Index (singa-simulation 0.2.2 API)

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

A

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
ActiveMembraneTransport - Class in de.bioforscher.singa.simulation.modules.membranetransport
ActiveMembraneTransport() - Constructor for class de.bioforscher.singa.simulation.modules.membranetransport.ActiveMembraneTransport
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
addEdgeBetween(int, BioNode, BioNode) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
addEdgeBetween(BioNode, BioNode) - 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(BioNode) - 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
addNodeToObserve(BioNode) - Method in class de.bioforscher.singa.simulation.events.EpochUpdateWriter
addPermeability(ChemicalEntity, double) - Method in class de.bioforscher.singa.simulation.model.graphs.BioEdge
addSection(CellSection) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
AppliedExpression - Class in de.bioforscher.singa.simulation.model.rules
AppliedExpression(String, Unit<?>) - Constructor for class de.bioforscher.singa.simulation.model.rules.AppliedExpression
apply() - Method in class de.bioforscher.singa.simulation.modules.model.updates.PotentialUpdate
applyAssignmentRules() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
applyRule(BioNode) - Method in class de.bioforscher.singa.simulation.model.rules.AssignmentRule
applyTo(AutomatonGraph) - Method in class de.bioforscher.singa.simulation.modules.diffusion.FreeDiffusion
applyTo(AutomatonGraph) - Method in class de.bioforscher.singa.simulation.modules.membranetransport.ActiveMembraneTransport
applyTo(AutomatonGraph) - Method in class de.bioforscher.singa.simulation.modules.membranetransport.PassiveMembraneTransport
applyTo(AutomatonGraph) - Method in interface de.bioforscher.singa.simulation.modules.model.Module
applyTo(AutomatonGraph) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactions
areViableParametersForDiffusion(double, double, int, Quantity<MolarConcentration>, Quantity<Diffusivity>) - Static method in class de.bioforscher.singa.simulation.modules.diffusion.DiffusionUtilities
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
AutomatonGraph - Class in de.bioforscher.singa.simulation.model.graphs
AutomatonGraph() - Constructor for class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
AutomatonGraph(int, int) - Constructor for class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
AutomatonGraphs - Class in de.bioforscher.singa.simulation.model.graphs

B

BiochemicalReaction - Class in de.bioforscher.singa.simulation.modules.reactions.implementations
BiochemicalReaction(KineticLaw) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.BiochemicalReaction
BiochemicalReaction(Enzyme) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.BiochemicalReaction
BioEdge - Class in de.bioforscher.singa.simulation.model.graphs
BioEdge() - Constructor for class de.bioforscher.singa.simulation.model.graphs.BioEdge
BioEdge(int) - Constructor for class de.bioforscher.singa.simulation.model.graphs.BioEdge
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
BioNode - Class in de.bioforscher.singa.simulation.model.graphs
BioNode(int) - Constructor for class de.bioforscher.singa.simulation.model.graphs.BioNode

C

calculateAcceleration(BioNode, CellSection) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.BiochemicalReaction
calculateAcceleration(BioNode, CellSection) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
calculateAcceleration(BioNode, CellSection) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.EquilibriumReaction
calculateAcceleration(BioNode, CellSection) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.DynamicKineticLaw
calculateAcceleration(BioNode, CellSection) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelisMentenWithKCat
calculateAcceleration(BioNode, CellSection) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
calculateAcceleration(BioNode, CellSection) - Method in interface de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticLaw
calculateAcceleration(BioNode, CellSection) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.NthOrderReaction
calculateAcceleration(BioNode, CellSection) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction: Determines the actual acceleration of concentration that would result in a change in concentration if the reaction is occurring in the given BioNode.
calculateThresholdForDistance(Quantity<Time>, int, Quantity<MolarConcentration>, Quantity<Diffusivity>) - Static method in class de.bioforscher.singa.simulation.modules.diffusion.DiffusionUtilities
calculateUpdate(BioNode, CellSection, ChemicalEntity) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactions
calculateUpdates(BioNode) - Method in class de.bioforscher.singa.simulation.modules.diffusion.FreeDiffusion
calculateUpdates(BioNode) - Method in class de.bioforscher.singa.simulation.modules.membranetransport.ActiveMembraneTransport
calculateUpdates(BioNode) - Method in class de.bioforscher.singa.simulation.modules.membranetransport.PassiveMembraneTransport
calculateUpdates(BioNode) - Method in interface de.bioforscher.singa.simulation.modules.model.updates.UpdateBehavior
calculateUpdates(BioNode) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactions
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
CLOSE_BRACKET - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for closing brackets
collectAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.modules.diffusion.FreeDiffusion
collectAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.modules.membranetransport.ActiveMembraneTransport
collectAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.modules.membranetransport.PassiveMembraneTransport
collectAllReferencedEntities() - Method in interface de.bioforscher.singa.simulation.modules.model.Module
collectAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
collectAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.BiochemicalReaction
collectAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
collectAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.EquilibriumReaction
collectAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.NthOrderReaction
collectAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
collectAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactions
collectChanges(BioNode) - Static method in class de.bioforscher.singa.simulation.modules.model.updates.PotentialUpdates
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.graphs: 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
copyStructureToBioGraph(UndirectedGraph) - Static method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraphs: Copies the structure (nodes and edges) of an UndirectedGraph to a AutomatonGraph.
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.
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 BiochemicalReaction, 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).
CumulativeUpdateBehavior - Interface in de.bioforscher.singa.simulation.modules.model.updates: This UpdateBehavior calculates all updates first and than applies them.

