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

S

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

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

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

saveCellDesigner(SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner

Save org.sbml.x2001.ns.celldesigner.SbmlDocument to file

saveModel(Model, String, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities

Save OWL model to the file

saveModel(Model, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXUtilities

saveSBML(SbmlDocument, String) - Static method in class fr.curie.BiNoM.pathways.wrappers.SBML

Saves org.sbml.sbml.level2.SbmlDocument to file

saveToFile(String, OntModel) - Static method in class fr.curie.BiNoM.pathways.test.TestBioPAX

saveToFile(String, OntModel) - Static method in class fr.curie.BiNoM.pathways.wrappers.BioPAX

Save an OntModel object to file

saveToFile(String, Model) - Static method in class fr.curie.BiNoM.pathways.wrappers.BioPAX

Save Model object to file

saveToXGMML(GraphDocument, String) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML

Saves XGMML to fil

saveToXGMML(Graph, String) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML

saveToXMGML(GraphDocument, String) - Static method in class fr.curie.BiNoM.pathways.utils.XGMMLExport

sbml - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

Java xml-beans mapping of CellDesigner file

sbml - Variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter.Graph

sbml - Variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

Java xml-beans mapping of CellDesigner file

SBML - Class in fr.curie.BiNoM.pathways.wrappers

Wrapper of 'pure' SBML represented by org.sbml.sbml.level2.SbmlDocument object

SBML() - Constructor for class fr.curie.BiNoM.pathways.wrappers.SBML

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

Result of conversion

SBMLExport - Class in fr.curie.BiNoM.cytoscape.sbml

SBMLExport(File) - Constructor for class fr.curie.BiNoM.cytoscape.sbml.SBMLExport

SBMLExportTask - Class in fr.curie.BiNoM.cytoscape.sbml

SBMLExportTask(File) - Constructor for class fr.curie.BiNoM.cytoscape.sbml.SBMLExportTask

SBMLExportToFile - Class in fr.curie.BiNoM.cytoscape.sbml

SBMLExportToFile() - Constructor for class fr.curie.BiNoM.cytoscape.sbml.SBMLExportToFile

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

ScaleSizes(SbmlDocument, float) - Static method in class fr.curie.BiNoM.pathways.test.test

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

SELECT_ENTITIES - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

Identifying entities by names and XREFs in the index

selectComplex - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions

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

SelectEdgesBetweenSelectedNodes() - Constructor for class fr.curie.BiNoM.cytoscape.utils.SelectEdgesBetweenSelectedNodes

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

SelectedNodes - Variable in class fr.curie.BiNoM.cytoscape.analysis.IndexPathAnalysisTask

SelectedNodes - Variable in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisTask

selectPublications - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions

selectReactions - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions

selectSpecies - Variable in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions

SEMANTIC - Static variable in class fr.curie.BiNoM.pathways.wrappers.Transpath

SEQUENCE_DASH_FEATURE_DASH_LISTAdded(sequenceParticipant, sequenceFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipantListener

Called when a value of SEQUENCE_DASH_FEATURE_DASH_LIST has been added

SEQUENCE_DASH_FEATURE_DASH_LISTProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipant

The Jena Property for SEQUENCE_DASH_FEATURE_DASH_LIST

SEQUENCE_DASH_FEATURE_DASH_LISTRemoved(sequenceParticipant, sequenceFeature) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipantListener

Called when a value of SEQUENCE_DASH_FEATURE_DASH_LIST has been removed

SEQUENCE_DASH_INTERVAL_DASH_BEGINChanged(sequenceInterval) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceIntervalListener

Called when SEQUENCE_DASH_INTERVAL_DASH_BEGIN has changed

SEQUENCE_DASH_INTERVAL_DASH_BEGINProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.sequenceInterval

The Jena Property for SEQUENCE_DASH_INTERVAL_DASH_BEGIN

SEQUENCE_DASH_INTERVAL_DASH_ENDChanged(sequenceInterval) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceIntervalListener

Called when SEQUENCE_DASH_INTERVAL_DASH_END has changed

SEQUENCE_DASH_INTERVAL_DASH_ENDProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.sequenceInterval

The Jena Property for SEQUENCE_DASH_INTERVAL_DASH_END

SEQUENCE_DASH_POSITIONChanged(sequenceSite) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceSiteListener

Called when SEQUENCE_DASH_POSITION has changed

SEQUENCE_DASH_POSITIONProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.sequenceSite

