has been removed
leftRemoved(Conversion, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of left has been removed
leftRemoved(Degradation, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of left has been removed
leftRemoved(Transport, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of left has been removed
leftRemoved(TransportWithBiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of left has been removed
length - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
LinearizeNetwork - Class in fr.curie.BiNoM.celldesigner.analysis
 
LinearizeNetwork(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.LinearizeNetwork
 
LinearizeNetwork - Class in fr.curie.BiNoM.cytoscape.analysis
 
LinearizeNetwork() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.LinearizeNetwork
 
LinearizeNetwork(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
LinearizeNetworkTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
LinearizeNetworkTask(CellDesignerPlugin, GraphDocument) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.LinearizeNetworkTask
 
LinearizeNetworkTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
LinearizeNetworkTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.LinearizeNetworkTask
 
link - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
Some object associated.
LIST_COMPLEXES - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Simply lists the proteins from the input to the query log
LIST_GENES - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Simply lists the dnas from the input to the query log
LIST_PROTEINS - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Simply lists the proteins from the input to the query log
LIST_PUBLICATIONS - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Simply lists the publications from the input to the query log
LIST_REACTIONS - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Simply lists the reactions from the input to the query log
LIST_SMALL_MOLECULES - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Simply lists the smallMolecules from the input to the query log
ListAllNodes - Class in fr.curie.BiNoM.cytoscape.utils
 
ListAllNodes() - Constructor for class fr.curie.BiNoM.cytoscape.utils.ListAllNodes
 
ListAllNodesDialog - Class in fr.curie.BiNoM.cytoscape.utils
 
ListAllNodesDialog() - Constructor for class fr.curie.BiNoM.cytoscape.utils.ListAllNodesDialog
 
ListAllReactions - Class in fr.curie.BiNoM.cytoscape.utils
 
ListAllReactions() - Constructor for class fr.curie.BiNoM.cytoscape.utils.ListAllReactions
 
ListAllReactionsDialog - Class in fr.curie.BiNoM.cytoscape.utils
 
ListAllReactionsDialog() - Constructor for class fr.curie.BiNoM.cytoscape.utils.ListAllReactionsDialog
 
listCompatibleInterfaces(com.hp.hpl.jena.rdf.model.Resource) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory
Return a list of compatible interfaces for the given type.
ListComponents - Class in fr.curie.BiNoM.cytoscape.nestmanager
List component in current network and nests from species described as BiNoM syntax Network generally converted from a CellDesigner file or URL Species are identified by attribute CELLDESIGNER_SPECIES
ListComponents() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ListComponents
 
ListDialog - Class in fr.curie.BiNoM.cytoscape.utils
A dialog box to select strings in a sorted list displaying selected strings
ListDialog(JFrame, String, String, String[]) - Constructor for class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
ListNodesByNest - Class in fr.curie.BiNoM.cytoscape.nestmanager
List nodes in current network inside nest or not Result in a text box
ListNodesByNest() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ListNodesByNest
 
listOfNodesInitial - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
listOfRankedGenes - Variable in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
lists - Variable in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
listSetsIncludingSet(String, String[]) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
listSetsIncludingSet(String, HashSet<String>) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
listSetsIncludingSet(HashSet<String>) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
listSpeciesForGeneList(SbmlDocument, Vector<String>) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ChemicalStructureImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceLocationImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.UtilityClassImpl
 
listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
load(String) - Method in class fr.curie.BiNoM.pathways.utils.GMTFile
 
load_config(File) - Static method in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
load_xrefs(BufferedReader, String) - Static method in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
loadAttribTable(String) - Method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
loadAttribTable(String) - Method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies
 
loadAttribTable(String) - Method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
loadBioPAX(String) - Method in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Loads BioPAX content from file fn
loadBioPAX(InputStream) - Method in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Loads BioPAX content from InputStream is
loadBioPAXFromString(String) - Method in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Loads BioPAX content from String
loadCellDesigner(String) - Method in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
loadCellDesigner() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
loadCellDesigner(String) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner
Loads org.sbml.x2001.ns.celldesigner.SbmlDocument from file
loadCellDesignerFromText(String) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner
Load org.sbml.x2001.ns.celldesigner.SbmlDocument from String
loadConfigFile(String) - Method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
Load the configuration file.
loadCSML(String) - Static method in class fr.curie.BiNoM.pathways.test.testCSML
 
loadCSML(String) - Static method in class fr.curie.BiNoM.pathways.wrappers.CSML
 
loadDataTable(String) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
loadDataTable(String, String) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
loadFromFile(String) - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
LoadFromSimpleDatFile(String, boolean, String) - Method in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
LoadFromSimpleDatFile(Reader, boolean, String) - Method in class fr.curie.BiNoM.pathways.utils.SimpleTable
Loads the table from the file.
LoadFromSimpleDatFileString(String, boolean, String) - Method in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
loadFromXMGML(String) - Static method in class fr.curie.BiNoM.pathways.utils.XGMMLExport
 
loadFromXMGML(String) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML
Loads XGMML from file
loadGeneList() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
loadGenePositions(String) - Method in class fr.curie.BiNoM.pathways.test.AgilentCGHMapping
 
loadGraph(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
loadGroupsOfProteins(String) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
loadHPRD(String) - Method in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
loadKEGGasGMTString(Vector<String>) - Static method in class fr.curie.BiNoM.pathways.utils.KEGGAccess
 
loadMap(String) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
loadMatrixFromFile(String) - Static method in class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
loadModel(String, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
Load the OWL model from file
loadNetwork(String) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
LoadNewOrderedList(String) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
loadRandkedGeneList(String) - Method in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
loadRandkedGeneList(String) - Static method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
loadReactions() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
loadReferenceGraph() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
loadSBML(String) - Static method in class fr.curie.BiNoM.pathways.wrappers.SBML
Loads SbmlDocument from file
LoadSetsFromGMT(String) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
loadSetsFromTable(String) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
loadSpecies() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
loadString(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Load a text file into memory and returns String
loadString(InputStream) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Converts InputStream into String
loadStringListFromFile(String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
loadTable(String) - Method in class fr.curie.BiNoM.pathways.utils.AccessionNumberTable
Loads tab delimited two-columns table \t
lostOwnership(Clipboard, Transferable) - Method in class fr.curie.BiNoM.cytoscape.utils.TextBox
 
lostOwnership(Clipboard, Transferable) - Method in class fr.curie.BiNoM.cytoscape.utils.TextBoxDialog
 

M

main(String[]) - Static method in class fr.curie.BiNoM.celldesigner.lib.testNetworkFactory
 
main(String[]) - Static method in class fr.curie.BiNoM.cytoscape.utils.SelectNodesByAttributeSubstringDialog
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.Skeleton
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.testPath
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.BioPAX2CellDesigner
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.BioPAX2Cytoscape
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.BioPAX2SBML
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.BioPAXIndex2Tables
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.CellDesigner2BioPAX
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.CellDesigner2Cytoscape
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.Cytoscape2BioPAX
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.Cytoscape2CellDesigner
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.Cytoscape2SBML
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.SimpleTextInfluence2BioPAX
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.Transpath2BioPAX
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.CSMLToCytoscapeConverter
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.navicell.WordPressTest
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.parseBioPAX
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.AgilentCGHMapping
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.analyzeSBMLFile
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.BioPAXConnectedComponents
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.examples.BioPAXConnectedComponents
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.examples.BioPAXPathAnalysis
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.examples.BioPAXStandardQuery
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.examples.CDesigner2BioPAX
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.test
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.test1
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.test2
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestAIN
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestAutomaticStructureAnalysis
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioBasePathway
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestBioPAX
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAX1
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAXExtract
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAXExtractAPO
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestBioPAXGraphMapper
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAXManipulation
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAXMerge
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAXQueryEngine
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestBioPAXQueryEngineEB
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testCellDesigner
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testChangeProteinSize
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testCSML
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestDialog
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testDialogs
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestEB
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testExtractBioPAX
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestFindAllPaths
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testFindingPath
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestGraphAlgo
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testGraphMappingService
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testGraphPruning
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testJastor
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestJastorEB
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testJavolution
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestMaterialComponents
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestMergeMapsACSN
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testMergeNetworksAndFilter
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestMergingMapsCD
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestMergingMapsDialog
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestMinCutSet
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestModuleDecomposition
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testNamingService
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestNIPath
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestOPtCutSet
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestPiquantDialog
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testRBpathway
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testRemoveEditPoints
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testSAX
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestSetSet
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testStructureAnalysis
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testTranspath
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestWordPress
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestXGMML
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.workMatlabOvidiu
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ConnectionToDatabases
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.DatabaseComparison
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.analyseInstallSpyLog
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.CellDesignerGenerator
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.CheckCellDesignerFile
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.ComputeNaviCellMaps
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.ExtractGMTFromCellDesigner
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.GeneticInteractionNetworks
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.GMTFile
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.InsertCellDesignerParameters
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.insertMassActionLaws
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.KEGGAccess
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.LaplaceMatToSif
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.Pair
Simple example test program.
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.prepareCellDesignerFile
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.SignsOfPaths
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.SpeciesStructure
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.testCellDesignerFile
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.XGMMLExport
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner
Save org.sbml.x2001.ns.celldesigner.SbmlDocument to file
main(String[]) - Static method in class fr.curie.BiNoM.pathways.wrappers.SBML
 
main(String[]) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML
 
mainBerge(boolean) - Method in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Implementation of Berge's algorithm to find minimal cut sets.
mainfile - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXMerge
The base BioPAX com.hp.hpl.jena.rdf.model.Model object
makeActiveNodeNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
makeAttrDesc(BioPAX, BioPAXClassDescFactory) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto
 
makeAttrDescV(BioPAX) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProtoFactory
 
makeBackupNetwork(CyNetwork, String) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
 
makeBackupNetwork(CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
 
makeBioPAX(String, Vector) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
Construct BioPAX object from AIN data.
MakeCanonicalView - Class in fr.curie.BiNoM.pathways.utils.acsn
 
MakeCanonicalView() - Constructor for class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
makeClassesDesc(BioPAX) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDescFactory
 
makeColorTransparent(Image, Color) - Static method in class fr.curie.BiNoM.pathways.utils.Utils.Transparency
 
makeComment(Iterator) - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Compile comments in a string from an iterator, with each comment on a different line.
makeCompactnessTest(String, Vector<Integer>, int, boolean, Vector<String>) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
makeCompactnessTest(String, Vector<Integer>, int, boolean, String, int, Vector<String>) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
makeCompartments() - Method in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Adds some standard compartments
makeComplexProfile(String) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
makeConnectivityTable - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
makeCopy() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
makeCopy() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Node
Clones the node
makeCopy(Model, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
Clones the source Model
makeEdgeDoubleSense(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
Add an edge from edgeId.Target to edgeId.Source.
makeEditPanel(BioPAXObject, Object, int, Component) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
makeEditPanel(BioPAXObject, Object, int, Component) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
makeEditPanel(BioPAXObject, Object, int, Component) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
makeEditPanel(BioPAXObject, Object, int, Component) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
makeEditPanel(BioPAXObject, Object, int, Component) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringListAttrDesc
 
makeEditPanelPerform(BioPAXAttrDesc, Vector<BioPAXClassDesc>, BioPAXObject, Object, int, Component) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
makeEditPanelPerform(BioPAXAttrDesc, BioPAXObject, Object, int, Component) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
makeGMTEntityHUGO() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
makeGMTOfReactionRegulators(String, Graph, String[]) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
makeGraph(int) - Method in class fr.curie.BiNoM.biopax.BioPAXImportBaseTask
 
makeGridBagConstraints(int, int, int, int) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
makeGridBagConstraints(int, int) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
makeHumanizedBioGrid() - Static method in class fr.curie.BiNoM.pathways.utils.GeneticInteractionNetworks
 
makeIdentifiersTable(String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ConnectionToDatabases
 
makeLists() - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Fills hashmaps(URI, Object) with Protein, Dna, Rna and SmallMolecule Objects for needed conversion.
makeMemberFamilyMap() - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
makeMetaOFTENFromRandkedGeneListFiles(Vector<String>, int[]) - Method in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
makeName(int, String) - Method in class fr.curie.BiNoM.biopax.BioPAXImportBaseTask
 
makenamelayer - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
makeNameLayer() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
makeNameLayerImage(Vector<String>, HashMap<String, String>) - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
makeOFTENAnalysis(int[]) - Method in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
makePathNetwork(Vector<Path>) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
makeReactionGraph() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
makeReactionListFromLink(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
makeReactionNotes(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.prepareCellDesignerFile
 
makeReactionsGrey - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
makeRedGreenColorFromNumbers(float[], float) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
makeRegularPoints() - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
makeRootPathwayNode - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option
 
makeSizeSignificanceTest - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
makeSLNetworkFromYeastScreen() - Static method in class fr.curie.BiNoM.pathways.utils.GeneticInteractionNetworks
 
makesubmap - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
makeSubMap() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
makeTargetNetwork() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
makeTestOfConnectivity(int, boolean, String, int, Vector<String>) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
makeUpperCaseInIndex - Variable in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
map() - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
The mapping implementation
mapBioPAXToGraph(BioPAX) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMappingService
Creates BioPAX index as XGMML file from BioPAX object
mapClassesToNodeProps(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
MapEntitiesId(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
mapFromTokenToFamily - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
mappedEntities - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
mapProfile(String) - Method in class fr.curie.BiNoM.pathways.test.AgilentCGHMapping
 
mapSignOfConservationCoeffs - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
MapSpeciesAliases(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
MapSpeciesId(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
markMissingInformation - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
MaterialComponents - Class in fr.curie.BiNoM.celldesigner.analysis
 
MaterialComponents(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.MaterialComponents
 
MaterialComponents - Class in fr.curie.BiNoM.cytoscape.analysis
 
MaterialComponents() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.MaterialComponents
 
MaterialComponentsTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
MaterialComponentsTask(CellDesignerPlugin, GraphDocument) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.MaterialComponentsTask
 
MaterialComponentsTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
MaterialComponentsTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.MaterialComponentsTask
 
Matrix2Color - Class in fr.curie.BiNoM.pathways.coloring
 
Matrix2Color() - Constructor for class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
matrix2Vector(float[][]) - Static method in class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
maxHitSetSize - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Maximum intervention set size for partial search.
maxNbHitSet - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Maximum number of sets for partial search.
maxSetNb - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Maximum set number cutoff value
maxSetSize - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Maximum set size cutoff value.
memberEntityReferenceAdded(DnaReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceAdded(DnaReference, DnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceAdded(DnaRegionReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceAdded(EntityReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceAdded(ProteinReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceAdded(ProteinReference, ProteinReference) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceAdded(RnaReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceAdded(RnaReference, RnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceAdded(RnaRegionReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceAdded(SmallMoleculeReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceAdded(SmallMoleculeReference, SmallMoleculeReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of memberEntityReference has been added
memberEntityReferenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityReference
The Jena Property for memberEntityReference
memberEntityReferenceRemoved(DnaReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of memberEntityReference has been removed
memberEntityReferenceRemoved(DnaReference, DnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of memberEntityReference has been removed
memberEntityReferenceRemoved(DnaRegionReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of memberEntityReference has been removed
memberEntityReferenceRemoved(EntityReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of memberEntityReference has been removed
memberEntityReferenceRemoved(ProteinReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of memberEntityReference has been removed
memberEntityReferenceRemoved(ProteinReference, ProteinReference) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of memberEntityReference has been removed
memberEntityReferenceRemoved(RnaReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of memberEntityReference has been removed
memberEntityReferenceRemoved(RnaReference, RnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of memberEntityReference has been removed
memberEntityReferenceRemoved(RnaRegionReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of memberEntityReference has been removed
memberEntityReferenceRemoved(SmallMoleculeReference, EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of memberEntityReference has been removed
memberEntityReferenceRemoved(SmallMoleculeReference, SmallMoleculeReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of memberEntityReference has been removed
memberFeatureAdded(BindingFeature, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when a value of memberFeature has been added
memberFeatureAdded(CovalentBindingFeature, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when a value of memberFeature has been added
memberFeatureAdded(EntityFeature, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeatureListener
Called when a value of memberFeature has been added
memberFeatureAdded(FragmentFeature, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.FragmentFeatureListener
Called when a value of memberFeature has been added
memberFeatureAdded(ModificationFeature, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when a value of memberFeature has been added
memberFeatureProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
The Jena Property for memberFeature
memberFeatureRemoved(BindingFeature, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeatureListener
Called when a value of memberFeature has been removed
memberFeatureRemoved(CovalentBindingFeature, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when a value of memberFeature has been removed
memberFeatureRemoved(EntityFeature, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeatureListener
Called when a value of memberFeature has been removed
memberFeatureRemoved(FragmentFeature, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.FragmentFeatureListener
Called when a value of memberFeature has been removed
memberFeatureRemoved(ModificationFeature, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when a value of memberFeature has been removed
memberPhysicalEntityAdded(Complex, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(Complex, Complex) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(Dna, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(Dna, Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(DnaRegion, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(DnaRegion, DnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(PhysicalEntity, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(Protein, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(Protein, Protein) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(Rna, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(Rna, Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(RnaRegion, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(RnaRegion, RnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(SmallMolecule, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityAdded(SmallMolecule, SmallMolecule) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of memberPhysicalEntity has been added
memberPhysicalEntityProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
The Jena Property for memberPhysicalEntity
memberPhysicalEntityRemoved(Complex, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(Complex, Complex) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(Dna, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(Dna, Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(DnaRegion, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(DnaRegion, DnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(PhysicalEntity, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(Protein, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(Protein, Protein) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(Rna, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(Rna, Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(RnaRegion, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(RnaRegion, RnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(SmallMolecule, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of memberPhysicalEntity has been removed
memberPhysicalEntityRemoved(SmallMolecule, SmallMolecule) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of memberPhysicalEntity has been removed
mergeAll(String) - Method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
Merge all maps into one.
mergeCellDesignerFiles(SbmlDocument, SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Merges two CellDesigner SbmlDocuments, the result of merging is in sbout
mergeDiagrams(SbmlDocument, SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
mergeFamilies() - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
MergeGraphs(Vector<Graph>) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
mergeIfFileExists - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
mergeImages - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.MergingMapsTask.MergingMapsOptions
 
mergeMainWithReferences() - Method in class fr.curie.BiNoM.pathways.utils.BioPAXMerge
Merging of the base file with reference files.
mergeMapImages(String, int, int, int) - Method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
 
MergeNetworkAndFilter(Vector<Graph>, float) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
MergeNetworksAndFilter - Class in fr.curie.BiNoM.cytoscape.utils
 
MergeNetworksAndFilter() - Constructor for class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilter
 
MergeNetworksAndFilterTask - Class in fr.curie.BiNoM.cytoscape.utils
 
MergeNetworksAndFilterTask(int[], StructureAnalysisUtils.Option, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilterTask
 
MergeNetworksAndFilterTaskFactory - Class in fr.curie.BiNoM.cytoscape.utils
 
MergeNetworksAndFilterTaskFactory() - Constructor for class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilterTaskFactory
 
MergeSelectedNests - Class in fr.curie.BiNoM.cytoscape.nestmanager
Merge selected nests using NestMerging
MergeSelectedNests() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.MergeSelectedNests
 
MergingMaps - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
MergingMaps() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.MergingMaps
 
mergingMaps - Class in fr.curie.BiNoM.pathways.test
 
mergingMaps() - Constructor for class fr.curie.BiNoM.pathways.test.mergingMaps
 
MergingMapsDialog - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
MergingMapsDialog() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.MergingMapsDialog
Constructor
MergingMapsProcessor - Class in fr.curie.BiNoM.pathways.utils
Cell Designer merging maps procedures.
MergingMapsProcessor() - Constructor for class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
Constructor
MergingMapsTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
MergingMapsTask(String, String, MergingMapsTask.MergingMapsOptions) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.MergingMapsTask
 
MergingMapsTask.MergingMapsOptions - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
MergingMapsTask.MergingMapsOptions() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.MergingMapsTask.MergingMapsOptions
 
metaNodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
methodOfSubnetworkExtraction - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
minByComp(ShortPathClustering.Distance) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Distance
 
missingValueColor - Static variable in class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
MLLabel - Class in fr.curie.BiNoM.lib
 
MLLabel() - Constructor for class fr.curie.BiNoM.lib.MLLabel
 
MLLabel(String) - Constructor for class fr.curie.BiNoM.lib.MLLabel
 
MLLabel(int) - Constructor for class fr.curie.BiNoM.lib.MLLabel
 
MLLabel(String, int) - Constructor for class fr.curie.BiNoM.lib.MLLabel
 
model - Variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
BioPAX OWL as com.hp.hpl.jena.rdf.Model
modelClosed(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin.BiNoMPlugin
 
modelClosed(jp.sbi.celldesigner.plugin.PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin2.Plugin
 
modelClosed(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.sample.SamplePlugin
 
modelOpened(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin.BiNoMPlugin
 
modelOpened(jp.sbi.celldesigner.plugin.PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin2.Plugin
 
modelOpened(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.sample.SamplePlugin
 
modelSelectChanged(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin.BiNoMPlugin
 
modelSelectChanged(jp.sbi.celldesigner.plugin.PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin2.Plugin
 
modelSelectChanged(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.sample.SamplePlugin
 
modeOfSubNetworkConstruction - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
modification_type - Variable in class fr.curie.BiNoM.pathways.utils.SpeciesStructure.SpeciesStructureComponentModification
 
ModificationFeature - Interface in fr.curie.BiNoM.pathways.biopax
Interface for ModificationFeature ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ModificationFeatureImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of ModificationFeature Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ModificationFeatureListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.ModificationFeature to receive notification when properties changed, added or removed.
modifications - Variable in class fr.curie.BiNoM.pathways.utils.SpeciesStructure.SpeciesStructureComponent
 
modificationTypeChanged(CovalentBindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureListener
Called when modificationType has changed
modificationTypeChanged(ModificationFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeatureListener
Called when modificationType has changed
modificationTypeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.ModificationFeature
The Jena Property for modificationType
modifyCellDesignerNotes - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
modifyCellDesignerNotes() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.modifyCellDesignerNotes
 
