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

T

takenaliases - Static variable in class fr.curie.BiNoM.pathways.CellDesignerToCytoscapeConverter

Map from a key in the form reaction_id+"_"+species_alias_id to ReactionDocument.Reaction object

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

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

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

Called when TAXON_DASH_XREF has changed

TAXON_DASH_XREFProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.bioSource

The Jena Property for TAXON_DASH_XREF

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

Called when a value of TEMPERATURE has been added

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

Called when a value of TEMPERATURE has been added

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

The Jena Property for TEMPERATURE

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

The Jena Property for TEMPERATURE

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

Called when a value of TEMPERATURE has been removed

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

Called when a value of TEMPERATURE has been removed

TERMAdded(openControlledVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabularyListener

Called when a value of TERM has been added

TERMProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

The Jena Property for TERM

TERMRemoved(openControlledVocabulary, String) - Method in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabularyListener

Called when a value of TERM has been removed

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

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

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

test1 - Class in fr.curie.BiNoM.pathways.test

test1() - Constructor for class fr.curie.BiNoM.pathways.test.test1

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

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

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

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

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

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

testBioPAX1 - Class in fr.curie.BiNoM.pathways.test

testBioPAX1() - Constructor for class fr.curie.BiNoM.pathways.test.testBioPAX1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

TestNetworkOP - Class in fr.curie.BiNoM.cytoscape.netwop

TestNetworkOP(String) - Constructor for class fr.curie.BiNoM.cytoscape.netwop.TestNetworkOP

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

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

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

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

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

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

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

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

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

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

Called when TISSUE has changed

TISSUEProperty - Static variable in interface fr.curie.BiNoM.pathways.biopax.bioSource

The Jena Property for TISSUE

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

TITLEChanged(publicationXref) - Method in interface fr.curie.BiNoM.pathways.biopax.publicationXrefListener

Called when TITLE has changed

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

The Jena Property for TITLE

toId(String) - Static method in class fr.curie.BiNoM.cytoscape.lib.NetworkFactory

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

toString() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleAttrDesc

toString() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXDoubleListAttrDesc

toString() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerAttrDesc

toString() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXIntegerListAttrDesc

toString() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectAttrDesc

toString() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXObjectListAttrDesc

toString() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringAttrDesc

toString() - Method in class fr.curie.BiNoM.cytoscape.biopax.propedit.BioPAXStringListAttrDesc

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

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

Experimental converter from Transpath to BioPAX

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

Transpath2BioPAX - Class in fr.curie.BiNoM.pathways.converters

Transpath2BioPAX() - Constructor for class fr.curie.BiNoM.pathways.converters.Transpath2BioPAX

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

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

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

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

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

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

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

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

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

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

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

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

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

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.biochemicalReaction

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.bioSource

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.catalysis

The rdf:type for this ontology class

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

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.complex

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.complexAssembly

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.confidence

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.control

The rdf:type for this ontology class

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

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.dataSource

The rdf:type for this ontology class

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

The rdf:type for this ontology class

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

The rdf:type for this ontology class

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

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.evidence

The rdf:type for this ontology class

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

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.externalReferenceUtilityClass

The rdf:type for this ontology class

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

The rdf:type for this ontology class

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

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.modulation

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.openControlledVocabulary

The rdf:type for this ontology class

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

The rdf:type for this ontology class

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

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.physicalEntity

The rdf:type for this ontology class

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

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.physicalInteraction

The rdf:type for this ontology class

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

The rdf:type for this ontology class

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

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.relationshipXref

The rdf:type for this ontology class

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

The rdf:type for this ontology class

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

The rdf:type for this ontology class

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

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.sequenceLocation

The rdf:type for this ontology class

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

The rdf:type for this ontology class

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

The rdf:type for this ontology class

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

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.transport

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReaction

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.unificationXref

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.utilityClass

The rdf:type for this ontology class

TYPE - Static variable in interface fr.curie.BiNoM.pathways.biopax.xref

The rdf:type for this ontology class

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

Type of BioPAX object linked to the species (protein, complex, dna)

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