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

B

backforwStates() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserFrame

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

BiNoMPlugin - Class in fr.curie.BiNoM.cytoscape.plugin

BiNoMPlugin() - Constructor for class fr.curie.BiNoM.cytoscape.plugin.BiNoMPlugin

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

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

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

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

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

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

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

Set of functions using specific graph node semantics of BiNoM

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

biopax - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Graph

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

Input for conversion

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

The result of the conversion

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

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

Input BioPAX object

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

BioPAX wrapper with some utilities implemented

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

BioPAX(String, String, String) - Constructor for class fr.curie.BiNoM.pathways.wrappers.BioPAX

Non-standard constructor with some prefixes

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

BioPAX2Cytoscape - Class in fr.curie.BiNoM.pathways.converters

BioPAX2Cytoscape() - Constructor for class fr.curie.BiNoM.pathways.converters.BioPAX2Cytoscape

BioPAX2SBML - Class in fr.curie.BiNoM.pathways.converters

BioPAX2SBML() - Constructor for class fr.curie.BiNoM.pathways.converters.BioPAX2SBML

biopax_DASH_level2_DOT_owlFactory - Class in fr.curie.BiNoM.pathways.biopax

Factory for instantiating objects for ontology classes in the biopax-level2.owl ontology.

biopax_DASH_level2_DOT_owlFactory() - Constructor for class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

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

A map from BioPAX file key to static set of BioPAX objects

BioPAXAssociateSource - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXAssociateSourceTask - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXAssociateSourceTask(File, String) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXAssociateSourceTask

BioPAXAttrDesc - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXClassDesc - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXClassDesc(BioPAX, Class) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc

BioPAXClassDesc.HierarchyScanner - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXClassDesc.HierarchyScanner() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDesc.HierarchyScanner

BioPAXClassDescFactory - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXClassTree - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXClassTree() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassTree

BioPAXClassTreeFrame - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXConnectedComponents - Class in fr.curie.BiNoM.pathways.test.examples

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

BioPAXDBRepository - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXDBRepository() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDBRepository

BioPAXDisplayIndexInfo - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXDisplayIndexInfo() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDisplayIndexInfo

BioPAXDisplayIndexInfoDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXDisplayIndexInfoDialog() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXDisplayIndexInfoDialog

BioPAXDoubleAttrDesc - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXDoubleAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleAttrDesc

BioPAXDoubleListAttrDesc - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXDoubleListAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleListAttrDesc

BioPAXExport - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXExport(File) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXExport

BioPAXExportTask - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXExportTask(File, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportTask

BioPAXExportToFile - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXExportToFile() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportToFile

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

Standard BioPAX v.2 prefix

BioPAXGenerateIndex - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXGenerateIndex() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndex

BioPAXGenerateIndexDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXGenerateIndexTask - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXGenerateIndexTask(String, String) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXGenerateIndexTask

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

Creates a BioPAX index - mapping of BioPAX content onto an attributed (di)graph

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

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

Service class performing creating BioPAX index

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

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

A simple container of the BioPAX standard query

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

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

The actual implementation of the standard query

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

BioPAXImport - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXImport(File, URL, String, int[], BioPAXToCytoscapeConverter.Option) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXImport

BioPAXImportDialog - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXImportFromFile - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXImportFromFile() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportFromFile

BioPAXImportFromURL - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXImportFromURL() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportFromURL

BioPAXImportTask - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXImportTask(File, URL, String, int[], BioPAXToCytoscapeConverter.Option, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXImportTask

BioPAXIndexPathAnalysis - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXIndexPathAnalysis() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexPathAnalysis

BioPAXIndexRepository - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXIndexRepository() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXIndexRepository

BioPAXIntegerAttrDesc - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXIntegerAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerAttrDesc

BioPAXIntegerListAttrDesc - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXIntegerListAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerListAttrDesc

BioPAXLoadIndex - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXLoadIndex() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndex

BioPAXLoadIndexDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXLoadIndexTask - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXLoadIndexTask(String, String) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXLoadIndexTask

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

Utilities for merging BioPAX objects

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

biopaxmodel - Variable in class fr.curie.BiNoM.pathways.wrappers.BioPAX

BioPAX OWL as com.hp.hpl.jena.ontology.OntModel

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

Naming service used for the mapping

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

BioPAX Naming Service.