ModifyCellDesignerNotes - Class in fr.curie.BiNoM.pathways.utils
 
ModifyCellDesignerNotes() - Constructor for class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
ModifyCellDesignerNotes() - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
ModifyCellDesignerNotes.AnnotationSection - Class in fr.curie.BiNoM.pathways.utils
 
ModifyCellDesignerNotes.AnnotationSection() - Constructor for class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes.AnnotationSection
 
modifyCellDesignerNotesDialog - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
modifyCellDesignerNotesTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
modifyCellDesignerNotesTask(String, String) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.modifyCellDesignerNotesTask
 
ModifyIfSeveralEntitiesForTheSameReference(Entity, String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
 
modifyPositionOfSpecies(SbmlDocument, GraphDocument) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
modifyPositionOfSpecies(SbmlDocument, GraphDocument) - Static method in class fr.curie.BiNoM.pathways.test.testCellDesigner
 
modifyPositionOfSpecies(SbmlDocument, GraphDocument) - Static method in class fr.curie.BiNoM.pathways.test.TestMergingMapsCD
 
ModularView - Class in fr.curie.BiNoM.celldesigner.analysis
 
ModularView(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.ModularView
 
ModularView - Class in fr.curie.BiNoM.cytoscape.analysis
 
ModularView() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ModularView
 
ModularViewDialog - Class in fr.curie.BiNoM.analysis
 
ModularViewTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
ModularViewTask(PluginModel, CellDesignerPlugin, int, int[], boolean, boolean) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.ModularViewTask
 
ModularViewTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
ModularViewTask(int, int[], boolean, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ModularViewTask
 
ModularViewTaskFactory - Class in fr.curie.BiNoM.celldesigner.analysis
 
ModularViewTaskFactory - Class in fr.curie.BiNoM.cytoscape.analysis
 
ModularViewTaskFactory() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ModularViewTaskFactory
 
Modulation - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Modulation ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ModulationImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Modulation Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ModulationListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Modulation to receive notification when properties changed, added or removed.
moduleGMTFileName - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask.extractingNotesOptions
 
moduleGMTFileName - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
ModuleVisualStyle - Class in fr.curie.BiNoM.cytoscape.nestmanager
Create a style to visualize nest networks
ModuleVisualStyle() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ModuleVisualStyle
 
MOLECULAR_EVIDENCE - Static variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
MolecularInteraction - Interface in fr.curie.BiNoM.pathways.biopax
Interface for MolecularInteraction ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
MolecularInteractionImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of MolecularInteraction Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
MolecularInteractionListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.MolecularInteraction to receive notification when properties changed, added or removed.
molecularWeightChanged(SmallMoleculeReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when molecularWeight has changed
molecularWeightProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
The Jena Property for molecularWeight
moleculeEnd - Static variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
moleculeHash - Variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
molecules - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
moleculeStart - Static variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
MonoMolecularReactionsAsEdges - Class in fr.curie.BiNoM.celldesigner.analysis
 
MonoMolecularReactionsAsEdges(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.MonoMolecularReactionsAsEdges
 
MonoMolecularReactionsAsEdges - Class in fr.curie.BiNoM.cytoscape.analysis
 
MonoMolecularReactionsAsEdges() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.MonoMolecularReactionsAsEdges
 
MonoMolecularReactionsAsEdgesTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
MonoMolecularReactionsAsEdgesTask(CellDesignerPlugin, GraphDocument) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.MonoMolecularReactionsAsEdgesTask
 
MonoMolecularReactionsAsEdgesTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
MonoMolecularReactionsAsEdgesTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.MonoMolecularReactionsAsEdgesTask
 
mouseClicked(MouseEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassTreeFrame
 
mouseClicked(MouseEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserPanel
 
mouseEntered(MouseEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassTreeFrame
 
mouseEntered(MouseEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserPanel
 
mouseExited(MouseEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassTreeFrame
 
mouseExited(MouseEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserPanel
 
mousePressed(MouseEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassTreeFrame
 
mousePressed(MouseEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserPanel
 
mouseReleased(MouseEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassTreeFrame
 
mouseReleased(MouseEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserPanel
 
moveNonannotatedTextToReferenceSection - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask.extractingNotesOptions
 
moveNonannotatedTextToReferenceSection - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
moveSpeciesNotesToProteinNotes(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.testCellDesigner
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.ClusterNetworks
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.ConnectedComponents
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.CycleDecomposition
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.ExcludeIntermediateNodes
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.ExtractReactionNetwork
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.LinearizeNetwork
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.MaterialComponents
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.ModularView
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.MonoMolecularReactionsAsEdges
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.PruneGraph
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.analysis.StronglyConnectedComponents
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.biopax.BioPAXImportFromFile
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.biopax.propedit.BioPAXClassTree
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.biopax.propedit.BioPAXPropertyBrowser
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginAction
 
myActionPerformed(ActionEvent) - Method in class fr.curie.BiNoM.celldesigner.sample.SampleAction
 

N

N - Static variable in class fr.curie.BiNoM.cytoscape.utils.GridBagDialog
 
name - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
NAME - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.ModuleVisualStyle
 
name - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Attribute
 
name - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
name - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter.BioPAXSpecies
 
name - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes.AnnotationSection
 
name - Variable in class fr.curie.BiNoM.pathways.utils.SpeciesStructure.SpeciesStructureComponent
 
name - Variable in class fr.curie.BiNoM.pathways.utils.SpeciesStructure.SpeciesStructureComponentModification
 
nameAdded(BiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of name has been added
nameAdded(BioSource, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSourceListener
Called when a value of name has been added
nameAdded(Catalysis, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of name has been added
nameAdded(ComplexAssembly, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of name has been added
nameAdded(Complex, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of name has been added
nameAdded(Control, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of name has been added
nameAdded(Conversion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of name has been added
nameAdded(Degradation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of name has been added
nameAdded(Dna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of name has been added
nameAdded(DnaReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of name has been added
nameAdded(DnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of name has been added
nameAdded(DnaRegionReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of name has been added
nameAdded(Entity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityListener
Called when a value of name has been added
nameAdded(EntityReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of name has been added
nameAdded(Gene, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of name has been added
nameAdded(GeneticInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of name has been added
nameAdded(Interaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of name has been added
nameAdded(Modulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of name has been added
nameAdded(MolecularInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of name has been added
nameAdded(Pathway, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of name has been added
nameAdded(PhysicalEntity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of name has been added
nameAdded(Protein, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of name has been added
nameAdded(ProteinReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of name has been added
nameAdded(Provenance, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProvenanceListener
Called when a value of name has been added
nameAdded(Rna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of name has been added
nameAdded(RnaReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of name has been added
nameAdded(RnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of name has been added
nameAdded(RnaRegionReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of name has been added
nameAdded(SmallMolecule, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of name has been added
nameAdded(SmallMoleculeReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of name has been added
nameAdded(TemplateReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of name has been added
nameAdded(TemplateReactionRegulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of name has been added
nameAdded(Transport, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of name has been added
nameAdded(TransportWithBiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of name has been added
nameElements - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
nameEntity - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
nameEntity - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
nameFeatures - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
nameFeatures - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
nameid - Variable in class fr.curie.BiNoM.pathways.utils.AccessionNumberTable
Map from name in the table used to the Vector of database ids/names
nameParticipant - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
nameParticipant - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
nameProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BioSource
The Jena Property for name
nameProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Entity
The Jena Property for name
nameProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityReference
The Jena Property for name
nameProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Provenance
The Jena Property for name
nameReactions - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
nameReactions - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
nameRemoved(BiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of name has been removed
nameRemoved(BioSource, String) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSourceListener
Called when a value of name has been removed
nameRemoved(Catalysis, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of name has been removed
nameRemoved(ComplexAssembly, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of name has been removed
nameRemoved(Complex, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of name has been removed
nameRemoved(Control, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of name has been removed
nameRemoved(Conversion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of name has been removed
nameRemoved(Degradation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of name has been removed
nameRemoved(Dna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of name has been removed
nameRemoved(DnaReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of name has been removed
nameRemoved(DnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of name has been removed
nameRemoved(DnaRegionReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of name has been removed
nameRemoved(Entity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityListener
Called when a value of name has been removed
nameRemoved(EntityReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of name has been removed
nameRemoved(Gene, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of name has been removed
nameRemoved(GeneticInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of name has been removed
nameRemoved(Interaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of name has been removed
nameRemoved(Modulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of name has been removed
nameRemoved(MolecularInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of name has been removed
nameRemoved(Pathway, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of name has been removed
nameRemoved(PhysicalEntity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of name has been removed
nameRemoved(Protein, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of name has been removed
nameRemoved(ProteinReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of name has been removed
nameRemoved(Provenance, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProvenanceListener
Called when a value of name has been removed
nameRemoved(Rna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of name has been removed
nameRemoved(RnaReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of name has been removed
nameRemoved(RnaRegion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of name has been removed
nameRemoved(RnaRegionReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of name has been removed
nameRemoved(SmallMolecule, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of name has been removed
nameRemoved(SmallMoleculeReference, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of name has been removed
nameRemoved(TemplateReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of name has been removed
nameRemoved(TemplateReactionRegulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of name has been removed
nameRemoved(Transport, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of name has been removed
nameRemoved(TransportWithBiochemicalReaction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of name has been removed
namespaceFileString - Static variable in class fr.curie.BiNoM.pathways.test.TestBioPAX
 
namespaceFileString - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Standard BioPAX v.3 prefix
namespaceString - Static variable in class fr.curie.BiNoM.pathways.test.TestBioPAX
 
namespaceString - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Standard BioPAX v.3 prefix
nameType - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
nbTopSets - Variable in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetVisuDialog
 
neighboursOfNodeHash(Graph, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
Sub-routine for Dijkstra's algorithm Returns vector (of length number of nodes) of vectors of outgoing edges numbers
NestInNodeAttribute - Class in fr.curie.BiNoM.cytoscape.nestmanager
Create a node attribute containing nest name where it is in the current network
NestInNodeAttribute() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.NestInNodeAttribute
 
NestMerging - Class in fr.curie.BiNoM.cytoscape.nestmanager
Merge several nests and create merged networks Replace selected nodes by one merged and delete edges in nest network Transfer positions to created network
NestMerging(CyNetwork, CyNetworkView) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.NestMerging
 
NestUtils - Class in fr.curie.BiNoM.cytoscape.nestmanager
Class gathering useful functions shared by several classes of nest manager: - Access by different structure to list of nodes or edges - Edges linking nodes - Reconnection between 2 nodes by copy an edge from a reference network - Create network made of nests - Pack part of network in nest keeping connections - Transfer positions, delete edges - Dialog to select one or several networks
NestUtils() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
network - Variable in class fr.curie.BiNoM.cytoscape.analysis.createNeighborhoodSetsDialog
 
network - Variable in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph
 
network - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
network - Variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
NetworkDifference - Class in fr.curie.BiNoM.cytoscape.netwop
 
NetworkDifference(CyNetwork, CyNetwork) - Constructor for class fr.curie.BiNoM.cytoscape.netwop.NetworkDifference
 
networkDistanceMatrix - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
NetworkFactory - Class in fr.curie.BiNoM.celldesigner.lib
 
NetworkFactory() - Constructor for class fr.curie.BiNoM.celldesigner.lib.NetworkFactory
 
NetworkFactory - Class in fr.curie.BiNoM.cytoscape.lib
 
NetworkFactory() - Constructor for class fr.curie.BiNoM.cytoscape.lib.NetworkFactory
 
NetworkIntersection - Class in fr.curie.BiNoM.cytoscape.netwop
 
NetworkIntersection(CyNetwork, CyNetwork) - Constructor for class fr.curie.BiNoM.cytoscape.netwop.NetworkIntersection
 
NetworkOperation - Class in fr.curie.BiNoM.cytoscape.netwop
 
NetworkOperation(String, String) - Constructor for class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation
 
NetworkOperation.Estimator - Class in fr.curie.BiNoM.cytoscape.netwop
 
NetworkOperation.Estimator() - Constructor for class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
 
NetworksUpdate - Class in fr.curie.BiNoM.cytoscape.netwop
 
NetworksUpdate() - Constructor for class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdate
 
NetworksUpdateConfirmDialog - Class in fr.curie.BiNoM.cytoscape.netwop
 
NetworksUpdateDialog - Class in fr.curie.BiNoM.cytoscape.netwop
 
NetworksUpdateTask - Class in fr.curie.BiNoM.cytoscape.netwop
 
NetworksUpdateTask(CyNetwork[], CyNetwork, CyNetwork) - Constructor for class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateTask
 
NetworkUnion - Class in fr.curie.BiNoM.cytoscape.netwop
 
NetworkUnion(CyNetwork, CyNetwork) - Constructor for class fr.curie.BiNoM.cytoscape.netwop.NetworkUnion
 
NetworkUtils - Class in fr.curie.BiNoM.celldesigner.lib
 
NetworkUtils() - Constructor for class fr.curie.BiNoM.celldesigner.lib.NetworkUtils
 
NetworkUtils - Class in fr.curie.BiNoM.cytoscape.lib
 
NetworkUtils() - Constructor for class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
 
newFamilies - Variable in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogFamily
 
newline - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
System independent newline character
nextElement() - Method in class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer
Returns the next token from the input string.
nextStepAdded(BiochemicalPathwayStep, PathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of nextStep has been added
nextStepAdded(PathwayStep, PathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStepListener
Called when a value of nextStep has been added
nextStepProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
The Jena Property for nextStep
nextStepRemoved(BiochemicalPathwayStep, PathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of nextStep has been removed
nextStepRemoved(PathwayStep, PathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStepListener
Called when a value of nextStep has been removed
nextToken() - Method in class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer
Returns the next token from the input string.
Node - Class in fr.curie.BiNoM.pathways.analysis.structure
 
Node() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Node
 
Node1 - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
Source node
Node2 - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
Target node
NODE_ATTR - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_ATTR - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_BIOCHEMICAL_REACTION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_CATALYSIS - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_CATALYSIS - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_COMPLEX - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_COMPLEX - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_COMPLEX_ASSEMBLY - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_CONTROL - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_CONVERSION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_DNA - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_DNAREGION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_GENE - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_GENE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_GENETIC_INTERACTION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_HETERODIMER_ASSOCIATION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_HETERODIMER_DISSOCIATION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_INTERACTION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_ION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_KNOWN_TRANSITION_OMITTED - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_MODULATION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_NEGATIVE_INFLUENCE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_PATHWAY - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_PATHWAY - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_PATHWAY_STEP - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_PHENOTYPE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_PHYSICAL_ENTITY - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_PHYSICAL_INTERACTION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_POSITIVE_INFLUENCE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_PROTEIN - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_PROTEIN - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_PUBLICATION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_RNA - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_RNA - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_RNAREGION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_SIMPLE_MOLECULE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_SMALL_MOLECULE - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_STATE_TRANSITION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_TEMPLATE_REACTION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_TRANSCRIPTION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_TRANSCRIPTIONAL_ACTIVATION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_TRANSCRIPTIONAL_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_TRANSLATION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_TRANSLATIONAL_ACTIVATION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_TRANSLATIONAL_INHIBITION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_TRANSPORT - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_TRANSPORT - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_TRANSPORT_WITH_BIOCHEMICAL_REACTION - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition
 
NODE_TRUNCATION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_UNKNOWN_NEGATIVE_INFLUENCE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_UNKNOWN_POSITIVE_INFLUENCE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_UNKNOWN_REACTION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
NODE_UNKNOWN_TRANSITION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition
 
nodeAttr - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
NodeBorderColor - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
nodeBorderColorMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
nodeBorderLineStyleMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
nodeBorderLineWidthMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
NodeBorderWidth - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
NodeClass - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
0 - species 1 - reaction 2 - cycle 3 - metanode
NodeClassInfo - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
NodeColor - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
nodeColorMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
NodeHash - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
nodeId - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OmegaScoreData
Node ID
nodeID2attribute - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Node Id to attribute value map
nodeImageMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
nodeInconsistencies - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
NodeIndexHash - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
NodeInfo - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
NodeLabel - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
nodeNameArray - Variable in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetGenesDialog
 
nodes - Variable in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph
 
nodes - Variable in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
Nodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
nodes - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
Map from node ids and object uris to Node objects
NodesAndEdgesClipboard - Class in fr.curie.BiNoM.cytoscape.utils
 
nodeSequence - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
NodeShape - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
nodeShapeMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
NodeSize - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
nodeSizeMapping - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
nodesToExclude - Variable in class fr.curie.BiNoM.analysis.ExcludeIntermediateNodesDialog
 
noGraphTest() - Static method in class fr.curie.BiNoM.pathways.test.TestOPtCutSet
 
normalizeColumnValues - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
normalizeToZValues - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask.stainingOptions
 
notFeatureAdded(Complex, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of notFeature has been added
notFeatureAdded(Dna, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of notFeature has been added
notFeatureAdded(DnaRegion, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of notFeature has been added
notFeatureAdded(PhysicalEntity, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of notFeature has been added
notFeatureAdded(Protein, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of notFeature has been added
notFeatureAdded(Rna, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of notFeature has been added
notFeatureAdded(RnaRegion, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of notFeature has been added
notFeatureAdded(SmallMolecule, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of notFeature has been added
notFeatureAdded(SmallMolecule, BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of notFeature has been added
notFeatureProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
The Jena Property for notFeature
notFeatureRemoved(Complex, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of notFeature has been removed
notFeatureRemoved(Dna, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of notFeature has been removed
notFeatureRemoved(DnaRegion, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of notFeature has been removed
notFeatureRemoved(PhysicalEntity, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of notFeature has been removed
notFeatureRemoved(Protein, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of notFeature has been removed
notFeatureRemoved(Rna, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of notFeature has been removed
notFeatureRemoved(RnaRegion, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of notFeature has been removed
notFeatureRemoved(SmallMolecule, EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of notFeature has been removed
notFeatureRemoved(SmallMolecule, BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of notFeature has been removed
numberOfActiveNodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
numberOfPermutations - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
numberOfPermutations - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
numberOfPermutationsForSizeTest - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
numberOfPermutationsForSizeTest - Variable in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
numberOfStatements(com.ibm.adtech.jastor.Thing) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
 
numberOfStatements(Model) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
 
numberOfTimesToScale - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.MergingMapsTask.MergingMapsOptions
 

O

o1 - Variable in class fr.curie.BiNoM.pathways.utils.Pair
 
o2 - Variable in class fr.curie.BiNoM.pathways.utils.Pair
 
OCS_BERGE - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Ocsana search option: Berge's algorithm
OCS_PARTIAL - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Ocsana search option: partial search
OCS_SEED - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Ocsana search option: seed based search
ocsanaScore() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Determine paths for optimal combinations sets analysis and calculate the scores for elementary nodes.
ocsanaSearch() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Performs optimal intervention set search.
ocsSearch - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Ocsana search option by default
OCTAGON - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
OFTENAnalysis - Class in fr.curie.BiNoM.pathways.utils
 
OFTENAnalysis() - Constructor for class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
OmegaScoreData - Class in fr.curie.BiNoM.pathways.analysis.structure
Simple class to store Omega score data for optimal intervention sets elementary nodes.
OmegaScoreData(String, double) - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.OmegaScoreData
 
omegaScoreList - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Ordered list of nodes nodes with their corresponding omega scores.
omegaScoreMap - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Omega score per elementary node = OCSANA Score
omegaScores - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Ocsana Omega scores
ontology - Variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
com.hp.hpl.jena.ontology.Ontology object
open_file(File) - Static method in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
open_local_file(String) - Static method in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
optCutSet - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer.optCutSetData
 
optCutSetReport - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Report for the optimal intervention set search
optCutSetSize - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer.optCutSetData
 
OptimalCombinationAnalyzer - Class in fr.curie.BiNoM.pathways.analysis.structure
Optimal Combinations of intervention strategies for network analysis (OCSANA) class.
OptimalCombinationAnalyzer() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Constructor
OptimalCutSetAnalyzer - Class in fr.curie.BiNoM.cytoscape.analysis
Root class for the optimal intervention set analysis.
OptimalCutSetAnalyzer() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzer
 
OptimalCutSetAnalyzerDialog - Class in fr.curie.BiNoM.cytoscape.analysis
Graphical interface for the input parameters of the Optimal Intervention Set algorithm.
OptimalCutSetAnalyzerDialog(JFrame, String, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerDialog
Constructor
OptimalCutSetAnalyzerTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
OptimalCutSetAnalyzerTask(DataPathConsistencyAnalyzer) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerTask
 
OptimalCutSetGenesDialog - Class in fr.curie.BiNoM.cytoscape.analysis
Paste box for a list of items to be selected in a JList.
OptimalCutSetGenesDialog(JFrame, String, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetGenesDialog
 
OptimalCutSetReportDialog - Class in fr.curie.BiNoM.cytoscape.analysis
A simple dialog window to show the optimal intervention set search report.
OptimalCutSetReportDialog(DataPathConsistencyAnalyzer) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetReportDialog
 
OptimalCutSetVisuDialog - Class in fr.curie.BiNoM.cytoscape.analysis
Dialog for setting options for the visualization of optimal intervention sets in Cytoscape graphs.
OptimalCutSetVisuDialog(JFrame, String, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetVisuDialog
 
optIntSets - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
List of optimal intervention sets as node objects.
OptionParser - Class in fr.curie.BiNoM.pathways.utils
 
OptionParser(String, String[], String) - Constructor for class fr.curie.BiNoM.pathways.utils.OptionParser
 