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.model.compartments - package de.bioforscher.singa.simulation.model.compartments
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.diffusion - package de.bioforscher.singa.simulation.modules.diffusion
de.bioforscher.singa.simulation.modules.membranetransport - package de.bioforscher.singa.simulation.modules.membranetransport
de.bioforscher.singa.simulation.modules.model - package de.bioforscher.singa.simulation.modules.model
de.bioforscher.singa.simulation.modules.model.updates - package de.bioforscher.singa.simulation.modules.model.updates
de.bioforscher.singa.simulation.modules.reactions.implementations - package de.bioforscher.singa.simulation.modules.reactions.implementations
de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations - package de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations
de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model - package de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model
de.bioforscher.singa.simulation.modules.reactions.model - package de.bioforscher.singa.simulation.modules.reactions.model
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
de.bioforscher.singa.simulation.research - package de.bioforscher.singa.simulation.research
determineConcentration(BioNode, CellSection, ReactantRole) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction: Determines the concentration of reactants that influence the velocity of the reaction.
DiffusionGridSearch - Class in de.bioforscher.singa.simulation.research
DiffusionGridSearch(List<UniqueParameterList<?>>) - Constructor for class de.bioforscher.singa.simulation.research.DiffusionGridSearch
DiffusionResearch - Class in de.bioforscher.singa.simulation.research
DiffusionResearch() - Constructor for class de.bioforscher.singa.simulation.research.DiffusionResearch
DiffusionUtilities - Class in de.bioforscher.singa.simulation.modules.diffusion
DynamicKineticLaw - Class in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations
DynamicKineticLaw(AppliedExpression) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.DynamicKineticLaw
DynamicReaction - Class in de.bioforscher.singa.simulation.modules.reactions.implementations
DynamicReaction(DynamicKineticLaw) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction

E

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
EntityDependentKineticParameter<ParameterType extends javax.measure.Quantity<ParameterType>> - Class in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model
EntityDependentKineticParameter(KineticParameterType, Quantity<ParameterType>) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.EntityDependentKineticParameter
EntityDependentKineticParameter(KineticParameterType, Quantity<ParameterType>, ChemicalEntity) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.EntityDependentKineticParameter
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(Quantity<ReactionRate>, Quantity<ReactionRate>) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.EquilibriumReaction
estimateSimulationAccuracy(double, double) - Static method in class de.bioforscher.singa.simulation.modules.diffusion.DiffusionUtilities
estimateSimulationSpeed(double, int) - Static method in class de.bioforscher.singa.simulation.modules.diffusion.DiffusionUtilities
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

