Index (singa-simulation 0.2.3 API)

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

A

AbstractNeighbourDependentModule - Class in de.bioforscher.singa.simulation.modules.model
AbstractNeighbourDependentModule(Simulation) - Constructor for class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
AbstractNeighbourIndependentModule - Class in de.bioforscher.singa.simulation.modules.model
AbstractNeighbourIndependentModule() - Constructor for class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
AbstractNeighbourIndependentModule(Simulation) - Constructor for class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
AbstractSectionSpecificModule - Class in de.bioforscher.singa.simulation.modules.model
AbstractSectionSpecificModule() - Constructor for class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
AbstractSectionSpecificModule(Simulation) - Constructor for class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.AdditionExpressionNode: Implementation of the visitor design pattern.
accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.ConstantExpressionNode: Implementation of the visitor design pattern.
accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.ExponentiationExpressionNode: Implementation of the visitor design pattern.
accept(ExpressionNodeVisitor) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNode: Method needed for the visitor design pattern
accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.FunctionExpressionNode: Implementation of the visitor design pattern.
accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode: Implementation of the visitor design pattern.
accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode: Implementation of the visitor design pattern.
acceptValue(String, double) - Method in class de.bioforscher.singa.simulation.model.rules.AppliedExpression
add(ExpressionNode, boolean) - Method in class uk.co.cogitolearning.cogpar.SequenceExpressionNode: Add another term to the sequence
add(String, int) - Method in class uk.co.cogitolearning.cogpar.Tokenizer: Add a regular expression and a token id to the internal list of recognized tokens
addCellSection(CellSection) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph: Adds a cell section to this graph but does not associate any node to it.
addDelta(Delta) - Method in class de.bioforscher.singa.simulation.model.concentrations.DeltaContainer: Adds a delta to the container.
addDeltaFunction(Function<ConcentrationContainer, Delta>) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
addDeltaFunction(Function<ConcentrationContainer, Delta>, Predicate<ConcentrationContainer>) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
addDeltaFunction(Function<ConcentrationContainer, List<Delta>>, Predicate<ConcentrationContainer>) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
addEdgeBetween(int, AutomatonNode, AutomatonNode) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
addEdgeBetween(AutomatonNode, AutomatonNode) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
ADDITION_NODE - Static variable in interface uk.co.cogitolearning.cogpar.ExpressionNode: Node id for addition nodes
AdditionExpressionNode - Class in uk.co.cogitolearning.cogpar: An ExpressionNode that handles additions and subtractions.
AdditionExpressionNode(ExpressionNode, boolean) - Constructor for class uk.co.cogitolearning.cogpar.AdditionExpressionNode: Constructor to create an addition with the first term already added.
addNode(AutomatonNode) - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection: Adds a node to the section, without altering the state of the node.
addNodesToCompartment(EnclosedCompartment, Rectangle) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph: Adds nodes in a rectangular region to the cell section.
addNodeToObserve(AutomatonNode) - Method in class de.bioforscher.singa.simulation.events.EpochUpdateWriter
addPotentialDelta(Delta) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Adds a potential delta to this node.
addPotentialDeltas(List<Delta>) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Adds a list of potential deltas to this node.
AppliedExpression - Class in de.bioforscher.singa.simulation.model.rules
AppliedExpression(String, Unit<?>) - Constructor for class de.bioforscher.singa.simulation.model.rules.AppliedExpression
AppliedScale - Class in de.bioforscher.singa.simulation.features.scale
AppliedScale(Double, FeatureOrigin) - Constructor for class de.bioforscher.singa.simulation.features.scale.AppliedScale
AppliedScale() - Constructor for class de.bioforscher.singa.simulation.features.scale.AppliedScale
applyAlways() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
applyAlways() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
applyAlways() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
applyAssignmentRules() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Apply all referenced assignment rules.
applyDeltas() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Applies all final deltas and clears the delta list.
applyRule(AutomatonNode) - Method in class de.bioforscher.singa.simulation.model.rules.AssignmentRule
AssignmentRule - Class in de.bioforscher.singa.simulation.model.rules
AssignmentRule(ChemicalEntity<?>, AppliedExpression) - Constructor for class de.bioforscher.singa.simulation.model.rules.AssignmentRule
AssignmentRules - Class in de.bioforscher.singa.simulation.model.rules
AutomatonEdge - Class in de.bioforscher.singa.simulation.model.graphs
AutomatonEdge(int) - Constructor for class de.bioforscher.singa.simulation.model.graphs.AutomatonEdge
AutomatonGraph - Class in de.bioforscher.singa.simulation.model.graphs: The Automaton graph class is the underlying graph of cellular graph automaton Simulations.
AutomatonGraph() - Constructor for class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph: Creates a new empty graph.
AutomatonGraph(int, int) - Constructor for class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph: Creates a new empty graph, initialized with node and edge capacity.
AutomatonGraphs - Class in de.bioforscher.singa.simulation.model.graphs
AutomatonNode - Class in de.bioforscher.singa.simulation.model.graphs: A node of the AutomatonGraph.
AutomatonNode(int) - Constructor for class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Creates a new plain automaton node.
availableFeatures - Variable in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction

B

BIOMODELS_FETCH_URL - Static variable in class de.bioforscher.singa.simulation.parser.sbml.BioModelsParserService
BioModelsParserService - Class in de.bioforscher.singa.simulation.parser.sbml
BioModelsParserService() - Constructor for class de.bioforscher.singa.simulation.parser.sbml.BioModelsParserService

C

calculateDeltas(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
calculateVelocity(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicKineticLaw
calculateVelocity(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
calculateVelocity(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.EquilibriumReaction
calculateVelocity(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.MichaelisMentenReaction
calculateVelocity(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.NthOrderReaction
calculateVelocity(ConcentrationContainer) - Method in interface de.bioforscher.singa.simulation.modules.reactions.model.KineticLaw
calculateVelocity(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
CatalyticReactant - Class in de.bioforscher.singa.simulation.modules.reactions.model: CatalyticReactants are Reactants that are not consumed or produced during Reactions, but influence its velocity (reaction rate).
CatalyticReactant(ChemicalEntity, ReactantRole) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.model.CatalyticReactant
CellSection - Class in de.bioforscher.singa.simulation.model.compartments: A CellSection is everything that can be considered a part of the cell.
CellSection(String, String) - Constructor for class de.bioforscher.singa.simulation.model.compartments.CellSection: Creates a new CellSection with the given identifier and name.
characters(char[], int, int) - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
clear() - Method in class de.bioforscher.singa.simulation.model.concentrations.DeltaContainer: Removes all deltas from this container.
clearPotentialDeltas() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Clears the list of potential deltas.
CLOSE_BRACKET - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for closing brackets
CompartmentHandler - Class in de.bioforscher.singa.simulation.parser.sbml.converter
CompartmentHandler() - Constructor for class de.bioforscher.singa.simulation.parser.sbml.converter.CompartmentHandler
ConcentrationContainer - Interface in de.bioforscher.singa.simulation.model.concentrations: Concentration containers are used to manage the concentration inside of a node.
CONSTANT_NODE - Static variable in interface uk.co.cogitolearning.cogpar.ExpressionNode: Node id for constant nodes
ConstantExpressionNode - Class in uk.co.cogitolearning.cogpar: An ExpressionNode that stores a constant value
ConstantExpressionNode(double) - Constructor for class uk.co.cogitolearning.cogpar.ConstantExpressionNode: Construct with the fixed value.
ConstantExpressionNode(String) - Constructor for class uk.co.cogitolearning.cogpar.ConstantExpressionNode: Convenience constructor that takes a string and converts it to a double before storing the value.
convertAssignmentRule(AssignmentRule) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLAssignmentRuleConverter
convertKineticLaw(KineticLaw) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLKineticLawConverter
convertLocalParameter(LocalParameter) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLParameterConverter
convertRawExpression(ASTNode, ListOf<LocalParameter>, Unit<?>) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLExpressionConverter
convertRawExpression(ASTNode, Unit<?>) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLExpressionConverter
convertReaction(Reaction) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLReactionConverter
convertReactions(ListOf<Reaction>) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLReactionConverter
convertSimulationParameter(Parameter) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLParameterConverter
convertSimulationParameters(ListOf<Parameter>) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLParameterConverter
convertUnit(UnitDefinition) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLUnitConverter
convertUnits(ListOf<UnitDefinition>) - Method in class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLUnitConverter
createCompartmentTestEnvironment() - Static method in class de.bioforscher.singa.simulation.modules.model.SimulationExamples
createDecompositionReactionExample() - Static method in class de.bioforscher.singa.simulation.modules.model.SimulationExamples: This simulation simulates the thermal decomposition of dinitrogen pentaoxide.
createDiffusionAndMembraneTransportExample() - Static method in class de.bioforscher.singa.simulation.modules.model.SimulationExamples
createDiffusionModuleExample(int, Quantity<Time>) - Static method in class de.bioforscher.singa.simulation.modules.model.SimulationExamples: This simulation simulates a diffusion of small molecules in a rectangular gird graph.
createEquilibriumReactionExample() - Static method in class de.bioforscher.singa.simulation.modules.model.SimulationExamples: This simulation simulates a equilibrium reaction.
createIodineMultiReactionExample() - Static method in class de.bioforscher.singa.simulation.modules.model.SimulationExamples: This simulation simulates a multiple reactions involving iodine.
createMichaelisMentenReactionExample() - Static method in class de.bioforscher.singa.simulation.modules.model.SimulationExamples: This simulation simulates a MichaelisMentenReaction, where D-Fructose 1-phosphate is convertet to glycerone phosphate and D-glyceraldehyde using fructose bisphosphate aldolase.
createPassiveMembraneTransportExample() - Static method in class de.bioforscher.singa.simulation.modules.model.SimulationExamples
createRectangularAutomatonGraph(int, int) - Static method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraphs
createSimulationFromSBML() - Static method in class de.bioforscher.singa.simulation.modules.model.SimulationExamples
createSynthesisReactionExample() - Static method in class de.bioforscher.singa.simulation.modules.model.SimulationExamples: This simulation simulates the synthesis of 1,3,5-octatriene (C8H12) from Buta-1,3-diene (C4H6).

D

de.bioforscher.singa.simulation.events - package de.bioforscher.singa.simulation.events
de.bioforscher.singa.simulation.features.permeability - package de.bioforscher.singa.simulation.features.permeability
de.bioforscher.singa.simulation.features.scale - package de.bioforscher.singa.simulation.features.scale
de.bioforscher.singa.simulation.model.compartments - package de.bioforscher.singa.simulation.model.compartments
de.bioforscher.singa.simulation.model.concentrations - package de.bioforscher.singa.simulation.model.concentrations
de.bioforscher.singa.simulation.model.graphs - package de.bioforscher.singa.simulation.model.graphs
de.bioforscher.singa.simulation.model.parameters - package de.bioforscher.singa.simulation.model.parameters
de.bioforscher.singa.simulation.model.rules - package de.bioforscher.singa.simulation.model.rules
de.bioforscher.singa.simulation.modules.model - package de.bioforscher.singa.simulation.modules.model
de.bioforscher.singa.simulation.modules.reactions.implementations - package de.bioforscher.singa.simulation.modules.reactions.implementations
de.bioforscher.singa.simulation.modules.reactions.model - package de.bioforscher.singa.simulation.modules.reactions.model
de.bioforscher.singa.simulation.modules.transport - package de.bioforscher.singa.simulation.modules.transport
de.bioforscher.singa.simulation.parser.graphs - package de.bioforscher.singa.simulation.parser.graphs
de.bioforscher.singa.simulation.parser.sbml - package de.bioforscher.singa.simulation.parser.sbml
de.bioforscher.singa.simulation.parser.sbml.converter - package de.bioforscher.singa.simulation.parser.sbml.converter
decreaseTimeStep() - Method in class de.bioforscher.singa.simulation.modules.model.TimeStepHarmonizer
Delta - Class in de.bioforscher.singa.simulation.model.concentrations: The delta object signifies the change that will be applied to the concentration of a specific ChemicalEntity in a specific CellSection.
Delta(CellSection, ChemicalEntity, Quantity<MolarConcentration>) - Constructor for class de.bioforscher.singa.simulation.model.concentrations.Delta: Creates a new delta for a specific ChemicalEntity in a specific CellSection.
DeltaContainer - Class in de.bioforscher.singa.simulation.model.concentrations: The container for the final Deltas that are applied to a AutomatonNode.
DeltaContainer() - Constructor for class de.bioforscher.singa.simulation.model.concentrations.DeltaContainer: Creates a new empty delta container.
determineAllDeltas() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
determineAllDeltas() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
determineAllDeltas() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
determineAllDeltas() - Method in interface de.bioforscher.singa.simulation.modules.model.Module
determineConcentration(ConcentrationContainer, ReactantRole) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction: Determines the concentration of reactants that influence the velocity of the reaction.
determineDeltas(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
determineDeltas(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
determineDeltasForNode(AutomatonNode) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
determineDeltasForNode(AutomatonNode) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
determineDeltasForNode(AutomatonNode) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
determineDeltasForNode(AutomatonNode) - Method in interface de.bioforscher.singa.simulation.modules.model.Module
determineFullDeltas(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
DynamicKineticLaw - Class in de.bioforscher.singa.simulation.modules.reactions.implementations
DynamicKineticLaw(AppliedExpression) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicKineticLaw
DynamicReaction - Class in de.bioforscher.singa.simulation.modules.reactions.implementations
DynamicReaction(Simulation, DynamicKineticLaw) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
DynamicReaction(DynamicKineticLaw) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction

E

emitNextEpochEvent(AutomatonNode) - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Emits the NodeUpdatedEvent to all listeners.
EnclosedCompartment - Class in de.bioforscher.singa.simulation.model.compartments: An EnclosedCompartment is a CellSection that is bordered or enclosed by a Membrane.
EnclosedCompartment(String, String) - Constructor for class de.bioforscher.singa.simulation.model.compartments.EnclosedCompartment: Creates a new EnclosedCompartment with the given identifier and name.
endDocument() - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
endElement(String, String, String) - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
endPrefixMapping(String) - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
EpochUpdateWriter - Class in de.bioforscher.singa.simulation.events: This class can be used to write the concentrations of a node to a file while simulating.
EpochUpdateWriter(Path, Path, Set<ChemicalEntity<?>>) - Constructor for class de.bioforscher.singa.simulation.events.EpochUpdateWriter
EpochUpdateWriter(Path, Path, Set<ChemicalEntity<?>>, boolean) - Constructor for class de.bioforscher.singa.simulation.events.EpochUpdateWriter
EPSILON - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for the epsilon terminal
equals(Object) - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection
EquilibriumReaction - Class in de.bioforscher.singa.simulation.modules.reactions.implementations
EquilibriumReaction(Simulation, Quantity<Frequency>, Quantity<Frequency>) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.EquilibriumReaction
evaluate() - Method in class de.bioforscher.singa.simulation.model.rules.AppliedExpression
EvaluationException - Exception in uk.co.cogitolearning.cogpar: A simple subclass of RuntimeException that indicates errors when trying to evaluate an expression.
EvaluationException(String) - Constructor for exception uk.co.cogitolearning.cogpar.EvaluationException: Construct the evaluation exception with a message.
EXPONENTIATION_NODE - Static variable in interface uk.co.cogitolearning.cogpar.ExpressionNode: Node id for exponentiation nodes
ExponentiationExpressionNode - Class in uk.co.cogitolearning.cogpar: An ExpressionNode that handles exponentiation.
ExponentiationExpressionNode(ExpressionNode, ExpressionNode) - Constructor for class uk.co.cogitolearning.cogpar.ExponentiationExpressionNode: Construct the ExponentiationExpressionNode with base and exponent
exportGraph(AutomatonGraph, File) - Static method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLExportService: Exports a Graph to a GraphML file.
expression - Variable in class uk.co.cogitolearning.cogpar.SequenceExpressionNode.Term: the expression node
ExpressionNode - Interface in uk.co.cogitolearning.cogpar: An interface for expression nodes.
ExpressionNodeVisitor - Interface in uk.co.cogitolearning.cogpar: An interface for the visitor design pattern.

F

forCompartment(EnclosedCompartment) - Static method in class de.bioforscher.singa.simulation.model.compartments.Membrane
FreeDiffusion - Class in de.bioforscher.singa.simulation.modules.transport: Diffusion is the net movement of molecules or atoms from a region of high concentration to a region of low concentration.
FreeDiffusion(Simulation) - Constructor for class de.bioforscher.singa.simulation.modules.transport.FreeDiffusion
FUNCTION - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for function names
FUNCTION_NODE - Static variable in interface uk.co.cogitolearning.cogpar.ExpressionNode: Node id for function nodes
FunctionExpressionNode - Class in uk.co.cogitolearning.cogpar: An ExpressionNode that handles mathematical functions.
FunctionReference - Class in de.bioforscher.singa.simulation.parser.sbml
FunctionReference(String, String, List<String>) - Constructor for class de.bioforscher.singa.simulation.parser.sbml.FunctionReference
FunctionReference(String, String) - Constructor for class de.bioforscher.singa.simulation.parser.sbml.FunctionReference

G

generateMapOfEntities(AutomatonGraph) - Static method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraphs: Creates and returns a map that contains all chemical entities that are present in the given graph as values and with the name of the entity as key.
generateMembrane() - Method in class de.bioforscher.singa.simulation.model.compartments.EnclosedCompartment: Tries to generate a Membrane around the contents of this compartment.
getAllConcentrations() - Method in interface de.bioforscher.singa.simulation.model.concentrations.ConcentrationContainer: Returns the representative concentrations of all referenced chemical entities.
getAllConcentrations() - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getAllConcentrations() - Method in class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
getAllConcentrations() - Method in class de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer
getAllConcentrations() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Returns all concentrations of all chemical entities.
getAllConcentrationsForSection(CellSection) - Method in interface de.bioforscher.singa.simulation.model.concentrations.ConcentrationContainer: Returns all concentrations for a particular CellSection.
getAllConcentrationsForSection(CellSection) - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getAllConcentrationsForSection(CellSection) - Method in class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
getAllConcentrationsForSection(CellSection) - Method in class de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer
getAllConcentrationsForSection(CellSection) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Returns all concentrations of all chemical entities in the given cell section.
getAllReferencedEntities() - Method in interface de.bioforscher.singa.simulation.model.concentrations.ConcentrationContainer: Returns all ChemicalEntities that are referenced in this container.
getAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
getAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer
getAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Returns all chemical entities referenced in this node.
getAllReferencedSections() - Method in interface de.bioforscher.singa.simulation.model.concentrations.ConcentrationContainer: Returns all Compartments that are referenced in this container.
getAllReferencedSections() - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getAllReferencedSections() - Method in class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
getAllReferencedSections() - Method in class de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer
getAllReferencedSections() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Returns all referenced sections in this node.
getAnnotations() - Method in class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
getAppliedScale() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicKineticLaw
getAssignmentRules() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Returns the assignment rules.
getAssignmentRules() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getAvailableConcentration(CellSection, ChemicalEntity) - Method in interface de.bioforscher.singa.simulation.model.concentrations.ConcentrationContainer: Returns the concentration of the specified ChemicalEntity available in the CellSection.
getAvailableConcentration(CellSection, ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getAvailableConcentration(CellSection, ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
getAvailableConcentration(CellSection, ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer
getAvailableConcentration(ChemicalEntity, CellSection) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Returns the concentration of the given chemical entity in the given compartment.
getAvailableFeatures() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
getCatalyticReactants() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
getCellSection() - Method in class de.bioforscher.singa.simulation.model.concentrations.Delta: Returns the cell section.
getCellSection(String) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph: Return the cell section with the given identifier.
getCellSection() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Returns the primary cell section of this node (Membrane nodes may belong to multiple sections).
getCellSections() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph: Returns all CellSections referenced in this graph.
getChemicalEntities() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Returns the chemical entities.
getChemicalEntities() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getChemicalEntity() - Method in class de.bioforscher.singa.simulation.model.concentrations.Delta: Returns the chemical entity.
getCompartments() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getConcentration(ChemicalEntity) - Method in interface de.bioforscher.singa.simulation.model.concentrations.ConcentrationContainer: Returns the representative concentration of a chemical entity.
getConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
getConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer
getConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Gets the concentration of the given chemical entity.
getConcentrationContainer() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Returns the ConcentrationContainer used by this node.
getContent() - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection: Returns the nodes belonging to this cell section.
getCopy() - Method in interface de.bioforscher.singa.simulation.model.concentrations.ConcentrationContainer: Returns a copy of this concentration container.
getCopy() - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getCopy() - Method in class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
getCopy() - Method in class de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer
getCurrentCellSection() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
getCurrentCellSection() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
getCurrentCellSection() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
getCurrentCellSection() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicKineticLaw
getCurrentChemicalEntity() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
getCurrentChemicalEntity() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
getCurrentNode() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
getCurrentNode() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
getCurrentNode() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
getDeltas() - Method in class de.bioforscher.singa.simulation.model.concentrations.DeltaContainer: Returns all deltas.
getDeltas() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Returns all deltas that are going to be applied to this node.
getDisplayString() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
getElapsedTime() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Returns the elapsed time after the deltas of the current epoch are applied.
getEnclosingMembrane() - Method in class de.bioforscher.singa.simulation.model.compartments.EnclosedCompartment
getEntity() - Method in class de.bioforscher.singa.simulation.modules.model.LocalError
getEntity() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactant: Gets the entity representing this reactant.
getEntityReference() - Method in class de.bioforscher.singa.simulation.model.rules.AssignmentRule
getEntityReference() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicKineticLaw
getEpoch() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Returns the current epoch number.
getEpsilon() - Method in class de.bioforscher.singa.simulation.modules.model.TimeStepHarmonizer
getExpression() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicKineticLaw
getExpressionString() - Method in class de.bioforscher.singa.simulation.model.rules.AppliedExpression
getExpressionTokenizer() - Static method in class uk.co.cogitolearning.cogpar.Tokenizer: A static method that returns a tokenizer for mathematical expressions
getFeature(Featureable, Class<? extends ScalableFeature<FeatureContent>>) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
getFeature(ChemicalEntity<?>, Class<? extends ScalableFeature<FeatureContent>>) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
getFeature(ChemicalEntity<?>, Class<? extends ScalableFeature<FeatureContent>>) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
getFeature(Class<FeatureType>) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
getFeatures() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
getGlobalParameters() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getGraph() - Method in class de.bioforscher.singa.simulation.events.GraphUpdatedEvent
getGraph() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Returns the simulation graph.
getGraph() - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
getHalfScaledQuantity() - Method in class de.bioforscher.singa.simulation.features.permeability.MembraneEntry
getHalfScaledQuantity() - Method in class de.bioforscher.singa.simulation.features.permeability.MembraneExit
getHalfScaledQuantity() - Method in class de.bioforscher.singa.simulation.features.permeability.MembraneFlipFlop
getHalfScaledQuantity() - Method in class de.bioforscher.singa.simulation.features.scale.AppliedScale
getIdentifier() - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection: Returns the identifier of this cell section.
getIdentifier() - Method in class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
getInnerCompartment() - Method in class de.bioforscher.singa.simulation.model.compartments.Membrane
getInnerLayer() - Method in class de.bioforscher.singa.simulation.model.compartments.Membrane
getInnerLayerSection() - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getInnerMembraneLayerConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getInnerPhaseConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getInnerPhaseSection() - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getKineticLaw() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
getLargestLocalError() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
getLargestLocalError() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
getLargestLocalError() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
getLargestLocalError() - Method in interface de.bioforscher.singa.simulation.modules.model.Module
getListeners() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
getMembrane() - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getMessage() - Method in exception uk.co.cogitolearning.cogpar.ParserException: Overrides RuntimeException.getMessage to add the token information into the error message.
getModules() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Returns the modules.
getName() - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection
getName() - Method in class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
getName() - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode
getNode() - Method in class de.bioforscher.singa.simulation.events.NodeUpdatedEvent
getNode() - Method in class de.bioforscher.singa.simulation.modules.model.LocalError
getOuterLayer() - Method in class de.bioforscher.singa.simulation.model.compartments.Membrane
getOuterLayerSection() - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getOuterMembraneLayerConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getOuterPhaseConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getOuterPhaseSection() - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
getParameters() - Method in class de.bioforscher.singa.simulation.model.rules.AppliedExpression
getProducts() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
getQuantity() - Method in class de.bioforscher.singa.simulation.model.concentrations.Delta: Returns the quantity of the change.
getQuantity() - Method in class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
getReactionOrder() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
getReactions() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getRole() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactant: Gets the role of this reactant.
getScaledFeature(Class<? extends ScalableFeature<FeatureContent>>) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
getScaledQuantity() - Method in class de.bioforscher.singa.simulation.features.permeability.MembraneEntry
getScaledQuantity() - Method in class de.bioforscher.singa.simulation.features.permeability.MembraneExit
getScaledQuantity() - Method in class de.bioforscher.singa.simulation.features.permeability.MembraneFlipFlop
getScaledQuantity() - Method in class de.bioforscher.singa.simulation.features.scale.AppliedScale
getSimulation() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
getSimulation() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
getStartingConcentrations() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getState() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Returns the node state.
getStoichiometricNumber() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
getStoichiometricReactants() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction: Returns the list of reactants for this reaction.
getStrength() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.CatalyticReactant: Gets the strength of this Reactant.
getSubstrates() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
getTargetEntity() - Method in class de.bioforscher.singa.simulation.model.rules.AssignmentRule
getTime() - Method in class de.bioforscher.singa.simulation.events.NodeUpdatedEvent
getToken() - Method in exception uk.co.cogitolearning.cogpar.ParserException: Get the token.
getTokens() - Method in class uk.co.cogitolearning.cogpar.Tokenizer: Get the tokens generated in the last call to tokenize.
getType() - Method in class uk.co.cogitolearning.cogpar.AdditionExpressionNode: Returns the type of the node, in this case ExpressionNode.ADDITION_NODE
getType() - Method in class uk.co.cogitolearning.cogpar.ConstantExpressionNode: Returns the type of the node, in this case ExpressionNode.CONSTANT_NODE
getType() - Method in class uk.co.cogitolearning.cogpar.ExponentiationExpressionNode: Returns the type of the node, in this case ExpressionNode.EXPONENTIATION_NODE
getType() - Method in interface uk.co.cogitolearning.cogpar.ExpressionNode: Returns the type of the node.ExpressionNode Each class derived from ExpressionNode representing a specific role in the expression should return the type according to that role.
getType() - Method in class uk.co.cogitolearning.cogpar.FunctionExpressionNode: Returns the type of the node, in this case ExpressionNode.FUNCTION_NODE
getType() - Method in class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode: Returns the type of the node, in this case ExpressionNode.MULTIPLICATION_NODE
getType() - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode: Returns the type of the node, in this case ExpressionNode.VARIABLE_NODE
getValue() - Method in class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
getValue() - Method in class de.bioforscher.singa.simulation.modules.model.LocalError
getValue() - Method in class uk.co.cogitolearning.cogpar.AdditionExpressionNode: Returns the value of the sub-expression that is rooted at this node.
getValue() - Method in class uk.co.cogitolearning.cogpar.ConstantExpressionNode: Returns the value of the constant
getValue() - Method in class uk.co.cogitolearning.cogpar.ExponentiationExpressionNode: Returns the value of the sub-expression that is rooted at this node.
getValue() - Method in interface uk.co.cogitolearning.cogpar.ExpressionNode: Calculates and returns the value of the sub-expression represented by the node.
getValue() - Method in class uk.co.cogitolearning.cogpar.FunctionExpressionNode: Returns the value of the sub-expression that is rooted at this node.
getValue() - Method in class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode: Returns the value of the sub-expression that is rooted at this node.
getValue() - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode: Returns the value of the variable but throws an exception if the value has not been set
GraphMLContentHandler - Class in de.bioforscher.singa.simulation.parser.graphs: Currently supports parsing nodes and connecting them with the given edges.
GraphMLContentHandler() - Constructor for class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
GraphMLExportService - Class in de.bioforscher.singa.simulation.parser.graphs: This class contains a single static method to export a Graph to a GraphML file.
GraphMLExportService() - Constructor for class de.bioforscher.singa.simulation.parser.graphs.GraphMLExportService
GraphMLParserService - Class in de.bioforscher.singa.simulation.parser.graphs
GraphMLParserService(String) - Constructor for class de.bioforscher.singa.simulation.parser.graphs.GraphMLParserService
GraphUpdatedEvent - Class in de.bioforscher.singa.simulation.events
GraphUpdatedEvent(AutomatonGraph) - Constructor for class de.bioforscher.singa.simulation.events.GraphUpdatedEvent