OptionParser(String[], String) - Constructor for class fr.curie.BiNoM.pathways.utils.OptionParser
 
orderedNodesByScore - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
List of nodes ordered by decreasing Ocsana score
organismChanged(DnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when organism has changed
organismChanged(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when organism has changed
organismChanged(Gene) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when organism has changed
organismChanged(Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when organism has changed
organismChanged(ProteinReference) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when organism has changed
organismChanged(RnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when organism has changed
organismChanged(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when organism has changed
organismProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaReference
The Jena Property for organism
organismProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
The Jena Property for organism
organismProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Gene
The Jena Property for organism
organismProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Pathway
The Jena Property for organism
organismProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
The Jena Property for organism
organismProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaReference
The Jena Property for organism
organismProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
The Jena Property for organism
outcomingEdges - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
List of all out-going edges.
OUTPUT_CURRENT_NETWORK - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask
 
OUTPUT_NEW_NETWORK - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask
 
overwriteModuleSection - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
OWLExtensionFilter - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
OWLExtensionFilter() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.OWLExtensionFilter
 

P

PackInNestNode - Class in fr.curie.BiNoM.cytoscape.nestmanager
Pack nodes inside selected networks in nest pointing to these networks Position of nest are the mean position of nodes Edges are recreated between nests and nodes with the same attributes
PackInNestNode() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.PackInNestNode
 
paintStaining(String, String) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
Pair - Class in fr.curie.BiNoM.pathways.utils
 
Pair(Object, Object) - Constructor for class fr.curie.BiNoM.pathways.utils.Pair
 
PARALLELOGRAM - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
parse(String) - Method in class fr.curie.BiNoM.pathways.utils.GraphXGMMLParser
Parses fn file
parseAccessionTable(String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
deprecated
parseBioPAX - Class in fr.curie.BiNoM.pathways
 
parseBioPAX() - Constructor for class fr.curie.BiNoM.pathways.parseBioPAX
 
parseCellDesigner - Class in fr.curie.BiNoM.pathways
Utility class for listing some CellDesigner information as a readable text
parseCellDesigner() - Constructor for class fr.curie.BiNoM.pathways.parseCellDesigner
 
parseXGMML(String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Loads BioPAXGraphQuery from a XGMML file
participantAdded(BiochemicalReaction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of participant has been added
participantAdded(BiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of participant has been added
participantAdded(Catalysis, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of participant has been added
participantAdded(ComplexAssembly, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of participant has been added
participantAdded(ComplexAssembly, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of participant has been added
participantAdded(Control, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of participant has been added
participantAdded(Conversion, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of participant has been added
participantAdded(Conversion, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of participant has been added
participantAdded(Degradation, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of participant has been added
participantAdded(Degradation, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of participant has been added
participantAdded(GeneticInteraction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of participant has been added
participantAdded(GeneticInteraction, Gene) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of participant has been added
participantAdded(Interaction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of participant has been added
participantAdded(Modulation, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of participant has been added
participantAdded(MolecularInteraction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of participant has been added
participantAdded(MolecularInteraction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of participant has been added
participantAdded(TemplateReaction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of participant has been added
participantAdded(TemplateReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of participant has been added
participantAdded(TemplateReactionRegulation, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of participant has been added
participantAdded(Transport, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of participant has been added
participantAdded(Transport, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of participant has been added
participantAdded(TransportWithBiochemicalReaction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of participant has been added
participantAdded(TransportWithBiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of participant has been added
participantProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Interaction
The Jena Property for participant
participantRemoved(BiochemicalReaction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of participant has been removed
participantRemoved(BiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of participant has been removed
participantRemoved(Catalysis, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of participant has been removed
participantRemoved(ComplexAssembly, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of participant has been removed
participantRemoved(ComplexAssembly, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of participant has been removed
participantRemoved(Control, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of participant has been removed
participantRemoved(Conversion, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of participant has been removed
participantRemoved(Conversion, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of participant has been removed
participantRemoved(Degradation, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of participant has been removed
participantRemoved(Degradation, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of participant has been removed
participantRemoved(GeneticInteraction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of participant has been removed
participantRemoved(GeneticInteraction, Gene) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of participant has been removed
participantRemoved(Interaction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of participant has been removed
participantRemoved(Modulation, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of participant has been removed
participantRemoved(MolecularInteraction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of participant has been removed
participantRemoved(MolecularInteraction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of participant has been removed
participantRemoved(TemplateReaction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of participant has been removed
participantRemoved(TemplateReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of participant has been removed
participantRemoved(TemplateReactionRegulation, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of participant has been removed
participantRemoved(Transport, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of participant has been removed
participantRemoved(Transport, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of participant has been removed
participantRemoved(TransportWithBiochemicalReaction, Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of participant has been removed
participantRemoved(TransportWithBiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of participant has been removed
participantStoichiometryAdded(BiochemicalReaction, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of participantStoichiometry has been added
participantStoichiometryAdded(ComplexAssembly, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of participantStoichiometry has been added
participantStoichiometryAdded(Conversion, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of participantStoichiometry has been added
participantStoichiometryAdded(Degradation, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of participantStoichiometry has been added
participantStoichiometryAdded(Transport, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of participantStoichiometry has been added
participantStoichiometryAdded(TransportWithBiochemicalReaction, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of participantStoichiometry has been added
participantStoichiometryProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Conversion
The Jena Property for participantStoichiometry
participantStoichiometryRemoved(BiochemicalReaction, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of participantStoichiometry has been removed
participantStoichiometryRemoved(ComplexAssembly, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of participantStoichiometry has been removed
participantStoichiometryRemoved(Conversion, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of participantStoichiometry has been removed
participantStoichiometryRemoved(Degradation, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of participantStoichiometry has been removed
participantStoichiometryRemoved(Transport, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of participantStoichiometry has been removed
participantStoichiometryRemoved(TransportWithBiochemicalReaction, Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of participantStoichiometry has been removed
PasteNodesAndEdges - Class in fr.curie.BiNoM.cytoscape.utils
 
PasteNodesAndEdges() - Constructor for class fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdges
 
PasteNodesAndEdgesDialog - Class in fr.curie.BiNoM.cytoscape.utils
 
PasteNodesAndEdgesDialog() - Constructor for class fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog
 
Path - Class in fr.curie.BiNoM.pathways.analysis.structure
 
Path() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Path
 
Path(Graph, String) - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Path
 
path - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
PathAnalysis - Class in fr.curie.BiNoM.cytoscape.analysis
 
PathAnalysis() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PathAnalysis
 
PathAnalysisDialog - Class in fr.curie.BiNoM.cytoscape.analysis
 
PathAnalysisTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
PathAnalysisTask(GraphDocument, Vector<String>, Vector<String>, StructureAnalysisUtils.Option, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisTask
 
PathConsistencyAnalyzer - Class in fr.curie.BiNoM.cytoscape.analysis
 
PathConsistencyAnalyzer() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzer
 
PathConsistencyAnalyzerBootstrapDialog - Class in fr.curie.BiNoM.cytoscape.analysis
 
PathConsistencyAnalyzerBootstrapDialog(JFrame, String, boolean, DataPathConsistencyAnalyzer) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerBootstrapDialog
 
PathConsistencyAnalyzerBootstrapTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
PathConsistencyAnalyzerBootstrapTask(DataPathConsistencyAnalyzer) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerBootstrapTask
 
PathConsistencyAnalyzerDialog - Class in fr.curie.BiNoM.cytoscape.analysis
 
PathConsistencyAnalyzerDialog(JFrame, String, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerDialog
 
PathConsistencyAnalyzerPathDialog - Class in fr.curie.BiNoM.cytoscape.analysis
 
PathConsistencyAnalyzerPathDialog(JFrame, String, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
PathConsistencyAnalyzerReportDialog - Class in fr.curie.BiNoM.cytoscape.analysis
Report dialog box for optimal intervention set results.
PathConsistencyAnalyzerReportDialog(String) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerReportDialog
 
PathConsistencyAnalyzerTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
PathConsistencyAnalyzerTask(DataPathConsistencyAnalyzer) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerTask
 
pathFindMode - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
pathMatrix - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Elementary paths matrix
pathMatrix - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Path matrix (without target nodes).
pathMatrixNbCol - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Path matrix number of rows and columns
pathMatrixNbCol - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Path matrix number of columns
pathMatrixNbRow - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Path matrix number of rows and columns
pathMatrixNbRow - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Path matrix number of rows
pathMatrixNodeList - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Elementary paths matrix node names list
pathMatrixNodeList - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Node labels for path matrix (columns)
Pathway - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Pathway ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
PATHWAY_STEP - Static variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
PATHWAY_STRUCTURE_CONVERSION - Static variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
Mode of conversion: from BioPAX to Pathway Structure BioPAX interface
pathwayComponentAdded(Pathway, Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of pathwayComponent has been added
pathwayComponentAdded(Pathway, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of pathwayComponent has been added
pathwayComponentProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Pathway
The Jena Property for pathwayComponent
pathwayComponentRemoved(Pathway, Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of pathwayComponent has been removed
pathwayComponentRemoved(Pathway, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of pathwayComponent has been removed
PathwayImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Pathway Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
PathwayListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Pathway to receive notification when properties changed, added or removed.
pathwayNodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
pathwayOrderAdded(Pathway, PathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of pathwayOrder has been added
pathwayOrderProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Pathway
The Jena Property for pathwayOrder
pathwayOrderRemoved(Pathway, PathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of pathwayOrder has been removed
pathways - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
Map from complete uris to pathway objects
pathwaysAdded - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
 
pathwaysAdded - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
 
pathwayStainingCellDesigner - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
pathwayStainingCellDesigner() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesigner
 
pathwayStainingCellDesignerDialog - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
pathwayStainingCellDesignerTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
pathwayStainingCellDesignerTask(String, String, String, String, pathwayStainingCellDesignerTask.stainingOptions) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask
 
pathwayStainingCellDesignerTask.stainingOptions - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
pathwayStainingCellDesignerTask.stainingOptions() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask.stainingOptions
 
PathwayStep - Interface in fr.curie.BiNoM.pathways.biopax
Interface for PathwayStep ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
PathwayStepImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of PathwayStep Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
PathwayStepListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.PathwayStep to receive notification when properties changed, added or removed.
pathwaySteps - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
Map from complete uris to pathwaySteps objects
patoDataChanged(PhenotypeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyListener
Called when patoData has changed
patoDataProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabulary
The Jena Property for patoData
PavingData - Class in fr.curie.BiNoM.cytoscape.utils
Data structure for Paving Dialog used too for displaying arrays xNames: column names yNames: row names stateNames: state names for discrete visualization stateAbbrev: short names of states to displaying in text window stateArray: array of states for discrete visualization stateColors: colors used for displaying states values: continue states values for continue visualization from blue to red (negative to positive)
PavingData() - Constructor for class fr.curie.BiNoM.cytoscape.utils.PavingData
 
PavingDialog - Class in fr.curie.BiNoM.cytoscape.utils
Create a paved window where colors depend on - a state defined by an array of integer,stateNotValue=true - a value from an array of values, 2 options: 1 negative in green, positive in red and zero in black, with a progressive gradation 2 negative in blue, positive in red and zero in white, with a progressive gradation Selection of squares writes in text window data of selected squares there is a geometric cooking to adjust square, the result is not always perfect
PavingDialog(Window, String, String, PavingData, boolean, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.utils.PavingDialog
 
perform() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSource
 
perform() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSource
 
perform(ArrayList<CyNode>) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.NestMerging
 
PERMUTE_NODE_ACTIVITIES - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
phChanged(DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaGListener
Called when ph has changed
phChanged(KPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrimeListener
Called when ph has changed
phenotypeChanged(GeneticInteraction) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when phenotype has changed
phenotypeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
The Jena Property for phenotype
phenotypes - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
phenotypes - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
PhenotypeVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for PhenotypeVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
PhenotypeVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of PhenotypeVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
PhenotypeVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.PhenotypeVocabulary to receive notification when properties changed, added or removed.
phProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DeltaG
The Jena Property for ph
phProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.KPrime
The Jena Property for ph
PhysicalEntity - Interface in fr.curie.BiNoM.pathways.biopax
Interface for PhysicalEntity ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
physicalEntityChanged(Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.StoichiometryListener
Called when physicalEntity has changed
PhysicalEntityImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of PhysicalEntity Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
PhysicalEntityListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.PhysicalEntity to receive notification when properties changed, added or removed.
physicalEntityProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Stoichiometry
The Jena Property for physicalEntity
piquantAbsSetScoreMap - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
plug - Static variable in class fr.curie.BiNoM.celldesigner.plugin.BiNoMPluginDialog
 
plug - Static variable in class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
plugin - Variable in class fr.curie.BiNoM.celldesigner.biopax.propedit.BioPAXPropertyManager
 
Plugin - Class in fr.curie.BiNoM.celldesigner.plugin2
 
Plugin() - Constructor for class fr.curie.BiNoM.celldesigner.plugin2.Plugin
 
pMgChanged(DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaGListener
Called when pMg has changed
pMgChanged(KPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrimeListener
Called when pMg has changed
pMgProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DeltaG
The Jena Property for pMg
pMgProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.KPrime
The Jena Property for pMg
pop() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc.HierarchyScanner
 
pop() - Method in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogConstitutiveReactions
 
pop() - Method in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetReportDialog
 
pop() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerReportDialog
 
pop(GraphDocument, org.sbml.x2001.ns.celldesigner.SbmlDocument, BioPAX) - Method in class fr.curie.BiNoM.cytoscape.utils.ListAllNodesDialog
 
pop(Graph, org.sbml.x2001.ns.celldesigner.SbmlDocument, BioPAX) - Method in class fr.curie.BiNoM.cytoscape.utils.ListAllNodesDialog
 
pop(GraphDocument, org.sbml.x2001.ns.celldesigner.SbmlDocument, BioPAX) - Method in class fr.curie.BiNoM.cytoscape.utils.ListAllReactionsDialog
 
pop(HashMap, HashMap, HashMap) - Method in class fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog
 
pop(Graph) - Method in class fr.curie.BiNoM.cytoscape.utils.SelectNodesByAttributeSubstringDialog
 
pop(HashMap, HashMap, HashMap) - Method in class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContentsDialog
 
pop(String, String) - Method in class fr.curie.BiNoM.cytoscape.utils.ShowTextDialog
 
populateModel() - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
populateModelnew() - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
The converter itself
populateSbml() - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Performs actual BioPAX->SBML conversion Requires this.biopax object to be specified
positionStatusChanged(SequenceSite) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceSiteListener
Called when positionStatus has changed
positionStatusProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.SequenceSite
The Jena Property for positionStatus
post_link_base(int, StringBuffer) - Method in class fr.curie.BiNoM.pathways.navicell.WordPressBlogCreator
 
postProcessAnnotations(String) - Method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
 
postProcessMergedMap(String) - Method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
 
PowerfulTokenizer - Class in fr.curie.BiNoM.pathways.utils
A Powerful Tokenizer Author Bhabani Padhi Extension of the standard StringTokenizer
PowerfulTokenizer(String, String) - Constructor for class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer
Constructor
PowerfulTokenizer(String, String, boolean) - Constructor for class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer
Constructor
prefixLength - Variable in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
 
prepareCellDesignerFile - Class in fr.curie.BiNoM.pathways.utils
 
prepareCellDesignerFile() - Constructor for class fr.curie.BiNoM.pathways.utils.prepareCellDesignerFile
 
prepareDatabaseCopyForIndexPathAnalysis() - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
Prepares a copy of database for Index Path Analysis.
prepareFamilies(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
preProcessMergedMaps() - Method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
 
preprocessText(String) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
print(String, StringBuffer) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
print() - Method in class fr.curie.BiNoM.pathways.utils.AccessionNumberTable
Prints the whole table in the form \t
printAllToAllInfluenceTable(float[][]) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
printAntisenseRNAList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
printDump(Model) - Static method in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Prints the content of the BioPAX Model object as readable text
printEntityName(Entity) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
 
printGeneList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
printGraphList() - Static method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
printMassif(float[]) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
printPaths(ArrayList<Path>) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Print out elementary path matrix data.
printPhenotypeList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
printPropertyURIs(Entity) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Simply prints all statement uris in the entity res
printPropertyURIs(UtilityClass) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Simply prints all statement uris in the utilityClass res
printProteinsList(SbmlDocument.Sbml, boolean) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
printReactionList(SbmlDocument.Sbml, boolean) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
printRNAList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
printSetIntersections(String) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
printSetIntersectionsInFolder(String) - Static method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
printSetSizes() - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
printSignificanceAnalysisReport() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
printSmallMoleculeList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
printSpeciesList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
printSpeciesReactions(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
 
printStatements() - Method in class fr.curie.BiNoM.pathways.utils.BioPAXMerge
Prints all statements of the base Model
printUsedMemory() - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Prints how much memory is used
printUsedMemorySinceLastTime() - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Prints a difference in used memory since last call of printUsedMemory,printUsedMemorySinceLastTime, getUsedMemorySinceLastTime,printUsedMemorySinceLastTimeByte functions
printUsedMemorySinceLastTimeByte() - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Same ad printUsedMemorySinceLastTime but in bytes
printUtilityClassName(UtilityClass) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
 
processAnnotation(String, String, HashMap<String, Vector<String>>) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
processAnnotation(String, String, HashMap<String, Vector<String>>) - Method in class fr.curie.BiNoM.pathways.utils.ExtractGMTFromCellDesigner
 
processAnnotations(String, String, String, String[], boolean) - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
processAnnotations(String, String, String, String[], boolean, StringBuffer, Vector<ModifyCellDesignerNotes.AnnotationSection>) - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
produceCandidateMergeLists(SbmlDocument, SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
ProduceClickableMap - Class in fr.curie.BiNoM.pathways.navicell
 
ProduceClickableMap(String, File) - Constructor for class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
ProduceClickableMap.NaviCellException - Exception in fr.curie.BiNoM.pathways.navicell
 
produceConnectionsSecondOrder(Graph, String) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
produceConnectionsSecondOrderFromDistMatrix(Graph) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
ProduceNaviCellMapFiles - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
ProduceNaviCellMapFiles() - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.ProduceNaviCellMapFiles
 
ProduceNaviCellMapFilesDialog - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
ProduceNaviCellMapFilesTask - Class in fr.curie.BiNoM.cytoscape.celldesigner
 
ProduceNaviCellMapFilesTask(String, String, String, String, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.celldesigner.ProduceNaviCellMapFilesTask
 
productAdded(TemplateReaction, Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of product has been added
productAdded(TemplateReaction, Protein) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of product has been added
productAdded(TemplateReaction, Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of product has been added
productProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
The Jena Property for product
productRemoved(TemplateReaction, Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of product has been removed
productRemoved(TemplateReaction, Protein) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of product has been removed
productRemoved(TemplateReaction, Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of product has been removed
projectName - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMappingService
 
Protein - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Protein ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
proteinComplexMap - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
ProteinImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Protein Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
proteinList - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cut uris (after # separator) to 'protein' entities
ProteinListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Protein to receive notification when properties changed, added or removed.
proteinMap - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
ProteinReference - Interface in fr.curie.BiNoM.pathways.biopax
Interface for ProteinReference ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ProteinReferenceImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of ProteinReference Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ProteinReferenceListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.ProteinReference to receive notification when properties changed, added or removed.
proteins - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Map of CellDesigner Celldesigner entity objects
Provenance - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Provenance ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ProvenanceImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Provenance Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ProvenanceListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Provenance to receive notification when properties changed, added or removed.
PruneEdges(Graph, Vector<Float>, float) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
PruneGraph - Class in fr.curie.BiNoM.celldesigner.analysis
 
PruneGraph(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.PruneGraph
 
PruneGraph - Class in fr.curie.BiNoM.cytoscape.analysis
 
PruneGraph() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PruneGraph
 
PruneGraph(Graph, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
Graph pruning (eliminataing IN and OUT layers)
PruneGraphTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
PruneGraphTask(CellDesignerPlugin, GraphDocument) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.PruneGraphTask
 
PruneGraphTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
PruneGraphTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.PruneGraphTask
 
ptintComplexList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
pub1 - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
pub1 - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
pub2 - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
pub2 - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
publications - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
publications - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
PublicationXref - Interface in fr.curie.BiNoM.pathways.biopax
Interface for PublicationXref ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
PublicationXrefImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of PublicationXref Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
PublicationXrefListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.PublicationXref to receive notification when properties changed, added or removed.
pubmedrefsHash - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Map from Pubmed ids to publicationXref objects
push(BioPAXClassDesc) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc.HierarchyScanner
 
putCytoscapeColorsOnReactions - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
putCytoscapeColorsOnSpecies - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
putEntity(Entity) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Adds an entity for naming
putID(String, String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
 
putName(String, String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Adds a (uri,name) pair
putSpeciesNotesIntoProteinNotes(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
putSpeciesNotesIntoProteinNotes(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
putUtilityClass(UtilityClass) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService
Adds an utilityClass for naming

Q

query - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
The query to be made
queryType - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Predefined query type

R

raise(String[]) - Method in class fr.curie.BiNoM.analysis.ClusterNetworksDialog
 
raise(AbstractExcludeIntermediateNodesTaskFactory, Graph, Vector) - Method in class fr.curie.BiNoM.analysis.ExcludeIntermediateNodesDialog
 
raise(AbstractModularViewTaskFactory, String[]) - Method in class fr.curie.BiNoM.analysis.ModularViewDialog
 
raise(AbstractBioPAXImportTaskFactory, File, String) - Method in class fr.curie.BiNoM.biopax.BioPAXImportDialog
 
raise(AbstractBioPAXImportTaskFactory, URL, String) - Method in class fr.curie.BiNoM.biopax.BioPAXImportDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.analysis.createNeighborhoodSetsDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetworkDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisDialog
 
raise(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSyncNetworksDialog
 
raise(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDisplayIndexInfoDialog
 
raise(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexDialog
 
raise(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexDialog
 
raise(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesDialog
 
raise(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXViewQueryLogDialog
 
raise(File) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.checkCellDesignerFileDialog
 
raise(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.colorCellDesignerProteinsDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.modifyCellDesignerNotesDialog
 
raise(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerDialog
 
raise(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.ProduceNaviCellMapFilesDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.netwop.DoubleNetworkDifferenceDialog
 
raise(CyNetwork, CyNetwork, int[]) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateConfirmDialog
 
raise() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateDialog
 
rankedGeneList - Variable in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
reachArea(double) - Method in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
reachAreaFromStarts(double, double[]) - Method in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
reachParameter() - Method in class fr.curie.BiNoM.cytoscape.influence.FromToNodes
 