The Jena Property for SEQUENCE_DASH_POSITION

SEQUENCEAdded(dna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.dnaListener

Called when a value of SEQUENCE has been added

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

Called when SEQUENCE has changed

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

Called when SEQUENCE has changed

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

SEQUENCEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.dna

The Jena Property for SEQUENCE

SEQUENCEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.protein

The Jena Property for SEQUENCE

SEQUENCEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.rna

The Jena Property for SEQUENCE

SEQUENCERemoved(dna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.dnaListener

Called when a value of SEQUENCE has been removed

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

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

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

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

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

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

setAccessionNumberTable(AccessionNumberTable) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository

setAccNumberFileName(String) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository

setAttrDescV(Vector<BioPAXAttrDesc>) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc

setAttribute(GraphicEdge, String, String, String, ObjectType.Enum) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Set attribute value for GraphicEdge

setAttribute(GraphicNode, String, String, String, ObjectType.Enum) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Set attribute value for GraphicNode

setAttributeValueUnique(String, String) - Method in class fr.curie.BiNoM.pathways.analysis.structure.Element

Checks if the attribute with such a name already attached and if yes, then changes its value, if no then creates a new one

setAveragePositionForXGMML(GraphicNode, Vector, HashMap) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

Place node 'nod' into the average of 'nodes' positions

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

setBioPAX(CyNetwork, BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXSourceDB

setBioPAXGraphQueryEngine(BioPAXGraphQueryEngine) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository

setCellDesigner(CyNetwork, SbmlDocument) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerSourceDB

setCELLTYPE(openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource

Sets the 'CELLTYPE' property value

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

Sets the 'CELLTYPE' property value to an anonymous node

setCELLTYPE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource

Sets the 'CELLTYPE' property value to the given resource, and add's rdf:type properties.

setCELLTYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl

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

setCELLTYPE(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl

setCELLULAR_DASH_LOCATION(openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant

Sets the 'CELLULAR_DASH_LOCATION' property value

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

Sets the 'CELLULAR_DASH_LOCATION' property value to an anonymous node

setCELLULAR_DASH_LOCATION(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant

Sets the 'CELLULAR_DASH_LOCATION' property value to the given resource, and add's rdf:type properties.

setCELLULAR_DASH_LOCATION(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl

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

setCELLULAR_DASH_LOCATION(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl

setCELLULAR_DASH_LOCATION(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl

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

setCELLULAR_DASH_LOCATION(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl

setCHEMICAL_DASH_FORMULA(String) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMolecule

Sets the 'CHEMICAL_DASH_FORMULA' property value

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

setCONFIDENCE_DASH_VALUE(String) - Method in interface fr.curie.BiNoM.pathways.biopax.confidence

Sets the 'CONFIDENCE_DASH_VALUE' property value

setCONFIDENCE_DASH_VALUE(String) - Method in class fr.curie.BiNoM.pathways.biopax.confidenceImpl

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

setCONTROL_DASH_TYPE(String) - Method in interface fr.curie.BiNoM.pathways.biopax.control

Sets the 'CONTROL_DASH_TYPE' property value

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

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

setCONTROLLED(conversion) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysis

Sets the 'CONTROLLED' property value

setCONTROLLED(conversion) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

setCONTROLLED(interaction) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

setCONTROLLED(pathway) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

setCONTROLLED(interaction) - Method in interface fr.curie.BiNoM.pathways.biopax.control

Sets the 'CONTROLLED' property value

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

Sets the 'CONTROLLED' property value

setCONTROLLED(interaction) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

setCONTROLLED(pathway) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

setCONTROLLED(catalysis) - Method in interface fr.curie.BiNoM.pathways.biopax.modulation

Sets the 'CONTROLLED' property value

setCONTROLLED(catalysis) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

setCONTROLLED(interaction) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

setCONTROLLED(pathway) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

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

Sets the 'CONTROLLED' property value to an anonymous node

setCONTROLLED_ascatalysis(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.modulation

Sets the 'CONTROLLED' property value to the given resource, and add's rdf:type properties.

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

setCONTROLLED_ascatalysis(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

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

Sets the 'CONTROLLED' property value to an anonymous node

setCONTROLLED_asconversion(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysis

Sets the 'CONTROLLED' property value to the given resource, and add's rdf:type properties.

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

setCONTROLLED_asconversion(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

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

setCONTROLLED_asinteraction(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

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

Sets the 'CONTROLLED' property value to an anonymous node

setCONTROLLED_asinteraction(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.control

Sets the 'CONTROLLED' property value to the given resource, and add's rdf:type properties.

