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

N

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

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

Called when a value of NAME has been added

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

Called when NAME has changed

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

Called when NAME has changed

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

Called when NAME has changed

NAMEChanged(complexAssembly) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when NAME has changed

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

Called when NAME has changed

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

Called when NAME has changed

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

Called when NAME has changed

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

Called when NAME has changed

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

Called when NAME has changed

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

Called when NAME has changed

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

Called when NAME has changed

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

Called when NAME has changed

NAMEChanged(physicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityListener

Called when NAME has changed

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

Called when NAME has changed

NAMEChanged(protein) - Method in interface fr.curie.BiNoM.pathways.biopax.proteinListener

Called when NAME has changed

NAMEChanged(rna) - Method in interface fr.curie.BiNoM.pathways.biopax.rnaListener

Called when NAME has changed

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

Called when NAME has changed

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

Called when NAME has changed

NAMEChanged(transport) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when NAME has changed

NAMEChanged(transportWithBiochemicalReaction) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when NAME has changed

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

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 - 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.dataSource

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.sequenceFeature

The Jena Property for NAME

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

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

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.2 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.2 prefix

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

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

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.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.cytoscape.lib

NetworkUtils() - Constructor for class fr.curie.BiNoM.cytoscape.lib.NetworkUtils

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

Called when a value of NEXT_DASH_STEP has been added

NEXT_DASH_STEPProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

The Jena Property for NEXT_DASH_STEP

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

Called when a value of NEXT_DASH_STEP has been removed

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

Returns the next token from the input string.

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_GENE - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition

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_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_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_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_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_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_REACTION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition

NODE_UNKNOWN_TRANSITION - Static variable in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerVisualStyleDefinition

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

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

NodeHash - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Graph

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

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 to GraphicNode objects

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

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

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

numberOfStatements(Thing) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities

numberOfStatements(Model) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities