Index (singa-simulation 0.5.0 API)

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

A

AbstractDeltaFunction<FunctionReturnType> - Class in bio.singa.simulation.model.modules.concentration.functions: Delta Functions are used to calculate updates for Updatables during simulation.
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.
ACTIN_ATTACHED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
ACTIN_PROPELLED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
ACTIN_TETHERED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
ActinBoostVelocity - Class in bio.singa.simulation.features
ActinBoostVelocity(Quantity<Speed>, Evidence) - Constructor for class bio.singa.simulation.features.ActinBoostVelocity
ActinBoostVelocity(double, Evidence) - Constructor for class bio.singa.simulation.features.ActinBoostVelocity
ActinCortex - Class in bio.singa.simulation.model.agents.volumelike
ActinCortex(Polygon) - Constructor for class bio.singa.simulation.model.agents.volumelike.ActinCortex
ActinCortexAttachment - Class in bio.singa.simulation.model.modules.qualitative.implementations
ActinCortexAttachment() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexAttachment
ActinCortexDiffusivityScaling - Class in bio.singa.simulation.model.modules.qualitative.implementations
ActinCortexDiffusivityScaling() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexDiffusivityScaling
add(double) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDelta
add(String, Parameter) - Static method in class bio.singa.simulation.model.parameters.ParameterStorage
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
addActin(Vector2D, Vector2D) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
addAssociatedNode(AutomatonNode, double) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
addCellRegion(CellRegion) - Method in class bio.singa.simulation.model.graphs.AutomatonGraph: Adds a cell section to this graph but does not associate any node to it.
addDeltaFunction(DeltaFunctionType) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Adds a delta function to the module.
addDeltaFunction(EntityDeltaFunction) - Method in class bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific
addDeltaFunction(SectionDeltaFunction) - Method in class bio.singa.simulation.model.modules.concentration.specifity.SectionSpecific
addDeltaFunction(UpdatableDeltaFunction) - Method in class bio.singa.simulation.model.modules.concentration.specifity.UpdatableSpecific
addDeltaFunction(DeltaFunctionType) - Method in interface bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity: Adds the implementation of a AbstractDeltaFunction to be calculated during simulation.
addDeltaFunction(Function<Vesicle, DisplacementDelta>, Predicate<Vesicle>) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
addEdgeBetween(int, AutomatonNode, AutomatonNode) - Method in class bio.singa.simulation.model.graphs.AutomatonGraph
addEdgeBetween(AutomatonNode, AutomatonNode) - Method in class bio.singa.simulation.model.graphs.AutomatonGraph
addGraphUpdateListener(UpdateEventListener<GraphUpdatedEvent>) - Method in class bio.singa.simulation.model.simulation.SimulationManager: Adds a new listener for graph based events.
addInitialConcentration(InitialConcentration) - Method in class bio.singa.simulation.model.sections.concentration.ConcentrationInitializer
addInitialConcentration(CellRegion, CellSubsection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.concentration.ConcentrationInitializer
addInitialConcentration(CellSubsection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.concentration.ConcentrationInitializer
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.
addLineLikeAgentSegment(LineLikeAgent, Vector2D) - Method in class bio.singa.simulation.model.graphs.AutomatonNode
addMembrane(Membrane) - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneLayer
addMembraneCargo(Quantity<Area>, double, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
addMembranes(Collection<Membrane>) - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneLayer
addMembraneSegment(MembraneSegment) - Method in class bio.singa.simulation.model.graphs.AutomatonNode
addMicrotubule(Vector2D, Vector2D) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
addModuleToSimulation() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: References the module and referenced entities to the referenced simulation.
addNodeToObserve(AutomatonNode) - Method in class bio.singa.simulation.events.EpochUpdateWriter: Initializes a node that will be observed during simulation.
addNodeUpdateListener(UpdateEventListener<UpdatableUpdatedEvent>) - Method in class bio.singa.simulation.model.simulation.SimulationManager: Adds a new listener for node based events.
addPotentialDelta(ConcentrationDelta) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
addPotentialDelta(ConcentrationDelta) - Method in class bio.singa.simulation.model.graphs.AutomatonNode: Adds a potential delta to this node.
addPotentialDelta(ConcentrationDelta) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Adds a potential delta to this updatable.
addPotentialDelta(ConcentrationDelta) - Method in interface bio.singa.simulation.model.simulation.Updatable
addPotentialDisplacementDelta(DisplacementDelta) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager: Adds a displacement delta.
addPotentialSpatialDelta(DisplacementDelta) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
addProduct(ChemicalEntity, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
addProduct(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
addProduct(ChemicalEntity, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
addReactant(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
addReferencedEntities(Collection<? extends ChemicalEntity>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Adds multiple referenced chemical entities.
addReferencedEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Adds a referenced chemical entity.
addReferencedEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.simulation.Simulation
addSegment(AutomatonNode, LineSegment) - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
addState(VesicleStateRegistry.VesicleState) - Static method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
addStochiometricReactant(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction
addSubSection(CellTopology, CellSubsection) - Method in class bio.singa.simulation.model.sections.CellRegion
addSubsectionRepresentation(CellSubsection, Polygon) - Method in class bio.singa.simulation.model.graphs.AutomatonNode
addSubstrate(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
addSubstrate(ChemicalEntity, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
addSubstrate(ChemicalEntity, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
addSubstrate(ChemicalEntity, CellTopology, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
addSubstrate(ChemicalEntity, double, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
addTrajectoryData(Double, TrajectoryData) - Method in class bio.singa.simulation.trajectories.Trajectories
addVariation(FeatureType) - Method in class bio.singa.simulation.features.variation.Variation
addVariation(Variation<?>) - Method in class bio.singa.simulation.features.variation.VariationSet
addVesicle(Vesicle) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
allEntities() - Method in interface bio.singa.simulation.events.EpochUpdateWriter.EntitiesStep
allEntities() - Method in class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
allModules() - Method in class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
allModules() - Method in interface bio.singa.simulation.events.EpochUpdateWriter.ModulesStep
AppliedScale - Class in bio.singa.simulation.features
AppliedScale(double, Evidence) - Constructor for class bio.singa.simulation.features.AppliedScale
AppliedScale() - Constructor for class bio.singa.simulation.features.AppliedScale
applyAssignmentRules() - Method in class bio.singa.simulation.model.simulation.Simulation: Apply all referenced assignment rules.
applyDeltas() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
applyDeltas() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
applyDeltas() - Method in class bio.singa.simulation.model.graphs.AutomatonNode: Applies all final deltas and clears the delta list.
applyDeltas() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Applies all final deltas and clears the delta list.
applyDeltas() - Method in interface bio.singa.simulation.model.simulation.Updatable
applyRule(AutomatonNode) - Method in class bio.singa.simulation.model.rules.AssignmentRule
area - Variable in class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent
AssignmentRule - Class in bio.singa.simulation.model.rules
AssignmentRule(ChemicalEntity) - Constructor for class bio.singa.simulation.model.rules.AssignmentRule
AssignmentRules - Class in bio.singa.simulation.model.rules
associateInGraph(AutomatonGraph) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
associateInGraph(AutomatonGraph) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate
associateVesicles() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
AttachedFilament - Class in bio.singa.simulation.features
AttachedFilament(LineLikeAgent.FilamentType, Evidence) - Constructor for class bio.singa.simulation.features.AttachedFilament
AttachedMotor - Class in bio.singa.simulation.features
AttachedMotor(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.AttachedMotor
AttachmentDistance - Class in bio.singa.simulation.features
AttachmentDistance(Quantity<Length>, Evidence) - Constructor for class bio.singa.simulation.features.AttachmentDistance
AttachmentDistance(double, Evidence) - Constructor for class bio.singa.simulation.features.AttachmentDistance
AutomatonEdge - Class in bio.singa.simulation.model.graphs
AutomatonEdge(int) - Constructor for class bio.singa.simulation.model.graphs.AutomatonEdge
AutomatonGraph - Class in bio.singa.simulation.model.graphs: The Automaton graph class is the underlying graph of cellular graph automaton Simulations.
AutomatonGraph(int, int) - Constructor for class bio.singa.simulation.model.graphs.AutomatonGraph: Creates a new empty graph, initialized with node and edge capacity.
AutomatonGraphRenderer - Class in bio.singa.simulation.renderer
AutomatonGraphRenderer(AutomatonGraph) - Constructor for class bio.singa.simulation.renderer.AutomatonGraphRenderer
AutomatonGraphRenderer() - Constructor for class bio.singa.simulation.renderer.AutomatonGraphRenderer
AutomatonGraphs - Class in bio.singa.simulation.model.graphs
AutomatonNode - Class in bio.singa.simulation.model.graphs: A node of the AutomatonGraph.
AutomatonNode(RectangularCoordinate) - Constructor for class bio.singa.simulation.model.graphs.AutomatonNode
AutomatonNode(int, int) - Constructor for class bio.singa.simulation.model.graphs.AutomatonNode
availableFeatures - Static variable in class bio.singa.simulation.model.agents.pointlike.Vesicle

B

backwardsRateConstant(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.ReversibleReactionBuilder
BINESH2015 - Static variable in class bio.singa.simulation.features.DefaultFeatureSources
bio.singa.simulation - package bio.singa.simulation: The simulations allows for the definition of models and simulations based on modules, that define cellular processes.
bio.singa.simulation.events - package bio.singa.simulation.events
bio.singa.simulation.exceptions - package bio.singa.simulation.exceptions
bio.singa.simulation.features - package bio.singa.simulation.features
bio.singa.simulation.features.variation - package bio.singa.simulation.features.variation
bio.singa.simulation.model.agents - package bio.singa.simulation.model.agents
bio.singa.simulation.model.agents.linelike - package bio.singa.simulation.model.agents.linelike
bio.singa.simulation.model.agents.organelles - package bio.singa.simulation.model.agents.organelles
bio.singa.simulation.model.agents.pointlike - package bio.singa.simulation.model.agents.pointlike
bio.singa.simulation.model.agents.surfacelike - package bio.singa.simulation.model.agents.surfacelike
bio.singa.simulation.model.agents.volumelike - package bio.singa.simulation.model.agents.volumelike
bio.singa.simulation.model.graphs - package bio.singa.simulation.model.graphs
bio.singa.simulation.model.modules - package bio.singa.simulation.model.modules
bio.singa.simulation.model.modules.concentration - package bio.singa.simulation.model.modules.concentration
bio.singa.simulation.model.modules.concentration.functions - package bio.singa.simulation.model.modules.concentration.functions
bio.singa.simulation.model.modules.concentration.imlementations - package bio.singa.simulation.model.modules.concentration.imlementations
bio.singa.simulation.model.modules.concentration.reactants - package bio.singa.simulation.model.modules.concentration.reactants
bio.singa.simulation.model.modules.concentration.scope - package bio.singa.simulation.model.modules.concentration.scope
bio.singa.simulation.model.modules.concentration.specifity - package bio.singa.simulation.model.modules.concentration.specifity
bio.singa.simulation.model.modules.displacement - package bio.singa.simulation.model.modules.displacement
bio.singa.simulation.model.modules.displacement.implementations - package bio.singa.simulation.model.modules.displacement.implementations
bio.singa.simulation.model.modules.qualitative - package bio.singa.simulation.model.modules.qualitative
bio.singa.simulation.model.modules.qualitative.implementations - package bio.singa.simulation.model.modules.qualitative.implementations
bio.singa.simulation.model.parameters - package bio.singa.simulation.model.parameters
bio.singa.simulation.model.rules - package bio.singa.simulation.model.rules
bio.singa.simulation.model.sections - package bio.singa.simulation.model.sections
bio.singa.simulation.model.sections.concentration - package bio.singa.simulation.model.sections.concentration
bio.singa.simulation.model.simulation - package bio.singa.simulation.model.simulation
bio.singa.simulation.renderer - package bio.singa.simulation.renderer
bio.singa.simulation.trajectories - package bio.singa.simulation.trajectories
BioGraphRenderOptions - Class in bio.singa.simulation.renderer
BioGraphRenderOptions() - Constructor for class bio.singa.simulation.renderer.BioGraphRenderOptions
build() - Method in interface bio.singa.simulation.events.EpochUpdateWriter.BuildStep
build() - Method in interface bio.singa.simulation.events.EpochUpdateWriter.ConcentrationUnitStep
build() - Method in interface bio.singa.simulation.events.EpochUpdateWriter.EntitiesStep
build() - Method in class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
build() - Method in interface bio.singa.simulation.events.EpochUpdateWriter.ModulesStep
build() - Method in interface bio.singa.simulation.events.EpochUpdateWriter.TimeUnitStep
build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BuilderStep
build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.BuildStep
build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.DiffusionBuilder
build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.BuildStep
build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.ParameterStep
build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.BuildStep
build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.MembraneDiffusionBuilder
build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.BuildStep
build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder
build() - Method in interface bio.singa.simulation.model.modules.concentration.ModuleBuilder
Builder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
by(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BinderSelection
by(ChemicalEntity, RateConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BinderSelection
by(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
by(ChemicalEntity, RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder

C

calculateDeltas(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction
calculateDeltas(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction: Calculates all deltas for all reactants for the reaction.
calculateDisplacement(Vesicle) - Method in class bio.singa.simulation.model.modules.displacement.implementations.EndocytosisActinBoost
calculateDisplacement(Vesicle) - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleConfinedDiffusion
calculateDisplacement(Vesicle) - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleCytoplasmDiffusion
calculateDisplacement(Vesicle) - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleTransport
calculateMembraneBasedVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction
calculateTotalDisplacement() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
calculateTotalDisplacement() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager: Calculates the total displacement resulting from the potential deltas and sets the result as the next position.
calculateUpdates() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
calculateUpdates() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
calculateUpdates() - Method in class bio.singa.simulation.model.modules.displacement.implementations.EndocytosisActinBoost
calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexAttachment
calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexDiffusivityScaling
calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment
calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion
calculateUpdates() - Method in interface bio.singa.simulation.model.modules.UpdateModule
calculateVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction
calculateVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction
calculateVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction: Calculates the reaction velocity, depending on the kinetic law.
calculateVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction
calculateVelocity(ConcentrationContainer, boolean) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw: Calculates the velocity of the reaction based on the entities in the concentration container.
call() - Method in class bio.singa.simulation.model.simulation.SimulationManager
Cargo - Class in bio.singa.simulation.features
Cargo(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.Cargo
cargo(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.CargoStep
cargo(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.MembraneDiffusionBuilder
cargo(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.CargoStep
cargo(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder
CargoAdditionRate - Class in bio.singa.simulation.features
CargoAdditionRate(Quantity<FirstOrderRate>, Evidence) - Constructor for class bio.singa.simulation.features.CargoAdditionRate
CargoAdditionRate(double, Unit<FirstOrderRate>, Evidence) - Constructor for class bio.singa.simulation.features.CargoAdditionRate
Cargoes - Class in bio.singa.simulation.features
Cargoes(Set<ChemicalEntity>, Evidence) - Constructor for class bio.singa.simulation.features.Cargoes
CELL_OUTER_MEMBRANE - Static variable in class bio.singa.simulation.model.sections.CellSubsections
CELL_OUTER_MEMBRANE_REGION - Static variable in class bio.singa.simulation.model.sections.CellRegions
CellRegion - Class in bio.singa.simulation.model.sections
CellRegion(String) - Constructor for class bio.singa.simulation.model.sections.CellRegion
CellRegion(String, GoTerm) - Constructor for class bio.singa.simulation.model.sections.CellRegion
CellRegions - Class in bio.singa.simulation.model.sections
CellRegions() - Constructor for class bio.singa.simulation.model.sections.CellRegions
CellSubsection - Class in bio.singa.simulation.model.sections: A cell subsection organizes the contents of a Updatable.
CellSubsection(String) - Constructor for class bio.singa.simulation.model.sections.CellSubsection: Creates a new cell subsection with the given identifier and dynamic preferred concentration unit.
CellSubsection(String, GoTerm) - Constructor for class bio.singa.simulation.model.sections.CellSubsection
CellSubsections - Class in bio.singa.simulation.model.sections
CellSubsections() - Constructor for class bio.singa.simulation.model.sections.CellSubsections
CellTopology - Enum in bio.singa.simulation.model.sections: The cell topology defines how the subsections are spatially organized.
checkFeatures() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
checkFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
checkFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction
checkFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction
checkFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction
checkFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport
checkFeatures() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
checkFeatures() - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleTransport
checkFeatures() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
checkFeatures() - Method in interface bio.singa.simulation.model.modules.UpdateModule
circleRegion(AutomatonGraph, CellRegion, RectangularCoordinate, int) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs
ClathrinMediatedEndocytosis - Class in bio.singa.simulation.model.modules.qualitative.implementations
ClathrinMediatedEndocytosis() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
ClathrinMediatedEndocytosis.Pit - Class in bio.singa.simulation.model.modules.qualitative.implementations
clear() - Static method in class bio.singa.simulation.model.parameters.ParameterStorage
clearAssociatedNodes() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
clearDeltas() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Clears all full end half deltas.
clearPotentialConcentrationDeltas() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
clearPotentialConcentrationDeltas() - Method in class bio.singa.simulation.model.graphs.AutomatonNode: Clears the list of potential deltas.
clearPotentialConcentrationDeltas() - Method in interface bio.singa.simulation.model.simulation.Updatable
clearPotentialDeltas() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Clears the list of potential deltas.
clearPotentialDeltas(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.DependentUpdate
clearPotentialDeltas(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.IndependentUpdate
clearPotentialDeltas(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate
clearPotentialDeltas(Updatable) - Method in interface bio.singa.simulation.model.modules.concentration.scope.UpdateScope: Clears all concentration deltas that may be assigned to the given updatable.
clearPotentialDeltasBut(UpdateModule) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
clearPotentialDeltasBut(UpdateModule) - Method in class bio.singa.simulation.model.graphs.AutomatonNode
clearPotentialDeltasBut(UpdateModule) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Clears the list of potential deltas retaining updates from a specific module.
clearPotentialDeltasBut(UpdateModule) - Method in interface bio.singa.simulation.model.simulation.Updatable
clearPotentialDisplacementDeltas() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
clearPotentialDisplacementDeltas() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager: Clears all potential displacement deltas.
clearPreviouslyObservedDeltas() - Method in class bio.singa.simulation.model.simulation.Simulation
clearUpdates() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
CLOSE_BRACKET - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for closing brackets
closeWriters() - Method in class bio.singa.simulation.events.EpochUpdateWriter: Close all associated writers.
collectProductsString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction
collectSubstrateString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction
collectUpdatables() - Method in class bio.singa.simulation.model.simulation.Simulation
combineToGif() - Method in class bio.singa.simulation.events.GraphImageWriter
ComplexBuildingReaction - Class in bio.singa.simulation.model.modules.concentration.imlementations: Complex building or breaking reactions are a special kind of ReversibleReaction.
ComplexBuildingReaction() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
ComplexBuildingReaction.BindeeSectionSelection - Interface in bio.singa.simulation.model.modules.concentration.imlementations