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

setCONTROLLED_asinteraction(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

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

setCONTROLLED_asinteraction(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

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

setCONTROLLED_aspathway(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

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

Sets the 'CONTROLLED' property value to an anonymous node

setCONTROLLED_aspathway(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.control

Sets the 'CONTROLLED' property value to the given resource, and add's rdf:type properties.

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

setCONTROLLED_aspathway(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

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

setCONTROLLED_aspathway(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

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

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

setCONTROLLER(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

setCONTROLLER(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.control

Sets the 'CONTROLLER' property value

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

Sets the 'CONTROLLER' property value to an anonymous node

setCONTROLLER(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.control

Sets the 'CONTROLLER' property value to the given resource, and add's rdf:type properties.

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

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

setCONTROLLER(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

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

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

setCONTROLLER(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

setDatabase(GraphDocument) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine

Setting the BioPAX index file for performing the query

setDatabase(Graph) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQueryEngine

Setting the BioPAX index file for performing the query

setDatabaseFileName(String) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository

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

setDB(String) - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl

setDB(String) - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl

setDB(String) - Method in interface fr.curie.BiNoM.pathways.biopax.xref

Sets the 'DB' property value

setDB(String) - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl

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

setDB_DASH_VERSION(String) - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl

setDB_DASH_VERSION(String) - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl

setDB_DASH_VERSION(String) - Method in interface fr.curie.BiNoM.pathways.biopax.xref

Sets the 'DB_DASH_VERSION' property value

setDB_DASH_VERSION(String) - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl

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

Sets the 'DELTA_DASH_G_DASH_PRIME_DASH_O' property value

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

setDIRECTION(String) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysis

Sets the 'DIRECTION' property value

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

setEntityId(CelldesignerSpeciesIdentityDocument.CelldesignerSpeciesIdentity, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

setFEATURE_DASH_TYPE(openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Sets the 'FEATURE_DASH_TYPE' property value

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

Sets the 'FEATURE_DASH_TYPE' property value to an anonymous node

setFEATURE_DASH_TYPE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

Sets the 'FEATURE_DASH_TYPE' property value to the given resource, and add's rdf:type properties.

setFEATURE_DASH_TYPE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl

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

setFEATURE_DASH_TYPE(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl

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

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

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

setID(String) - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl

setID(String) - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl

setID(String) - Method in interface fr.curie.BiNoM.pathways.biopax.xref

Sets the 'ID' property value

setID(String) - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl

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

setID_DASH_VERSION(String) - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl

setID_DASH_VERSION(String) - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl

setID_DASH_VERSION(String) - Method in interface fr.curie.BiNoM.pathways.biopax.xref

Sets the 'ID_DASH_VERSION' property value

setID_DASH_VERSION(String) - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl

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

Sets the 'K_DASH_PRIME' property value

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

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

Same as SetValue

setMOLECULAR_DASH_WEIGHT(Double) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMolecule

Sets the 'MOLECULAR_DASH_WEIGHT' property value

setMOLECULAR_DASH_WEIGHT(Double) - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl

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

setNAME(String) - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource

Sets the 'NAME' property value

setNAME(String) - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl

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

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

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

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

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

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

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

Sets the 'NAME' property value

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

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

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

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

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

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

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

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

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

Sets the 'NAME' property value

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

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

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

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

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

setNetworkContents(CyNetwork, CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils

setNetworkContentsAndReportPositions(CyNetwork, CyNetwork) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkUtils

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

Sets NotesDocument.Notes content

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

Sets the 'ORGANISM' property value

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

Sets the 'ORGANISM' property value to an anonymous node

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

Sets the 'ORGANISM' property value to the given resource, and add's rdf:type properties.

setORGANISM(bioSource) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

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

setORGANISM(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

setORGANISM(bioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.protein

Sets the 'ORGANISM' property value

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

Sets the 'ORGANISM' property value to an anonymous node

setORGANISM(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.protein

Sets the 'ORGANISM' property value to the given resource, and add's rdf:type properties.

setORGANISM(bioSource) - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl

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

setORGANISM(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl

setORGANISM(bioSource) - Method in interface fr.curie.BiNoM.pathways.biopax.rna

Sets the 'ORGANISM' property value

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

Sets the 'ORGANISM' property value to an anonymous node

setORGANISM(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.rna

Sets the 'ORGANISM' property value to the given resource, and add's rdf:type properties.

setORGANISM(bioSource) - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl

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

setORGANISM(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl

setParentClassDescV(Vector<BioPAXClassDesc>) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc

setPARTICIPANT(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalForm

Sets the 'PARTICIPANT' property value

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

Sets the 'PARTICIPANT' property value to an anonymous node

setPARTICIPANT(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.experimentalForm

Sets the 'PARTICIPANT' property value to the given resource, and add's rdf:type properties.

