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

I

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

Edge unique id

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

Node unique id

id - Variable in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter.BioPAXSpecies

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

Called when ID_DASH_VERSION has changed

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

Called when ID_DASH_VERSION has changed

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

Called when ID_DASH_VERSION has changed

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

Called when ID_DASH_VERSION has changed

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

The Jena Property for ID_DASH_VERSION

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

Called when ID has changed

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

Called when ID has changed

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

Called when ID has changed

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

Called when ID has changed

identicalNodes(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph

idname - Variable in class fr.curie.BiNoM.pathways.utils.AccessionNumberTable

Map from id used by a database to the Vector of names in the table (id - is database identifier, name - some common name or accession number)

idName - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX

Some identifier for this BioPAX

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

The Jena Property for ID

img - Variable in class fr.curie.BiNoM.cytoscape.lib.VisualStyleDefinition.ImageDefinition

importString - Static variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX

Standard BioPAX v.2 prefix

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

Auxillary property for analysis of conservation laws

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

Map from cutted uris (after # separator) to BioPAXSpecies included into entities (these species group complex components, for example)

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

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

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

includesNodes(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph

includesNodesPercentage(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph

inclusionGraph(Vector) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils

Creates a new graph where nodes represent other graphs and edges represent intersections in nodes between these graphs.

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

List of all in-going edges.

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

Auxilary map

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

Map from cutted uris (after # separator) to BioPAXSpecies

IndexPathAnalysisDialog - Class in fr.curie.BiNoM.cytoscape.analysis

IndexPathAnalysisTask - Class in fr.curie.BiNoM.cytoscape.analysis

IndexPathAnalysisTask(Vector<String>, Vector<String>, StructureAnalysisUtils.Option, VisualStyle, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask

init(boolean, boolean) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserPanel

initializeModel() - Method in class fr.curie.BiNoM.pathways.wrappers.Transpath

input - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

Input for the query

INPUT_CURRENT_NETWORK - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask

INPUT_LISTOF_NAMES - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask

insertMassActionLaws - Class in fr.curie.BiNoM.pathways.utils

insertMassActionLaws() - Constructor for class fr.curie.BiNoM.pathways.utils.insertMassActionLaws

insertMassActionLaws(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.insertMassActionLaws

instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.ModularViewDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSyncNetworksDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDisplayIndexInfoDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXViewQueryLogDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.netwop.DoubleNetworkDifferenceDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateConfirmDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog

instance - Static variable in class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContentsDialog

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

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

INTERACTION_DASH_TYPEAdded(biochemicalReaction, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of INTERACTION_DASH_TYPE has been added

INTERACTION_DASH_TYPEAdded(catalysis, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of INTERACTION_DASH_TYPE has been added

INTERACTION_DASH_TYPEAdded(complexAssembly, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of INTERACTION_DASH_TYPE has been added

INTERACTION_DASH_TYPEAdded(control, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of INTERACTION_DASH_TYPE has been added

INTERACTION_DASH_TYPEAdded(conversion, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of INTERACTION_DASH_TYPE has been added

INTERACTION_DASH_TYPEAdded(modulation, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of INTERACTION_DASH_TYPE has been added

INTERACTION_DASH_TYPEAdded(physicalInteraction, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of INTERACTION_DASH_TYPE has been added

INTERACTION_DASH_TYPEAdded(transport, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of INTERACTION_DASH_TYPE has been added

INTERACTION_DASH_TYPEAdded(transportWithBiochemicalReaction, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of INTERACTION_DASH_TYPE has been added

INTERACTION_DASH_TYPEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

The Jena Property for INTERACTION_DASH_TYPE

INTERACTION_DASH_TYPERemoved(biochemicalReaction, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of INTERACTION_DASH_TYPE has been removed

INTERACTION_DASH_TYPERemoved(catalysis, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of INTERACTION_DASH_TYPE has been removed

INTERACTION_DASH_TYPERemoved(complexAssembly, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of INTERACTION_DASH_TYPE has been removed

INTERACTION_DASH_TYPERemoved(control, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of INTERACTION_DASH_TYPE has been removed

INTERACTION_DASH_TYPERemoved(conversion, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of INTERACTION_DASH_TYPE has been removed

INTERACTION_DASH_TYPERemoved(modulation, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of INTERACTION_DASH_TYPE has been removed

INTERACTION_DASH_TYPERemoved(physicalInteraction, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of INTERACTION_DASH_TYPE has been removed

INTERACTION_DASH_TYPERemoved(transport, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of INTERACTION_DASH_TYPE has been removed

INTERACTION_DASH_TYPERemoved(transportWithBiochemicalReaction, openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of INTERACTION_DASH_TYPE has been removed

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

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

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

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

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

Map from complete uris to interaction objects

intersection(Graph) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Graph

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

IONIC_DASH_STRENGTHAdded(deltaGprimeO, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeOListener

Called when a value of IONIC_DASH_STRENGTH has been added

IONIC_DASH_STRENGTHAdded(kPrime, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrimeListener

Called when a value of IONIC_DASH_STRENGTH has been added

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

The Jena Property for IONIC_DASH_STRENGTH

IONIC_DASH_STRENGTHProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.kPrime

The Jena Property for IONIC_DASH_STRENGTH

IONIC_DASH_STRENGTHRemoved(deltaGprimeO, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeOListener

Called when a value of IONIC_DASH_STRENGTH has been removed

IONIC_DASH_STRENGTHRemoved(kPrime, Float) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrimeListener

Called when a value of IONIC_DASH_STRENGTH has been removed

isBioPAXNetwork(CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImport

isBioPAXNetwork(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSourceDB

isCellDesignerNetwork(CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImport

isCellDesignerNetwork(CyNetwork) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerSourceDB

isEmpty() - Method in class fr.curie.BiNoM.cytoscape.utils.NodesAndEdgesClipboard

isNumber(String) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils

isRealReaction(ReactionDocument.Reaction, SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

Returns true if the reaction r describes real interaction (not influence on a phenotype, for example)