H

halfTime - Variable in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
halfTime - Variable in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
halfTime - Variable in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
hasFeature(Class<FeatureType>) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
hashCode() - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection

I

ignorableWhitespace(char[], int, int) - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
increaseTimeStep() - Method in class de.bioforscher.singa.simulation.modules.model.TimeStepHarmonizer
initializeNodes(AutomatonGraph) - Method in class de.bioforscher.singa.simulation.model.compartments.Membrane
initializeSpeciesWithConcentration(ChemicalEntity, double) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph: Initializes the concentration of the given chemical entity of every node in this graph to to the given concentration in mol/l.
initializeSpeciesWithConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph: Initializes the concentration of the given chemical entity of every node in this graph.
isAccelerator() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.CatalyticReactant: Returns true if this Reactant is increasing the velocity of the associated reaction, and false otherwise.
isElementary() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction: Returns true if this Reaction is considered elementary and false otherwise.
isInhibitor() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.CatalyticReactant: Returns true if this Reactant is decreasing the velocity of the associated reaction, and false otherwise.
isObserved() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Returns true if this node is observed.
isProduct() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
isRateDetermining() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
isSubsection() - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection: Returns true if this cell section is a subsection of another section.
isSubstrate() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant

K

KineticLaw - Interface in de.bioforscher.singa.simulation.modules.reactions.model

L

LocalError - Class in de.bioforscher.singa.simulation.modules.model
LocalError(AutomatonNode, ChemicalEntity<?>, double) - Constructor for class de.bioforscher.singa.simulation.modules.model.LocalError