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

BioPAXNamingService(BioPAX, boolean) - Constructor for class fr.curie.BiNoM.pathways.utils.BioPAXNamingService

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

BioPAXNamingServiceManager - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXNamingServiceManager() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXNamingServiceManager

BioPAXObject - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXObject(BioPAXClassDesc, Object, BioPAX) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObject

BioPAXObjectAttrDesc - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXObjectAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc

BioPAXObjectFactory - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXObjectListAttrDesc - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXObjectListAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc

BioPAXPathAnalysis - Class in fr.curie.BiNoM.pathways.test.examples

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

BioPAXPropertyBrowser - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXPropertyBrowser() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowser

BioPAXPropertyBrowserFrame - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXPropertyBrowserPanel - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXPropertyBrowserPanel(BioPAXObject, BioPAX, boolean, boolean, BioPAXPropertyBrowserFrame) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserPanel

BioPAXPropertyEditor - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXPropertyEditor() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyEditor

BioPAXPropertyManager - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

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

Map from cutted uris (after # separator) to BioPAX 'conversion' objects

BioPAXRepository - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXRepository() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXRepository

BioPAXSaveAssociated - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXSaveAssociated() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXSaveAssociated

BioPAXSelectEntities - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXSelectEntities() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntities

BioPAXSelectEntitiesDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXSelectEntitiesDialog() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesDialog

BioPAXSelectEntitiesTask - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXSelectEntitiesTask(BioPAXGraphQuery, int, int) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXSelectEntitiesTask

BioPAXSourceDB - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXStandardQuery - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXStandardQuery() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQuery

BioPAXStandardQuery - Class in fr.curie.BiNoM.pathways.test.examples

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

BioPAXStandardQueryDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXStandardQueryTask - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXStandardQueryTask(BioPAXStandardQueryTask.StandardQueryOptions, BioPAXGraphQuery, Vector, boolean) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask

BioPAXStandardQueryTask() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask

BioPAXStandardQueryTask.StandardQueryOptions - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXStandardQueryTask.StandardQueryOptions() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXStandardQueryTask.StandardQueryOptions

biopaxString - Static variable in class fr.curie.BiNoM.pathways.test.TestBioPAX

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

Standard BioPAX v.2 prefix

BioPAXStringAttrDesc - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXStringAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringAttrDesc

BioPAXStringListAttrDesc - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXStringListAttrDesc(BioPAXClassDesc, String, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>, Vector<BioPAXAttrDesc.CMethod>) - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringListAttrDesc

BioPAXSyncNetworks - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXSyncNetworks() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.BioPAXSyncNetworks

BioPAXSyncNetworksDialog - Class in fr.curie.BiNoM.cytoscape.biopax

BioPAXToCytoscapeConverter - Class in fr.curie.BiNoM.pathways

Converts BioPAX (represented by BioPAX object) to XGMML (represented by GraphDocument object)

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

BioPAXToCytoscapeConverter.Graph - Class in fr.curie.BiNoM.pathways

Little auxillary container for BioPAX and GraphDocument object

BioPAXToCytoscapeConverter.Option - Class in fr.curie.BiNoM.pathways

Set of conversion options

BioPAXToCytoscapeConverter.Option() - Constructor for class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option

BioPAXToggleNamingService - Class in fr.curie.BiNoM.cytoscape.biopax.propedit

BioPAXToggleNamingService() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXToggleNamingService

BioPAXToSBMLConverter - Class in fr.curie.BiNoM.pathways

Converts BioPAX (represented by BioPAX object) to SBML (represented by org.sbml.x2001.ns.celldesigner.SbmlDocument object)

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

BioPAXToSBMLConverter.BioPAXSpecies - Class in fr.curie.BiNoM.pathways

Represents BioPAX physicalEntityParticipants grouped into distinctive chemical species (entity, characterized by a definite location and a definite modification).

BioPAXToSBMLConverter.BioPAXSpecies() - Constructor for class fr.curie.BiNoM.pathways.BioPAXToSBMLConverter.BioPAXSpecies

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

Set of utilities for manipulating com.hp.hpl.jena.rdf.model.Model objects

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

BioPAXViewQueryLog - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXViewQueryLog() - Constructor for class fr.curie.BiNoM.cytoscape.biopax.query.BioPAXViewQueryLog

BioPAXViewQueryLogDialog - Class in fr.curie.BiNoM.cytoscape.biopax.query

BioPAXVisualStyleDefinition - Class in fr.curie.BiNoM.cytoscape.biopax

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

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

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

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

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

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

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

Was supposed to deal with Bi-partite graphs specifically but has not been used yet

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

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

BioPAX Naming service used for conversion

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

BioPAXToSBML Converter is needed to created the Reaction Network part of the index