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

F

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

FEATURE_DASH_LOCATIONAdded(sequenceFeature, sequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeatureListener

Called when a value of FEATURE_DASH_LOCATION has been added

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

The Jena Property for FEATURE_DASH_LOCATION

FEATURE_DASH_LOCATIONRemoved(sequenceFeature, sequenceLocation) - Method in interface fr.curie.BiNoM.pathways.biopax.sequenceFeatureListener

Called when a value of FEATURE_DASH_LOCATION has been removed

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

Called when FEATURE_DASH_TYPE has changed

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

The Jena Property for FEATURE_DASH_TYPE

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

fieldNumByName(String) - Method in class fr.curie.BiNoM.pathways.utils.SimpleTable

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

Name of CellDesigner file

filterIDs(BioPAX, GraphDocument) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter

filterIDs(BioPAX, Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter

filterIDs(SbmlDocument, GraphDocument) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter

filterIDs(SbmlDocument, Vector, Vector, Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter

filterIDsCompleteReactions(SbmlDocument, Vector, Vector, Vector, Vector) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter

filterPathwaySteps(BioPAX, HashMap, HashMap, HashMap) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToBioPAXConverter

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

Finds all CellDesigner species aliases

findAllMembers(String, Vector) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork

FindAllPaths(Graph, Node, Set<Node>, boolean, double) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.GraphAlgorithms

Note: searchRadius here is the number of edges from source (edge weights are not considered)

findAllPlacesInCellDesigner() - Method in class fr.curie.BiNoM.pathways.test.ProduceClickableMap

findBioPAXSpeciesAndReactions(Vector, Vector) - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExport

findBioPAXSpeciesAndReactions(Vector, Vector) - Static method in class fr.curie.BiNoM.cytoscape.biopax.BioPAXExportTask

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

Procedure of groupping physicalEntityParticipants into BioPAXSpecies (chemical species)

findPaths(GraphDocument, Vector<String>, Vector<String>, StructureAnalysisUtils.Option) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils

findPaths(Graph, Vector<String>, Vector<String>, StructureAnalysisUtils.Option) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.StructureAnalysisUtils

findSBMLSpeciesAndReactions(SbmlDocument, Vector, Vector, Vector, Vector) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExport

findSBMLSpeciesAndReactions(SbmlDocument, Vector, Vector, Vector, Vector) - Static method in class fr.curie.BiNoM.cytoscape.celldesigner.CellDesignerExportTask

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

fr.curie.BiNoM.cytoscape.analysis - package fr.curie.BiNoM.cytoscape.analysis

Cytoscape interface to BiNoM structural network analysis methods

fr.curie.BiNoM.cytoscape.biopax - package fr.curie.BiNoM.cytoscape.biopax

Cytoscape interface for working with BioPAX files

fr.curie.BiNoM.cytoscape.biopax.propedit - package fr.curie.BiNoM.cytoscape.biopax.propedit

BiNoM property editor implementation

fr.curie.BiNoM.cytoscape.biopax.query - package fr.curie.BiNoM.cytoscape.biopax.query

Cytoscape interface to BioPAX query engine

fr.curie.BiNoM.cytoscape.celldesigner - package fr.curie.BiNoM.cytoscape.celldesigner

Cytoscape interface for working with CellDesigner files

fr.curie.BiNoM.cytoscape.lib - package fr.curie.BiNoM.cytoscape.lib

General-purpose utilities

fr.curie.BiNoM.cytoscape.netwop - package fr.curie.BiNoM.cytoscape.netwop

Network manipulations directly with Cytoscape networks

fr.curie.BiNoM.cytoscape.plugin - package fr.curie.BiNoM.cytoscape.plugin

Cytoscape plugins

fr.curie.BiNoM.cytoscape.sbml - package fr.curie.BiNoM.cytoscape.sbml

Interface for exporting reaction network to SBML

fr.curie.BiNoM.cytoscape.utils - package fr.curie.BiNoM.cytoscape.utils

BiNoM network clipboard and other utilities

fr.curie.BiNoM.pathways - package fr.curie.BiNoM.pathways

Set of converters for conversion of one systems biology format into an other.

fr.curie.BiNoM.pathways.analysis.structure - package fr.curie.BiNoM.pathways.analysis.structure

Tools for structural analysis of biological graphs

fr.curie.BiNoM.pathways.biopax - package fr.curie.BiNoM.pathways.biopax

Java mapping of BioPAX version 2 (generated by Jastor)

fr.curie.BiNoM.pathways.converters - package fr.curie.BiNoM.pathways.converters

Little scripts for command-line file conversion

fr.curie.BiNoM.pathways.test - package fr.curie.BiNoM.pathways.test

Diverse scripts (used internally, but you can find some examples of use there)

fr.curie.BiNoM.pathways.test.examples - package fr.curie.BiNoM.pathways.test.examples

Source code of some examples of using BiNoM as a library independently from Cytoscape

fr.curie.BiNoM.pathways.utils - package fr.curie.BiNoM.pathways.utils

Utility classes

fr.curie.BiNoM.pathways.wrappers - package fr.curie.BiNoM.pathways.wrappers

Auxilary containers representing different systems biology formats

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

Mode of conversion: from BioPAX to full index (see BiNoM documentation)