M

Membrane - Class in de.bioforscher.singa.simulation.model.compartments
Membrane(String, String, EnclosedCompartment) - Constructor for class de.bioforscher.singa.simulation.model.compartments.Membrane
MembraneContainer - Class in de.bioforscher.singa.simulation.model.concentrations: In this representation of a membrane is divided into four parts.
MembraneContainer(CellSection, CellSection, Membrane) - Constructor for class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
MembraneContainer(MembraneContainer) - Constructor for class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
MembraneEntry - Class in de.bioforscher.singa.simulation.features.permeability
MembraneEntry(Quantity<Frequency>, FeatureOrigin) - Constructor for class de.bioforscher.singa.simulation.features.permeability.MembraneEntry
MembraneEntry(double, FeatureOrigin) - Constructor for class de.bioforscher.singa.simulation.features.permeability.MembraneEntry
MembraneExit - Class in de.bioforscher.singa.simulation.features.permeability
MembraneExit(Quantity<Frequency>, FeatureOrigin) - Constructor for class de.bioforscher.singa.simulation.features.permeability.MembraneExit
MembraneExit(double, FeatureOrigin) - Constructor for class de.bioforscher.singa.simulation.features.permeability.MembraneExit
MembraneFlipFlop - Class in de.bioforscher.singa.simulation.features.permeability
MembraneFlipFlop(Quantity<Frequency>, FeatureOrigin) - Constructor for class de.bioforscher.singa.simulation.features.permeability.MembraneFlipFlop
MembraneFlipFlop(double, FeatureOrigin) - Constructor for class de.bioforscher.singa.simulation.features.permeability.MembraneFlipFlop
MembraneProtein - Class in de.bioforscher.singa.simulation.model.compartments
MembraneProtein(SimpleStringIdentifier) - Constructor for class de.bioforscher.singa.simulation.model.compartments.MembraneProtein: Creates a new Chemical Entity with the given identifier.
merge(Delta) - Method in class de.bioforscher.singa.simulation.model.concentrations.Delta: Merges (adds) two deltas an returns a new delta.
MichaelisMentenReaction - Class in de.bioforscher.singa.simulation.modules.reactions.implementations
MichaelisMentenReaction(Simulation, Enzyme) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.MichaelisMentenReaction
MINIMAL_EMPTY_ERROR - Static variable in class de.bioforscher.singa.simulation.modules.model.LocalError
Module - Interface in de.bioforscher.singa.simulation.modules.model
MULTDIV - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for multiplication or division
MultiConcentrationContainer - Class in de.bioforscher.singa.simulation.model.concentrations
MultiConcentrationContainer(Set<CellSection>) - Constructor for class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
MultiConcentrationContainer(MultiConcentrationContainer) - Constructor for class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
MULTIPLICATION_NODE - Static variable in interface uk.co.cogitolearning.cogpar.ExpressionNode: Node id for multiplication nodes
MultiplicationExpressionNode - Class in uk.co.cogitolearning.cogpar: An ExpressionNode that handles multiplications and divisions.
MultiplicationExpressionNode() - Constructor for class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode: Default constructor.
MultiplicationExpressionNode(ExpressionNode, boolean) - Constructor for class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode: Constructor to create a multiplication with the first term already added.
multiply(double) - Method in class de.bioforscher.singa.simulation.model.concentrations.Delta: Multiplies (modifies) this delta .

N

nextEpoch() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Calculates the next epoch.
nextNodeIdentifier() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
NodeState - Enum in de.bioforscher.singa.simulation.model.compartments: The general state of a AutomatonNode.
NodeUpdatedEvent - Class in de.bioforscher.singa.simulation.events
NodeUpdatedEvent(Quantity<Time>, AutomatonNode) - Constructor for class de.bioforscher.singa.simulation.events.NodeUpdatedEvent
NthOrderReaction - Class in de.bioforscher.singa.simulation.modules.reactions.implementations
NthOrderReaction(Simulation, Quantity<Frequency>) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.NthOrderReaction
NUMBER - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for numbers

O

onEventReceived(NodeUpdatedEvent) - Method in class de.bioforscher.singa.simulation.events.EpochUpdateWriter
onlyApplyIf(Predicate<AutomatonNode>) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
onlyApplyIf(Predicate<AutomatonNode>) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
onlyApplyIf(Predicate<AutomatonNode>) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
OPEN_BRACKET - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for opening brackets

P

parse() - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLParserService
parse() - Method in class de.bioforscher.singa.simulation.parser.sbml.SabioRKParserService
parse() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
parse(String) - Method in class uk.co.cogitolearning.cogpar.Parser: Parse a mathematical expression in a string and return an ExpressionNode.
parse(LinkedList<Token>) - Method in class uk.co.cogitolearning.cogpar.Parser: Parse a mathematical expression in contained in a list of tokens and return an ExpressionNode.
parseModelById(String) - Static method in class de.bioforscher.singa.simulation.parser.sbml.BioModelsParserService
parseModelFromFile(String) - Static method in class de.bioforscher.singa.simulation.parser.sbml.BioModelsParserService
parseModelFromStream(InputStream) - Static method in class de.bioforscher.singa.simulation.parser.sbml.BioModelsParserService
Parser - Class in uk.co.cogitolearning.cogpar: A parser for mathematical expressions.
Parser() - Constructor for class uk.co.cogitolearning.cogpar.Parser
ParserException - Exception in uk.co.cogitolearning.cogpar: A simple subclass of RuntimeException that indicates errors when trying to parse the input to Parser.
ParserException(String) - Constructor for exception uk.co.cogitolearning.cogpar.ParserException: Construct the evaluation exception with a message.
ParserException(String, Token) - Constructor for exception uk.co.cogitolearning.cogpar.ParserException: Construct the evaluation exception with a message and a token.
PassiveMembraneTransport - Class in de.bioforscher.singa.simulation.modules.transport
PassiveMembraneTransport(Simulation) - Constructor for class de.bioforscher.singa.simulation.modules.transport.PassiveMembraneTransport
PLUSMINUS - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for plus or minus
pos - Variable in class uk.co.cogitolearning.cogpar.Token: the position of the token in the input string
positive - Variable in class uk.co.cogitolearning.cogpar.SequenceExpressionNode.Term: the boolean flag
processingInstruction(String, String) - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler

R

RAISED - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for the exponentiation symbol
Reactant - Class in de.bioforscher.singa.simulation.modules.reactions.model: A Reactant encapsulates a ChemicalEntity for the use in Reactions.
Reactant(ChemicalEntity<?>, ReactantRole) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.model.Reactant
ReactantRole - Enum in de.bioforscher.singa.simulation.modules.reactions.model
Reaction - Class in de.bioforscher.singa.simulation.modules.reactions.model: A chemical reaction is a process that leads to the transformation of one set of chemical substances to another.
Reaction(Simulation) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
Reaction() - Constructor for class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
referenceChemicalEntityToParameter(String, ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.rules.AssignmentRule
referenceChemicalEntityToParameter(String, ChemicalEntity) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicKineticLaw
replaceInEquation(String) - Method in class de.bioforscher.singa.simulation.parser.sbml.FunctionReference
rescaleDiffusivity(Quantity<Diffusivity>, Quantity<Time>, Quantity<Length>) - Static method in class de.bioforscher.singa.simulation.model.parameters.UnitScaler: Scales the diffusivity for the use with cellular graph automata.
rescaleParameters() - Method in class de.bioforscher.singa.simulation.modules.model.TimeStepHarmonizer
rescaleReactionRate(Quantity<Frequency>, Quantity<Time>) - Static method in class de.bioforscher.singa.simulation.model.parameters.UnitScaler: Scales the reaction rate for the use with cellular graph automata.
resetLargestLocalError() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourDependentModule
resetLargestLocalError() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
resetLargestLocalError() - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
resetLargestLocalError() - Method in interface de.bioforscher.singa.simulation.modules.model.Module

