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

R

raise() - Method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksDialog

raise() - Method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkDialog

raise() - Method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisDialog

raise() - Method in class fr.curie.BiNoM.cytoscape.analysis.ModularViewDialog

raise() - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisDialog

raise(File, String) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportDialog

raise(URL, String) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportDialog

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() - 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

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

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

List of CellDesigner ReactionDocument.Reaction objects

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.cytoscape.biopax.propedit.BioPAXClassTreeFrame

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

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.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.confidenceImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl

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.externalReferenceUtilityClassImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl

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.physicalEntityImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl

registerListener(ThingListener) - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl

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.sequenceFeatureImpl

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.sequenceParticipantImpl

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.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

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

Called when RELATIONSHIP_DASH_TYPE has changed

RELATIONSHIP_DASH_TYPEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.relationshipXref

The Jena Property for RELATIONSHIP_DASH_TYPE

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

Interface for relationshipXref ontology class
Use the fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_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_level2_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.

removeAll() - Method in class fr.curie.BiNoM.cytoscape.lib.MLLabel

removeAUTHORS(String) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXref

Remove a 'AUTHORS' property value.

removeAUTHORS(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.dnaImpl

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.interactionImpl

removeAVAILABILITY(String) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

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.physicalInteractionImpl

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.smallMoleculeImpl

removeAVAILABILITY(String) - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

removeAVAILABILITY(String) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removeCOFACTOR(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysis

Removes a value for the 'COFACTOR' property.

removeCOFACTOR(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

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.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.confidenceImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl

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.entityImpl

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.externalReferenceUtilityClassImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl

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.physicalEntityImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl

removeCOMMENT(String) - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl

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.sequenceFeatureImpl

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.sequenceParticipantImpl

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.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

removeCOMPONENTS(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.complex

Removes a value for the 'COMPONENTS' property.

removeCOMPONENTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl

removeCONFIDENCE(confidence) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Removes a value for the 'CONFIDENCE' property.

removeCONFIDENCE(confidence) - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl

removeConversion(conversion, HashMap, HashMap, Vector, HashMap, BioPAXToSBMLConverter) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl

removeDATA_DASH_SOURCE(dataSource) - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Removes a value for the 'DATA_DASH_SOURCE' property.

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

removeDATA_DASH_SOURCE(dataSource) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removeDELTA_DASH_G(deltaGprimeO) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Removes a value for the 'DELTA_DASH_G' property.

removeDELTA_DASH_G(deltaGprimeO) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removeDELTA_DASH_G(deltaGprimeO) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removeDELTA_DASH_H(Double) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Remove a 'DELTA_DASH_H' property value.

removeDELTA_DASH_H(Double) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removeDELTA_DASH_H(Double) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removeDELTA_DASH_S(Double) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Remove a 'DELTA_DASH_S' property value.

removeDELTA_DASH_S(Double) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removeDELTA_DASH_S(Double) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.chemicalStructureImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.confidenceImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.experimentalFormImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.externalReferenceUtilityClassImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayStepImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceIntervalImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceLocationImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceSiteImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.utilityClassImpl

removedStatement(Statement) - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl

removeEC_DASH_NUMBER(String) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

Remove a 'EC_DASH_NUMBER' property value.

removeEC_DASH_NUMBER(String) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removeEC_DASH_NUMBER(String) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

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.controlImpl

removeEVIDENCE(evidence) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

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

Removes a value for the 'EVIDENCE' property.

removeEVIDENCE(evidence) - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

removeEVIDENCE(evidence) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

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

Removes a value for the 'EVIDENCE' property.

removeEVIDENCE(evidence) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

removeEVIDENCE(evidence) - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

removeEVIDENCE(evidence) - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

removeEVIDENCE(evidence) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removeEVIDENCE_DASH_CODE(openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Removes a value for the 'EVIDENCE_DASH_CODE' property.

removeEVIDENCE_DASH_CODE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl

removeEXPERIMENTAL_DASH_FORM(experimentalForm) - Method in interface fr.curie.BiNoM.pathways.biopax.evidence

Removes a value for the 'EXPERIMENTAL_DASH_FORM' property.

removeEXPERIMENTAL_DASH_FORM(experimentalForm) - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl

removeEXPERIMENTAL_DASH_FORM_DASH_TYPE(openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalForm

Removes a value for the 'EXPERIMENTAL_DASH_FORM_DASH_TYPE' property.

removeEXPERIMENTAL_DASH_FORM_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.experimentalFormImpl

removeFEATURE_DASH_LOCATION(sequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Removes a value for the 'FEATURE_DASH_LOCATION' property.

removeFEATURE_DASH_LOCATION(sequenceLocation) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl

removeINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removeINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

removeINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl

removeINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

removeINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

removeINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

removeINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

Removes a value for the 'INTERACTION_DASH_TYPE' property.

removeINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

removeINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

removeINTERACTION_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removeIONIC_DASH_STRENGTH(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO

Remove a 'IONIC_DASH_STRENGTH' property value.

removeIONIC_DASH_STRENGTH(Float) - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl

removeIONIC_DASH_STRENGTH(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime

Remove a 'IONIC_DASH_STRENGTH' property value.

removeIONIC_DASH_STRENGTH(Float) - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl

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(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removeLEFT(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl

removeLEFT(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Removes a value for the 'LEFT' property.

removeLEFT(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

removeLEFT(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

removeLEFT(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removeNAME(String) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Remove a 'NAME' property value.

removeNAME(String) - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl

removeNEXT_DASH_STEP(pathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Removes a value for the 'NEXT_DASH_STEP' property.

removeNEXT_DASH_STEP(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

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

removeORGANISM(bioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.complex

Removes a value for the 'ORGANISM' property.

removeORGANISM(bioSource) - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl

removeORGANISM(bioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.dna

Removes a value for the 'ORGANISM' property.

removeORGANISM(bioSource) - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl

removePARTICIPANTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removePARTICIPANTS(entity) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removePARTICIPANTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

removePARTICIPANTS(entity) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

removePARTICIPANTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl

removePARTICIPANTS(entity) - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl

removePARTICIPANTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

removePARTICIPANTS(entity) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

removePARTICIPANTS(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Removes a value for the 'PARTICIPANTS' property.

removePARTICIPANTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

removePARTICIPANTS(entity) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

removePARTICIPANTS(entity) - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Removes a value for the 'PARTICIPANTS' property.

removePARTICIPANTS(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.interaction

Removes a value for the 'PARTICIPANTS' property.

removePARTICIPANTS(entity) - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

removePARTICIPANTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

removePARTICIPANTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

removePARTICIPANTS(entity) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

removePARTICIPANTS(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

Removes a value for the 'PARTICIPANTS' property.

removePARTICIPANTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

removePARTICIPANTS(entity) - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

removePARTICIPANTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

removePARTICIPANTS(entity) - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

removePARTICIPANTS(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removePARTICIPANTS(entity) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removePATHWAY_DASH_COMPONENTS(interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Removes a value for the 'PATHWAY_DASH_COMPONENTS' property.

removePATHWAY_DASH_COMPONENTS(pathwayStep) - Method in interface fr.curie.BiNoM.pathways.biopax.pathway

Removes a value for the 'PATHWAY_DASH_COMPONENTS' property.

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

Removes a value for the 'PATHWAY_DASH_COMPONENTS' property.

removePATHWAY_DASH_COMPONENTS(interaction) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

removePATHWAY_DASH_COMPONENTS(pathwayStep) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

removePATHWAY_DASH_COMPONENTS(pathway) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

removePH(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO

Remove a 'PH' property value.

removePH(Float) - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl

removePH(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime

Remove a 'PH' property value.

removePH(Float) - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl

removePMG(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO

Remove a 'PMG' property value.

removePMG(Float) - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl

removePMG(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime

Remove a 'PMG' property value.

removePMG(Float) - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl

RemoveResidueNames(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.test.test

removeRIGHT(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removeRIGHT(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl

removeRIGHT(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Removes a value for the 'RIGHT' property.

removeRIGHT(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

removeRIGHT(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

removeRIGHT(physicalEntityParticipant) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removeSEQUENCE(String) - Method in interface fr.curie.BiNoM.pathways.biopax.dna

Remove a 'SEQUENCE' property value.

removeSEQUENCE(String) - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl

removeSEQUENCE_DASH_FEATURE_DASH_LIST(sequenceFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipant

Removes a value for the 'SEQUENCE_DASH_FEATURE_DASH_LIST' property.