fixDiffusionCoefficientForEntity(ChemicalEntity, Quantity<Diffusivity>) - Method in class de.bioforscher.singa.simulation.modules.diffusion.FreeDiffusion
forCompartment(EnclosedCompartment) - Static method in class de.bioforscher.singa.simulation.model.compartments.Membrane
FreeDiffusion - Class in de.bioforscher.singa.simulation.modules.diffusion: Diffusion is the net movement of molecules or atoms from a region of high concentration to a region of low concentration.
FreeDiffusion() - Constructor for class de.bioforscher.singa.simulation.modules.diffusion.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 class de.bioforscher.singa.simulation.model.graphs.BioNode
getAllConcentrations() - Method in interface de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer: Returns the representative concentrations of all referenced chemical entities.
getAllConcentrations() - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
getAllConcentrations() - Method in class de.bioforscher.singa.simulation.model.graphs.MultiConcentrationContainer
getAllConcentrations() - Method in class de.bioforscher.singa.simulation.model.graphs.SimpleConcentrationContainer
getAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
getAllReferencedEntities() - Method in interface de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer: Returns all ChemicalEntities that are referenced in this container.
getAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
getAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.model.graphs.MultiConcentrationContainer
getAllReferencedEntities() - Method in class de.bioforscher.singa.simulation.model.graphs.SimpleConcentrationContainer
getAllReferencedSections() - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
getAllReferencedSections() - Method in interface de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer: Returns all Compartments that are referenced in this container.
getAllReferencedSections() - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
getAllReferencedSections() - Method in class de.bioforscher.singa.simulation.model.graphs.MultiConcentrationContainer
getAllReferencedSections() - Method in class de.bioforscher.singa.simulation.model.graphs.SimpleConcentrationContainer
getAnnotations() - Method in class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
getAppliedScale() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.DynamicKineticLaw
getAssignmentRules() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
getAssignmentRules() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getAvailableConcentration(ChemicalEntity, CellSection) - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
getAvailableConcentration(CellSection, ChemicalEntity) - Method in interface de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer: Returns the available concentration based on the given compartment.
getAvailableConcentration(CellSection, ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
getAvailableConcentration(CellSection, ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.MultiConcentrationContainer
getAvailableConcentration(CellSection, ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.SimpleConcentrationContainer
getBackwardsRateConstant() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.EquilibriumReaction
getCatalyticReactants() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
getCellSection() - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
getCellSection() - Method in class de.bioforscher.singa.simulation.modules.model.updates.PotentialUpdate
getChemicalEntities() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
getChemicalEntities() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getCompartments() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
getConcentration(ChemicalEntity) - Method in interface de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer: Returns the representative concentration of a chemical entity.
getConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
getConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.MultiConcentrationContainer
getConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.SimpleConcentrationContainer
getConcentrations() - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
getContent() - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection: Returns the nodes belonging to this cell section.
getDisplayString() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
getElapsedTime() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
getEnclosingMembrane() - Method in class de.bioforscher.singa.simulation.model.compartments.EnclosedCompartment
getEntity() - Method in class de.bioforscher.singa.simulation.modules.model.updates.PotentialUpdate
getEntity() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.EntityDependentKineticParameter
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.kineticLaws.implementations.DynamicKineticLaw
getEntityWithMaximalDiffusivity() - Method in class de.bioforscher.singa.simulation.modules.diffusion.FreeDiffusion
getEpoch() - Method in class de.bioforscher.singa.simulation.events.NodeUpdatedEvent
getEpoch() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
getExpression() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.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
getForwardsRateConstant() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.EquilibriumReaction
getFreeDiffusionModule() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
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
getGraph() - Method in class de.bioforscher.singa.simulation.parser.graphs.GraphMLContentHandler
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
getInnerMembraneLayerConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
getInnerPhaseConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
getKineticLaw() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
getKm() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
getListeners() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
getMaximalDiffusivity() - Method in class de.bioforscher.singa.simulation.modules.diffusion.FreeDiffusion
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
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 enum de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticParameterType
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.updates.PotentialUpdate
getOuterMembraneLayerConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
getOuterPhaseConcentration(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
getParameters() - Method in class de.bioforscher.singa.simulation.model.rules.AppliedExpression
getParameterType() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticParameter
getPermeability() - Method in class de.bioforscher.singa.simulation.model.graphs.BioEdge
getPermeability(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.BioEdge
getProducts() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
getQuantity() - Method in class de.bioforscher.singa.simulation.model.parameters.SimulationParameter
getQuantity() - Method in class de.bioforscher.singa.simulation.modules.model.updates.PotentialUpdate
getQuantity() - Method in enum de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticParameterType
getRateConstant() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.NthOrderReaction
getReactionOrder() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
getReactions() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactions
getReactions() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getRequiredParameters() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.DynamicKineticLaw
getRequiredParameters() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelisMentenWithKCat
getRequiredParameters() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
getRequiredParameters() - Method in interface de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticLaw
getRole() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactant: Gets the role of this reactant.
getSection(String) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
getSections() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
getStartingConcentrations() - Method in class de.bioforscher.singa.simulation.parser.sbml.SBMLParser
getState() - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
getSteepestDifference(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
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.
getSubstrate() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
getSubstrates() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
getSymbol() - Method in enum de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticParameterType
getTargetEntity() - Method in class de.bioforscher.singa.simulation.model.rules.AssignmentRule
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.reactions.implementations.kineticLaws.model.KineticParameter
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
getVMax() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
getWriter() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
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