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

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

setPARTICIPANT(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.experimentalFormImpl

setPHYSICAL_DASH_ENTITY(physicalEntity) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant

Sets the 'PHYSICAL_DASH_ENTITY' property value

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

Sets the 'PHYSICAL_DASH_ENTITY' property value to an anonymous node

setPHYSICAL_DASH_ENTITY(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant

Sets the 'PHYSICAL_DASH_ENTITY' property value to the given resource, and add's rdf:type properties.

setPHYSICAL_DASH_ENTITY(physicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl

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

setPHYSICAL_DASH_ENTITY(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl

setPHYSICAL_DASH_ENTITY(physicalEntity) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl

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

setPHYSICAL_DASH_ENTITY(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl

setPOSITION_DASH_STATUS(String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceSite

Sets the 'POSITION_DASH_STATUS' property value

setPOSITION_DASH_STATUS(String) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceSiteImpl

setReactionEffectAttribute(interaction, GraphicNode, String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper

If there is a comment with which contains substring+":", this comment is added as a value of an attribute named substring

setRELATIONSHIP_DASH_TYPE(String) - Method in interface fr.curie.BiNoM.pathways.biopax.relationshipXref

Sets the 'RELATIONSHIP_DASH_TYPE' property value

setRELATIONSHIP_DASH_TYPE(String) - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl

setReport(String) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository

setSEQUENCE(String) - Method in interface fr.curie.BiNoM.pathways.biopax.protein

Sets the 'SEQUENCE' property value

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

setSEQUENCE(String) - Method in interface fr.curie.BiNoM.pathways.biopax.rna

Sets the 'SEQUENCE' property value

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

setSEQUENCE_DASH_INTERVAL_DASH_BEGIN(sequenceSite) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceInterval

Sets the 'SEQUENCE_DASH_INTERVAL_DASH_BEGIN' property value

setSEQUENCE_DASH_INTERVAL_DASH_BEGIN() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceInterval

Sets the 'SEQUENCE_DASH_INTERVAL_DASH_BEGIN' property value to an anonymous node

setSEQUENCE_DASH_INTERVAL_DASH_BEGIN(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceInterval

Sets the 'SEQUENCE_DASH_INTERVAL_DASH_BEGIN' property value to the given resource, and add's rdf:type properties.

setSEQUENCE_DASH_INTERVAL_DASH_BEGIN(sequenceSite) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceIntervalImpl

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

setSEQUENCE_DASH_INTERVAL_DASH_BEGIN(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceIntervalImpl

setSEQUENCE_DASH_INTERVAL_DASH_END(sequenceSite) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceInterval

Sets the 'SEQUENCE_DASH_INTERVAL_DASH_END' property value

setSEQUENCE_DASH_INTERVAL_DASH_END() - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceInterval

Sets the 'SEQUENCE_DASH_INTERVAL_DASH_END' property value to an anonymous node

setSEQUENCE_DASH_INTERVAL_DASH_END(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceInterval

Sets the 'SEQUENCE_DASH_INTERVAL_DASH_END' property value to the given resource, and add's rdf:type properties.

setSEQUENCE_DASH_INTERVAL_DASH_END(sequenceSite) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceIntervalImpl

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

setSEQUENCE_DASH_INTERVAL_DASH_END(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceIntervalImpl

setSEQUENCE_DASH_POSITION(XSDBaseNumericType) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceSite

Sets the 'SEQUENCE_DASH_POSITION' property value

setSEQUENCE_DASH_POSITION(XSDBaseNumericType) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceSiteImpl

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

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

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

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

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

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

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

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

Sets the 'SHORT_DASH_NAME' property value

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

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

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

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

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

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

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

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

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

Sets the 'SHORT_DASH_NAME' property value

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

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

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

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

setSpeciesPositionForXGMML(String, GraphicNode, SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

Reads the position information for a node from CellDesigner

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

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

setSPONTANEOUS(String) - Method in interface fr.curie.BiNoM.pathways.biopax.conversion

Sets the 'SPONTANEOUS' property value

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

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

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

setSTOICHIOMETRIC_DASH_COEFFICIENT(Double) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant

