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

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DATA_DASH_SOURCEAdded(biochemicalReaction, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(catalysis, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(complexAssembly, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(complex, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.complexListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(control, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(conversion, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(dna, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.dnaListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(entity, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.entityListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(interaction, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.interactionListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(modulation, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(pathway, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(physicalEntity, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(physicalInteraction, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(protein, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.proteinListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(rna, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.rnaListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(smallMolecule, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMoleculeListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(transport, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of DATA_DASH_SOURCE has been added

DATA_DASH_SOURCEAdded(transportWithBiochemicalReaction, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of DATA_DASH_SOURCE has been added

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

The Jena Property for DATA_DASH_SOURCE

DATA_DASH_SOURCERemoved(biochemicalReaction, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(catalysis, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(complexAssembly, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(complex, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.complexListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(control, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(conversion, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(dna, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.dnaListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(entity, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.entityListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(interaction, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.interactionListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(modulation, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(pathway, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(physicalEntity, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(physicalInteraction, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(protein, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.proteinListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(rna, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.rnaListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(smallMolecule, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMoleculeListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(transport, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of DATA_DASH_SOURCE has been removed

DATA_DASH_SOURCERemoved(transportWithBiochemicalReaction, dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of DATA_DASH_SOURCE has been removed

database - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine

The index with which the query is performed

databaseCopyForPathAnalysis - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine

Copy of the database to perform index path analysis

dataSource - Interface in fr.curie.BiNoM.pathways.biopax

Interface for dataSource ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

dataSourceImpl - Class in fr.curie.BiNoM.pathways.biopax

Implementation of dataSource Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

dataSourceListener - Interface in fr.curie.BiNoM.pathways.biopax

Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.dataSource to receive notification when properties changed, added or removed.

DB_DASH_VERSIONChanged(publicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXrefListener

Called when DB_DASH_VERSION has changed

DB_DASH_VERSIONChanged(relationshipXref) - Method in interface fr.curie.BiNoM.pathways.biopax.relationshipXrefListener

Called when DB_DASH_VERSION has changed

DB_DASH_VERSIONChanged(unificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.unificationXrefListener

Called when DB_DASH_VERSION has changed

DB_DASH_VERSIONChanged(xref) - Method in interface fr.curie.BiNoM.pathways.biopax.xrefListener

Called when DB_DASH_VERSION has changed

DB_DASH_VERSIONProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.xref

The Jena Property for DB_DASH_VERSION

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

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

DELTA_DASH_G_DASH_PRIME_DASH_OChanged(deltaGprimeO) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeOListener

Called when DELTA_DASH_G_DASH_PRIME_DASH_O has changed

DELTA_DASH_G_DASH_PRIME_DASH_OProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO

The Jena Property for DELTA_DASH_G_DASH_PRIME_DASH_O

DELTA_DASH_GAdded(biochemicalReaction, deltaGprimeO) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of DELTA_DASH_G has been added

DELTA_DASH_GAdded(transportWithBiochemicalReaction, deltaGprimeO) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of DELTA_DASH_G has been added

DELTA_DASH_GProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

The Jena Property for DELTA_DASH_G

DELTA_DASH_GRemoved(biochemicalReaction, deltaGprimeO) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of DELTA_DASH_G has been removed

DELTA_DASH_GRemoved(transportWithBiochemicalReaction, deltaGprimeO) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of DELTA_DASH_G has been removed

DELTA_DASH_HAdded(biochemicalReaction, Double) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of DELTA_DASH_H has been added

DELTA_DASH_HAdded(transportWithBiochemicalReaction, Double) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of DELTA_DASH_H has been added

DELTA_DASH_HProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

The Jena Property for DELTA_DASH_H

DELTA_DASH_HRemoved(biochemicalReaction, Double) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of DELTA_DASH_H has been removed

DELTA_DASH_HRemoved(transportWithBiochemicalReaction, Double) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of DELTA_DASH_H has been removed

DELTA_DASH_SAdded(biochemicalReaction, Double) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of DELTA_DASH_S has been added

DELTA_DASH_SAdded(transportWithBiochemicalReaction, Double) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of DELTA_DASH_S has been added

DELTA_DASH_SProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

The Jena Property for DELTA_DASH_S

DELTA_DASH_SRemoved(biochemicalReaction, Double) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of DELTA_DASH_S has been removed

DELTA_DASH_SRemoved(transportWithBiochemicalReaction, Double) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of DELTA_DASH_S has been removed

deltaGprimeO - Interface in fr.curie.BiNoM.pathways.biopax

Interface for deltaGprimeO ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this interface.

deltaGprimeOImpl - Class in fr.curie.BiNoM.pathways.biopax

Implementation of deltaGprimeO Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory to create instances of this class.

deltaGprimeOListener - Interface in fr.curie.BiNoM.pathways.biopax

Implementations of this listener may be registered with instances of fr.curie.BiNoM.pathways.biopax.deltaGprimeO to receive notification when properties changed, added or removed.

describe() - Method in class fr.curie.BiNoM.cytoscape.plugin.BiNoMPlugin

Gives a description of this plugin.

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

DijkstraProcedure(Graph, int, int, 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

directedGraph - Variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option

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

Called when DIRECTION has changed

DIRECTIONProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.catalysis

The Jena Property for DIRECTION

distinguishCompartments - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option

distinguishModifications - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option

dna - Interface in fr.curie.BiNoM.pathways.biopax

Interface for dna ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_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_level2_DOT_owlFactory to create instances of this class.

dnaList - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

Map from cutted 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.

doQuery(BioPAXGraphQuery, int) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine

Performs a query of queryType

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