REACTION_NETWORK_CONVERSION - Static variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter
Mode of conversion: from BioPAX to Reaction Network BioPAX interface
reactionAll - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions
 
reactionComplete - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions
 
reactionConnecting - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions
 
reactionEdgeTypes - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
 
reactionGraph - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
reactionList(String, HashMap) - Method in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
reactionNodeTypes - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX
 
reactionNodeTypes - Static variable in class fr.curie.BiNoM.pathways.wrappers.CellDesigner
 
reactions - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from BioPAX conversion (cutted) uris to SBML reactions (represented by ReactionDocument.Reaction objects)
reactions - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Map of CellDesigner ReactionDocument.Reaction objects
reactionString(SbmlDocument.Sbml, String, boolean, boolean) - Method in class fr.curie.BiNoM.pathways.parseBioPAX
 
reactionString(SbmlDocument.Sbml, String, boolean) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner
 
readComplexes(String, int) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
readComplexProfile(String, int) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
readConservationLaws(Graph, String, boolean) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
Reads a file produced by Structural Analysis GUI software in SB Workbench and finds subgraphs, corresponding to the conservation laws (P-invariants?)
recompute() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassTreeFrame
 
reconnect2Nodes(Node, Node, CyEdge) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
RecreateLostConnectionsInsideNests - Class in fr.curie.BiNoM.cytoscape.nestmanager
Create edges inside nested network from a reference network Delete all old edges of nested network Search edges which nodes belong to the nested network Copy edges attributes included from the reference network to every nested network
RecreateLostConnectionsInsideNests() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.RecreateLostConnectionsInsideNests
 
RecreateLostConnectionsInsideNestsTask - Class in fr.curie.BiNoM.cytoscape.nestmanager
Task of updating edges inside all nests
RecreateLostConnectionsInsideNestsTask(RecreateLostConnectionsInsideNests) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.RecreateLostConnectionsInsideNestsTask
 
recreateNodeEdgeHash() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
RECTANGLE - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
RECTANGLE_ROUNDED - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
referenceFiles - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXMerge
List of com.hp.hpl.jena.rdf.model.Model objects to merge with the base Model
referenceGraph - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
regionTypeChanged(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when regionType has changed
regionTypeChanged(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when regionType has changed
regionTypeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
The Jena Property for regionType
regionTypeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
The Jena Property for regionType
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ChemicalStructureImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceLocationImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.UtilityClassImpl
 
registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
regularpoints - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
relationshipTypeAdded(RelationshipXref, RelationshipTypeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXrefListener
Called when a value of relationshipType has been added
relationshipTypeProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.RelationshipXref
The Jena Property for relationshipType
relationshipTypeRemoved(RelationshipXref, RelationshipTypeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXrefListener
Called when a value of relationshipType has been removed
RelationshipTypeVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for RelationshipTypeVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
RelationshipTypeVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of RelationshipTypeVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
RelationshipTypeVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabulary to receive notification when properties changed, added or removed.
RelationshipXref - Interface in fr.curie.BiNoM.pathways.biopax
Interface for RelationshipXref ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
RelationshipXrefImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of RelationshipXref Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
RelationshipXrefListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.RelationshipXref to receive notification when properties changed, added or removed.
REMOVE - Static variable in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyEditFrame
 
REMOVE_ADD - Static variable in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyEditFrame
 
removeAll() - Method in class fr.curie.BiNoM.lib.MLLabel
 
removeAuthor(String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
Remove a 'author' property value.
removeAuthor(String) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removeAvailability(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Remove a 'availability' property value.
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeAvailability(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeCofactor(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Catalysis
Removes a value for the 'cofactor' property.
removeCofactor(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ChemicalStructureImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
removeComment(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Remove a 'comment' property value.
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceLocationImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
removeComment(String) - Method in interface fr.curie.BiNoM.pathways.biopax.UtilityClass
Remove a 'comment' property value.
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.UtilityClassImpl
 
removeComment(String) - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
removeCompartmentSuffix(String) - Static method in class fr.curie.BiNoM.pathways.BioPAXToCellDesignerConverter
 
removeComplexNames - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
removeComponent(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Removes a value for the 'component' property.
removeComponent(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeComponentStoichiometry(Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Removes a value for the 'componentStoichiometry' property.
removeComponentStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeConfidence(Score) - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Removes a value for the 'confidence' property.
removeConfidence(Score) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
removeController(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removeController(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removeController(Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Removes a value for the 'controller' property.
removeController(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Removes a value for the 'controller' property.
removeController(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
removeController(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
removeController(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Modulation
Removes a value for the 'controller' property.
removeController(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
removeController(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
removeController(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation
Removes a value for the 'controller' property.
removeController(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
removeController(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
removeConversion(Conversion, HashMap, HashMap, Vector, HashMap, BioPAXToSBMLConverter) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removeDataSource(Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Removes a value for the 'dataSource' property.
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeDataSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeDeltaG(DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Removes a value for the 'deltaG' property.
removeDeltaG(DeltaG) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeDeltaG(DeltaG) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeDeltaH(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Remove a 'deltaH' property value.
removeDeltaH(Float) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeDeltaH(Float) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeDeltaS(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Remove a 'deltaS' property value.
removeDeltaS(Float) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeDeltaS(Float) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeDoubleEdges() - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ChemicalStructureImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceLocationImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.UtilityClassImpl
 
removedStatement(com.hp.hpl.jena.rdf.model.Statement) - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
removeECNumber(String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Remove a 'eCNumber' property value.
removeECNumber(String) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeECNumber(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeEdge(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
removeEditPoints(SbmlDocument) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
removeEditPoints(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.testRemoveEditPoints
 
removeEmptySections - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask.extractingNotesOptions
 
removeEmptySections - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
removeEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
removeEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
removeEntityFeature(EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Removes a value for the 'entityFeature' property.
removeEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
removeEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
removeEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
removeEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
removeEntityFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
removeEvidence(Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Removes a value for the 'evidence' property.
removeEvidence(Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Removes a value for the 'evidence' property.
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
removeEvidence(Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Removes a value for the 'evidence' property.
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
removeEvidence(Evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Removes a value for the 'evidence' property.
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeEvidence(Evidence) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeEvidenceCode(EvidenceCodeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Removes a value for the 'evidenceCode' property.
removeEvidenceCode(EvidenceCodeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
removeExperimentalFeature(EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Removes a value for the 'experimentalFeature' property.
removeExperimentalFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
removeExperimentalForm(ExperimentalForm) - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Removes a value for the 'experimentalForm' property.
removeExperimentalForm(ExperimentalForm) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
removeExperimentalFormDescription(ExperimentalFormVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Removes a value for the 'experimentalFormDescription' property.
removeExperimentalFormDescription(ExperimentalFormVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
removeExperimentalFormEntity(Gene) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Removes a value for the 'experimentalFormEntity' property.
removeExperimentalFormEntity(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
Removes a value for the 'experimentalFormEntity' property.
removeExperimentalFormEntity(Gene) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
removeExperimentalFormEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
removeFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removeFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removeFeature(EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Removes a value for the 'feature' property.
removeFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
removeFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removeFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removeFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removeFeature(BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Removes a value for the 'feature' property.
removeFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeFeature(BindingFeature) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeFeatureLocation(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
removeFeatureLocation(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
removeFeatureLocation(SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Removes a value for the 'featureLocation' property.
removeFeatureLocation(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
removeFeatureLocation(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
removeFeatureLocation(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
removeFeatureLocationType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
removeFeatureLocationType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
removeFeatureLocationType(SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Removes a value for the 'featureLocationType' property.
removeFeatureLocationType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
removeFeatureLocationType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
removeFeatureLocationType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
removeInteractionScore(Score) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Removes a value for the 'interactionScore' property.
removeInteractionScore(Score) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
removeInvalidTags - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask.extractingNotesOptions
 
removeInvalidTags - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
removeKEQ(KPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
Removes a value for the 'kEQ' property.
removeKEQ(KPrime) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeKEQ(KPrime) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeLeft(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Removes a value for the 'left' property.
removeLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeLeft(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeLineBreakPoints - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
removeMemberEntityReference(DnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Removes a value for the 'memberEntityReference' property.
removeMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
removeMemberEntityReference(DnaReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
removeMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
removeMemberEntityReference(EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Removes a value for the 'memberEntityReference' property.
removeMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
removeMemberEntityReference(ProteinReference) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
Removes a value for the 'memberEntityReference' property.
removeMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
removeMemberEntityReference(ProteinReference) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
removeMemberEntityReference(RnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Removes a value for the 'memberEntityReference' property.
removeMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
removeMemberEntityReference(RnaReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
removeMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
removeMemberEntityReference(SmallMoleculeReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Removes a value for the 'memberEntityReference' property.
removeMemberEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
removeMemberEntityReference(SmallMoleculeReference) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
removeMemberFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
removeMemberFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
removeMemberFeature(EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
Removes a value for the 'memberFeature' property.
removeMemberFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
removeMemberFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
removeMemberFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
removeMemberPhysicalEntity(Complex) - Method in interface fr.curie.BiNoM.pathways.biopax.Complex
Removes a value for the 'memberPhysicalEntity' property.
removeMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeMemberPhysicalEntity(Complex) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeMemberPhysicalEntity(Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Removes a value for the 'memberPhysicalEntity' property.
removeMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removeMemberPhysicalEntity(Dna) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removeMemberPhysicalEntity(DnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Removes a value for the 'memberPhysicalEntity' property.
removeMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removeMemberPhysicalEntity(DnaRegion) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removeMemberPhysicalEntity(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Removes a value for the 'memberPhysicalEntity' property.
removeMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
removeMemberPhysicalEntity(Protein) - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Removes a value for the 'memberPhysicalEntity' property.
removeMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removeMemberPhysicalEntity(Protein) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removeMemberPhysicalEntity(Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Removes a value for the 'memberPhysicalEntity' property.
removeMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removeMemberPhysicalEntity(Rna) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removeMemberPhysicalEntity(RnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Removes a value for the 'memberPhysicalEntity' property.
removeMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removeMemberPhysicalEntity(RnaRegion) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removeMemberPhysicalEntity(SmallMolecule) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Removes a value for the 'memberPhysicalEntity' property.
removeMemberPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeMemberPhysicalEntity(SmallMolecule) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeName(String) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Remove a 'name' property value.
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
removeName(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Remove a 'name' property value.
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
removeName(String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Remove a 'name' property value.
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
removeName(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Remove a 'name' property value.
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeName(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
RemoveNames(SbmlDocument) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
RemoveNames(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.test
 
RemoveNames(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
removeNextStep(PathwayStep) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
removeNextStep(PathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Removes a value for the 'nextStep' property.
removeNextStep(PathwayStep) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
removeNode(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
removeNodes(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
RemoveNodesOfType(Graph, String, String) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
Removes nodes which have an attribute with substringAttName in its name and substringAttValue in its value
RemoveNonExpressedProteins - Class in fr.curie.BiNoM.pathways.test
 
RemoveNonExpressedProteins() - Constructor for class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
removeNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removeNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removeNotFeature(EntityFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Removes a value for the 'notFeature' property.
removeNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
removeNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removeNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removeNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removeNotFeature(BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Removes a value for the 'notFeature' property.
removeNotFeature(EntityFeature) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeNotFeature(BindingFeature) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeObsoleteEdges() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeParticipant(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeParticipant(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
removeParticipant(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Removes a value for the 'participant' property.
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeParticipant(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeParticipant(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeParticipant(Gene) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Removes a value for the 'participant' property.
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
removeParticipant(Gene) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
removeParticipant(Entity) - Method in interface fr.curie.BiNoM.pathways.biopax.Interaction
Removes a value for the 'participant' property.
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
removeParticipant(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteraction
Removes a value for the 'participant' property.
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
removeParticipant(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
removeParticipant(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Removes a value for the 'participant' property.
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeParticipant(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeParticipant(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeParticipant(Entity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeParticipant(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeParticipantStoichiometry(Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Removes a value for the 'participantStoichiometry' property.
removeParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeParticipantStoichiometry(Stoichiometry) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removePathwayComponent(Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Removes a value for the 'pathwayComponent' property.
removePathwayComponent(Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Removes a value for the 'pathwayComponent' property.
removePathwayComponent(Interaction) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
removePathwayComponent(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
removePathwayOrder(PathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Removes a value for the 'pathwayOrder' property.
removePathwayOrder(PathwayStep) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
removeProduct(Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Removes a value for the 'product' property.
removeProduct(Protein) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Removes a value for the 'product' property.
removeProduct(Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Removes a value for the 'product' property.
removeProduct(Dna) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeProduct(Protein) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeProduct(Rna) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeReciprocalEdges(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
 
removeRelationshipType(RelationshipTypeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipXref
Removes a value for the 'relationshipType' property.
removeRelationshipType(RelationshipTypeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
RemoveResidueNames(SbmlDocument) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
RemoveResidueNames(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.test
 
RemoveResidueNames(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
removeResiduesNames - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
removeRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeRight(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Removes a value for the 'right' property.
removeRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeRight(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
removeSelfInteractions(Graph) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
removeSource(String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
Remove a 'source' property value.
removeSource(String) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
removeStepProcess(Control) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Removes a value for the 'stepProcess' property.
removeStepProcess(Control) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
removeStepProcess(Interaction) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
removeStepProcess(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
removeStepProcess(Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Removes a value for the 'stepProcess' property.
removeStepProcess(Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
Removes a value for the 'stepProcess' property.
removeStepProcess(Interaction) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
removeStepProcess(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
removeSubRegion(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Removes a value for the 'subRegion' property.
removeSubRegion(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Removes a value for the 'subRegion' property.
removeSubRegion(DnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
removeSubRegion(RnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
removeSubRegion(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Removes a value for the 'subRegion' property.
removeSubRegion(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Removes a value for the 'subRegion' property.
removeSubRegion(DnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
removeSubRegion(RnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
removeSubRegion(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Removes a value for the 'subRegion' property.
removeSubRegion(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Removes a value for the 'subRegion' property.
removeSubRegion(RnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
removeSubRegion(DnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
removeSubRegion(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Removes a value for the 'subRegion' property.
removeSubRegion(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Removes a value for the 'subRegion' property.
removeSubRegion(RnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
removeSubRegion(DnaRegionReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
removeTerm(String) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Remove a 'term' property value.
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
removeTerm(String) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
removeUrl(String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
Remove a 'url' property value.
removeUrl(String) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
removeValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
removeValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
removeValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringListAttrDesc
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
removeXref(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Removes a value for the 'xref' property.
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
removeXref(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Removes a value for the 'xref' property.
removeXref(UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
Removes a value for the 'xref' property.
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
removeXref(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.Entity
Removes a value for the 'xref' property.
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
removeXref(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Removes a value for the 'xref' property.
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
removeXref(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.Evidence
Removes a value for the 'xref' property.
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
removeXref(Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Removes a value for the 'xref' property.
removeXref(PublicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Removes a value for the 'xref' property.
removeXref(UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.Provenance
Removes a value for the 'xref' property.
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
removeXref(PublicationXref) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
removeXref(UnificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
removeXref(Xref) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
renameSpecies(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.prepareCellDesignerFile
 
repl(String) - Static method in class fr.curie.BiNoM.pathways.utils.InsertCellDesignerParameters
 
replaceByList(String, HashMap<String, String>) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
replaceCellDesignerByList(String, HashMap<String, String>) - Static method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
 
replaceCellDesignerPrefix(String, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
 
replaceCellDesignerPrefixList(String, Vector<String>, String) - Static method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
 
replaceString(String, String, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorProteins
 
replaceString(String, String, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies
 
replaceString(String, String, String) - Static method in class fr.curie.BiNoM.pathways.test.RemoveNonExpressedProteins
 
replaceString(String, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
replaceString(String, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
In source string replaces shabl substring with val
replaceStringChar(String, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
replaceStringCount(String, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
In source string replaces shabl substring with val and providing some info about the number of changes made
report - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
A report to log events on.
report - Variable in class fr.curie.BiNoM.pathways.utils.CheckCellDesignerFile
 
reportPosition(CyNode, CyNetworkView, CyNetworkView) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
 
reportPosition(CyNetworkView, CyNetworkView) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
reset() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
 
reset() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
 
reset() - Method in class fr.curie.BiNoM.pathways.utils.CombinationGenerator
 
resetAnalyzer() - Method in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerDialog
 
reshuffleSets(int, boolean) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
restrictBerge - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Flag for restricting Berge's algorithm search
restrictBerge - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
flag to indicate if Berge's search is restricted, default is false
result - Variable in class fr.curie.BiNoM.analysis.ExcludeIntermediateNodesDialog
 
result - Variable in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogConstitutiveReactions
 
result - Variable in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogFamily
 
result - Variable in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerDialog
 
result - Variable in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerDialog
 
result - Variable in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
result - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Output of the query
resultAsXgmml() - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
Result of the query as GraphDocument object
rewireDiagram(SbmlDocument, Vector<String>, Vector<String>) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
rightAdded(BiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of right has been added
rightAdded(ComplexAssembly, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of right has been added
rightAdded(Conversion, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of right has been added
rightAdded(Degradation, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of right has been added
rightAdded(Transport, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of right has been added
rightAdded(TransportWithBiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of right has been added
rightProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Conversion
The Jena Property for right
rightRemoved(BiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of right has been removed
rightRemoved(ComplexAssembly, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of right has been removed
rightRemoved(Conversion, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of right has been removed
rightRemoved(Degradation, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of right has been removed
rightRemoved(Transport, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of right has been removed
rightRemoved(TransportWithBiochemicalReaction, PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of right has been removed
Rna - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Rna ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
RnaImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Rna Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
rnaList - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cut uris (after # separator) to 'rna' entities
RnaListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Rna to receive notification when properties changed, added or removed.
RnaReference - Interface in fr.curie.BiNoM.pathways.biopax
Interface for RnaReference ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
RnaReferenceImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of RnaReference Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
RnaReferenceListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.RnaReference to receive notification when properties changed, added or removed.
RnaRegion - Interface in fr.curie.BiNoM.pathways.biopax
Interface for RnaRegion ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
RnaRegionImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of RnaRegion Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
rnaRegionList - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cut uris (after # separator) to 'rnaRegion' entities
RnaRegionListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.RnaRegion to receive notification when properties changed, added or removed.
RnaRegionReference - Interface in fr.curie.BiNoM.pathways.biopax
Interface for RnaRegionReference ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
RnaRegionReferenceImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of RnaRegionReference Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
RnaRegionReferenceListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.RnaRegionReference to receive notification when properties changed, added or removed.
rnas - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
 
rowCount - Variable in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
run() - Method in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.CalcCentralityTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponentsTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.ConvertReactionNetworkToEntityNetworkTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.ConvertToUndirectedGraphTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.CycleDecompositionTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExcludeIntermediateNodesTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetworkTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetworkTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.LinearizeNetworkTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.MaterialComponentsTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.ModularViewTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.MonoMolecularReactionsAsEdgesTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerBootstrapTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.PruneGraphTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.analysis.StronglyConnectedComponentsTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSourceTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSourceTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.checkCellDesignerFileTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.colorCellDesignerProteinsTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CSMLImportTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.MergingMapsTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.modifyCellDesignerNotesTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.ProduceNaviCellMapFilesTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ClusterByShortPathTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.DestroyUnusedNetworksAsNestTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.RecreateLostConnectionsInsideNestsTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExportTask
 
run() - Method in class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilterTask
 
run(String, String, String, String) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
run(String, File, boolean, boolean, String, ProduceClickableMap.AtlasInfo, String[][], boolean, String, String, String, String, File, boolean) - Static method in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
runScript() - Method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
User specific script for manipulating map

S

SA_activities - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
SA_observedPathScores - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
SA_observedTargetScores - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
SA_pathScoresRandomDistribution - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
SA_targetScoreRandomDistribution - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
same(Object, Object) - Static method in class fr.curie.BiNoM.pathways.utils.Pair
 
SampleAction - Class in fr.curie.BiNoM.celldesigner.sample
 
SampleAction(SamplePlugin) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SampleAction
 
SamplePlugin - Class in fr.curie.BiNoM.celldesigner.sample
SamplePlugin This plugin opens a simple dialog.
SamplePlugin() - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePlugin
 
SamplePluginDialog - Class in fr.curie.BiNoM.celldesigner.sample
 
SamplePluginDialog(SamplePlugin) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
This is the default constructor
SamplePluginDialog(Frame) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
SamplePluginDialog(Frame, boolean) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
SamplePluginDialog(Frame, String) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
SamplePluginDialog(Frame, String, boolean) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
SamplePluginDialog(Frame, String, boolean, GraphicsConfiguration) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
SamplePluginDialog(Dialog) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
SamplePluginDialog(Dialog, boolean) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
SamplePluginDialog(Dialog, String) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
SamplePluginDialog(Dialog, String, boolean) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
SamplePluginDialog(Dialog, String, boolean, GraphicsConfiguration) - Constructor for class fr.curie.BiNoM.celldesigner.sample.SamplePluginDialog
 
sampling - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
saveAllNamesToFile(String) - Method in class fr.curie.BiNoM.pathways.utils.GMTFile
 
saveAsCytoscapeGML(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
saveAsCytoscapeSif(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
saveAsCytoscapeXGMML(String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
saveCellDesigner() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
saveCellDesigner(SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner
 
saveDistanceMatrix(double[][], String, boolean) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
saveModel(Model, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
Save OWL model to the file
saveModel(Model, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities
 
saveOptCutSetData(File) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
save optimal intervention set list to a text file.
saveSampling() - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
saveSBML(org.sbml.sbml.level2.SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.wrappers.SBML
Saves org.sbml.sbml.level2.SbmlDocument to file
saveSetsAsGMT(String, int) - Method in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
saveStringToFile(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
saveToFile(String, OntModel) - Static method in class fr.curie.BiNoM.pathways.test.TestBioPAX
 
saveToFile(String, OntModel) - Static method in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Save an OntModel object to file
saveToFile(String, Model) - Static method in class fr.curie.BiNoM.pathways.wrappers.BioPAX
Save Model object to file
saveToSimpleTxtTabDelimited(String) - Method in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
saveToXGMML(GraphDocument, String) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML
Saves XGMML to fil
saveToXMGML(GraphDocument, String) - Static method in class fr.curie.BiNoM.pathways.utils.XGMMLExport
 