Sets the 'STOICHIOMETRIC_DASH_COEFFICIENT' property value

setSTOICHIOMETRIC_DASH_COEFFICIENT(Double) - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl

setSTOICHIOMETRIC_DASH_COEFFICIENT(Double) - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl

setSTRUCTURE_DASH_DATA(String) - Method in interface fr.curie.BiNoM.pathways.biopax.chemicalStructure

Sets the 'STRUCTURE_DASH_DATA' property value

setSTRUCTURE_DASH_DATA(String) - Method in class fr.curie.BiNoM.pathways.biopax.chemicalStructureImpl

setSTRUCTURE_DASH_FORMAT(String) - Method in interface fr.curie.BiNoM.pathways.biopax.chemicalStructure

Sets the 'STRUCTURE_DASH_FORMAT' property value

setSTRUCTURE_DASH_FORMAT(String) - Method in class fr.curie.BiNoM.pathways.biopax.chemicalStructureImpl

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ClusterNetworksTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ConnectedComponentsTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.CycleDecompositionTask

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

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

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

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.MaterialComponentsTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.ModularViewTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.MonoMolecularReactionsAsEdgesTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.PathAnalysisTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.PruneGraphTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.analysis.StronglyConnectedComponentsTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSourceTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExport

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

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

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSourceTask

setTaskMonitor(TaskMonitor) - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExport

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

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

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

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

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

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

setTAXON_DASH_XREF(unificationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource

Sets the 'TAXON_DASH_XREF' property value

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

Sets the 'TAXON_DASH_XREF' property value to an anonymous node

setTAXON_DASH_XREF(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource

Sets the 'TAXON_DASH_XREF' property value to the given resource, and add's rdf:type properties.

setTAXON_DASH_XREF(unificationXref) - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl

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

setTAXON_DASH_XREF(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl

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

setTISSUE(openControlledVocabulary) - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource

Sets the 'TISSUE' property value

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

Sets the 'TISSUE' property value to an anonymous node

setTISSUE(Resource) - Method in interface fr.curie.BiNoM.pathways.biopax.bioSource

Sets the 'TISSUE' property value to the given resource, and add's rdf:type properties.

setTISSUE(openControlledVocabulary) - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl

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

setTISSUE(Resource) - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl

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

Sets the 'TITLE' property value

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

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

setValue(BioPAXObject, Double) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleAttrDesc

setValue(BioPAXObject, Integer) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerAttrDesc

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

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

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

Set a string value for XmlObject

setYEAR(Integer) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXref

Sets the 'YEAR' property value

setYEAR(Integer) - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl

SHARP - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

Called when SHORT_DASH_NAME has changed

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

The Jena Property for SHORT_DASH_NAME

SHORT_DASH_NAMEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

The Jena Property for SHORT_DASH_NAME

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

ShowClipboardContents() - Constructor for class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContents

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

ShowClipboardContentsDialog() - Constructor for class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContentsDialog

ShowMonoMolecularReactionsAsEdges(Graph) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils

Finds all reactions on the graph gri having only one reactant and one product and no modifiers and substitutes them by edge.

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

Simple implementation of a table of entries

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

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

List of identical (from the point of view of SBML) physicalEntityParticipants

Skeleton - Class in fr.curie.BiNoM.pathways.analysis.structure

Some old and forgotten idea

Skeleton() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.Skeleton

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

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

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

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

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

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

Map from cutted uris (after # separator) to 'smallMolecule' entities

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

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

SOURCEAdded(publicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXrefListener

Called when a value of SOURCE has been added

SOURCEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.publicationXref

The Jena Property for SOURCE

SOURCERemoved(publicationXref, String) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXrefListener

Called when a value of SOURCE has been removed

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

Map from SBML species ids to SpeciesDocument.Species objects

species - Variable in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

List of CellDesigner SpeciesDocument.Species objects

speciesFilter - Variable in class fr.curie.BiNoM.pathways.wrappers.Transpath

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

Called when SPONTANEOUS has changed

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

Called when SPONTANEOUS has changed

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

Called when SPONTANEOUS has changed

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

Called when SPONTANEOUS has changed

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

Called when SPONTANEOUS has changed

SPONTANEOUSProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.conversion

The Jena Property for SPONTANEOUS

SQUARE - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.Edge

startElement(String, String, String, Attributes) - Method in class fr.curie.BiNoM.pathways.utils.GraphXGMMLParser

