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

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main(String[]) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils

main(String[]) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.Graph

main(String[]) - Static method in class fr.curie.BiNoM.pathways.analysis.structure.Skeleton

main(String[]) - Static method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies

main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.BioPAX2Cytoscape

main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.BioPAX2SBML

main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.CellDesigner2BioPAX

main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.CellDesigner2Cytoscape

main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.Cytoscape2BioPAX

main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.Cytoscape2CellDesigner

main(String[]) - Static method in class fr.curie.BiNoM.pathways.converters.Transpath2BioPAX

main(String[]) - Static method in class fr.curie.BiNoM.pathways.CytoscapeToCellDesignerConverter

main(String[]) - Static method in class fr.curie.BiNoM.pathways.parseBioPAX

main(String[]) - Static method in class fr.curie.BiNoM.pathways.parseCellDesigner

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.analyzeSBMLFile

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.examples.BioPAXConnectedComponents

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.examples.BioPAXPathAnalysis

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.examples.BioPAXStandardQuery

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.examples.CDesigner2BioPAX

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.ProduceClickableMap

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.test

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.test1

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestAutomaticStructureAnalysis

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioBasePathway

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestBioPAX

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAX1

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAXExtract

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAXMerge

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testBioPAXQueryEngine

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testCellDesigner

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testEwingNetwork

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testExtractBioPAX

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testGraphMappingService

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testJastor

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testJavolution

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.TestModuleDecomposition

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testNamingService

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testRBpathway

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testSAX

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testStructureAnalysis

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.testTranspath

main(String[]) - Static method in class fr.curie.BiNoM.pathways.test.workMatlabOvidiu

main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.analyseInstallSpyLog

main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.insertMassActionLaws

main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.LaplaceMatToSif

main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.PowerfulTokenizer

main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.prepareCellDesignerFile

main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.SimpleTable

main(String[]) - Static method in class fr.curie.BiNoM.pathways.utils.XGMMLExport

main(String[]) - Static method in class fr.curie.BiNoM.pathways.wrappers.SBML

main(String[]) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML

mainfile - Variable in class fr.curie.BiNoM.pathways.utils.BioPAXMerge

The base BioPAX com.hp.hpl.jena.rdf.model.Model object

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

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

makeClassesDesc(BioPAX) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassDescFactory

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

makeCompartments() - Method in class fr.curie.BiNoM.pathways.wrappers.BioPAX

Adds some standard compartments

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

makeCopy() - Method in class fr.curie.BiNoM.pathways.analysis.structure.Node

Clones the node

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

Clones the source Model

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

Add an edge from edgeId.Target to edgeId.Source.

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

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

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

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

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

makeEditPanelPerform(BioPAXAttrDesc, Vector<BioPAXClassDesc>, BioPAXObject, Object, int, Component) - Static method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc

makeEditPanelPerform(BioPAXAttrDesc, BioPAXObject, Object, int, Component) - Static method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringAttrDesc

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

Fills all maps for needed conversion

makeReactionNotes(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.utils.prepareCellDesignerFile

makeRootPathwayNode - Variable in class fr.curie.BiNoM.pathways.BioPAXToCytoscapeConverter.Option

map() - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMapper

The mapping implementation

mapBioPAXToGraph(BioPAX) - Method in class fr.curie.BiNoM.pathways.utils.BioPAXGraphMappingService

Creates BioPAX index as XGMML file from BioPAX object

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

MapEntitiesId(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

mapSignOfConservationCoeffs - Static variable in class fr.curie.BiNoM.pathways.analysis.structure.BiographUtils

MapSpeciesAliases(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

MapSpeciesId(SbmlDocument) - Static method in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

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

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

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

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

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

Merges two CellDesigner SbmlDocuments, the result of merging is in sbout

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

Merging of the base file with reference files.

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

MLLabel - Class in fr.curie.BiNoM.cytoscape.lib

MLLabel() - Constructor for class fr.curie.BiNoM.cytoscape.lib.MLLabel

MLLabel(String) - Constructor for class fr.curie.BiNoM.cytoscape.lib.MLLabel

MLLabel(int) - Constructor for class fr.curie.BiNoM.cytoscape.lib.MLLabel

MLLabel(String, int) - Constructor for class fr.curie.BiNoM.cytoscape.lib.MLLabel

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

BioPAX OWL as com.hp.hpl.jena.rdf.Model

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

not yet used

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

not yet used

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

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

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

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

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

ModularViewTask(GraphDocument, Vector<GraphDocument>, boolean, boolean, VisualStyle) - Constructor for class fr.curie.BiNoM.cytoscape.analysis.ModularViewTask

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

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

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

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

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

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

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

Called when MOLECULAR_DASH_WEIGHT has changed

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

The Jena Property for MOLECULAR_DASH_WEIGHT

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

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

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

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

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

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

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

mouseClicked(MouseEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassTreeFrame

mouseClicked(MouseEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserPanel

mouseEntered(MouseEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassTreeFrame

mouseEntered(MouseEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserPanel

mouseExited(MouseEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassTreeFrame

mouseExited(MouseEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserPanel

mousePressed(MouseEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassTreeFrame

mousePressed(MouseEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserPanel

mouseReleased(MouseEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXClassTreeFrame

mouseReleased(MouseEvent) - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXPropertyBrowserPanel