- 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
-
- 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
-
- 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
-
- 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
- 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
-
- 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 - 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
-
- 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
- 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
- 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
-
- 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
-
- 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
-
- 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
-