ComplexBuildingReaction.BindeeSelection - Interface in bio.singa.simulation.model.modules.concentration.imlementations
ComplexBuildingReaction.BinderSectionSelection - Interface in bio.singa.simulation.model.modules.concentration.imlementations
ComplexBuildingReaction.BinderSelection - Interface in bio.singa.simulation.model.modules.concentration.imlementations
ComplexBuildingReaction.BuilderStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
ComplexBuildingReaction.ComplexBuildingReactionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations
ComplexBuildingReactionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
ConcentrationBasedModule<DeltaFunctionType extends AbstractDeltaFunction> - Class in bio.singa.simulation.model.modules.concentration: Concentration based modules handle updates that are applied to the concentrations in Updatables during a simulation.
ConcentrationBasedModule() - Constructor for class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Creates a new concentration based module.
ConcentrationContainer - Class in bio.singa.simulation.model.sections: The concentration container manages the concentrations of one updatable.
ConcentrationContainer() - Constructor for class bio.singa.simulation.model.sections.ConcentrationContainer: Creates a new concentration container.
ConcentrationData - Class in bio.singa.simulation.trajectories
ConcentrationDelta - Class in bio.singa.simulation.model.modules.concentration: The delta object manages the change that will be applied to the concentration of a specific ChemicalEntity in a CellSubsection.
ConcentrationDelta(UpdateModule, CellSubsection, ChemicalEntity, Quantity<MolarConcentration>) - Constructor for class bio.singa.simulation.model.modules.concentration.ConcentrationDelta: Creates a new concentration delta.
ConcentrationDeltaIdentifier - Class in bio.singa.simulation.model.modules.concentration: Used to identify changes to concentrations (ConcentrationDeltas) (mostly in maps).
ConcentrationDeltaIdentifier(Updatable, CellSubsection, ChemicalEntity) - Constructor for class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier: Creates a new DeltaIdentifier.
ConcentrationDeltaManager - Class in bio.singa.simulation.model.modules.concentration: The ConcentrationDeltaManager handles current concentrations of an updatable and the updates to those concentrations that should be applied during simulation.
ConcentrationDeltaManager(ConcentrationContainer) - Constructor for class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Creates a new Concentration Delta Manager.
concentrationFormat(QuantityFormatter<MolarConcentration>) - Method in interface bio.singa.simulation.events.EpochUpdateWriter.ConcentrationUnitStep
concentrationFormat(QuantityFormatter<MolarConcentration>) - Method in class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
ConcentrationInitializer - Class in bio.singa.simulation.model.sections.concentration
ConcentrationInitializer() - Constructor for class bio.singa.simulation.model.sections.concentration.ConcentrationInitializer
ConcentrationInitializer(Set<InitialConcentration>) - Constructor for class bio.singa.simulation.model.sections.concentration.ConcentrationInitializer
ConcentrationPool - Class in bio.singa.simulation.model.sections: The concentration pool manages the MolarConcentration of ChemicalEntitys in CellSubsections.
ConcentrationPool() - Constructor for class bio.singa.simulation.model.sections.ConcentrationPool: Creates a new, empty concentration pool.
ConcentrationVariation - Class in bio.singa.simulation.features.variation
ConcentrationVariation(CellRegion, CellSubsection, ChemicalEntity) - Constructor for class bio.singa.simulation.features.variation.ConcentrationVariation
ConcentrationVariation(CellSubsection, ChemicalEntity) - Constructor for class bio.singa.simulation.features.variation.ConcentrationVariation
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.
containsEntity(CellTopology, ChemicalEntity) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer
CortexDiffusivity - Class in bio.singa.simulation.features
CortexDiffusivity(Quantity<Diffusivity>, Evidence) - Constructor for class bio.singa.simulation.features.CortexDiffusivity
create() - Static method in class bio.singa.simulation.events.EpochUpdateWriter
create(Object) - Method in class bio.singa.simulation.features.variation.ConcentrationVariation
create(Object) - Method in class bio.singa.simulation.features.variation.EntityFeatureVariation
create(Object) - Method in class bio.singa.simulation.features.variation.ModuleFeatureVariation
create(Object) - Method in class bio.singa.simulation.features.variation.Variation
create() - Method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes
createActinCortex(Membrane, MooreRectangularDirection, Quantity<Length>, Quantity<Length>) - Static method in class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgentFactory
createActinCortex(Membrane, Quantity<Length>, Quantity<Length>) - Static method in class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgentFactory
createClosedMembrane(Collection<Vector2D>, CellRegion, CellRegion, AutomatonGraph, Map<Vector2D, CellRegion>) - Static method in class bio.singa.simulation.model.agents.surfacelike.MembraneFactory
createCompartmentTestEnvironment() - Static method in class bio.singa.simulation.model.simulation.SimulationExamples
createDecompositionReactionExample() - Static method in class bio.singa.simulation.model.simulation.SimulationExamples: This simulation simulates the thermal decomposition of dinitrogen pentaoxide.
createDiffusionModuleExample(int, Quantity<Time>) - Static method in class bio.singa.simulation.model.simulation.SimulationExamples: This simulation simulates a diffusion of small molecules in a rectangular gird graph.
createEquilibriumReactionExample() - Static method in class bio.singa.simulation.model.simulation.SimulationExamples: This simulation simulates a equilibrium reaction.
createIodineMultiReactionExample() - Static method in class bio.singa.simulation.model.simulation.SimulationExamples: This simulation simulates a multiple reactions involving iodine.
createLinearMembrane(Collection<Vector2D>, CellRegion, CellRegion, NeumannRectangularDirection, AutomatonGraph, Map<Vector2D, CellRegion>, Rectangle) - Static method in class bio.singa.simulation.model.agents.surfacelike.MembraneFactory
createMichaelisMentenReactionExample() - Static method in class bio.singa.simulation.model.simulation.SimulationExamples: This simulation simulates a MichaelisMentenReaction, where D-Fructose 1-phosphate is convertet to glycerone phosphate and D-glyceraldehyde using fructose bisphosphate aldolase.
createModule(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
createModule(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.DiffusionBuilder
createModule(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
createModule(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.MembraneDiffusionBuilder
createModule(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
createModule(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder
createModule(Simulation) - Method in interface bio.singa.simulation.model.modules.concentration.ModuleBuilder
createObject(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction.MichaelisMentenReactionBuilder
createObject(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction.NthOrderReactionBuilder
createObject(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
createObject(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.ReversibleReactionBuilder
createRectangularAutomatonGraph(int, int) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs
createSynthesisReactionExample() - Static method in class bio.singa.simulation.model.simulation.SimulationExamples: This simulation simulates the synthesis of 1,3,5-octatriene (C8H12) from Buta-1,3-diene (C4H6).
CYTOPLASM - Static variable in class bio.singa.simulation.model.sections.CellSubsections
CytoplasmDiffusivity - Class in bio.singa.simulation.features
CytoplasmDiffusivity(Quantity<Diffusivity>, Evidence) - Constructor for class bio.singa.simulation.features.CytoplasmDiffusivity
CYTOSOL_A - Static variable in class bio.singa.simulation.model.sections.CellRegion
CYTOSOL_B - Static variable in class bio.singa.simulation.model.sections.CellRegion