SBaseAdded(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin.BiNoMPlugin
 
SBaseAdded(jp.sbi.celldesigner.plugin.PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin2.Plugin
 
SBaseAdded(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.sample.SamplePlugin
 
SBaseChanged(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin.BiNoMPlugin
 
SBaseChanged(jp.sbi.celldesigner.plugin.PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin2.Plugin
 
SBaseChanged(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.sample.SamplePlugin
 
SBaseDeleted(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin.BiNoMPlugin
 
SBaseDeleted(jp.sbi.celldesigner.plugin.PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.plugin2.Plugin
 
SBaseDeleted(PluginSBase) - Method in class fr.curie.BiNoM.celldesigner.sample.SamplePlugin
 
sbml - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Java xml-beans mapping of CellDesigner file
sbml - Variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter.Graph
 
sbml - Variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Java xml-beans mapping of CellDesigner file
SBML - Class in fr.curie.BiNoM.pathways.wrappers
Wrapper of 'pure' SBML represented by org.sbml.sbml.level2.SbmlDocument object
SBML() - Constructor for class fr.curie.BiNoM.pathways.wrappers.SBML
 
sbmlDoc - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Result of conversion
sbmlDoc - Variable in class fr.curie.BiNoM.pathways.utils.CheckCellDesignerFile
 
sbmlDoc - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
SBMLExportTask - Class in fr.curie.BiNoM.cytoscape.sbml
 
SBMLExportTask(File) - Constructor for class fr.curie.BiNoM.cytoscape.sbml.SBMLExportTask
 
SBMLExportToFile - Class in fr.curie.BiNoM.cytoscape.sbml
 
SBMLExportToFile() - Constructor for class fr.curie.BiNoM.cytoscape.sbml.SBMLExportToFile
 
scale - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition.ImageDefinition
 
scale - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
scaleDiagram(SbmlDocument, float) - Static method in class fr.curie.BiNoM.pathways.test.mergingMaps
 
scaleFactor - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
ScaleSizes(SbmlDocument, float, boolean) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
ScaleSizes(SbmlDocument, float, boolean) - Static method in class fr.curie.BiNoM.pathways.test.test
 
SCALING_POSITION - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
SCALING_SHAPE - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 
scanHierarchy(BioPAXClassDesc.HierarchyScanner) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
scanHierarchy(int, BioPAXClassDesc.HierarchyScanner) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
score - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer.optCutSetData
 
score - Variable in class fr.curie.BiNoM.pathways.analysis.structure.OmegaScoreData
Ocsana overall omega score.
Score - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Score ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
ScoreImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Score Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
ScoreListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Score to receive notification when properties changed, added or removed.
scoreSourceChanged(Score) - Method in interface fr.curie.BiNoM.pathways.biopax.ScoreListener
Called when scoreSource has changed
scoreSourceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Score
The Jena Property for scoreSource
scriptFile - Static variable in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
searchHitSetPartial() - Method in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Search for minimal intervention sets by partial enumeration.
searchHitSetSizeOne() - Method in class fr.curie.BiNoM.pathways.analysis.structure.OptimalCombinationAnalyzer
Search for hit sets of size 1.
searchPathMode - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
searchRadius - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
searchRadius - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
secondaryIndex - Variable in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
select - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
SELECT_ENTITIES - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery
Identifying entities by names and XREFs in the index
SelectAllPaths() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
selectAllReferencesType(Graph, String) - Method in class fr.curie.BiNoM.pathways.utils.acsn.DatabaseComparison
 
selectComplex - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions
 
SelectDownstreamNeighbours - Class in fr.curie.BiNoM.cytoscape.utils
 
SelectDownstreamNeighbours() - Constructor for class fr.curie.BiNoM.cytoscape.utils.SelectDownstreamNeighbours
 
selected - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
SelectEdgesBetweenSelectedNodes - Class in fr.curie.BiNoM.cytoscape.utils
 
SelectEdgesBetweenSelectedNodes() - Constructor for class fr.curie.BiNoM.cytoscape.utils.SelectEdgesBetweenSelectedNodes
 
selectedIds - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
selectedIds - Variable in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
SelectedNodes - Variable in class fr.curie.BiNoM.cytoscape.analysis.CalcCentralityTask
 
selectedNodes - Variable in class fr.curie.BiNoM.cytoscape.analysis.createNeighborhoodSetsDialog
 
SelectedNodes - Variable in class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetworkTask
 
SelectedNodes - Variable in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask
 
SelectedNodes - Variable in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisTask
 
selectEntityReferencesByXREFList(Graph, Vector<String>, String) - Method in class fr.curie.BiNoM.pathways.utils.acsn.DatabaseComparison
 
selectFamily(String) - Method in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogFamily
 
selectNetworks(TreeMap<String, CyNetwork>, String, String) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
SelectNodesByAttributeSubstring - Class in fr.curie.BiNoM.cytoscape.utils
 
SelectNodesByAttributeSubstring() - Constructor for class fr.curie.BiNoM.cytoscape.utils.SelectNodesByAttributeSubstring
 
SelectNodesByAttributeSubstringDialog - Class in fr.curie.BiNoM.cytoscape.utils
 
SelectNodesByAttributeSubstringDialog() - Constructor for class fr.curie.BiNoM.cytoscape.utils.SelectNodesByAttributeSubstringDialog
 
selectNodesFromList(Vector<String>) - Method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
selectNodesFromList(Graph, Vector<String>) - Static method in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
selectOneNetwork(TreeMap<String, CyNetwork>, String, String) - Static method in class fr.curie.BiNoM.cytoscape.nestmanager.NestUtils
 
selectPublications - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions
 
selectReactions - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions
 
selectSpecies - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions
 
selectSpeciesAndReactions() - Method in class fr.curie.BiNoM.pathways.utils.acsn.MakeCanonicalView
 
SelectUpstreamNeighbours - Class in fr.curie.BiNoM.cytoscape.utils
 
SelectUpstreamNeighbours() - Constructor for class fr.curie.BiNoM.cytoscape.utils.SelectUpstreamNeighbours
 
SEMANTIC - Static variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
sequenceChanged(DnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when sequence has changed
sequenceChanged(DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when sequence has changed
sequenceChanged(ProteinReference) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when sequence has changed
sequenceChanged(RnaReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when sequence has changed
sequenceChanged(RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when sequence has changed
SequenceInterval - Interface in fr.curie.BiNoM.pathways.biopax
Interface for SequenceInterval ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
sequenceIntervalBeginChanged(SequenceInterval) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceIntervalListener
Called when sequenceIntervalBegin has changed
sequenceIntervalBeginProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
The Jena Property for sequenceIntervalBegin
sequenceIntervalEndChanged(SequenceInterval) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceIntervalListener
Called when sequenceIntervalEnd has changed
sequenceIntervalEndProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
The Jena Property for sequenceIntervalEnd
SequenceIntervalImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of SequenceInterval Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
SequenceIntervalListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.SequenceInterval to receive notification when properties changed, added or removed.
SequenceLocation - Interface in fr.curie.BiNoM.pathways.biopax
Interface for SequenceLocation ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
SequenceLocationImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of SequenceLocation Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
SequenceLocationListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.SequenceLocation to receive notification when properties changed, added or removed.
SequenceModificationVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for SequenceModificationVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
SequenceModificationVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of SequenceModificationVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
SequenceModificationVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabulary to receive notification when properties changed, added or removed.
sequencePositionChanged(SequenceSite) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceSiteListener
Called when sequencePosition has changed
sequencePositionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.SequenceSite
The Jena Property for sequencePosition
sequenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaReference
The Jena Property for sequence
sequenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
The Jena Property for sequence
sequenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
The Jena Property for sequence
sequenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaReference
The Jena Property for sequence
sequenceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
The Jena Property for sequence
SequenceRegionVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for SequenceRegionVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
SequenceRegionVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of SequenceRegionVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
SequenceRegionVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabulary to receive notification when properties changed, added or removed.
SequenceSite - Interface in fr.curie.BiNoM.pathways.biopax
Interface for SequenceSite ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
SequenceSiteImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of SequenceSite Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
SequenceSiteListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.SequenceSite to receive notification when properties changed, added or removed.
set(int) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph.IntEdge
 
set(ShortPathClustering.Distance) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Distance
 
setAbsoluteRegion(SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Sets the 'absoluteRegion' property value
setAbsoluteRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Sets the 'absoluteRegion' property value to an anonymous node
setAbsoluteRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Sets the 'absoluteRegion' property value to the given resource, and add's rdf:type properties.
setAbsoluteRegion(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setAbsoluteRegion() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setAbsoluteRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setAbsoluteRegion(SequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Sets the 'absoluteRegion' property value
setAbsoluteRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Sets the 'absoluteRegion' property value to an anonymous node
setAbsoluteRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Sets the 'absoluteRegion' property value to the given resource, and add's rdf:type properties.
setAbsoluteRegion(SequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setAbsoluteRegion() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setAbsoluteRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setAccessionNumberTable(AccessionNumberTable) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
setAccNumberFileName(String) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
setAttrDescV(Vector<BioPAXAttrDesc>) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
setAttribute(GraphicEdge, String, String, String, ObjectType.Enum) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Set attribute value for GraphicEdge
setAttribute(GraphicNode, String, String, String, ObjectType.Enum) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Set attribute value for GraphicNode
setAttributeValueUnique(String, String, int) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Element
Checks if the attribute with such a name already attached and if yes, then changes its value, if no then creates a new one
setAveragePositionForXGMML(GraphicNode, Vector, HashMap) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Place node 'nod' into the average of 'nodes' positions
setBackground(Color) - Method in class fr.curie.BiNoM.lib.MLLabel
 
setBindsTo(BindingFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeature
Sets the 'bindsTo' property value
setBindsTo() - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeature
Sets the 'bindsTo' property value to an anonymous node
setBindsTo(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeature
Sets the 'bindsTo' property value to the given resource, and add's rdf:type properties.
setBindsTo(BindingFeature) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
setBindsTo() - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
setBindsTo(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
setBindsTo(BindingFeature) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
setBindsTo() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
setBindsTo(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
setBioPAX(Object, BioPAX) - Method in class fr.curie.BiNoM.biopax.BioPAXSourceDB
 
setBioPAX(BioPAX, String) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassTreeFrame
 
setBioPAXGraphQueryEngine(BioPAXGraphQueryEngine) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
setButtons(String) - Method in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogFamily
 
setCatalysisDirection(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Catalysis
Sets the 'catalysisDirection' property value
setCatalysisDirection(String) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setCellDesigner(CyNetwork, SbmlDocument) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerSourceDB
 
setCellType(CellVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Sets the 'cellType' property value
setCellType() - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Sets the 'cellType' property value to an anonymous node
setCellType(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Sets the 'cellType' property value to the given resource, and add's rdf:type properties.
setCellType(CellVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
setCellType() - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
setCellType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
setCellularLocation(CellularLocationVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
setCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
setCellularLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
setCellularLocation(CellularLocationVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
setCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
setCellularLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
setCellularLocation(CellularLocationVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
setCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
setCellularLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
setCellularLocation(CellularLocationVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Sets the 'cellularLocation' property value
setCellularLocation() - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Sets the 'cellularLocation' property value to an anonymous node
setCellularLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
Sets the 'cellularLocation' property value to the given resource, and add's rdf:type properties.
setCellularLocation(CellularLocationVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
setCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
setCellularLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
setCellularLocation(CellularLocationVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
setCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
setCellularLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
setCellularLocation(CellularLocationVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
setCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
setCellularLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
setCellularLocation(CellularLocationVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
setCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
setCellularLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
setCellularLocation(CellularLocationVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
setCellularLocation() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
setCellularLocation(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
setChemicalFormula(String) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Sets the 'chemicalFormula' property value
setChemicalFormula(String) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
setClipboardContents(String) - Method in class fr.curie.BiNoM.cytoscape.utils.TextBox
 
setClipboardContents(String) - Method in class fr.curie.BiNoM.cytoscape.utils.TextBoxDialog
 
setColor(Color) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
setControlled(Conversion) - Method in interface fr.curie.BiNoM.pathways.biopax.Catalysis
Sets the 'controlled' property value
setControlled(Conversion) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setControlled(Interaction) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setControlled(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setControlled(Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Sets the 'controlled' property value
setControlled(Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Sets the 'controlled' property value
setControlled(Interaction) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
setControlled(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
setControlled(Catalysis) - Method in interface fr.curie.BiNoM.pathways.biopax.Modulation
Sets the 'controlled' property value
setControlled(Catalysis) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setControlled(Interaction) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setControlled(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setControlled(TemplateReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation
Sets the 'controlled' property value
setControlled(TemplateReaction) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setControlled(Interaction) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setControlled(Pathway) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setControlled_asCatalysis() - Method in interface fr.curie.BiNoM.pathways.biopax.Modulation
Sets the 'controlled' property value to an anonymous node
setControlled_asCatalysis(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Modulation
Sets the 'controlled' property value to the given resource, and add's rdf:type properties.
setControlled_asCatalysis() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setControlled_asCatalysis(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setControlled_asConversion() - Method in interface fr.curie.BiNoM.pathways.biopax.Catalysis
Sets the 'controlled' property value to an anonymous node
setControlled_asConversion(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Catalysis
Sets the 'controlled' property value to the given resource, and add's rdf:type properties.
setControlled_asConversion() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setControlled_asConversion(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setControlled_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setControlled_asInteraction(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setControlled_asInteraction() - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Sets the 'controlled' property value to an anonymous node
setControlled_asInteraction(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Sets the 'controlled' property value to the given resource, and add's rdf:type properties.
setControlled_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
setControlled_asInteraction(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
setControlled_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setControlled_asInteraction(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setControlled_asInteraction() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setControlled_asInteraction(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setControlled_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setControlled_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setControlled_asPathway() - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Sets the 'controlled' property value to an anonymous node
setControlled_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Sets the 'controlled' property value to the given resource, and add's rdf:type properties.
setControlled_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
setControlled_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
setControlled_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setControlled_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setControlled_asPathway() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setControlled_asPathway(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setControlled_asTemplateReaction() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation
Sets the 'controlled' property value to an anonymous node
setControlled_asTemplateReaction(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation
Sets the 'controlled' property value to the given resource, and add's rdf:type properties.
setControlled_asTemplateReaction() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setControlled_asTemplateReaction(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setControlType(String) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setControlType(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Control
Sets the 'controlType' property value
setControlType(String) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
setControlType(String) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setControlType(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setConversionDirection(String) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
setConversionDirection(String) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
setConversionDirection(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Sets the 'conversionDirection' property value
setConversionDirection(String) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
setConversionDirection(String) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
setConversionDirection(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
setConversionDirection(String) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
setCurrentModelSize(int, int) - Static method in class fr.curie.BiNoM.celldesigner.lib.NetworkUtils
 
setDatabase(edu.rpi.cs.xgmml.GraphDocument) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine
Setting the BioPAX index file for performing the query
setDatabaseFileName(String) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
setDb(String) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
setDb(String) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
setDb(String) - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
setDb(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Xref
Sets the 'db' property value
setDb(String) - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
setDbVersion(String) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
setDbVersion(String) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
setDbVersion(String) - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
setDbVersion(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Xref
Sets the 'dbVersion' property value
setDbVersion(String) - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
setDeltaGPrime0(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaG
Sets the 'deltaGPrime0' property value
setDeltaGPrime0(Float) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
setDisplayAll(boolean) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserFrame
 
setDistance(ShortPathClustering.Distance) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Distance
 
setEditMode(boolean) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyBrowserFrame
 
setEntityId(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
setEntityReference(EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Sets the 'entityReference' property value
setEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Sets the 'entityReference' property value to an anonymous node
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
setEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
setEntityReference(EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Sets the 'entityReference' property value
setEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Sets the 'entityReference' property value to an anonymous node
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
setEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
setEntityReference(EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Sets the 'entityReference' property value
setEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Sets the 'entityReference' property value to an anonymous node
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
setEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
setEntityReference(EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Sets the 'entityReference' property value
setEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Sets the 'entityReference' property value to an anonymous node
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
setEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
setEntityReference(EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Sets the 'entityReference' property value
setEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Sets the 'entityReference' property value to an anonymous node
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
setEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
setEntityReference(EntityReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Sets the 'entityReference' property value
setEntityReference() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Sets the 'entityReference' property value to an anonymous node
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference(EntityReference) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
setEntityReference() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
setEntityReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
setEntityReference_asDnaReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Sets the 'entityReference' property value to an anonymous node
setEntityReference_asDnaReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Dna
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference_asDnaReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
setEntityReference_asDnaReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
setEntityReference_asDnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Sets the 'entityReference' property value to an anonymous node
setEntityReference_asDnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference_asDnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
setEntityReference_asDnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
setEntityReference_asProteinReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Sets the 'entityReference' property value to an anonymous node
setEntityReference_asProteinReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Protein
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference_asProteinReference() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
setEntityReference_asProteinReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
setEntityReference_asRnaReference() - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Sets the 'entityReference' property value to an anonymous node
setEntityReference_asRnaReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Rna
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference_asRnaReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
setEntityReference_asRnaReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
setEntityReference_asRnaRegionReference() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Sets the 'entityReference' property value to an anonymous node
setEntityReference_asRnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference_asRnaRegionReference() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
setEntityReference_asRnaRegionReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
setEntityReference_asSmallMoleculeReference() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Sets the 'entityReference' property value to an anonymous node
setEntityReference_asSmallMoleculeReference(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
Sets the 'entityReference' property value to the given resource, and add's rdf:type properties.
setEntityReference_asSmallMoleculeReference() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
setEntityReference_asSmallMoleculeReference(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
setEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
setEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
setEntityReferenceType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
setEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setEntityReferenceType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setEntityReferenceType(EntityReferenceTypeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Sets the 'entityReferenceType' property value
setEntityReferenceType() - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Sets the 'entityReferenceType' property value to an anonymous node
setEntityReferenceType(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReference
Sets the 'entityReferenceType' property value to the given resource, and add's rdf:type properties.
setEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
setEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
setEntityReferenceType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
setEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
setEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
setEntityReferenceType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
setEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
setEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
setEntityReferenceType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
setEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setEntityReferenceType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setEntityReferenceType(EntityReferenceTypeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
setEntityReferenceType() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
setEntityReferenceType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
setFont(Font) - Method in class fr.curie.BiNoM.lib.MLLabel
 
setForeground(Color) - Method in class fr.curie.BiNoM.lib.MLLabel
 
setId(String) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
setId(String) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
setId(String) - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
setId(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Xref
Sets the 'id' property value
setId(String) - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
setIdVersion(String) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
setIdVersion(String) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
setIdVersion(String) - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
setIdVersion(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Xref
Sets the 'idVersion' property value
setIdVersion(String) - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
setInteractionType(InteractionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.Interaction
Sets the 'interactionType' property value
setInteractionType() - Method in interface fr.curie.BiNoM.pathways.biopax.Interaction
Sets the 'interactionType' property value to an anonymous node
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Interaction
Sets the 'interactionType' property value to the given resource, and add's rdf:type properties.
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
setInteractionType(InteractionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
setInteractionType() - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
setInteractionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
setIntraMolecular(Boolean) - Method in interface fr.curie.BiNoM.pathways.biopax.BindingFeature
Sets the 'intraMolecular' property value
setIntraMolecular(Boolean) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
setIntraMolecular(Boolean) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
setIonicStrength(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaG
Sets the 'ionicStrength' property value
setIonicStrength(Float) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
setIonicStrength(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrime
Sets the 'ionicStrength' property value
setIonicStrength(Float) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
setKPrime(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrime
Sets the 'kPrime' property value
setKPrime(Float) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
setListwithAttributeName() - Method in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerDialog
Add attribute information to node IDs in the source, target and side-effect node lists.
setLitValue(XmlObject, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Same as SetValue
setMapSize(int, int) - Method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
Set size values for new map
setModificationType(SequenceModificationVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
setModificationType() - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
setModificationType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
setModificationType(SequenceModificationVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeature
Sets the 'modificationType' property value
setModificationType() - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeature
Sets the 'modificationType' property value to an anonymous node
setModificationType(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.ModificationFeature
Sets the 'modificationType' property value to the given resource, and add's rdf:type properties.
setModificationType(SequenceModificationVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
setModificationType() - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
setModificationType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
setMolecularWeight(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Sets the 'molecularWeight' property value
setMolecularWeight(Float) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
setName(String) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Cluster
 
setnames - Variable in class fr.curie.BiNoM.pathways.utils.GMTFile
 
setnames - Variable in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
setNamingServiceMode(boolean) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
setNetwork(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard
 
setNetworkContents(CyNetwork, CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
 
setNetworkContentsAndReportPositions(CyNetwork, CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils
 
setNoteHtmlBodyValue(NotesDocument.Notes, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Sets NotesDocument.Notes content
setOrganism(BioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Sets the 'organism' property value
setOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Sets the 'organism' property value to an anonymous node
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Sets the 'organism' property value to the given resource, and add's rdf:type properties.
setOrganism(BioSource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
setOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
setOrganism(BioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Sets the 'organism' property value
setOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Sets the 'organism' property value to an anonymous node
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Sets the 'organism' property value to the given resource, and add's rdf:type properties.
setOrganism(BioSource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setOrganism(BioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.Gene
Sets the 'organism' property value
setOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.Gene
Sets the 'organism' property value to an anonymous node
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Gene
Sets the 'organism' property value to the given resource, and add's rdf:type properties.
setOrganism(BioSource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
setOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
setOrganism(BioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Sets the 'organism' property value
setOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Sets the 'organism' property value to an anonymous node
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Pathway
Sets the 'organism' property value to the given resource, and add's rdf:type properties.
setOrganism(BioSource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
setOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
setOrganism(BioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
Sets the 'organism' property value
setOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
Sets the 'organism' property value to an anonymous node
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
Sets the 'organism' property value to the given resource, and add's rdf:type properties.
setOrganism(BioSource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
setOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
setOrganism(BioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Sets the 'organism' property value
setOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Sets the 'organism' property value to an anonymous node
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Sets the 'organism' property value to the given resource, and add's rdf:type properties.
setOrganism(BioSource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
setOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
setOrganism(BioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Sets the 'organism' property value
setOrganism() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Sets the 'organism' property value to an anonymous node
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Sets the 'organism' property value to the given resource, and add's rdf:type properties.
setOrganism(BioSource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setOrganism() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setOrganism(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
SetOverlapAnalysis - Class in fr.curie.BiNoM.pathways.utils
 