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
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
initializeSpeciesWithConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
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.BioNode
isProduct() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
isRateDetermining() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant
isSubstrate() - Method in class de.bioforscher.singa.simulation.modules.reactions.model.StoichiometricReactant

K

KCAT - Static variable in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelisMentenWithKCat
KineticLaw - Interface in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model
KineticParameter<ParameterType extends javax.measure.Quantity<ParameterType>> - Class in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model
KineticParameter(KineticParameterType, Quantity<ParameterType>) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticParameter
KineticParameterType - Enum in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model
KM - Static variable in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM

M

main(String[]) - Static method in class de.bioforscher.singa.simulation.research.DiffusionGridSearch
main(String[]) - Static method in class de.bioforscher.singa.simulation.research.DiffusionResearch
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.graphs: In this representation of a membrane is divided into four parts.
MembraneContainer(CellSection, CellSection, Membrane) - Constructor for class de.bioforscher.singa.simulation.model.graphs.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.
MichaelisMentenWithKCat - Class in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations
MichaelisMentenWithKCat(ChemicalEntity, Enzyme) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelisMentenWithKCat
MichaelisMentenWithKCat(ChemicalEntity, Enzyme, EntityDependentKineticParameter<MolarConcentration>, KineticParameter<ReactionRate>) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelisMentenWithKCat
MichaelsMentenWithKM - Class in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations
MichaelsMentenWithKM(ChemicalEntity) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
MichaelsMentenWithKM(ChemicalEntity, EntityDependentKineticParameter<MolarConcentration>, KineticParameter<ReactionRate>) - Constructor for class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
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.graphs
MultiConcentrationContainer(CellSection) - Constructor for class de.bioforscher.singa.simulation.model.graphs.MultiConcentrationContainer
MultiConcentrationContainer(Set<CellSection>) - Constructor for class de.bioforscher.singa.simulation.model.graphs.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.

N

nextEpoch() - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
nextNodeIdentifier() - Method in class de.bioforscher.singa.simulation.model.graphs.AutomatonGraph
NodeState - Enum in de.bioforscher.singa.simulation.model.compartments
NodeUpdatedEvent - Class in de.bioforscher.singa.simulation.events
NodeUpdatedEvent(int, BioNode) - Constructor for class de.bioforscher.singa.simulation.events.NodeUpdatedEvent
NthOrderReaction - Class in de.bioforscher.singa.simulation.modules.reactions.implementations
NthOrderReaction(Quantity<ReactionRate>) - 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
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.membranetransport
PassiveMembraneTransport() - Constructor for class de.bioforscher.singa.simulation.modules.membranetransport.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
PotentialUpdate - Class in de.bioforscher.singa.simulation.modules.model.updates
PotentialUpdate(BioNode, CellSection, ChemicalEntity, Quantity<MolarConcentration>) - Constructor for class de.bioforscher.singa.simulation.modules.model.updates.PotentialUpdate
PotentialUpdates - Class in de.bioforscher.singa.simulation.modules.model.updates
prepareAppliedRateConstant() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.NthOrderReaction
prepareAppliedRateConstants() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.EquilibriumReaction
prepareAppliedRateConstants() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.DynamicKineticLaw
prepareAppliedRateConstants() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelisMentenWithKCat
prepareAppliedRateConstants() - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
prepareAppliedRateConstants() - Method in interface de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticLaw
prepareCoefficients(Set<ChemicalEntity<?>>) - Method in class de.bioforscher.singa.simulation.modules.membranetransport.PassiveMembraneTransport
prepareDiffusionCoefficients(Set<ChemicalEntity<?>>) - Method in class de.bioforscher.singa.simulation.modules.diffusion.FreeDiffusion
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() - Constructor for class de.bioforscher.singa.simulation.modules.reactions.model.Reaction
Reactions - Class in de.bioforscher.singa.simulation.modules.reactions.model: The Reactions module defines the entirety of chemical conversions that take place in the Simulation.
Reactions() - Constructor for class de.bioforscher.singa.simulation.modules.reactions.model.Reactions
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.kineticLaws.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.
rescaleReactionRate(Quantity<ReactionRate>, Quantity<Time>) - Static method in class de.bioforscher.singa.simulation.model.parameters.UnitScaler: Scales the reaction rate for the use with cellular graph automata.

