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

P

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

parse(String) - Method in class fr.curie.BiNoM.pathways.utils.GraphXGMMLParser

Parses fn file

parseAccessionTable(String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

deprecated

parseBioPAX - Class in fr.curie.BiNoM.pathways

Utility class for listing some BioPAX information as a readable text

parseBioPAX() - Constructor for class fr.curie.BiNoM.pathways.parseBioPAX

parseCellDesigner - Class in fr.curie.BiNoM.pathways

Utility class for listing some CellDesigner information as a readable text

parseCellDesigner() - Constructor for class fr.curie.BiNoM.pathways.parseCellDesigner

parseXGMML(String) - Static method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

Loads BioPAXGraphQuery from a XGMML file

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

Called when PARTICIPANT has changed

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

The Jena Property for PARTICIPANT

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

Map from complete uris to physicalEntityParticipants

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

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(biochemicalReaction, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(catalysis, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(catalysis, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of PARTICIPANTS has been added

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

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(complexAssembly, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(control, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(control, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of PARTICIPANTS has been added

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

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(conversion, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of PARTICIPANTS has been added

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

Called when a value of PARTICIPANTS has been added

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

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(modulation, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(modulation, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(physicalInteraction, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(physicalInteraction, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of PARTICIPANTS has been added

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

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(transport, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(transportWithBiochemicalReaction, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of PARTICIPANTS has been added

PARTICIPANTSAdded(transportWithBiochemicalReaction, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of PARTICIPANTS has been added

PARTICIPANTSProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.interaction

The Jena Property for PARTICIPANTS

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

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(biochemicalReaction, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.biochemicalReactionListener

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(catalysis, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(catalysis, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.catalysisListener

Called when a value of PARTICIPANTS has been removed

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

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(complexAssembly, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.complexAssemblyListener

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(control, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(control, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.controlListener

Called when a value of PARTICIPANTS has been removed

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

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(conversion, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.conversionListener

Called when a value of PARTICIPANTS has been removed

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

Called when a value of PARTICIPANTS has been removed

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

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(modulation, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(modulation, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.modulationListener

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(physicalInteraction, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(physicalInteraction, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.physicalInteractionListener

Called when a value of PARTICIPANTS has been removed

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

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(transport, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.transportListener

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(transportWithBiochemicalReaction, physicalEntityParticipant) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of PARTICIPANTS has been removed

PARTICIPANTSRemoved(transportWithBiochemicalReaction, entity) - Method in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionListener

Called when a value of PARTICIPANTS has been removed

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

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

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

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

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

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

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

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

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

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

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

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

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

Called when a value of PATHWAY_DASH_COMPONENTS has been added

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

Called when a value of PATHWAY_DASH_COMPONENTS has been added

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

Called when a value of PATHWAY_DASH_COMPONENTS has been added

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

The Jena Property for PATHWAY_DASH_COMPONENTS

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

Called when a value of PATHWAY_DASH_COMPONENTS has been removed

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

Called when a value of PATHWAY_DASH_COMPONENTS has been removed

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

Called when a value of PATHWAY_DASH_COMPONENTS has been removed

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

PATHWAY_STRUCTURE_CONVERSION - Static variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter

Mode of conversion: from BioPAX to Pathway Structure BioPAX interface

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

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

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

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

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

Map from complete uris to pathway objects

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

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

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

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

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

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

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

Map from complete uris to pathwaySteps objects

perform() - Method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSource

perform() - Method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerAssociateSource

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

Called when a value of PH has been added

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

Called when a value of PH has been added

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

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

The Jena Property for PH

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

The Jena Property for PH

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

Called when a value of PH has been removed

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

Called when a value of PH has been removed

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

Called when PHYSICAL_DASH_ENTITY has changed

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

Called when PHYSICAL_DASH_ENTITY has changed

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

The Jena Property for PHYSICAL_DASH_ENTITY

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

placeMap - Variable in class fr.curie.BiNoM.pathways.test.ProduceClickableMap

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

Called when a value of PMG has been added

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

Called when a value of PMG has been added

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

The Jena Property for PMG

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

The Jena Property for PMG

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

Called when a value of PMG has been removed

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

Called when a value of PMG has been removed

pop() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc.HierarchyScanner

pop(HashMap, HashMap, HashMap) - Method in class fr.curie.BiNoM.cytoscape.utils.PasteNodesAndEdgesDialog

pop(HashMap, HashMap, HashMap) - Method in class fr.curie.BiNoM.cytoscape.utils.ShowClipboardContentsDialog

populateModel() - Method in class fr.curie.BiNoM.pathways.CellDesignerToBioPAXConverter

The converter itself

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

populateSbml() - Method in class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter

Performs actual BioPAX->SBML conversion Requires this.biopax object to be specified

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

Called when POSITION_DASH_STATUS has changed

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

The Jena Property for POSITION_DASH_STATUS

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

A Powerful Tokenizer Author Bhabani Padhi Extension of the standard StringTokenizer

PowerfulTokenizer(String, String) - Constructor for class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer

Constructor

PowerfulTokenizer(String, String, boolean) - Constructor for class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer

Constructor

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

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

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

Prepares a copy of database for Index Path Analysis.

print() - Method in class fr.curie.BiNoM.pathways.utils.AccessionNumberTable

Prints the whole table in the form \t

printAntisenseRNAList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner

printDump(Model) - Static method in class fr.curie.BiNoM.pathways.wrappers.BioPAX

Prints the content of the BioPAX Model object as readable text

printEntityName(entity) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

printGeneList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner

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

printPhenotypeList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner

printPropertyURIs(entity) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Simply prints all statement uris in the entity res

printPropertyURIs(utilityClass) - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Simply prints all statement uris in the utilityClass res

printProteinsList(SbmlDocument.Sbml, boolean) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner

printReactionList(SbmlDocument.Sbml, boolean) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner

printRNAList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner

printSmallMoleculeList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner

printSpeciesList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner

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

printStatements() - Method in class fr.curie.BiNoM.pathways.utils.BioPAXMerge

Prints all statements of the base Model

printUsedMemory() - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Prints how much memory is used

printUsedMemorySinceLastTime() - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Prints a difference in used memory since last call of printUsedMemory,printUsedMemorySinceLastTime, getUsedMemorySinceLastTime,printUsedMemorySinceLastTimeByte functions

printUsedMemorySinceLastTimeByte() - Static method in class fr.curie.BiNoM.pathways.utils.Utils

Same ad printUsedMemorySinceLastTime but in bytes

printUtilityClassName(utilityClass) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

ProduceClickableMap - Class in fr.curie.BiNoM.pathways.test

ProduceClickableMap() - Constructor for class fr.curie.BiNoM.pathways.test.ProduceClickableMap

projectName - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMappingService

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

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

PROTEIN_PROTEIN_INTERACTION_CONVERSION - Static variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter

Mode of conversion: from BioPAX to Protein-protein interaction BioPAX interface

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

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

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

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

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

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

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

List of CellDesigner CelldesignerProteinDocument.CelldesignerProtein objects

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

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

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

Graph pruning (eliminataing IN and OUT layers)

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

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

ptintComplexList(SbmlDocument.Sbml) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner

pub1 - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork

pub2 - Static variable in class fr.curie.BiNoM.pathways.test.testEwingNetwork

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

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

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

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

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

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

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

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

Map from Pubmed ids to publicationXref objects

push(BioPAXClassDesc) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc.HierarchyScanner

putEntity(entity) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

Adds an entity for naming

putID(String, String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

putName(String, String) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

Adds a (uri,name) pair

putUtilityClass(utilityClass) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

Adds an utilityClass for naming