SetOverlapAnalysis() - Constructor for class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
setParentClassDescV(Vector<BioPAXClassDesc>) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
setPatoData(String) - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabulary
Sets the 'patoData' property value
setPatoData(String) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
setPh(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaG
Sets the 'ph' property value
setPh(Float) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
setPh(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrime
Sets the 'ph' property value
setPh(Float) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
setPhenotype(PhenotypeVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Sets the 'phenotype' property value
setPhenotype() - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Sets the 'phenotype' property value to an anonymous node
setPhenotype(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
Sets the 'phenotype' property value to the given resource, and add's rdf:type properties.
setPhenotype(PhenotypeVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
setPhenotype() - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
setPhenotype(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
setPhysicalEntity(PhysicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.Stoichiometry
Sets the 'physicalEntity' property value
setPhysicalEntity() - Method in interface fr.curie.BiNoM.pathways.biopax.Stoichiometry
Sets the 'physicalEntity' property value to an anonymous node
setPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Stoichiometry
Sets the 'physicalEntity' property value to the given resource, and add's rdf:type properties.
setPhysicalEntity(PhysicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
setPhysicalEntity() - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
setPhysicalEntity(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
setPMg(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaG
Sets the 'pMg' property value
setPMg(Float) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
setPMg(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrime
Sets the 'pMg' property value
setPMg(Float) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
setPositionStatus(String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceSite
Sets the 'positionStatus' property value
setPositionStatus(String) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
setReactionEffectAttribute(Interaction, Node, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
If there is a comment with which contains substring+":", this comment is added as a value of an attribute named substring
setReactionEffectAttribute(Interaction, GraphicNode, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper
 
setRegionType(SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Sets the 'regionType' property value
setRegionType() - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Sets the 'regionType' property value to an anonymous node
setRegionType(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Sets the 'regionType' property value to the given resource, and add's rdf:type properties.
setRegionType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setRegionType() - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setRegionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setRegionType(SequenceRegionVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Sets the 'regionType' property value
setRegionType() - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Sets the 'regionType' property value to an anonymous node
setRegionType(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Sets the 'regionType' property value to the given resource, and add's rdf:type properties.
setRegionType(SequenceRegionVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setRegionType() - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setRegionType(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setReport(String) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository
 
sets - Variable in class fr.curie.BiNoM.pathways.utils.GMTFile
 
sets - Variable in class fr.curie.BiNoM.pathways.utils.SetOverlapAnalysis
 
setScoreSource(Provenance) - Method in interface fr.curie.BiNoM.pathways.biopax.Score
Sets the 'scoreSource' property value
setScoreSource() - Method in interface fr.curie.BiNoM.pathways.biopax.Score
Sets the 'scoreSource' property value to an anonymous node
setScoreSource(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.Score
Sets the 'scoreSource' property value to the given resource, and add's rdf:type properties.
setScoreSource(Provenance) - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
setScoreSource() - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
setScoreSource(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
setSequence(String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReference
Sets the 'sequence' property value
setSequence(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
setSequence(String) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
Sets the 'sequence' property value
setSequence(String) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
setSequence(String) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
Sets the 'sequence' property value
setSequence(String) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
setSequence(String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReference
Sets the 'sequence' property value
setSequence(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
setSequence(String) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
Sets the 'sequence' property value
setSequence(String) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
setSequenceIntervalBegin(SequenceSite) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
Sets the 'sequenceIntervalBegin' property value
setSequenceIntervalBegin() - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
Sets the 'sequenceIntervalBegin' property value to an anonymous node
setSequenceIntervalBegin(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
Sets the 'sequenceIntervalBegin' property value to the given resource, and add's rdf:type properties.
setSequenceIntervalBegin(SequenceSite) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
setSequenceIntervalBegin() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
setSequenceIntervalBegin(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
setSequenceIntervalEnd(SequenceSite) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
Sets the 'sequenceIntervalEnd' property value
setSequenceIntervalEnd() - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
Sets the 'sequenceIntervalEnd' property value to an anonymous node
setSequenceIntervalEnd(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
Sets the 'sequenceIntervalEnd' property value to the given resource, and add's rdf:type properties.
setSequenceIntervalEnd(SequenceSite) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
setSequenceIntervalEnd() - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
setSequenceIntervalEnd(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
setSequencePosition(Integer) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceSite
Sets the 'sequencePosition' property value
setSequencePosition(Integer) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
setSpeciesPositionForXGMML(String, GraphicNode, SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Reads the position information for a node from CellDesigner
setSpontaneous(Boolean) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
setSpontaneous(Boolean) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
setSpontaneous(Boolean) - Method in interface fr.curie.BiNoM.pathways.biopax.Conversion
Sets the 'spontaneous' property value
setSpontaneous(Boolean) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
setSpontaneous(Boolean) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
setSpontaneous(Boolean) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
setSpontaneous(Boolean) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
setStepConversion(Conversion) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Sets the 'stepConversion' property value
setStepConversion() - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Sets the 'stepConversion' property value to an anonymous node
setStepConversion(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Sets the 'stepConversion' property value to the given resource, and add's rdf:type properties.
setStepConversion(Conversion) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
setStepConversion() - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
setStepConversion(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
setStepDirection(String) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
Sets the 'stepDirection' property value
setStepDirection(String) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
setStoichiometricCoefficient(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.Stoichiometry
Sets the 'stoichiometricCoefficient' property value
setStoichiometricCoefficient(Float) - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
setStructure(ChemicalStructure) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Sets the 'structure' property value
setStructure() - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Sets the 'structure' property value to an anonymous node
setStructure(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
Sets the 'structure' property value to the given resource, and add's rdf:type properties.
setStructure(ChemicalStructure) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
setStructure() - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
setStructure(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
setStructureData(String) - Method in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructure
Sets the 'structureData' property value
setStructureData(String) - Method in class fr.curie.BiNoM.pathways.biopax.ChemicalStructureImpl
 
setStructureFormat(String) - Method in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructure
Sets the 'structureFormat' property value
setStructureFormat(String) - Method in class fr.curie.BiNoM.pathways.biopax.ChemicalStructureImpl
 
setSubType(BioPAXAttrDescProto.SubType) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.CalcCentralityTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponentsTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ConvertReactionNetworkToEntityNetworkTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ConvertToUndirectedGraphTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.CycleDecompositionTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ExcludeIntermediateNodesTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetworkTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractSubnetworkTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.LinearizeNetworkTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.MaterialComponentsTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ModularViewTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.MonoMolecularReactionsAsEdgesTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.OptimalCutSetAnalyzerTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerBootstrapTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.PruneGraphTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.StronglyConnectedComponentsTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSourceTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSourceTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.checkCellDesignerFileTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.colorCellDesignerProteinsTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CSMLImportTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.MergingMapsTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.modifyCellDesignerNotesTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.ProduceNaviCellMapFilesTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ClusterByShortPathTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.DestroyUnusedNetworksAsNestTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.nestmanager.RecreateLostConnectionsInsideNestsTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExportTask
 
setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.utils.MergeNetworksAndFilterTask
 
setTemperature(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaG
Sets the 'temperature' property value
setTemperature(Float) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
setTemperature(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrime
Sets the 'temperature' property value
setTemperature(Float) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
setTemplate(Dna) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value
setTemplate(DnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value
setTemplate(Rna) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value
setTemplate(RnaRegion) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value
setTemplate(Dna) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate(DnaRegion) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate(Rna) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate(RnaRegion) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate_asDna() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value to an anonymous node
setTemplate_asDna(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value to the given resource, and add's rdf:type properties.
setTemplate_asDna() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate_asDna(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate_asDnaRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value to an anonymous node
setTemplate_asDnaRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value to the given resource, and add's rdf:type properties.
setTemplate_asDnaRegion() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate_asDnaRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate_asRna() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value to an anonymous node
setTemplate_asRna(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value to the given resource, and add's rdf:type properties.
setTemplate_asRna() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate_asRna(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate_asRnaRegion() - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value to an anonymous node
setTemplate_asRnaRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'template' property value to the given resource, and add's rdf:type properties.
setTemplate_asRnaRegion() - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplate_asRnaRegion(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setTemplateDirection(String) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
Sets the 'templateDirection' property value
setTemplateDirection(String) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
setText(String) - Method in class fr.curie.BiNoM.lib.MLLabel
 
setTissue(TissueVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Sets the 'tissue' property value
setTissue() - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Sets the 'tissue' property value to an anonymous node
setTissue(com.hp.hpl.jena.rdf.model.Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSource
Sets the 'tissue' property value to the given resource, and add's rdf:type properties.
setTissue(TissueVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
setTissue() - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
setTissue(com.hp.hpl.jena.rdf.model.Resource) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
setTitle(String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
Sets the 'title' property value
setTitle(String) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
setURI(Object, String) - Method in class fr.curie.BiNoM.biopax.BioPAXSourceDB
 
setValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXAttrDesc
 
setValue(BioPAXObject, Double) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleAttrDesc
 
setValue(BioPAXObject, Integer) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerAttrDesc
 
setValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
setValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
setValue(String) - Method in interface fr.curie.BiNoM.pathways.biopax.Score
Sets the 'value' property value
setValue(String) - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
setValue(XmlObject, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
Set a string value for XmlObject
setYear(Integer) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
Sets the 'year' property value
setYear(Integer) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
SHARP - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
 
shiftCoordinates(SbmlDocument, float, float) - Static method in class fr.curie.BiNoM.pathways.test.TestMergingMapsCD
 
SHORTEST_PATHS - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
ShortPathClustering - Class in fr.curie.BiNoM.cytoscape.nestmanager
Algorithm of clustering based on a distance computed by minimum linkage of the oriented shortest path when shortest paths are equal, the bigger number of links is get as minimum The ceiling size of cluster and the max length of shortest paths are parameters the condition to stop clustering is the - the maximal length of shortest paths is reached - the number of clusters remaining in the queue is less than 2 When the size of an union of clusters exceed the ceiling size, it is not created and the biggest is out of the queue and kept apart the start list of nodes is sorted by in degree, so sources are first every created cluster is placed at the end of the queue to slow the increasing of size
ShortPathClustering() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering
 
ShortPathClustering(CyNetwork) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering
 
ShortPathClustering.Cluster - Class in fr.curie.BiNoM.cytoscape.nestmanager
 
ShortPathClustering.Cluster() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Cluster
 
ShortPathClustering.Cluster(Integer) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Cluster
 
ShortPathClustering.Cluster(ShortPathClustering.Cluster, ShortPathClustering.Cluster, ShortPathClustering.Distance) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Cluster
 
ShortPathClustering.Distance - Class in fr.curie.BiNoM.cytoscape.nestmanager
 
ShortPathClustering.Distance() - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Distance
 
ShortPathClustering.Distance(Integer, Integer) - Constructor for class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Distance
 
shortPathMatrix() - Method in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
shortPathMatrixByBFS() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph
 
showAlsoSynonyms - Variable in class fr.curie.BiNoM.cytoscape.utils.ListAllNodesDialog
 
ShowClipboardContents - Class in fr.curie.BiNoM.cytoscape.utils
 
ShowClipboardContents() - Constructor for class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContents
 
ShowClipboardContentsDialog - Class in fr.curie.BiNoM.cytoscape.utils
 
ShowClipboardContentsDialog() - Constructor for class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContentsDialog
 
ShowMonoMolecularReactionsAsEdges(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils
Finds all reactions on the graph gri having only one reactant and one product and no modifiers and substitutes them by edge.
showOnlyEntityNames - Variable in class fr.curie.BiNoM.cytoscape.utils.ListAllNodesDialog
 
ShowTextDialog - Class in fr.curie.BiNoM.cytoscape.utils
 
ShowTextDialog() - Constructor for class fr.curie.BiNoM.cytoscape.utils.ShowTextDialog
 
sideNodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
List of nodes to be considered for scoring side effects
sideScoreMap - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
significanceAnalysis(int, int) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
significanceAnalysisDoPermutation(int) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
significanceOfConnectedComponents - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
SignsOfPaths - Class in fr.curie.BiNoM.pathways.utils
 
SignsOfPaths() - Constructor for class fr.curie.BiNoM.pathways.utils.SignsOfPaths
 
SimpleEdgePruning(Graph, Vector<Float>, Vector<Float>, int, Vector<Graph>) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
SimpleEdgePruningLOOCrossValidation(Graph, Vector<Float>, Vector<Float>, int, Vector<Graph>) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
SimpleTable - Class in fr.curie.BiNoM.pathways.utils
Simple implementation of a table of entries
SimpleTable() - Constructor for class fr.curie.BiNoM.pathways.utils.SimpleTable
 
SimpleTextInfluence2BioPAX - Class in fr.curie.BiNoM.pathways.converters
 
SimpleTextInfluence2BioPAX() - Constructor for class fr.curie.BiNoM.pathways.converters.SimpleTextInfluence2BioPAX
 
SimpleTextInfluenceToBioPAX - Class in fr.curie.BiNoM.pathways
 
SimpleTextInfluenceToBioPAX() - Constructor for class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
SIMPLY_CONNECT - Static variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
SIMPLY_CONNECT_WITH_COMPLEX_NODES - Static variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
SIMPLY_CONNECT_WITH_SECOND_ORDER_CONNECTIONS - Static variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
sinonymSpecies - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter.BioPAXSpecies
List of identical (from the point of view of SBML) physicalEntityParticipants
sizesToTest - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
Skeleton - Class in fr.curie.BiNoM.pathways.analysis.structure
Some old and forgotten idea
Skeleton() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Skeleton
 
smallestCycleSize - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
SmallMolecule - Interface in fr.curie.BiNoM.pathways.biopax
Interface for SmallMolecule ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
SmallMoleculeImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of SmallMolecule Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
smallMoleculeList - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from cut uris (after # separator) to 'smallMolecule' entities
SmallMoleculeListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.SmallMolecule to receive notification when properties changed, added or removed.
SmallMoleculeReference - Interface in fr.curie.BiNoM.pathways.biopax
Interface for SmallMoleculeReference ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
SmallMoleculeReferenceImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of SmallMoleculeReference Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
SmallMoleculeReferenceListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference to receive notification when properties changed, added or removed.
snp - Variable in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
sort(Vector<BioPAXClassDesc>) - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
SortMass(float[]) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
sortPathsByActivities() - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
sortPathsByActivities(float[]) - Method in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
source - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
source - Variable in class fr.curie.BiNoM.pathways.test.TestGraphAlgo.ElemScore
 
sourceAdded(PublicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when a value of source has been added
sourceGraphs - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Ocsana list of "source" graphs
sourceNodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
List of source nodes
sourceProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
The Jena Property for source
sourceRemoved(PublicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when a value of source has been removed
species - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
Map from SBML species ids to SpeciesDocument.Species objects
species - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
Map of CellDesigner SpeciesDocument.Species objects
speciesAliasIdMap - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
speciesAliasMap - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
speciesFilter - Variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
speciesMap - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
speciesModularModuleNameMap - Variable in class fr.curie.BiNoM.pathways.navicell.ProduceClickableMap
 
SpeciesStructure - Class in fr.curie.BiNoM.pathways.utils
 
SpeciesStructure() - Constructor for class fr.curie.BiNoM.pathways.utils.SpeciesStructure
 
SpeciesStructure.SpeciesStructureComponent - Class in fr.curie.BiNoM.pathways.utils
 
SpeciesStructure.SpeciesStructureComponent() - Constructor for class fr.curie.BiNoM.pathways.utils.SpeciesStructure.SpeciesStructureComponent
 
SpeciesStructure.SpeciesStructureComponentModification - Class in fr.curie.BiNoM.pathways.utils
 
SpeciesStructure.SpeciesStructureComponentModification() - Constructor for class fr.curie.BiNoM.pathways.utils.SpeciesStructure.SpeciesStructureComponentModification
 
spontaneousChanged(BiochemicalReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when spontaneous has changed
spontaneousChanged(ComplexAssembly) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when spontaneous has changed
spontaneousChanged(Conversion) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when spontaneous has changed
spontaneousChanged(Degradation) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when spontaneous has changed
spontaneousChanged(Transport) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when spontaneous has changed
spontaneousChanged(TransportWithBiochemicalReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when spontaneous has changed
spontaneousProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Conversion
The Jena Property for spontaneous
SQUARE - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
 
srcs - Variable in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
staining - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
startElement(String, String, String, Attributes) - Method in class fr.curie.BiNoM.pathways.utils.GraphXGMMLParser
 
startId - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
stateAbbrev - Variable in class fr.curie.BiNoM.cytoscape.utils.PavingData
 
stateArray - Variable in class fr.curie.BiNoM.cytoscape.utils.PavingData
 
stateColors - Variable in class fr.curie.BiNoM.cytoscape.utils.PavingData
 
stateNames - Variable in class fr.curie.BiNoM.cytoscape.utils.PavingData
 
stepConversionChanged(BiochemicalPathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when stepConversion has changed
stepConversionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
The Jena Property for stepConversion
stepDirectionChanged(BiochemicalPathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when stepDirection has changed
stepDirectionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
The Jena Property for stepDirection
stepProcessAdded(BiochemicalPathwayStep, Control) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of stepProcess has been added
stepProcessAdded(BiochemicalPathwayStep, Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of stepProcess has been added
stepProcessAdded(BiochemicalPathwayStep, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of stepProcess has been added
stepProcessAdded(PathwayStep, Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStepListener
Called when a value of stepProcess has been added
stepProcessAdded(PathwayStep, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStepListener
Called when a value of stepProcess has been added
stepProcessProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
The Jena Property for stepProcess
stepProcessRemoved(BiochemicalPathwayStep, Control) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of stepProcess has been removed
stepProcessRemoved(BiochemicalPathwayStep, Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of stepProcess has been removed
stepProcessRemoved(BiochemicalPathwayStep, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepListener
Called when a value of stepProcess has been removed
stepProcessRemoved(PathwayStep, Interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStepListener
Called when a value of stepProcess has been removed
stepProcessRemoved(PathwayStep, Pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayStepListener
Called when a value of stepProcess has been removed
stoichiometricCoefficientChanged(Stoichiometry) - Method in interface fr.curie.BiNoM.pathways.biopax.StoichiometryListener
Called when stoichiometricCoefficient has changed
stoichiometricCoefficientProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Stoichiometry
The Jena Property for stoichiometricCoefficient
Stoichiometry - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Stoichiometry ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
StoichiometryImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Stoichiometry Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
StoichiometryListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Stoichiometry to receive notification when properties changed, added or removed.
stringOption(String, String) - Method in class fr.curie.BiNoM.pathways.utils.OptionParser
 
stringRequiredOption(String, String) - Method in class fr.curie.BiNoM.pathways.utils.OptionParser
 
stringTable - Variable in class fr.curie.BiNoM.pathways.utils.SimpleTable
 
StronglyConnectedComponents - Class in fr.curie.BiNoM.celldesigner.analysis
 
StronglyConnectedComponents(CellDesignerPlugin) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.StronglyConnectedComponents
 
StronglyConnectedComponents - Class in fr.curie.BiNoM.cytoscape.analysis
 
StronglyConnectedComponents() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.StronglyConnectedComponents
 
StronglyConnectedComponentsTarjan(Graph, int) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
StronglyConnectedComponentsTask - Class in fr.curie.BiNoM.celldesigner.analysis
 
StronglyConnectedComponentsTask(CellDesignerPlugin, GraphDocument) - Constructor for class fr.curie.BiNoM.celldesigner.analysis.StronglyConnectedComponentsTask
 
StronglyConnectedComponentsTask - Class in fr.curie.BiNoM.cytoscape.analysis
 
StronglyConnectedComponentsTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.StronglyConnectedComponentsTask
 
StructureAnalysisUtils - Class in fr.curie.BiNoM.pathways.analysis.structure
Connector class between GraphAlgorithms and BiographUtils and Cytoscape interface
StructureAnalysisUtils() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils
 
StructureAnalysisUtils.Option - Class in fr.curie.BiNoM.pathways.analysis.structure
Options container
StructureAnalysisUtils.Option() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
structureChanged(SmallMoleculeReference) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when structure has changed
structureDataChanged(ChemicalStructure) - Method in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructureListener
Called when structureData has changed
structureDataProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructure
The Jena Property for structureData
structureFormatChanged(ChemicalStructure) - Method in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructureListener
Called when structureFormat has changed
structureFormatProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructure
The Jena Property for structureFormat
structureProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
The Jena Property for structure
subnetwork - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
SubnetworkComplexProfile - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
subnetworkDistanceMatrix - Variable in class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
SubnetworkProperties - Class in fr.curie.BiNoM.pathways.utils
 