D

DecayingEntity - Class in bio.singa.simulation.features
DecayingEntity(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.DecayingEntity
decreaseTimeStep() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler
DEFAULT_ACTIN_VELOCITY - Static variable in class bio.singa.simulation.features.ActinBoostVelocity: Average lateral displacement velocity after scission for 11 seconds.
DEFAULT_BUDDING_RATE - Static variable in class bio.singa.simulation.features.PitFormationRate: About three events per 10^8 nm^2 s^-1, developing into actual vesicles.
DEFAULT_CORTEX_DIFFUSIVITY - Static variable in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexDiffusivityScaling
DEFAULT_CYTOPLASM_DIFFUSIFITY - Static variable in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexDiffusivityScaling
DEFAULT_DYNEIN_ATTACHMENT_DISTANCE - Static variable in class bio.singa.simulation.features.AttachmentDistance: Size of the dynein complex fom vesicle surface to microtubule.
DEFAULT_MATURATION_TIME - Static variable in class bio.singa.simulation.features.MaturationTime: Average maturation time is 100 seconds.
DEFAULT_MOTOR_VELOCITY - Static variable in class bio.singa.simulation.features.MotorMovementVelocity: Average lateral displacement velocity after scission for 11 seconds.
DEFAULT_TETHERING_TIME - Static variable in class bio.singa.simulation.features.TetheringTime: Average maturation time is 100 seconds.
DEFAULT_VESICLE_RADIUS - Static variable in class bio.singa.simulation.features.VesicleRadius
DefaultFeatureSources - Class in bio.singa.simulation.features
deltaIsValid(ConcentrationDelta) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns true if the delta is valid, i.e.
deltasAreBelowDisplacementCutoff() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
DependentUpdate - Class in bio.singa.simulation.model.modules.concentration.scope: Dependent Updatable ConcentrationBasedModules require an integer state of basically all updatables in a simulation.
DependentUpdate(ConcentrationBasedModule<?>) - Constructor for class bio.singa.simulation.model.modules.concentration.scope.DependentUpdate: Initializes the update scope for the corresponding module.
determineDeltas(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific
determineDeltas(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.specifity.SectionSpecific
determineDeltas(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.specifity.UpdatableSpecific
determineDeltas(ConcentrationContainer) - Method in interface bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity: Determines all deltas for a Concentration container.
determineDeltas(Vesicle) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
determineLargestLocalError() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: The local error is calculated and the largest local error of the current epoch resulting from the executing module is returned.
Diffusion - Class in bio.singa.simulation.model.modules.concentration.imlementations: Diffusion is the fundamental force governing the random movement of molecules in cells.
Diffusion() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion
Diffusion.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
Diffusion.DiffusionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations
Diffusion.SelectionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
DiffusionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.DiffusionBuilder
DisplacementBasedModule - Class in bio.singa.simulation.model.modules.displacement
DisplacementBasedModule() - Constructor for class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
DisplacementDelta - Class in bio.singa.simulation.model.modules.displacement
DisplacementDelta(DisplacementBasedModule, Vector2D) - Constructor for class bio.singa.simulation.model.modules.displacement.DisplacementDelta
DisplacementDeltaManager - Class in bio.singa.simulation.model.modules.displacement: The DisplacementDeltaManager handles the current position an updatable amd the updates to this position during simulation.
DisplacementDeltaManager(Vector2D) - Constructor for class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager: Creates a new Displacement Delta Manager.
done() - Method in class bio.singa.simulation.model.simulation.SimulationManager
drawEdge(AutomatonEdge) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer
drawNode(AutomatonNode) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer
DynamicReaction - Class in bio.singa.simulation.model.modules.concentration.imlementations
DynamicReaction() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
DynamicReaction.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
DynamicReaction.DynamicReactionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations
DynamicReaction.KineticLawStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
DynamicReaction.ParameterStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
DynamicReactionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder

E

EARLY_ENDOSOME_LUMEN - Static variable in class bio.singa.simulation.model.sections.CellSubsections
EARLY_ENDOSOME_MEMBRANE - Static variable in class bio.singa.simulation.model.sections.CellSubsections
EARLY_ENDOSOME_VESICLE_REGION - Static variable in class bio.singa.simulation.model.sections.CellRegions
EHRLICH2004 - Static variable in class bio.singa.simulation.features.DefaultFeatureSources
emitGraphEvent(Simulation) - Method in class bio.singa.simulation.model.simulation.SimulationManager
emitNodeEvent(Simulation, Updatable) - Method in class bio.singa.simulation.model.simulation.SimulationManager
emptyCopy() - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns a empty copy of this container, keeping subsections and cell topologies associated.
EndocytosisActinBoost - Class in bio.singa.simulation.model.modules.displacement.implementations
EndocytosisActinBoost() - Constructor for class bio.singa.simulation.model.modules.displacement.implementations.EndocytosisActinBoost
EndocytosisCheckpointTime - Class in bio.singa.simulation.features
EndocytosisCheckpointTime(Quantity<Time>, Evidence) - Constructor for class bio.singa.simulation.features.EndocytosisCheckpointTime
EndocytosisCheckpointTime(double, Evidence) - Constructor for class bio.singa.simulation.features.EndocytosisCheckpointTime
EndocytosisCkeckpointConcentration - Class in bio.singa.simulation.features
EndocytosisCkeckpointConcentration(Quantity<MolarConcentration>, Evidence) - Constructor for class bio.singa.simulation.features.EndocytosisCkeckpointConcentration
EndocytosisPlayground - Class in bio.singa.simulation.model.agents
EndocytosisPlayground() - Constructor for class bio.singa.simulation.model.agents.EndocytosisPlayground
entities(Set<ChemicalEntity>) - Method in interface bio.singa.simulation.events.EpochUpdateWriter.EntitiesStep
entities(Set<ChemicalEntity>) - Method in class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
EntityDeltaFunction - Class in bio.singa.simulation.model.modules.concentration.functions: Entity delta functions are AbstractDeltaFunctions which return only one concentration delta.
EntityDeltaFunction(Function<ConcentrationContainer, ConcentrationDelta>, Predicate<ConcentrationContainer>) - Constructor for class bio.singa.simulation.model.modules.concentration.functions.EntityDeltaFunction: Creates a new entity delta function with the specified condition and function.
EntityFeatureVariation<FeatureType> - Class in bio.singa.simulation.features.variation
EntityFeatureVariation(ChemicalEntity, Class<? extends Feature<FeatureType>>) - Constructor for class bio.singa.simulation.features.variation.EntityFeatureVariation
EntityFeatureVariationEntry - Class in bio.singa.simulation.features.variation
EntityFeatureVariationEntry(ChemicalEntity, Feature<?>) - Constructor for class bio.singa.simulation.features.variation.EntityFeatureVariationEntry
EntitySpecific - Class in bio.singa.simulation.model.modules.concentration.specifity: Entity specific ConcentrationBasedModules calculate their AbstractDeltaFunction for every chemical entity and every subsection of an updatable.
EntitySpecific(ConcentrationBasedModule<EntityDeltaFunction>) - Constructor for class bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific: Initializes the update specificity for the corresponding module.
enzyme(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction.MichaelisMentenReactionBuilder
EpochUpdateWriter - Class in bio.singa.simulation.events: This class can be used to write the concentration of chemical entities of a node and the changes applied to the node to a file.
EpochUpdateWriter() - Constructor for class bio.singa.simulation.events.EpochUpdateWriter
EpochUpdateWriter.BuildStep - Interface in bio.singa.simulation.events
EpochUpdateWriter.ConcentrationUnitStep - Interface in bio.singa.simulation.events
EpochUpdateWriter.EntitiesStep - Interface in bio.singa.simulation.events
EpochUpdateWriter.EpochUpdateWriterBuilder - Class in bio.singa.simulation.events
EpochUpdateWriter.FolderStep - Interface in bio.singa.simulation.events
EpochUpdateWriter.ModulesStep - Interface in bio.singa.simulation.events
EpochUpdateWriter.SimulationStep - Interface in bio.singa.simulation.events
EpochUpdateWriter.TimeUnitStep - Interface in bio.singa.simulation.events
EpochUpdateWriter.WorkspaceStep - Interface in bio.singa.simulation.events
EpochUpdateWriterBuilder() - Constructor for class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
EPSILON - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for the epsilon terminal
equals(Object) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry.VesicleState
equals(Object) - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
equals(Object) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier
equals(Object) - Method in class bio.singa.simulation.model.sections.CellRegion
equals(Object) - Method in class bio.singa.simulation.model.sections.CellSubsection
equals(Object) - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
equals(Object) - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
estimateDiffusivity(Vesicle) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexDiffusivityScaling
evaluateModuleState() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
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
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.
ExpressionParser - Class in uk.co.cogitolearning.cogpar: A parser for mathematical expressions.
ExpressionParser() - Constructor for class uk.co.cogitolearning.cogpar.ExpressionParser
EXTRACELLULAR_REGION - Static variable in class bio.singa.simulation.model.sections.CellRegions
EXTRACELLULAR_REGION - Static variable in class bio.singa.simulation.model.sections.CellSubsections

