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

Called when a value of EC_DASH_NUMBER has been added

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

Called when a value of EC_DASH_NUMBER has been added

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

The Jena Property for EC_DASH_NUMBER

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

Called when a value of EC_DASH_NUMBER has been removed

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

Called when a value of EC_DASH_NUMBER 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_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_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_NEXT - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition

EDGE_physicalInteraction - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXVisualStyleDefinition

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_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

EdgeArrowType - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge

Type of edge arrow (not used yet)

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

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 GraphicEdge 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

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

ELLIPSE - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Node

entities - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper

Map from complete uris to entity objects

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

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

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

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

Implementation of entity Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_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.

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

Map from node names and synonyms to the Vector of Node objects

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.cytoscape.biopax.propedit.BioPAXPropertyBrowserFrame

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_level2_DOT_owlFactory to create instances of this interface.

EVIDENCE_DASH_CODEAdded(evidence, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.evidenceListener

Called when a value of EVIDENCE_DASH_CODE has been added

EVIDENCE_DASH_CODEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.evidence

The Jena Property for EVIDENCE_DASH_CODE

EVIDENCE_DASH_CODERemoved(evidence, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.evidenceListener

Called when a value of EVIDENCE_DASH_CODE has been removed

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

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

Called when a value of EVIDENCE has been added

EVIDENCEAdded(physicalInteraction, evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

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

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

Implementation of evidence Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_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.interaction

The Jena Property for EVIDENCE

EVIDENCEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.pathway

The Jena Property for EVIDENCE

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

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

Called when a value of EVIDENCE has been removed

EVIDENCERemoved(physicalInteraction, evidence) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

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

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

If false, all smallMolecules are excluded in queries

executeTask(Task) - Static method in class fr.curie.BiNoM.cytoscape.lib.TaskManager

EXPERIMENTAL_DASH_FORM_DASH_TYPEAdded(experimentalForm, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalFormListener

Called when a value of EXPERIMENTAL_DASH_FORM_DASH_TYPE has been added

EXPERIMENTAL_DASH_FORM_DASH_TYPEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.experimentalForm

The Jena Property for EXPERIMENTAL_DASH_FORM_DASH_TYPE

EXPERIMENTAL_DASH_FORM_DASH_TYPERemoved(experimentalForm, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalFormListener

Called when a value of EXPERIMENTAL_DASH_FORM_DASH_TYPE has been removed

EXPERIMENTAL_DASH_FORMAdded(evidence, experimentalForm) - Method in interface fr.curie.BiNoM.pathways.biopax.evidenceListener

Called when a value of EXPERIMENTAL_DASH_FORM has been added

EXPERIMENTAL_DASH_FORMProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.evidence

The Jena Property for EXPERIMENTAL_DASH_FORM

EXPERIMENTAL_DASH_FORMRemoved(evidence, experimentalForm) - Method in interface fr.curie.BiNoM.pathways.biopax.evidenceListener

Called when a value of EXPERIMENTAL_DASH_FORM 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_level2_DOT_owlFactory to create instances of this interface.

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

Implementation of experimentalForm Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_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.

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

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

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

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

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

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

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

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

extractModificationsFromName(String) - Static method in class fr.curie.BiNoM.pathways.wrappers.Transpath

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.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.cytoscape.analysis

ExtractReactionNetworkTask(GraphDocument, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetworkTask

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

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