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

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

Called when a value of STEP_DASH_INTERACTIONS has been added

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

Called when a value of STEP_DASH_INTERACTIONS has been added

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

The Jena Property for STEP_DASH_INTERACTIONS

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

Called when a value of STEP_DASH_INTERACTIONS has been removed

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

Called when a value of STEP_DASH_INTERACTIONS has been removed

STOICHIOMETRIC_DASH_COEFFICIENTChanged(physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantListener

Called when STOICHIOMETRIC_DASH_COEFFICIENT has changed

STOICHIOMETRIC_DASH_COEFFICIENTChanged(sequenceParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceParticipantListener

Called when STOICHIOMETRIC_DASH_COEFFICIENT has changed

STOICHIOMETRIC_DASH_COEFFICIENTProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.physicalEntityParticipant

The Jena Property for STOICHIOMETRIC_DASH_COEFFICIENT

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

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

StronglyConnectedComponents() - Constructor for class fr.curie.BiNoM.cytoscape.analysis.StronglyConnectedComponents

StronglyConnectedComponentsTarjan(Graph, int) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms

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

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

STRUCTURE_DASH_DATAChanged(chemicalStructure) - Method in interface fr.curie.BiNoM.pathways.biopax.chemicalStructureListener

Called when STRUCTURE_DASH_DATA has changed

STRUCTURE_DASH_DATAProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.chemicalStructure

The Jena Property for STRUCTURE_DASH_DATA

STRUCTURE_DASH_FORMATChanged(chemicalStructure) - Method in interface fr.curie.BiNoM.pathways.biopax.chemicalStructureListener

Called when STRUCTURE_DASH_FORMAT has changed

STRUCTURE_DASH_FORMATProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.chemicalStructure

The Jena Property for STRUCTURE_DASH_FORMAT

STRUCTUREAdded(smallMolecule, chemicalStructure) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMoleculeListener

Called when a value of STRUCTURE has been added

StructureAnalysisUtils - Class in fr.curie.BiNoM.pathways.analysis.structure

Connector class between GraphAlgorithms and BiographUtils and Cytoscape interface

StructureAnalysisUtils() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils

StructureAnalysisUtils.Option - Class in fr.curie.BiNoM.pathways.analysis.structure

Options container

StructureAnalysisUtils.Option() - Constructor for class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option

STRUCTUREProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.smallMolecule

The Jena Property for STRUCTURE

STRUCTURERemoved(smallMolecule, chemicalStructure) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMoleculeListener

Called when a value of STRUCTURE has been removed

SUBOPTIMAL_SHORTEST_PATHS - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils.Option

substituteEntityId(SbmlDocument, String, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

substituteSpeciesId(SbmlDocument, String, String) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

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

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

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

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

Called when a value of SYNONYMS has been added

SYNONYMSAdded(catalysis, String) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(complexAssembly, String) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(complex, String) - Method in interface fr.curie.BiNoM.pathways.biopax.complexListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(control, String) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(conversion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(dna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.dnaListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(entity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.entityListener

Called when a value of SYNONYMS has been added

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

Called when a value of SYNONYMS has been added

SYNONYMSAdded(modulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of SYNONYMS has been added

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

Called when a value of SYNONYMS has been added

SYNONYMSAdded(physicalEntity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(physicalInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(protein, String) - Method in interface fr.curie.BiNoM.pathways.biopax.proteinListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(rna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.rnaListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(sequenceFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeatureListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(smallMolecule, String) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMoleculeListener

Called when a value of SYNONYMS has been added

SYNONYMSAdded(transport, String) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of SYNONYMS has been added

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

Called when a value of SYNONYMS has been added

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

The Jena Property for SYNONYMS

SYNONYMSProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.sequenceFeature

The Jena Property for SYNONYMS

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

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(catalysis, String) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(complexAssembly, String) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(complex, String) - Method in interface fr.curie.BiNoM.pathways.biopax.complexListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(control, String) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(conversion, String) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(dna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.dnaListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(entity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.entityListener

Called when a value of SYNONYMS has been removed

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

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(modulation, String) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of SYNONYMS has been removed

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

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(physicalEntity, String) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalEntityListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(physicalInteraction, String) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(protein, String) - Method in interface fr.curie.BiNoM.pathways.biopax.proteinListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(rna, String) - Method in interface fr.curie.BiNoM.pathways.biopax.rnaListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(sequenceFeature, String) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeatureListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(smallMolecule, String) - Method in interface fr.curie.BiNoM.pathways.biopax.smallMoleculeListener

Called when a value of SYNONYMS has been removed

SYNONYMSRemoved(transport, String) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of SYNONYMS has been removed

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

Called when a value of SYNONYMS has been removed