F

FeatureManager - Class in bio.singa.simulation.model.parameters
FeatureManager() - Constructor for class bio.singa.simulation.model.parameters.FeatureManager
FeatureRandomizer - Class in bio.singa.simulation.features
FeatureRandomizer() - Constructor for class bio.singa.simulation.features.FeatureRandomizer
features - Variable in class bio.singa.simulation.model.agents.pointlike.Vesicle
FieldSupplier - Class in bio.singa.simulation.model.modules.concentration: The field supplier manages all files required for different behaviours of a module.
fillRegion(AutomatonGraph, CellRegion, RectangularCoordinate, int) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs
folder(Path, boolean) - Method in class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
folder(Path, boolean) - Method in interface bio.singa.simulation.events.EpochUpdateWriter.FolderStep
forAll(ChemicalEntity...) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.DiffusionBuilder
forAll(Collection<ChemicalEntity>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.DiffusionBuilder
forAll(ChemicalEntity...) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.SelectionStep
forAll(Collection<ChemicalEntity>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.SelectionStep
formingComplex(ComplexedChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BuilderStep
formingComplex(ComplexedChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
forSolute(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder
forSolute(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SolutesStep
forSolutes(ChemicalEntity...) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder
forSolutes(Collection<ChemicalEntity>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder
forSolutes(ChemicalEntity...) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SolutesStep
forSolutes(Collection<ChemicalEntity>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SolutesStep
forVesicle(String) - Static method in class bio.singa.simulation.model.sections.CellRegion
forwardsRateConstant(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.ReversibleReactionBuilder
fullCopy() - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns a full copy of this container, keeping concentrations.
fullCopy() - Method in class bio.singa.simulation.model.sections.ConcentrationPool: Creates a copy of this concentration pool.
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.
FusionPairs - Class in bio.singa.simulation.features: Snare pairs required for fusion event to trigger
FusionPairs(Quantity<Dimensionless>, Evidence) - Constructor for class bio.singa.simulation.features.FusionPairs