S

SabioRKParserService - Class in de.bioforscher.singa.simulation.parser.sbml
SabioRKParserService(String) - Constructor for class de.bioforscher.singa.simulation.parser.sbml.SabioRKParserService
SBMLAssignmentRuleConverter - Class in de.bioforscher.singa.simulation.parser.sbml.converter
SBMLAssignmentRuleConverter(Map<String, Unit<?>>, Map<String, ChemicalEntity>, Map<String, FunctionReference>, Map<String, SimulationParameter<?>>) - Constructor for class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLAssignmentRuleConverter
SBMLExpressionConverter - Class in de.bioforscher.singa.simulation.parser.sbml.converter
SBMLExpressionConverter(Map<String, Unit<?>>, Map<String, FunctionReference>, Map<String, SimulationParameter<?>>) - Constructor for class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLExpressionConverter
SBMLKineticLawConverter - Class in de.bioforscher.singa.simulation.parser.sbml.converter: Converts JSBML KineticLaws to SiNGA KineticLaws
SBMLKineticLawConverter(Map<String, Unit<?>>, Map<String, FunctionReference>, Map<String, SimulationParameter<?>>) - Constructor for class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLKineticLawConverter
SBMLParameterConverter - Class in de.bioforscher.singa.simulation.parser.sbml.converter: Converts JSBML Parameters to SiNGA Parameters.
SBMLParameterConverter(Map<String, Unit<?>>) - Constructor for class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLParameterConverter
SBMLParser - Class in de.bioforscher.singa.simulation.parser.sbml
SBMLParser(InputStream) - Constructor for class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
SBMLReactionConverter - Class in de.bioforscher.singa.simulation.parser.sbml.converter: Converts JSBML Reactions to SiNGA Reactions
SBMLReactionConverter(Map<String, Unit<?>>, Map<String, ChemicalEntity>, Map<String, FunctionReference>, Map<String, SimulationParameter<?>>) - Constructor for class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLReactionConverter
SBMLUnitConverter - Class in de.bioforscher.singa.simulation.parser.sbml.converter: Converts JSBML Units to UnitsOfMeasurement Units.
SBMLUnitConverter() - Constructor for class de.bioforscher.singa.simulation.parser.sbml.converter.SBMLUnitConverter
scale(Quantity<Time>, Quantity<Length>) - Method in class de.bioforscher.singa.simulation.features.permeability.MembraneEntry
scale(Quantity<Time>, Quantity<Length>) - Method in class de.bioforscher.singa.simulation.features.permeability.MembraneExit
scale(Quantity<Time>, Quantity<Length>) - Method in class de.bioforscher.singa.simulation.features.permeability.MembraneFlipFlop
scale(Quantity<Time>, Quantity<Length>) - Method in class de.bioforscher.singa.simulation.features.scale.AppliedScale
sequence - Variable in class uk.co.cogitolearning.cogpar.Token: the string that the token was created from
SequenceExpressionNode - Class in uk.co.cogitolearning.cogpar: A base class for AdditionExpressionNode and MultiplicationExpressionNode.
SequenceExpressionNode() - Constructor for class uk.co.cogitolearning.cogpar.SequenceExpressionNode: Default constructor.
SequenceExpressionNode(ExpressionNode, boolean) - Constructor for class uk.co.cogitolearning.cogpar.SequenceExpressionNode: Constructor to create a sequence with the first term already added.
SequenceExpressionNode.Term - Class in uk.co.cogitolearning.cogpar: An inner class that defines a pair containing an ExpressionNode and a boolean flag.
setAppliedScale(Double) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicKineticLaw
setAssignmentRules(List<AssignmentRule>) - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Adds a list of assignment rules, sorting them by their dependencies.
setAvailableConcentration(CellSection, ChemicalEntity, Quantity<MolarConcentration>) - Method in interface de.bioforscher.singa.simulation.model.concentrations.ConcentrationContainer: Sets the available concentration based on the given compartment.
setAvailableConcentration(CellSection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
setAvailableConcentration(CellSection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
setAvailableConcentration(CellSection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer
setAvailableConcentration(ChemicalEntity, CellSection, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Gets the concentration of the given chemical entity in the given compartment.
setCatalyticReactants(List<CatalyticReactant>) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
setCellSection(CellSection) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Sets the cell section of this node and references the node in the corresponding section.
setChemicalEntities(Set<ChemicalEntity<?>>) - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Sets all chemical entities at once.
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in interface de.bioforscher.singa.simulation.model.concentrations.ConcentrationContainer: Sets the representative concentration of a chemical entity.
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.concentrations.MembraneContainer
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.concentrations.MultiConcentrationContainer
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer
setConcentration(ChemicalEntity, double) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Sets the concentration of the entity in mol/l.
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Sets the concentration of the entity.
setConcentrationContainer(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Sets the ConcentrationContainer for this node.
setConcentrations(double, ChemicalEntity...) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Sets the concentration of the given chemical entities.
setContent(Set<AutomatonNode>) - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection: Sets the content of this cell section.
setCurrentCellSection(CellSection) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicKineticLaw
setDocumentLocator(Locator) - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
setElementary(boolean) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction: Sets this Reaction as elementary.
setEnclosingMembrane(Membrane) - Method in class de.bioforscher.singa.simulation.model.compartments.EnclosedCompartment
setEntity(ChemicalEntity<?>) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactant: Sets the entity representing this reactant.
setEntityReference(Map<ChemicalEntity, String>) - Method in class de.bioforscher.singa.simulation.model.rules.AssignmentRule
setEpsilon(double) - Method in class de.bioforscher.singa.simulation.modules.model.TimeStepHarmonizer
setFeature(Class<FeatureType>) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
setFeature(FeatureType) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
setGraph(AutomatonGraph) - Method in class de.bioforscher.singa.simulation.modules.model.Simulation: Sets the simulation graph and adds all entities referenced in the graph to the chemical entities of the simulation.
setKineticLaw(DynamicKineticLaw) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
setObserved(boolean) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Sets the observed state of this node.
setParameter(SimulationParameter) - Method in class de.bioforscher.singa.simulation.model.rules.AppliedExpression
setParameters(List<SimulationParameter>) - Method in class de.bioforscher.singa.simulation.model.rules.AppliedExpression
setQuantity(Quantity<QuantityType>) - Method in class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
setRateDetermining(boolean) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
setReactionOrder(double) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
setRole(ReactantRole) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactant: Gets the role of this reactant.
setSimulation(Simulation) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractNeighbourIndependentModule
setSimulation(Simulation) - Method in class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule
setState(NodeState) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Sets the state.
setStoichiometricNumber(double) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
setStoichiometricReactants(List<StoichiometricReactant>) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction: Sets the list of reactants for this reaction.
setStrength(double) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.CatalyticReactant: Sets the strength of this Reactant.
setSubsection(boolean) - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection: Set true if this cell section is a subsection of another section.
setTargetEntity(ChemicalEntity<?>) - Method in class de.bioforscher.singa.simulation.model.rules.AssignmentRule
setValue(double) - Method in class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
setValue(double) - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode: Sets the value of the variable
SetVariable - Class in uk.co.cogitolearning.cogpar: A visitor that sets a variable with a specific name to a given value
SetVariable(String, double) - Constructor for class uk.co.cogitolearning.cogpar.SetVariable: Construct the visitor with the name and the value of the variable to set
shiftDeltas() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode: Shifts the deltas from the potential delta list to the final delta list.
SimpleConcentrationContainer - Class in de.bioforscher.singa.simulation.model.concentrations
SimpleConcentrationContainer(CellSection) - Constructor for class de.bioforscher.singa.simulation.model.concentrations.SimpleConcentrationContainer
Simulation - Class in de.bioforscher.singa.simulation.modules.model: The simulation calss encapsulates everything that is needed to perform a Simulation based on cellular graph automata.
Simulation() - Constructor for class de.bioforscher.singa.simulation.modules.model.Simulation: Creates a new plain simulation.
SimulationExamples - Class in de.bioforscher.singa.simulation.modules.model: A factory class that can be used to create different examples to test and explore certain aspects to the api.
SimulationExamples() - Constructor for class de.bioforscher.singa.simulation.modules.model.SimulationExamples
SimulationParameter<QuantityType extends javax.measure.Quantity<QuantityType>> - Class in de.bioforscher.singa.simulation.model.parameters
SimulationParameter(String) - Constructor for class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
SimulationParameter(String, Quantity<QuantityType>) - Constructor for class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
skippedEntity(String) - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
sortAssignmentRulesByPriority(List<AssignmentRule>) - Static method in class de.bioforscher.singa.simulation.model.rules.AssignmentRules: It is possible, that AssignmentRules depend on each other.
splitRectangularGraphWithMembrane(AutomatonGraph, GridCoordinateConverter, EnclosedCompartment, CellSection) - Static method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraphs
startDocument() - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
startElement(String, String, String, Attributes) - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
startPrefixMapping(String, String) - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
step() - Method in class de.bioforscher.singa.simulation.modules.model.TimeStepHarmonizer
StoichiometricReactant - Class in de.bioforscher.singa.simulation.modules.reactions.model: StoichiometricReactants are Reactants that are consumed or produced during the reaction.
StoichiometricReactant(ChemicalEntity, ReactantRole, double, double) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
StoichiometricReactant(ChemicalEntity, ReactantRole, double) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
StoichiometricReactant(ChemicalEntity, ReactantRole, boolean) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
StoichiometricReactant(ChemicalEntity, ReactantRole) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant

T

Term(boolean, ExpressionNode) - Constructor for class uk.co.cogitolearning.cogpar.SequenceExpressionNode.Term: Construct the Term object with some values.
terms - Variable in class uk.co.cogitolearning.cogpar.SequenceExpressionNode: the list of terms in the sequence
TimeStepHarmonizer - Class in de.bioforscher.singa.simulation.modules.model
TimeStepHarmonizer(Simulation, Quantity<Time>) - Constructor for class de.bioforscher.singa.simulation.modules.model.TimeStepHarmonizer
Token - Class in uk.co.cogitolearning.cogpar: A token that is produced by Tokenizer and fed into Parser.parse A token consists of a token identifier, a string that the token was created from and the position in the input string that the token was found.
Token(int, String, int) - Constructor for class uk.co.cogitolearning.cogpar.Token: Construct the token with its values
token - Variable in class uk.co.cogitolearning.cogpar.Token: the token identifier
tokenize(String) - Method in class uk.co.cogitolearning.cogpar.Tokenizer: Tokenize an input string.
Tokenizer - Class in uk.co.cogitolearning.cogpar: A class for reading an input string and separating it into tokens that can be fed into Parser.
Tokenizer() - Constructor for class uk.co.cogitolearning.cogpar.Tokenizer: Default constructor
toString() - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection
toString() - Method in class de.bioforscher.singa.simulation.model.concentrations.Delta
toString() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonNode
toString() - Method in class de.bioforscher.singa.simulation.modules.model.LocalError

U

uk.co.cogitolearning.cogpar - package uk.co.cogitolearning.cogpar
UnitScaler - Class in de.bioforscher.singa.simulation.model.parameters
UnitScaler() - Constructor for class de.bioforscher.singa.simulation.model.parameters.UnitScaler
useStructureFrom(UndirectedGraph) - Static method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraphs: Copies the structure (nodes and edges) of an UndirectedGraph to a AutomatonGraph.

V

valueOf(String) - Static method in enum de.bioforscher.singa.simulation.model.compartments.NodeState: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.bioforscher.singa.simulation.modules.reactions.model.ReactantRole: Returns the enum constant of this type with the specified name.
values() - Static method in enum de.bioforscher.singa.simulation.model.compartments.NodeState: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.bioforscher.singa.simulation.modules.reactions.model.ReactantRole: Returns an array containing the constants of this enum type, in the order they are declared.
VARIABLE - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for variable names
VARIABLE_NODE - Static variable in interface uk.co.cogitolearning.cogpar.ExpressionNode: Node id for variable nodes
VariableExpressionNode - Class in uk.co.cogitolearning.cogpar: An ExpressionNode that stores a named variable
VariableExpressionNode(String) - Constructor for class uk.co.cogitolearning.cogpar.VariableExpressionNode: Construct with the name of the variable.
visit(VariableExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor
visit(ConstantExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor
visit(AdditionExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor
visit(MultiplicationExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor
visit(ExponentiationExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor
visit(FunctionExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor
visit(VariableExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable: Checks the nodes name against the name to set and sets the value if the two strings match
visit(ConstantExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable: Do nothing
visit(AdditionExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable: Do nothing
visit(MultiplicationExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable: Do nothing
visit(ExponentiationExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable: Do nothing
visit(FunctionExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable: Do nothing

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