SubnetworkProperties() - Constructor for class fr.curie.BiNoM.pathways.utils.SubnetworkProperties
 
SUBOPTIMAL_SHORTEST_PATHS - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
SUBOPTIMAL_SHORTEST_PATHS - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option
 
subRegionAdded(DnaReference, DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of subRegion has been added
subRegionAdded(DnaReference, RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of subRegion has been added
subRegionAdded(DnaRegionReference, DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of subRegion has been added
subRegionAdded(DnaRegionReference, RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of subRegion has been added
subRegionAdded(RnaReference, RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of subRegion has been added
subRegionAdded(RnaReference, DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of subRegion has been added
subRegionAdded(RnaRegionReference, RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of subRegion has been added
subRegionAdded(RnaRegionReference, DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of subRegion has been added
subRegionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaReference
The Jena Property for subRegion
subRegionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
The Jena Property for subRegion
subRegionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaReference
The Jena Property for subRegion
subRegionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
The Jena Property for subRegion
subRegionRemoved(DnaReference, DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of subRegion has been removed
subRegionRemoved(DnaReference, RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of subRegion has been removed
subRegionRemoved(DnaRegionReference, DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of subRegion has been removed
subRegionRemoved(DnaRegionReference, RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of subRegion has been removed
subRegionRemoved(RnaReference, RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of subRegion has been removed
subRegionRemoved(RnaReference, DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of subRegion has been removed
subRegionRemoved(RnaRegionReference, RnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of subRegion has been removed
subRegionRemoved(RnaRegionReference, DnaRegionReference) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of subRegion has been removed
substituteEntityId(SbmlDocument, String, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
substituteSpeciesId(SbmlDocument, String, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
 
subtractNodes(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
summaryActivity - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
sumPiquantAbsSetScore - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer.optCutSetData
 
sumSideScore - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer.optCutSetData
 
suppressedEdge(CyEdge) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
 
suppressedNode(CyNode) - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator
 
syncFrames() - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
synchronizeAnnotations(ModifyCellDesignerNotes) - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
synchronizeSections(String, Vector<ModifyCellDesignerNotes.AnnotationSection>) - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 

T

table - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
tags - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
takenaliases - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter
Map from a key in the form reaction_id+"_"+species_alias_id to ReactionDocument.Reaction object
target - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
target - Variable in class fr.curie.BiNoM.pathways.test.TestGraphAlgo.ElemScore
 
targetNodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
List of target nodes
TaskManager - Class in fr.curie.BiNoM.cytoscape.lib
 
TaskManager() - Constructor for class fr.curie.BiNoM.cytoscape.lib.TaskManager
 
temperatureChanged(DeltaG) - Method in interface fr.curie.BiNoM.pathways.biopax.DeltaGListener
Called when temperature has changed
temperatureChanged(KPrime) - Method in interface fr.curie.BiNoM.pathways.biopax.KPrimeListener
Called when temperature has changed
temperatureProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.DeltaG
The Jena Property for temperature
temperatureProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.KPrime
The Jena Property for temperature
tempFamilies - Variable in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINDialogFamily
 
templateChanged(TemplateReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when template has changed
templateDirectionChanged(TemplateReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when templateDirection has changed
templateDirectionProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
The Jena Property for templateDirection
templateProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
The Jena Property for template
TemplateReaction - Interface in fr.curie.BiNoM.pathways.biopax
Interface for TemplateReaction ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
TemplateReactionImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of TemplateReaction Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
TemplateReactionListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.TemplateReaction to receive notification when properties changed, added or removed.
TemplateReactionRegulation - Interface in fr.curie.BiNoM.pathways.biopax
Interface for TemplateReactionRegulation ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
TemplateReactionRegulationImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of TemplateReactionRegulation Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
TemplateReactionRegulationListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation to receive notification when properties changed, added or removed.
termAdded(CellularLocationVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyListener
Called when a value of term has been added
termAdded(CellVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CellVocabularyListener
Called when a value of term has been added
termAdded(ControlledVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabularyListener
Called when a value of term has been added
termAdded(EntityReferenceTypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyListener
Called when a value of term has been added
termAdded(EvidenceCodeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyListener
Called when a value of term has been added
termAdded(ExperimentalFormVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyListener
Called when a value of term has been added
termAdded(InteractionVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionVocabularyListener
Called when a value of term has been added
termAdded(PhenotypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyListener
Called when a value of term has been added
termAdded(RelationshipTypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyListener
Called when a value of term has been added
termAdded(SequenceModificationVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyListener
Called when a value of term has been added
termAdded(SequenceRegionVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyListener
Called when a value of term has been added
termAdded(TissueVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TissueVocabularyListener
Called when a value of term has been added
termProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
The Jena Property for term
termRemoved(CellularLocationVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyListener
Called when a value of term has been removed
termRemoved(CellVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.CellVocabularyListener
Called when a value of term has been removed
termRemoved(ControlledVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabularyListener
Called when a value of term has been removed
termRemoved(EntityReferenceTypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyListener
Called when a value of term has been removed
termRemoved(EvidenceCodeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyListener
Called when a value of term has been removed
termRemoved(ExperimentalFormVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyListener
Called when a value of term has been removed
termRemoved(InteractionVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionVocabularyListener
Called when a value of term has been removed
termRemoved(PhenotypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyListener
Called when a value of term has been removed
termRemoved(RelationshipTypeVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyListener
Called when a value of term has been removed
termRemoved(SequenceModificationVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyListener
Called when a value of term has been removed
termRemoved(SequenceRegionVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyListener
Called when a value of term has been removed
termRemoved(TissueVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.TissueVocabularyListener
Called when a value of term has been removed
test - Class in fr.curie.BiNoM.pathways.test
 
test() - Constructor for class fr.curie.BiNoM.pathways.test.test
 
test(String) - Static method in class fr.curie.BiNoM.pathways.test.testNamingService
 
test1 - Class in fr.curie.BiNoM.pathways.test
 
test1() - Constructor for class fr.curie.BiNoM.pathways.test.test1
 
test2 - Class in fr.curie.BiNoM.pathways.test
 
test2() - Constructor for class fr.curie.BiNoM.pathways.test.test2
 
TestAIN - Class in fr.curie.BiNoM.pathways.test
 
TestAIN() - Constructor for class fr.curie.BiNoM.pathways.test.TestAIN
 
TestAutomaticStructureAnalysis - Class in fr.curie.BiNoM.pathways.test
 
TestAutomaticStructureAnalysis() - Constructor for class fr.curie.BiNoM.pathways.test.TestAutomaticStructureAnalysis
 
testBioBasePathway - Class in fr.curie.BiNoM.pathways.test
 
testBioBasePathway() - Constructor for class fr.curie.BiNoM.pathways.test.testBioBasePathway
 
TestBioPAX - Class in fr.curie.BiNoM.pathways.test
 
TestBioPAX() - Constructor for class fr.curie.BiNoM.pathways.test.TestBioPAX
 
testBioPAX1 - Class in fr.curie.BiNoM.pathways.test
 
testBioPAX1() - Constructor for class fr.curie.BiNoM.pathways.test.testBioPAX1
 
testBioPAXExtract - Class in fr.curie.BiNoM.pathways.test
 
testBioPAXExtract() - Constructor for class fr.curie.BiNoM.pathways.test.testBioPAXExtract
 
testBioPAXExtractAPO - Class in fr.curie.BiNoM.pathways.test
 
testBioPAXExtractAPO() - Constructor for class fr.curie.BiNoM.pathways.test.testBioPAXExtractAPO
 
TestBioPAXGraphMapper - Class in fr.curie.BiNoM.pathways.test
 
TestBioPAXGraphMapper() - Constructor for class fr.curie.BiNoM.pathways.test.TestBioPAXGraphMapper
 
testBioPAXManipulation - Class in fr.curie.BiNoM.pathways.test
 
testBioPAXManipulation() - Constructor for class fr.curie.BiNoM.pathways.test.testBioPAXManipulation
 
testBioPAXMerge - Class in fr.curie.BiNoM.pathways.test
 
testBioPAXMerge() - Constructor for class fr.curie.BiNoM.pathways.test.testBioPAXMerge
 
testBioPAXQueryEngine - Class in fr.curie.BiNoM.pathways.test
 
testBioPAXQueryEngine() - Constructor for class fr.curie.BiNoM.pathways.test.testBioPAXQueryEngine
 
TestBioPAXQueryEngineEB - Class in fr.curie.BiNoM.pathways.test
 
TestBioPAXQueryEngineEB() - Constructor for class fr.curie.BiNoM.pathways.test.TestBioPAXQueryEngineEB
 
testCellDesigner - Class in fr.curie.BiNoM.pathways.test
 
testCellDesigner() - Constructor for class fr.curie.BiNoM.pathways.test.testCellDesigner
 
testCellDesignerFile - Class in fr.curie.BiNoM.pathways.utils
 
testCellDesignerFile() - Constructor for class fr.curie.BiNoM.pathways.utils.testCellDesignerFile
 
testChangeProteinSize - Class in fr.curie.BiNoM.pathways.test
 
testChangeProteinSize() - Constructor for class fr.curie.BiNoM.pathways.test.testChangeProteinSize
 
testCSML - Class in fr.curie.BiNoM.pathways.test
 
testCSML() - Constructor for class fr.curie.BiNoM.pathways.test.testCSML
 
TestDialog - Class in fr.curie.BiNoM.pathways.test
 
TestDialog() - Constructor for class fr.curie.BiNoM.pathways.test.TestDialog
 
testDialogs - Class in fr.curie.BiNoM.pathways.test
 
testDialogs() - Constructor for class fr.curie.BiNoM.pathways.test.testDialogs
 
TestEB - Class in fr.curie.BiNoM.pathways.test
 
TestEB() - Constructor for class fr.curie.BiNoM.pathways.test.TestEB
 
testEwingNetwork - Class in fr.curie.BiNoM.pathways.test
 
testEwingNetwork() - Constructor for class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
testExtractBioPAX - Class in fr.curie.BiNoM.pathways.test
 
testExtractBioPAX() - Constructor for class fr.curie.BiNoM.pathways.test.testExtractBioPAX
 
TestFindAllPaths - Class in fr.curie.BiNoM.pathways.test
 
TestFindAllPaths() - Constructor for class fr.curie.BiNoM.pathways.test.TestFindAllPaths
 
testFindingPath - Class in fr.curie.BiNoM.pathways.test
 
testFindingPath() - Constructor for class fr.curie.BiNoM.pathways.test.testFindingPath
 
TestGraphAlgo - Class in fr.curie.BiNoM.pathways.test
 
TestGraphAlgo() - Constructor for class fr.curie.BiNoM.pathways.test.TestGraphAlgo
 
TestGraphAlgo.ElemScore - Class in fr.curie.BiNoM.pathways.test
 
TestGraphAlgo.ElemScore(Node, Node, Double) - Constructor for class fr.curie.BiNoM.pathways.test.TestGraphAlgo.ElemScore
 
testGraphMappingService - Class in fr.curie.BiNoM.pathways.test
 
testGraphMappingService() - Constructor for class fr.curie.BiNoM.pathways.test.testGraphMappingService
 
testGraphPruning - Class in fr.curie.BiNoM.pathways.test
 
testGraphPruning() - Constructor for class fr.curie.BiNoM.pathways.test.testGraphPruning
 
testJastor - Class in fr.curie.BiNoM.pathways.test
 
testJastor() - Constructor for class fr.curie.BiNoM.pathways.test.testJastor
 
TestJastorEB - Class in fr.curie.BiNoM.pathways.test
 
TestJastorEB() - Constructor for class fr.curie.BiNoM.pathways.test.TestJastorEB
 
testJavolution - Class in fr.curie.BiNoM.pathways.test
 
testJavolution() - Constructor for class fr.curie.BiNoM.pathways.test.testJavolution
 
TestMaterialComponents - Class in fr.curie.BiNoM.pathways.test
 
TestMaterialComponents() - Constructor for class fr.curie.BiNoM.pathways.test.TestMaterialComponents
 
TestMergeMapsACSN - Class in fr.curie.BiNoM.pathways.test
 
TestMergeMapsACSN() - Constructor for class fr.curie.BiNoM.pathways.test.TestMergeMapsACSN
 
testMergeNetworksAndFilter - Class in fr.curie.BiNoM.pathways.test
 
testMergeNetworksAndFilter() - Constructor for class fr.curie.BiNoM.pathways.test.testMergeNetworksAndFilter
 
TestMergingMapsCD - Class in fr.curie.BiNoM.pathways.test
 
TestMergingMapsCD() - Constructor for class fr.curie.BiNoM.pathways.test.TestMergingMapsCD
 
TestMergingMapsDialog - Class in fr.curie.BiNoM.pathways.test
 
TestMergingMapsDialog() - Constructor for class fr.curie.BiNoM.pathways.test.TestMergingMapsDialog
 
TestMinCutSet - Class in fr.curie.BiNoM.pathways.test
 
TestMinCutSet() - Constructor for class fr.curie.BiNoM.pathways.test.TestMinCutSet
 
TestModuleDecomposition - Class in fr.curie.BiNoM.pathways.test
 
TestModuleDecomposition() - Constructor for class fr.curie.BiNoM.pathways.test.TestModuleDecomposition
 
testNamingService - Class in fr.curie.BiNoM.pathways.test
 
testNamingService() - Constructor for class fr.curie.BiNoM.pathways.test.testNamingService
 
testNetworkFactory - Class in fr.curie.BiNoM.celldesigner.lib
 
testNetworkFactory() - Constructor for class fr.curie.BiNoM.celldesigner.lib.testNetworkFactory
 
TestNetworkOP - Class in fr.curie.BiNoM.cytoscape.netwop
 
TestNetworkOP(String) - Constructor for class fr.curie.BiNoM.cytoscape.netwop.TestNetworkOP
 
TestNIPath - Class in fr.curie.BiNoM.pathways.test
 
TestNIPath() - Constructor for class fr.curie.BiNoM.pathways.test.TestNIPath
 
TestOPtCutSet - Class in fr.curie.BiNoM.pathways.test
 
TestOPtCutSet() - Constructor for class fr.curie.BiNoM.pathways.test.TestOPtCutSet
 
testPath - Class in fr.curie.BiNoM.pathways.analysis.structure
 
testPath() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.testPath
 
TestPiquantDialog - Class in fr.curie.BiNoM.pathways.test
 
TestPiquantDialog() - Constructor for class fr.curie.BiNoM.pathways.test.TestPiquantDialog
 
testRBpathway - Class in fr.curie.BiNoM.pathways.test
 
testRBpathway() - Constructor for class fr.curie.BiNoM.pathways.test.testRBpathway
 
testRemoveEditPoints - Class in fr.curie.BiNoM.pathways.test
 
testRemoveEditPoints() - Constructor for class fr.curie.BiNoM.pathways.test.testRemoveEditPoints
 
testSAX - Class in fr.curie.BiNoM.pathways.test
 
testSAX() - Constructor for class fr.curie.BiNoM.pathways.test.testSAX
 
TestSetSet - Class in fr.curie.BiNoM.pathways.test
 
TestSetSet() - Constructor for class fr.curie.BiNoM.pathways.test.TestSetSet
 
testSignificance - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
testSignificanceMode - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
testStructureAnalysis - Class in fr.curie.BiNoM.pathways.test
 
testStructureAnalysis() - Constructor for class fr.curie.BiNoM.pathways.test.testStructureAnalysis
 
testTranspath - Class in fr.curie.BiNoM.pathways.test
 
testTranspath() - Constructor for class fr.curie.BiNoM.pathways.test.testTranspath
 
TestWordPress - Class in fr.curie.BiNoM.pathways.test
 
TestWordPress() - Constructor for class fr.curie.BiNoM.pathways.test.TestWordPress
 
TestXGMML - Class in fr.curie.BiNoM.pathways.test
 
TestXGMML() - Constructor for class fr.curie.BiNoM.pathways.test.TestXGMML
 
text - Variable in class fr.curie.BiNoM.cytoscape.ain.ImportFromAINTask
 
text - Variable in class fr.curie.BiNoM.cytoscape.utils.ShowTextDialog
 
TextBox - Class in fr.curie.BiNoM.cytoscape.utils
Not modal dialog displaying text and allowing to copy it in clipboard
TextBox(JFrame, String, String) - Constructor for class fr.curie.BiNoM.cytoscape.utils.TextBox
 
TextBoxDialog - Class in fr.curie.BiNoM.cytoscape.utils
Modal dialog displaying text, allowing to copy it in clipboard, displaying a message and proposing a choice
TextBoxDialog(JFrame, String, String, String) - Constructor for class fr.curie.BiNoM.cytoscape.utils.TextBoxDialog
 
tgts - Variable in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
threshold_zvalue - Static variable in class fr.curie.BiNoM.pathways.coloring.Matrix2Color
 
thresholdForComputingGradient - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask.stainingOptions
 
thresholdGradient - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
thresholdIntersectionOfGraphs - Variable in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
thresholdSelectionConnectedComponents - Variable in class fr.curie.BiNoM.pathways.utils.OFTENAnalysis
 
Tissue - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
Tissue - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
tissueChanged(BioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSourceListener
Called when tissue has changed
tissueProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BioSource
The Jena Property for tissue
tissueTypes - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
tissueTypes - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork
 
TissueVocabulary - Interface in fr.curie.BiNoM.pathways.biopax
Interface for TissueVocabulary ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
TissueVocabularyImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of TissueVocabulary Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
TissueVocabularyListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.TissueVocabulary to receive notification when properties changed, added or removed.
title - Variable in class fr.curie.BiNoM.analysis.ClusterNetworksDialog
 
title - Static variable in class fr.curie.BiNoM.cytoscape.influence.FromToNodes
 
title - Static variable in class fr.curie.BiNoM.cytoscape.influence.InfluenceAreaInArray
 
title - Static variable in class fr.curie.BiNoM.cytoscape.influence.InfluenceAreaInAttribute
 
title - Static variable in class fr.curie.BiNoM.cytoscape.influence.InfluenceArrayAsGraphic
 
title - Static variable in class fr.curie.BiNoM.cytoscape.influence.InfluenceArrayAsText
 
title - Static variable in class fr.curie.BiNoM.cytoscape.influence.InfluenceByAttribute
 
title - Static variable in class fr.curie.BiNoM.cytoscape.influence.InfluenceFeatures
 
title - Static variable in class fr.curie.BiNoM.cytoscape.influence.InputReachParameter
 
title - Static variable in class fr.curie.BiNoM.cytoscape.influence.UpdateInfluenceAttrib
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.ClusterByShortPath
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.CreateConnectionsBetweenNests
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.CreateNestNetwork
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.DestroyUnusedNetworksAsNest
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.FindCommonNodes
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.InterOf2SelectedNests
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.ListComponents
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.ListNodesByNest
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.MergeSelectedNests
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.NestInNodeAttribute
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.PackInNestNode
 
title - Static variable in class fr.curie.BiNoM.cytoscape.nestmanager.RecreateLostConnectionsInsideNests
 
title - Variable in class fr.curie.BiNoM.cytoscape.utils.ShowTextDialog
 
titleC - Static variable in class fr.curie.BiNoM.cytoscape.influence.InfluenceArrayAsText
 
titleChanged(PublicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when title has changed
titleF - Static variable in class fr.curie.BiNoM.cytoscape.influence.InfluenceArrayAsGraphic
 
titleOfArray() - Method in class fr.curie.BiNoM.cytoscape.influence.FromToNodes
 
titleProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
The Jena Property for title
titleT - Static variable in class fr.curie.BiNoM.cytoscape.influence.InfluenceArrayAsGraphic
 
titleV - Static variable in class fr.curie.BiNoM.cytoscape.influence.InfluenceArrayAsText
 
toggleNamingServiceMode() - Static method in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyUtils
 
toId(String) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkFactory
 
tokens - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
toString() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
toString() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleAttrDesc
 
toString() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXDoubleListAttrDesc
 
toString() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerAttrDesc
 
toString() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXIntegerListAttrDesc
 
toString() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectAttrDesc
 
toString() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXObjectListAttrDesc
 
toString() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringAttrDesc
 
toString() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXStringListAttrDesc
 
toString() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph.IntEdge
 
toString() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.InteractionGraph.NodeDegree
 
toString() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Cluster
 
toString() - Method in class fr.curie.BiNoM.cytoscape.nestmanager.ShortPathClustering.Distance
 
toString() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Edge
 
toString() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
toString() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Path
 
toString() - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter.BioPAXSpecies
 
toString() - Method in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes.AnnotationSection
 
toString() - Method in class fr.curie.BiNoM.pathways.utils.Pair
 
toString() - Method in class fr.curie.BiNoM.pathways.utils.SpeciesStructure.SpeciesStructureComponent
 
toString() - Method in class fr.curie.BiNoM.pathways.utils.SpeciesStructure.SpeciesStructureComponentModification
 
toString() - Method in class fr.curie.BiNoM.pathways.utils.SpeciesStructure
 
Transpath - Class in fr.curie.BiNoM.pathways.wrappers
Experimental converter from Transpath to BioPAX
Transpath() - Constructor for class fr.curie.BiNoM.pathways.wrappers.Transpath
 
Transpath2BioPAX - Class in fr.curie.BiNoM.pathways.converters
 
Transpath2BioPAX() - Constructor for class fr.curie.BiNoM.pathways.converters.Transpath2BioPAX
 