G

generateAllCombinations() - Method in class bio.singa.simulation.features.variation.VariationSet
generateMapOfEntities(AutomatonGraph) - Static method in class bio.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.
get(String) - Static method in class bio.singa.simulation.model.parameters.ParameterStorage
get(CellSubsection, ChemicalEntity) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns the concentration of the entity in the corresponding subsection.
get(CellTopology, ChemicalEntity) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns the concentration of the entity in the corresponding topology.
get(ChemicalEntity) - Method in class bio.singa.simulation.model.sections.ConcentrationPool: Returns the concentration of a entity.
getAdditionDelta() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit
getAffectedParameters() - Method in class bio.singa.simulation.features.variation.VariationSet
getAll() - Static method in class bio.singa.simulation.model.parameters.ParameterStorage
getAllChemicalEntities() - Method in class bio.singa.simulation.model.simulation.Simulation
getAllFeatures() - Method in class bio.singa.simulation.model.parameters.FeatureManager
getAllReferencedSections() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getAllReferencedSections() - Method in class bio.singa.simulation.model.graphs.AutomatonNode: Returns all referenced sections in this node.
getAllReferencedSections() - Method in interface bio.singa.simulation.model.simulation.Updatable
getApplicationCondition() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns the application condition for this module.The module is only evaluated if the updatable fulfills the given predicate.
getArea() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getArea() - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment
getArea() - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent
getArea() - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
getAspiringPits() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
getAssociatedLineLikeAgents() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
getAssociatedNode() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit
getAssociatedNodes() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
getAssociatedNodes() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getAttachedFilament() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getAvailableFeatures() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getAvailableFeatures() - Method in class bio.singa.simulation.model.parameters.FeatureManager
getBindee() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
getBindeeTopology() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
getBinder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
getBinderTopology() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
getBioRenderingOptions() - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer
getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion
getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion
getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction
getBuilder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction.MichaelisMentenReactionBuilder
getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction
getBuilder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction.NthOrderReactionBuilder
getBuilder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction
getBuilder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.ReversibleReactionBuilder
getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport
getCargoConcentration() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit
getCatalysts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
getCellRegion() - Method in class bio.singa.simulation.features.variation.ConcentrationVariation
getCellRegion() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getCellRegion(String) - Method in class bio.singa.simulation.model.graphs.AutomatonGraph: Return the cell section with the given identifier.
getCellRegion() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
getCellRegion() - Method in interface bio.singa.simulation.model.simulation.Updatable
getCellSections() - Method in class bio.singa.simulation.model.graphs.AutomatonGraph: Returns all CellSubsections referenced in this graph.
getCellSubsection() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDelta: Returns the subsection.
getCheckpointTime() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit
getChemicalEntities() - Method in class bio.singa.simulation.model.simulation.Simulation: Returns the chemical entities.
getChemicalEntity() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDelta: Returns the chemical entity.
getChemicalEntity() - Method in class bio.singa.simulation.model.modules.concentration.LocalError: Returns the chemical entity where the error occurred.
getChemicalEntity(String) - Method in class bio.singa.simulation.model.simulation.Simulation
getCircleRepresentation() - Method in class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre
getCircleRepresentation() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getColor(GoTerm) - Static method in class bio.singa.simulation.model.sections.CellSubsections
getColor(CellSubsection) - Static method in class bio.singa.simulation.model.sections.CellSubsections
getColor(CellRegion) - Static method in class bio.singa.simulation.model.sections.CellSubsections
getColorForUpdatable(Updatable) - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions
getComplex() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
getConcentration(ChemicalEntity) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getConcentration() - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
getConcentrationContainer() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getConcentrationContainer() - Method in class bio.singa.simulation.model.graphs.AutomatonNode: Returns the ConcentrationContainer used by this node.
getConcentrationContainer() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Returns the current concentration container.
getConcentrationContainer() - Method in interface bio.singa.simulation.model.simulation.Updatable
getConcentrationData() - Method in class bio.singa.simulation.trajectories.TrajectoryData
getConcentrationInitializer() - Method in class bio.singa.simulation.model.simulation.Simulation
getConcentrationMap() - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
getConcentrations() - Method in class bio.singa.simulation.model.sections.ConcentrationContainer
getConcentrations() - Method in class bio.singa.simulation.model.sections.ConcentrationPool
getConcentrations() - Method in class bio.singa.simulation.trajectories.ConcentrationData
getConcentrationUnit() - Method in class bio.singa.simulation.trajectories.Trajectories
getCondition() - Method in class bio.singa.simulation.model.modules.concentration.functions.AbstractDeltaFunction: Returns the application condition.
getConfinedVolume() - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleConfinedDiffusion
getConfiningState() - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleConfinedDiffusion
getCopy() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
getCortex() - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLayer
getCurrentEntity() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Returns the current chemical entity.
getCurrentFullDeltas() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Returns all currently available full deltas.
getCurrentHalfDeltas() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Returns all currently available half deltas.
getCurrentPosition() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getCurrentPosition() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager: Returns the current position.
getCurrentSubsection() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Returns the current subsection.
getCurrentUpdatable() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Returns the current updatable.
getDeltaCutoff() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns the cutoff where deltas are validated to be effectively zero.
getDeltaVector() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDelta
getDescription() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry.VesicleState
getDesity(Vector2D) - Method in class bio.singa.simulation.model.agents.volumelike.ActinCortex
getDrawingHeight() - Method in class bio.singa.simulation.events.GraphImageWriter
getDrawingHeight() - Method in class bio.singa.simulation.model.agents.EndocytosisPlayground
getDrawingHeight() - Method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground
getDrawingHeight() - Method in class bio.singa.simulation.model.agents.pointlike.VesiclePlayground
getDrawingWidth() - Method in class bio.singa.simulation.events.GraphImageWriter
getDrawingWidth() - Method in class bio.singa.simulation.model.agents.EndocytosisPlayground
getDrawingWidth() - Method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground
getDrawingWidth() - Method in class bio.singa.simulation.model.agents.pointlike.VesiclePlayground
getEdgeColor(AutomatonEdge) - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions
getElapsedTime() - Method in class bio.singa.simulation.events.GraphUpdatedEvent
getElapsedTime() - Method in class bio.singa.simulation.model.simulation.Simulation
getEndingPoint() - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment
getEntity() - Method in class bio.singa.simulation.features.variation.ConcentrationVariation
getEntity() - Method in class bio.singa.simulation.features.variation.EntityFeatureVariation
getEntity() - Method in class bio.singa.simulation.features.variation.EntityFeatureVariationEntry
getEntity() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier: Returns the chemical entity the delta is assigned to.
getEntity() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant: Gets the entity representing this reactant.
getEntity() - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
getEntity() - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
getEntityReference() - Method in class bio.singa.simulation.model.rules.AssignmentRule
getEpoch() - Method in class bio.singa.simulation.model.simulation.Simulation
getErrorCutoff() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns the cutoff where numerical errors to be considered irretrievably unstable.
getEvidence() - Method in interface bio.singa.simulation.model.sections.concentration.InitialConcentration
getEvidence() - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
getEvidence() - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
getExpressionString() - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
getExpressionTokenizer() - Static method in class uk.co.cogitolearning.cogpar.Tokenizer: A static method that returns a tokenizer for mathematical expressions
getFeature() - Method in class bio.singa.simulation.features.variation.VariationEntry
getFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns the requested feature.
getFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
getFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
getFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.parameters.FeatureManager
getFeatureClass() - Method in class bio.singa.simulation.features.variation.EntityFeatureVariation
getFeatureClass() - Method in class bio.singa.simulation.features.variation.ModuleFeatureVariation
getFeatureMap() - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
getFeatures() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getFeatures() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns all features of this module (not its entities).
getFeatures() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
getFeatures() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
getFeatures() - Method in interface bio.singa.simulation.model.modules.UpdateModule
getFeatures() - Method in class bio.singa.simulation.model.parameters.FeatureManager
getFilaments() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
getFilaments() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate
getFilaments(Path, String, NeumannRectangularDirection) - Static method in class bio.singa.simulation.model.agents.organelles.OrganelleImageParser
getFinalDeltas() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Returns all deltas that are going to be applied to this node.
getFunction() - Method in class bio.singa.simulation.model.modules.concentration.functions.EntityDeltaFunction: Returns the function.
getFunction() - Method in class bio.singa.simulation.model.modules.concentration.functions.SectionDeltaFunction: Returns the function.
getFunction() - Method in class bio.singa.simulation.model.modules.concentration.functions.UpdatableDeltaFunction: Returns the function.
getGoTerm() - Method in class bio.singa.simulation.model.sections.CellRegion
getGoTerm() - Method in class bio.singa.simulation.model.sections.CellSubsection
getGraph() - Method in class bio.singa.simulation.events.GraphUpdatedEvent: Returns the encapsulated graph.
getGraph() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
getGraph() - Method in class bio.singa.simulation.model.simulation.Simulation
getGraphicsContext() - Method in class bio.singa.simulation.model.agents.EndocytosisPlayground
getGraphicsContext() - Method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground
getGraphicsContext() - Method in class bio.singa.simulation.model.agents.pointlike.VesiclePlayground
getGraphListeners() - Method in class bio.singa.simulation.model.simulation.SimulationManager
getGroups() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
getHalfScaledQuantity() - Method in class bio.singa.simulation.features.AppliedScale
getHalfScaledQuantity() - Method in class bio.singa.simulation.model.parameters.Parameter
getHalfStepConcentration(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.DependentUpdate
getHalfStepConcentration(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.IndependentUpdate
getHalfStepConcentration(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate
getHalfStepConcentration(Updatable) - Method in interface bio.singa.simulation.model.modules.concentration.scope.UpdateScope: Return the half step concentration of a node after the full update has been calculated for the full step and the resulting delta is known.
getIdentifier() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry.VesicleState
getIdentifier() - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
getIdentifier() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns the identifier of this module.