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
search() - Method in class de.bioforscher.singa.simulation.research.DiffusionGridSearch
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.kineticLaws.implementations.DynamicKineticLaw
setAssignmentRules(List<AssignmentRule>) - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
setAvailableConcentration(ChemicalEntity, CellSection, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
setAvailableConcentration(CellSection, ChemicalEntity, Quantity<MolarConcentration>) - Method in interface de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer: Sets the available concentration based on the given compartment.
setAvailableConcentration(CellSection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
setAvailableConcentration(CellSection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.MultiConcentrationContainer
setAvailableConcentration(CellSection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.SimpleConcentrationContainer
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.BioNode
setChemicalEntities(Set<ChemicalEntity<?>>) - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
setConcentration(ChemicalEntity, double) - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in interface de.bioforscher.singa.simulation.model.graphs.ConcentrationContainer: Sets the representative concentration of a chemical entity.
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.MembraneContainer
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.MultiConcentrationContainer
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.model.graphs.SimpleConcentrationContainer
setConcentrations(double, ChemicalEntity...) - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
setConcentrations(ConcentrationContainer) - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
setContent(Set<BioNode>) - Method in class de.bioforscher.singa.simulation.model.compartments.CellSection: Sets the content of this cell section.
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.implementations.kineticLaws.model.EntityDependentKineticParameter
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
setGraph(AutomatonGraph) - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
setKineticLaw(DynamicKineticLaw) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction
setKm(EntityDependentKineticParameter<MolarConcentration>) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
setModules(Set<Module>) - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
setObserved(boolean) - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
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
setParameterType(KineticParameterType) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticParameter
setPermeability(Map<ChemicalEntity, Double>) - Method in class de.bioforscher.singa.simulation.model.graphs.BioEdge
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
setReactions(List<Reaction>) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactions
setRole(ReactantRole) - Method in class de.bioforscher.singa.simulation.modules.reactions.model.Reactant: Gets the role of this reactant.
setState(NodeState) - Method in class de.bioforscher.singa.simulation.model.graphs.BioNode
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.
setSubstrate(ChemicalEntity) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
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(Quantity<ParameterType>) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model.KineticParameter
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
setVMax(KineticParameter<ReactionRate>) - Method in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM
setWriter(EpochUpdateWriter) - Method in class de.bioforscher.singa.simulation.modules.model.Simulation
SimpleConcentrationContainer - Class in de.bioforscher.singa.simulation.model.graphs
SimpleConcentrationContainer(CellSection) - Constructor for class de.bioforscher.singa.simulation.model.graphs.SimpleConcentrationContainer
Simulation - Class in de.bioforscher.singa.simulation.modules.model
Simulation() - Constructor for class de.bioforscher.singa.simulation.modules.model.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 certain 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
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
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.graphs.BioNode

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
UpdateBehavior - Interface in de.bioforscher.singa.simulation.modules.model.updates
updateGraph(AutomatonGraph) - Method in class de.bioforscher.singa.simulation.modules.membranetransport.PassiveMembraneTransport
updateGraph(AutomatonGraph) - Method in interface de.bioforscher.singa.simulation.modules.model.updates.CumulativeUpdateBehavior: Calculates all updates and applies them afterwards.
updateGraph(AutomatonGraph) - Method in interface de.bioforscher.singa.simulation.modules.model.updates.UpdateBehavior

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.implementations.kineticLaws.model.KineticParameterType: 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.implementations.kineticLaws.model.KineticParameterType: 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
VMAX - Static variable in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelisMentenWithKCat
VMAX - Static variable in class de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations.MichaelsMentenWithKM

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