Transport - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Transport ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
TransportImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Transport Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
TransportListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Transport to receive notification when properties changed, added or removed.
TransportWithBiochemicalReaction - Interface in fr.curie.BiNoM.pathways.biopax
Interface for TransportWithBiochemicalReaction ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
TransportWithBiochemicalReactionImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of TransportWithBiochemicalReaction Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
TransportWithBiochemicalReactionListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReaction to receive notification when properties changed, added or removed.
TreschAlgorithm(Graph, Vector<Float>, Vector<Float>, Vector<Graph>, float) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
Tresch's algorithm for transitive graph reduction From Tresch et al., JCompBiol V14, N9 (2007) Takes as arguments a graph to be pruned, 'probabilities' of positive and negative regulations (as Vectors of Float in the order, corresponding to the graph Edges), depth is the depth of the directed path search (for example, if equals number of Edges then this is complete pruning, if equals 2 then it searches for edge 'explanations' with only one intermediate node) The algorithm returns a pruned Graph, and also fills the Vector of 'explanations' (paths as graphs) in the order of the initial graph edges
TRIANGLE - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
 
TwoListDialog - Class in fr.curie.BiNoM.cytoscape.utils
 
TwoListDialog(JFrame, String, String, String, String, String[], String[]) - Constructor for class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 
type - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Attribute
 
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.BindingFeature
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStep
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReaction
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.BioSource
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Catalysis
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.CellularLocationVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.CellVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.ChemicalStructure
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Complex
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.ComplexAssembly
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Control
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Conversion
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.CovalentBindingFeature
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Degradation
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.DeltaG
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Dna
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaReference
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaRegion
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReference
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Entity
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityFeature
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityReference
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Evidence
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.ExperimentalForm
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.FragmentFeature
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Gene
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.GeneticInteraction
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Interaction
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.InteractionVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.KPrime
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.ModificationFeature
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Modulation
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.MolecularInteraction
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Pathway
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.PathwayStep
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntity
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Protein
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.ProteinReference
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Provenance
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.RelationshipXref
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Rna
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaReference
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaRegion
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReference
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Score
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.SequenceInterval
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.SequenceLocation
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.SequenceSite
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.SmallMolecule
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReference
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Stoichiometry
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.TemplateReaction
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulation
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.TissueVocabulary
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Transport
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReaction
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.UnificationXref
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.UtilityClass
The rdf:type for this ontology class
TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.Xref
The rdf:type for this ontology class
type - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter.BioPAXSpecies
Type of BioPAX object linked to the species (protein, complex, dna, rna, dnaRegion, rnaRegion)
typeOfReactionExtraction - Variable in class fr.curie.BiNoM.pathways.wrappers.Transpath
 
typeOfScaling - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportToFileDialog.CellDesignerExportToFileOptions
 

U

UnificationXref - Interface in fr.curie.BiNoM.pathways.biopax
Interface for UnificationXref ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
UnificationXrefImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of UnificationXref Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
UnificationXrefListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.UnificationXref to receive notification when properties changed, added or removed.
UnionOfSets(Set, Set) - Static method in class fr.curie.BiNoM.pathways.utils.Utils
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.BindingFeatureImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalPathwayStepImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.BiochemicalReactionImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.BioSourceImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.CatalysisImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.CellVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ChemicalStructureImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexAssemblyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ComplexImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ControlImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ControlledVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ConversionImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.CovalentBindingFeatureImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DegradationImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DeltaGImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DnaImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DnaReferenceImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EntityFeatureImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EntityImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.EvidenceImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.FragmentFeatureImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.GeneImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.GeneticInteractionImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.InteractionVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.KPrimeImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ModificationFeatureImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ModulationImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.MolecularInteractionImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.PathwayStepImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.PhysicalEntityImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ProteinReferenceImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ProvenanceImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.PublicationXrefImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RelationshipXrefImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RnaImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RnaReferenceImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.ScoreImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceIntervalImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceLocationImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SequenceSiteImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.StoichiometryImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.TissueVocabularyImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.TransportImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.UnificationXrefImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.UtilityClassImpl
 
unregisterListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.XrefImpl
 
UPDATE - Static variable in class fr.curie.BiNoM.biopax.propedit.BioPAXPropertyEditFrame
 
updateAnnotations(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
updateAnnotations(SbmlDocument, SbmlDocument) - Method in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
 
updateColor() - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassDesc
 
UpdateInfluenceAttrib - Class in fr.curie.BiNoM.cytoscape.influence
Update Influence Attribute WEIGHT at +1 or -1 from an attribute, generally interaction
UpdateInfluenceAttrib() - Constructor for class fr.curie.BiNoM.cytoscape.influence.UpdateInfluenceAttrib
 
updateLabels() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
updateLinks(String, String) - Static method in class fr.curie.BiNoM.pathways.utils.acsn.ACSNProcedures
 
updateMainfileWithReferences() - Method in class fr.curie.BiNoM.pathways.utils.BioPAXMerge
Updating base file with references.
updateSelectedPaths() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathConsistencyAnalyzerPathDialog
 
url - Variable in class fr.curie.BiNoM.biopax.BioPAXImportBaseTask
 
urlAdded(PublicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when a value of url has been added
urlProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
The Jena Property for url
urlRemoved(PublicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when a value of url has been removed
useAllnodesAttributes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
useBiopaxModelOntology - Static variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter
not used
useBiopaxModelOntology - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter
not used
useHUGOIdsForModuleIdentification - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.extractCellDesignerNotesTask.extractingNotesOptions
 
useHUGOIdsForModuleIdentification - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
useIDsForOutput - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
useMaxSetSize - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
Flag for using maximum set size
useModuleDefinitionsFromCellDesignerFile - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask.stainingOptions
 
useModuleDefinitionsFromCellDesignerFile - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
useProteinNameIfHUGOisntFound - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.pathwayStainingCellDesignerTask.stainingOptions
 
useProteinNameIfHUGOisntFound - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
useProteinNameIfHUGOisntFound - Variable in class fr.curie.BiNoM.pathways.utils.ExtractGMTFromCellDesigner
 
userDefinedFamilies - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
userDefinedFamiliesExpand - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
userDefinedFamiliesNonSelectedMembers - Variable in class fr.curie.BiNoM.pathways.SimpleTextInfluenceToBioPAX
 
useSignAlgebra - Variable in class fr.curie.BiNoM.pathways.analysis.structure.DataPathConsistencyAnalyzer
 
UtilityClass - Interface in fr.curie.BiNoM.pathways.biopax
Interface for UtilityClass ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
UtilityClassImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of UtilityClass Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
UtilityClassListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.UtilityClass to receive notification when properties changed, added or removed.
Utils - Class in fr.curie.BiNoM.lib
 
Utils() - Constructor for class fr.curie.BiNoM.lib.Utils
 
Utils - Class in fr.curie.BiNoM.pathways.utils
Set of simple functions
Utils() - Constructor for class fr.curie.BiNoM.pathways.utils.Utils
 
Utils.Transparency - Class in fr.curie.BiNoM.pathways.utils
 
Utils.Transparency() - Constructor for class fr.curie.BiNoM.pathways.utils.Utils.Transparency
 

V

V - Static variable in class fr.curie.BiNoM.cytoscape.utils.GridBagDialog
 
value - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Attribute
 
value - Variable in class fr.curie.BiNoM.pathways.test.TestGraphAlgo.ElemScore
 
valueChanged(TreeSelectionEvent) - Method in class fr.curie.BiNoM.biopax.propedit.BioPAXClassTreeFrame
 
valueChanged(ListSelectionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
valueChanged(ListSelectionEvent) - Method in class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 
valueChanged(Score) - Method in interface fr.curie.BiNoM.pathways.biopax.ScoreListener
Called when value has changed
valueOf(String) - Static method in enum fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto.SubType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto.Type
Returns the enum constant of this type with the specified name.
valueProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Score
The Jena Property for value
values() - Static method in enum fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto.SubType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.curie.BiNoM.biopax.propedit.BioPAXAttrDescProto.Type
Returns an array containing the constants of this enum type, in the order they are declared.
values - Variable in class fr.curie.BiNoM.cytoscape.utils.PavingData
 
verbose - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms
 
verbose - Variable in class fr.curie.BiNoM.pathways.utils.MergingMapsProcessor
Print extended informations while merging elements
verbose - Variable in class fr.curie.BiNoM.pathways.utils.ModifyCellDesignerNotes
 
VisualStyleDefinition - Class in fr.curie.BiNoM.cytoscape.lib
 
VisualStyleDefinition(String) - Constructor for class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition
 
VisualStyleDefinition.ImageDefinition - Class in fr.curie.BiNoM.cytoscape.lib
 
VisualStyleDefinition.ImageDefinition(String, double) - Constructor for class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition.ImageDefinition
 
VisualStyleDefinition.ImageDefinition(String) - Constructor for class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition.ImageDefinition
 
VisualStyleDefinition.ObjectMapping - Class in fr.curie.BiNoM.cytoscape.lib
 
VisualStyleDefinition.ObjectMapping(String, Object) - Constructor for class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition.ObjectMapping
 
VisualStyleFactory - Class in fr.curie.BiNoM.cytoscape.lib
 

W

w - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
Node width
weight - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge
Edge weight
weigths - Variable in class fr.curie.BiNoM.cytoscape.utils.ComputingByBFS
 
width - Variable in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
WordPressBlogCreator - Class in fr.curie.BiNoM.pathways.navicell
 
WordPressBlogCreator(String, String, String, String, ProduceClickableMap.AtlasInfo) - Constructor for class fr.curie.BiNoM.pathways.navicell.WordPressBlogCreator
 
WordPressTest - Class in fr.curie.BiNoM.pathways.navicell
Main Application class for the command line interface.
WordPressTest() - Constructor for class fr.curie.BiNoM.pathways.navicell.WordPressTest
 
workMatlabOvidiu - Class in fr.curie.BiNoM.pathways.test
Title: Pathway library
workMatlabOvidiu() - Constructor for class fr.curie.BiNoM.pathways.test.workMatlabOvidiu
 
writeConnection(FileWriter, Node, String, int, Node, Node, Vector<Node>, int) - Static method in class fr.curie.BiNoM.pathways.converters.BioPAXIndex2Tables
 
writeHangingNodes - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph
 
writeListOfPoints(Vector<CellDesignerPathwayStaining.ColorPoint>, String, String, String) - Method in class fr.curie.BiNoM.pathways.coloring.CellDesignerPathwayStaining
 
writeToFiles(Vector, String) - Static method in class fr.curie.BiNoM.pathways.test.testStructureAnalysis
 

X

x - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
Node position x
XGMML - Class in fr.curie.BiNoM.pathways.wrappers
Wrapper of XGMML content represented by edu.rpi.cs.xgmml.GraphDocument object
XGMML() - Constructor for class fr.curie.BiNoM.pathways.wrappers.XGMML
 
XGMMLExport - Class in fr.curie.BiNoM.pathways.utils
deprecated
XGMMLExport() - Constructor for class fr.curie.BiNoM.pathways.utils.XGMMLExport
 
XGMMLExtensionFilter - Class in fr.curie.BiNoM.cytoscape.biopax.query
 
XGMMLExtensionFilter() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.XGMMLExtensionFilter
 
xNames - Variable in class fr.curie.BiNoM.cytoscape.utils.PavingData
 
Xref - Interface in fr.curie.BiNoM.pathways.biopax
Interface for Xref ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this interface.
xrefAdded(BiochemicalReaction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of xref has been added
xrefAdded(BioSource, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSourceListener
Called when a value of xref has been added
xrefAdded(Catalysis, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of xref has been added
xrefAdded(CellularLocationVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyListener
Called when a value of xref has been added
xrefAdded(CellularLocationVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyListener
Called when a value of xref has been added
xrefAdded(CellVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.CellVocabularyListener
Called when a value of xref has been added
xrefAdded(CellVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.CellVocabularyListener
Called when a value of xref has been added
xrefAdded(ComplexAssembly, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of xref has been added
xrefAdded(Complex, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of xref has been added
xrefAdded(ControlledVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabularyListener
Called when a value of xref has been added
xrefAdded(ControlledVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabularyListener
Called when a value of xref has been added
xrefAdded(Control, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of xref has been added
xrefAdded(Conversion, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of xref has been added
xrefAdded(Degradation, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of xref has been added
xrefAdded(Dna, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of xref has been added
xrefAdded(DnaReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of xref has been added
xrefAdded(DnaRegion, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of xref has been added
xrefAdded(DnaRegionReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of xref has been added
xrefAdded(Entity, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityListener
Called when a value of xref has been added
xrefAdded(EntityReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of xref has been added
xrefAdded(EntityReferenceTypeVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyListener
Called when a value of xref has been added
xrefAdded(EntityReferenceTypeVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyListener
Called when a value of xref has been added
xrefAdded(EvidenceCodeVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyListener
Called when a value of xref has been added
xrefAdded(EvidenceCodeVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyListener
Called when a value of xref has been added
xrefAdded(Evidence, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceListener
Called when a value of xref has been added
xrefAdded(ExperimentalFormVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyListener
Called when a value of xref has been added
xrefAdded(ExperimentalFormVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyListener
Called when a value of xref has been added
xrefAdded(Gene, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of xref has been added
xrefAdded(GeneticInteraction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of xref has been added
xrefAdded(Interaction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of xref has been added
xrefAdded(InteractionVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionVocabularyListener
Called when a value of xref has been added
xrefAdded(InteractionVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionVocabularyListener
Called when a value of xref has been added
xrefAdded(Modulation, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of xref has been added
xrefAdded(MolecularInteraction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of xref has been added
xrefAdded(Pathway, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of xref has been added
xrefAdded(PhenotypeVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyListener
Called when a value of xref has been added
xrefAdded(PhenotypeVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyListener
Called when a value of xref has been added
xrefAdded(PhysicalEntity, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of xref has been added
xrefAdded(Protein, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of xref has been added
xrefAdded(ProteinReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of xref has been added
xrefAdded(Provenance, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ProvenanceListener
Called when a value of xref has been added
xrefAdded(Provenance, PublicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.ProvenanceListener
Called when a value of xref has been added
xrefAdded(Provenance, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.ProvenanceListener
Called when a value of xref has been added
xrefAdded(RelationshipTypeVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyListener
Called when a value of xref has been added
xrefAdded(RelationshipTypeVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyListener
Called when a value of xref has been added
xrefAdded(Rna, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of xref has been added
xrefAdded(RnaReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of xref has been added
xrefAdded(RnaRegion, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of xref has been added
xrefAdded(RnaRegionReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of xref has been added
xrefAdded(SequenceModificationVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyListener
Called when a value of xref has been added
xrefAdded(SequenceModificationVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyListener
Called when a value of xref has been added
xrefAdded(SequenceRegionVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyListener
Called when a value of xref has been added
xrefAdded(SequenceRegionVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyListener
Called when a value of xref has been added
xrefAdded(SmallMolecule, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of xref has been added
xrefAdded(SmallMoleculeReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of xref has been added
xrefAdded(TemplateReaction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of xref has been added
xrefAdded(TemplateReactionRegulation, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of xref has been added
xrefAdded(TissueVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.TissueVocabularyListener
Called when a value of xref has been added
xrefAdded(TissueVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.TissueVocabularyListener
Called when a value of xref has been added
xrefAdded(Transport, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of xref has been added
xrefAdded(TransportWithBiochemicalReaction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of xref has been added
XrefImpl - Class in fr.curie.BiNoM.pathways.biopax
Implementation of Xref Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level3_DOT_owlFactory to create instances of this class.
XrefListener - Interface in fr.curie.BiNoM.pathways.biopax
Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.Xref to receive notification when properties changed, added or removed.
xrefProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.BioSource
The Jena Property for xref
xrefProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabulary
The Jena Property for xref
xrefProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Entity
The Jena Property for xref
xrefProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.EntityReference
The Jena Property for xref
xrefProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Evidence
The Jena Property for xref
xrefProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.Provenance
The Jena Property for xref
xrefRemoved(BiochemicalReaction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.BiochemicalReactionListener
Called when a value of xref has been removed
xrefRemoved(BioSource, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.BioSourceListener
Called when a value of xref has been removed
xrefRemoved(Catalysis, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.CatalysisListener
Called when a value of xref has been removed
xrefRemoved(CellularLocationVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyListener
Called when a value of xref has been removed
xrefRemoved(CellularLocationVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.CellularLocationVocabularyListener
Called when a value of xref has been removed
xrefRemoved(CellVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.CellVocabularyListener
Called when a value of xref has been removed
xrefRemoved(CellVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.CellVocabularyListener
Called when a value of xref has been removed
xrefRemoved(ComplexAssembly, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexAssemblyListener
Called when a value of xref has been removed
xrefRemoved(Complex, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ComplexListener
Called when a value of xref has been removed
xrefRemoved(ControlledVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabularyListener
Called when a value of xref has been removed
xrefRemoved(ControlledVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlledVocabularyListener
Called when a value of xref has been removed
xrefRemoved(Control, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ControlListener
Called when a value of xref has been removed
xrefRemoved(Conversion, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ConversionListener
Called when a value of xref has been removed
xrefRemoved(Degradation, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.DegradationListener
Called when a value of xref has been removed
xrefRemoved(Dna, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaListener
Called when a value of xref has been removed
xrefRemoved(DnaReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaReferenceListener
Called when a value of xref has been removed
xrefRemoved(DnaRegion, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionListener
Called when a value of xref has been removed
xrefRemoved(DnaRegionReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.DnaRegionReferenceListener
Called when a value of xref has been removed
xrefRemoved(Entity, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityListener
Called when a value of xref has been removed
xrefRemoved(EntityReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceListener
Called when a value of xref has been removed
xrefRemoved(EntityReferenceTypeVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyListener
Called when a value of xref has been removed
xrefRemoved(EntityReferenceTypeVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.EntityReferenceTypeVocabularyListener
Called when a value of xref has been removed
xrefRemoved(EvidenceCodeVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyListener
Called when a value of xref has been removed
xrefRemoved(EvidenceCodeVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceCodeVocabularyListener
Called when a value of xref has been removed
xrefRemoved(Evidence, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.EvidenceListener
Called when a value of xref has been removed
xrefRemoved(ExperimentalFormVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyListener
Called when a value of xref has been removed
xrefRemoved(ExperimentalFormVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.ExperimentalFormVocabularyListener
Called when a value of xref has been removed
xrefRemoved(Gene, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneListener
Called when a value of xref has been removed
xrefRemoved(GeneticInteraction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.GeneticInteractionListener
Called when a value of xref has been removed
xrefRemoved(Interaction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionListener
Called when a value of xref has been removed
xrefRemoved(InteractionVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionVocabularyListener
Called when a value of xref has been removed
xrefRemoved(InteractionVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.InteractionVocabularyListener
Called when a value of xref has been removed
xrefRemoved(Modulation, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ModulationListener
Called when a value of xref has been removed
xrefRemoved(MolecularInteraction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.MolecularInteractionListener
Called when a value of xref has been removed
xrefRemoved(Pathway, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.PathwayListener
Called when a value of xref has been removed
xrefRemoved(PhenotypeVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyListener
Called when a value of xref has been removed
xrefRemoved(PhenotypeVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.PhenotypeVocabularyListener
Called when a value of xref has been removed
xrefRemoved(PhysicalEntity, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.PhysicalEntityListener
Called when a value of xref has been removed
xrefRemoved(Protein, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinListener
Called when a value of xref has been removed
xrefRemoved(ProteinReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ProteinReferenceListener
Called when a value of xref has been removed
xrefRemoved(Provenance, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.ProvenanceListener
Called when a value of xref has been removed
xrefRemoved(Provenance, PublicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.ProvenanceListener
Called when a value of xref has been removed
xrefRemoved(Provenance, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.ProvenanceListener
Called when a value of xref has been removed
xrefRemoved(RelationshipTypeVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyListener
Called when a value of xref has been removed
xrefRemoved(RelationshipTypeVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.RelationshipTypeVocabularyListener
Called when a value of xref has been removed
xrefRemoved(Rna, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaListener
Called when a value of xref has been removed
xrefRemoved(RnaReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaReferenceListener
Called when a value of xref has been removed
xrefRemoved(RnaRegion, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionListener
Called when a value of xref has been removed
xrefRemoved(RnaRegionReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.RnaRegionReferenceListener
Called when a value of xref has been removed
xrefRemoved(SequenceModificationVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyListener
Called when a value of xref has been removed
xrefRemoved(SequenceModificationVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceModificationVocabularyListener
Called when a value of xref has been removed
xrefRemoved(SequenceRegionVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyListener
Called when a value of xref has been removed
xrefRemoved(SequenceRegionVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.SequenceRegionVocabularyListener
Called when a value of xref has been removed
xrefRemoved(SmallMolecule, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeListener
Called when a value of xref has been removed
xrefRemoved(SmallMoleculeReference, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.SmallMoleculeReferenceListener
Called when a value of xref has been removed
xrefRemoved(TemplateReaction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionListener
Called when a value of xref has been removed
xrefRemoved(TemplateReactionRegulation, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.TemplateReactionRegulationListener
Called when a value of xref has been removed
xrefRemoved(TissueVocabulary, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.TissueVocabularyListener
Called when a value of xref has been removed
xrefRemoved(TissueVocabulary, UnificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.TissueVocabularyListener
Called when a value of xref has been removed
xrefRemoved(Transport, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportListener
Called when a value of xref has been removed
xrefRemoved(TransportWithBiochemicalReaction, Xref) - Method in interface fr.curie.BiNoM.pathways.biopax.TransportWithBiochemicalReactionListener
Called when a value of xref has been removed
xw - Static variable in class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
xw - Static variable in class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 

Y

y - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node
Node position y
yearChanged(PublicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.PublicationXrefListener
Called when year has changed
yearProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.PublicationXref
The Jena Property for year
yNames - Variable in class fr.curie.BiNoM.cytoscape.utils.PavingData
 
yw - Static variable in class fr.curie.BiNoM.cytoscape.utils.ListDialog
 
yw - Static variable in class fr.curie.BiNoM.cytoscape.utils.TwoListDialog
 

Z

zoomLevel - Variable in class fr.curie.BiNoM.cytoscape.celldesigner.MergingMapsTask.MergingMapsOptions
 
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