removeSEQUENCE_DASH_FEATURE_DASH_LIST(sequenceFeature) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl

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

removeSTEP_DASH_INTERACTIONS(interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Removes a value for the 'STEP_DASH_INTERACTIONS' property.

removeSTEP_DASH_INTERACTIONS(pathway) - Method in interface fr.curie.BiNoM.pathways.biopax.pathwayStep

Removes a value for the 'STEP_DASH_INTERACTIONS' property.

removeSTEP_DASH_INTERACTIONS(interaction) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayStepImpl

removeSTEP_DASH_INTERACTIONS(pathway) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayStepImpl

removeSTRUCTURE(chemicalStructure) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMolecule

Removes a value for the 'STRUCTURE' property.

removeSTRUCTURE(chemicalStructure) - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl

removeSYNONYMS(String) - Method in interface fr.curie.BiNoM.pathways.biopax.entity

Remove a 'SYNONYMS' property value.

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl

removeSYNONYMS(String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Remove a 'SYNONYMS' property value.

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

removeSYNONYMS(String) - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

removeTEMPERATURE(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.deltaGprimeO

Remove a 'TEMPERATURE' property value.

removeTEMPERATURE(Float) - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl

removeTEMPERATURE(Float) - Method in interface fr.curie.BiNoM.pathways.biopax.kPrime

Remove a 'TEMPERATURE' property value.

removeTEMPERATURE(Float) - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl

removeTERM(String) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

Remove a 'TERM' property value.

removeTERM(String) - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl

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.cytoscape.biopax.propedit.BioPAXAttrDesc

removeValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc

removeValue(BioPAXObject, Object) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringListAttrDesc

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

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 interface fr.curie.BiNoM.pathways.biopax.confidence

Removes a value for the 'XREF' property.

removeXREF(publicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.confidence

Removes a value for the 'XREF' property.

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.confidenceImpl

removeXREF(publicationXref) - Method in class fr.curie.BiNoM.pathways.biopax.confidenceImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

removeXREF(xref) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Removes a value for the 'XREF' property.

removeXREF(publicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Removes a value for the 'XREF' property.

removeXREF(unificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.dataSource

Removes a value for the 'XREF' property.

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl

removeXREF(publicationXref) - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl

removeXREF(unificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl

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.evidence

Removes a value for the 'XREF' property.

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

removeXREF(xref) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

Removes a value for the 'XREF' property.

removeXREF(unificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

Removes a value for the 'XREF' property.

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl

removeXREF(unificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl

removeXREF(xref) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Removes a value for the 'XREF' property.

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl

removeXREF(xref) - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl

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

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.utils.SimpleTable

replaceString(String, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

In source string replaces shabl substring with val

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

reportPosition(CyNode, CyNetworkView, CyNetworkView) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils

reset() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworkOperation.Estimator

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

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

RIGHTAdded(biochemicalReaction, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of RIGHT has been added

RIGHTAdded(complexAssembly, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of RIGHT has been added

RIGHTAdded(conversion, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of RIGHT has been added

RIGHTAdded(transport, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of RIGHT has been added

RIGHTAdded(transportWithBiochemicalReaction, physicalEntityParticipant) - 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, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of RIGHT has been removed

RIGHTRemoved(complexAssembly, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of RIGHT has been removed

RIGHTRemoved(conversion, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of RIGHT has been removed

RIGHTRemoved(transport, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of RIGHT has been removed

RIGHTRemoved(transportWithBiochemicalReaction, physicalEntityParticipant) - 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_level2_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_level2_DOT_owlFactory to create instances of this class.

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

Map from cutted 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.

rowCount - Variable in class fr.curie.BiNoM.pathways.utils.SimpleTable

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.CycleDecompositionTask

run() - Method in class fr.curie.BiNoM.cytoscape.analysis.EdgesFromOtherNetworkTask

run() - Method in class fr.curie.BiNoM.cytoscape.analysis.ExtractReactionNetworkTask

run() - Method in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask

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.PathAnalysisTask

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.BioPAXExport

run() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportTask

run() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImport

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.CellDesignerExport

run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask

run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImport

run() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerImportTask

run() - Method in class fr.curie.BiNoM.cytoscape.netwop.NetworksUpdateTask

run() - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExport

run() - Method in class fr.curie.BiNoM.cytoscape.sbml.SBMLExportTask