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

L

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

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

lastUsedMemory - Static variable in class fr.curie.BiNoM.pathways.utils.Utils

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

Called when a value of LEFT has been added

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

Called when a value of LEFT has been added

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

Called when a value of LEFT has been added

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

Called when a value of LEFT has been added

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

Called when a value of LEFT has been added

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

The Jena Property for LEFT

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

Called when a value of LEFT has been removed

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

Called when a value of LEFT has been removed

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

Called when a value of LEFT has been removed

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

Called when a value of LEFT has been removed

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

Called when a value of LEFT has been removed

link - Variable in class fr.curie.BiNoM.pathways.analysis.structure.Node

Some object associated.

LIST_COMPLEXES - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

Simply lists the proteins from the input to the query log

LIST_GENES - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

Simply lists the dnas from the input to the query log

LIST_PROTEINS - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

Simply lists the proteins from the input to the query log

LIST_PUBLICATIONS - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

Simply lists the publications from the input to the query log

LIST_REACTIONS - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

Simply lists the reactions from the input to the query log

LIST_SMALL_MOLECULES - Static variable in class fr.curie.BiNoM.pathways.utils.BioPAXGraphQuery

Simply lists the smallMolecules from the input to the query log

listCompatibleInterfaces(Resource) - Static method in class fr.curie.BiNoM.pathways.biopax.biopax_DASH_level2_DOT_owlFactory

Return a list of compatible interfaces for the given type.

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.biochemicalReactionImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.bioSourceImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.catalysisImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.chemicalStructureImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.complexAssemblyImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.complexImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.confidenceImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.controlImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.conversionImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.dataSourceImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.deltaGprimeOImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.dnaImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.entityImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.evidenceImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.experimentalFormImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.externalReferenceUtilityClassImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.interactionImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.kPrimeImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.modulationImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.openControlledVocabularyImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.pathwayStepImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.physicalEntityParticipantImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.physicalInteractionImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.proteinImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.publicationXrefImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.relationshipXrefImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.rnaImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceFeatureImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceIntervalImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceLocationImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceParticipantImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.sequenceSiteImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.smallMoleculeImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.transportImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.transportWithBiochemicalReactionImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.unificationXrefImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.utilityClassImpl

listStatements() - Method in class fr.curie.BiNoM.pathways.biopax.xrefImpl

loadAttribTable(String) - Method in class fr.curie.BiNoM.pathways.CellDesignerColorSpecies

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

Loads BioPAX content from file fn

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

Loads BioPAX content from InputStream is

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

Loads BioPAX content from String

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

loadCellDesigner(String) - Static method in class fr.curie.BiNoM.pathways.wrappers.CellDesigner

Loads org.sbml.x2001.ns.celldesigner.SbmlDocument from file

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

LoadFromSimpleDatFile(String, boolean, String) - Method in class fr.curie.BiNoM.pathways.utils.SimpleTable

Loads the table from the file.

loadFromXMGML(String) - Static method in class fr.curie.BiNoM.pathways.utils.XGMMLExport

loadFromXMGML(String) - Static method in class fr.curie.BiNoM.pathways.wrappers.XGMML

Loads XGMML from file

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

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

Load the OWL model from file

loadSBML(String) - Static method in class fr.curie.BiNoM.pathways.wrappers.SBML

Loads SbmlDocument from file

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

Load a text file into memory and returns String

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

Converts InputStream into String

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

Loads tab delimited two-columns table \t