getIdentifier() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
getIdentifier() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
getIdentifier() - Method in interface bio.singa.simulation.model.modules.UpdateModule
getIdentifier() - Method in class bio.singa.simulation.model.parameters.Parameter
getIdentifier() - Method in class bio.singa.simulation.model.sections.CellRegion
getIdentifier() - Method in class bio.singa.simulation.model.sections.CellSubsection: Returns the identifier.
getInitialConcentrations() - Method in class bio.singa.simulation.model.sections.concentration.ConcentrationInitializer
getInnerRegion() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
getInnerRegion() - Method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes
getInnerRegion() - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
getInnerSubsection() - Method in class bio.singa.simulation.model.sections.CellRegion
getInnerSubsection() - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns the inner subsection.
getInverseRegionMap() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
getKineticLaw() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction: Returns the kinetic law.
getLargestError() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler
getLargestLocalError() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Returns the largest error as of yet.
getLineLayer() - Method in class bio.singa.simulation.model.simulation.Simulation
getListeners() - Method in class bio.singa.simulation.events.GraphEventEmitter
getListeners() - Method in class bio.singa.simulation.events.NodeEventEmitter
getMembraneArea() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
getMembraneLayer() - Method in class bio.singa.simulation.model.simulation.Simulation
getMembraneRegion() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
getMembraneRegion() - Method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes
getMembraneRegion() - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
getMembranes() - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneLayer
getMembraneSegments() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
getMembraneSubsection() - Method in class bio.singa.simulation.model.sections.CellRegion
getMembraneSubsection() - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns the membrane subsection.
getMessage() - Method in exception uk.co.cogitolearning.cogpar.ParserException: Overrides RuntimeException.getMessage to add the token information into the error message.
getMicrotubuleOrganizingCentre() - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneLayer
getMinusEnd() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
getMinusEndBehaviour() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
getModule() - Method in class bio.singa.simulation.features.variation.ModuleFeatureVariation
getModule() - Method in class bio.singa.simulation.features.variation.ModuleFeatureVariationEntry
getModule() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDelta: Returns the module, that calculated this delta.
getModule() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
getModule() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.DiffusionBuilder
getModule() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
getModule() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.MembraneDiffusionBuilder
getModule() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
getModule() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder
getModule() - Method in interface bio.singa.simulation.model.modules.concentration.ModuleBuilder
getModule() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDelta
getModules() - Method in class bio.singa.simulation.model.simulation.Simulation
getName() - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode
getNextPosition() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getNextPosition() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager: Returns the next position.
getNode() - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment
getNodeColorScale() - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions
getNodeHighlightEntity() - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions
getNodeListeners() - Method in class bio.singa.simulation.model.simulation.SimulationManager: Returns all currently registered node event listeners.
getNumberOfMolecules() - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
getObservedUpdatables() - Method in class bio.singa.simulation.model.simulation.Simulation
getOrganelleTemplate(String) - Static method in class bio.singa.simulation.model.agents.organelles.OrganelleImageParser
getOrigin() - Method in class bio.singa.simulation.model.parameters.Parameter
getOuterSubsection() - Method in class bio.singa.simulation.model.sections.CellRegion
getOuterSubsection() - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns the outer subsection.
getParameterMap() - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
getPath() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
getPlusEnd() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
getPlusEndBehaviour() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
getPolygon() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
getPool(CellSubsection) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns the topology and concentration pool for the subsection.
getPool(CellTopology) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns the subsection and concentration pool for the topology.
getPoolsOfConcentration() - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns all concentration pools in this container.
getPotentialConcentrationDeltas() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getPotentialConcentrationDeltas() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
getPotentialConcentrationDeltas() - Method in interface bio.singa.simulation.model.simulation.Updatable
getPotentialDeltas() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Returns all potential deltas that should be applied.
getPotentialDisplacementDelta(DisplacementBasedModule) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager: Returns a specific delta applied by the given module.
getPotentialDisplacementDeltas() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager: Returns the potential displacement deltas.
getPreferredConcentrationUnit() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant
getPreferredTopology() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant
getPreviousObservedDeltas(Updatable) - Method in class bio.singa.simulation.model.simulation.Simulation
getProductEntities() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction: Returns all products of this reaction.
getProducts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
getProducts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction
getQuantity() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDelta: Returns the quantity of the change.
getQuantity() - Method in class bio.singa.simulation.model.parameters.Parameter
getRadius() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getReactionOrder() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant: Returns the reaction order.
getReactionString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
getReactionString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction: Returns a nicely formatted string representation of the reaction.
getReactionString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction
getRecalculationCutoff() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler
getReferencedEntities() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns all chemical entities that might be accessed by this module.
getReferencedEntities() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
getReferencedEntities() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
getReferencedEntities() - Method in interface bio.singa.simulation.model.modules.UpdateModule
getReferencedEntities() - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns all entities referenced in any concentration pool.
getReferencedEntities() - Method in class bio.singa.simulation.model.sections.ConcentrationPool: Returns all entities referenced in this map.
getReferencedSubSections() - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns all subsections, referenced in this container.
getRegion(Vector2D) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
getRegion() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getRegion(Map<CellRegion, Set<Vector2D>>, Vector2D) - Static method in class bio.singa.simulation.model.agents.surfacelike.MembraneTracer
getRegion() - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
getRegion() - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
getRegionMap() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
getRegionMap() - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
getRegions() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
getRenderingMode() - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions
getRequiredFeatures() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
getRequiredFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
getRequiredFeatures() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
getRequiredFeatures() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
getRequiredFeatures() - Method in interface bio.singa.simulation.model.modules.UpdateModule
getRequiredFeatures() - Method in class bio.singa.simulation.model.parameters.FeatureManager
getRole() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant: Gets the role of this reactant.
getScale() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate
getScale() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
getScaledFeature(Class<? extends ScalableFeature<FeatureContentType>>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
getScaledFeature(ChemicalEntity, Class<? extends ScalableFeature<FeatureContentType>>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns the requested feature of the given chemical entities, scaled according to the current time step and spatial scaling.
getScaledFeature(Class<? extends ScalableFeature<FeatureContentType>>) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
getScaledFeature(ChemicalEntity, Class<? extends ScalableFeature<FeatureContentType>>) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
getScaledFeature(Class<? extends ScalableFeature<FeatureContentType>>) - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
getScaledFeature(Class<? extends ScalableFeature<FeatureContentType>>) - Method in interface bio.singa.simulation.model.modules.UpdateModule
getScaledQuantity() - Method in class bio.singa.simulation.features.AppliedScale
getScaledQuantity() - Method in class bio.singa.simulation.model.parameters.Parameter
getScheduler() - Method in class bio.singa.simulation.model.simulation.Simulation
getScope() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns the scope of this module.
getSegment() - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment
getSegmentIterator() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getSegments() - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
getSimulation() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
getSimulation() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns the referenced simulation.
getSimulation() - Method in class bio.singa.simulation.model.simulation.SimulationManager: Returns the simulation.
getSimulationRegion() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
getSimulationRegion() - Method in class bio.singa.simulation.model.simulation.Simulation
getSpatialDelta(DisplacementBasedModule) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getSpatialRepresentation() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
getSpawnRadius() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit
getSpawnSite() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit
getSpecificity() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns the specificity of this module.
getStartingPoint() - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment
getState(String) - Static method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
getState() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
getState() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
getState() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
getState() - Method in interface bio.singa.simulation.model.modules.UpdateModule
getStates() - Static method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
getStoichiometricNumber() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant: Returns the stoichiometric number (the number of molecules required for one reaction.).
getStoichiometricReactants() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction: Returns the list of reactants for this reaction.
getStringIdentifier() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getStringIdentifier() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
getStringIdentifier() - Method in interface bio.singa.simulation.model.simulation.Updatable
getSubsection() - Method in class bio.singa.simulation.features.variation.ConcentrationVariation
getSubsection() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier: Returns the cell section the delta is assigned to.
getSubsection() - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
getSubsection(CellTopology) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Returns the subsection corresponding to the topology.
getSubsectionRepresentations() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
getSubsections() - Method in class bio.singa.simulation.model.sections.CellRegion
getSubstrateEntities() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction: Returns all substrates of this reaction.
getSubstrates() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
getSubstrates() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction
getSupplier() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Returns the field supplier.
getSymbol() - Method in class bio.singa.simulation.features.ActinBoostVelocity
getSymbol() - Method in class bio.singa.simulation.features.AppliedScale
getSymbol() - Method in class bio.singa.simulation.features.AttachedFilament
getSymbol() - Method in class bio.singa.simulation.features.AttachedMotor
getSymbol() - Method in class bio.singa.simulation.features.AttachmentDistance
getSymbol() - Method in class bio.singa.simulation.features.Cargo
getSymbol() - Method in class bio.singa.simulation.features.CargoAdditionRate
getSymbol() - Method in class bio.singa.simulation.features.Cargoes
getSymbol() - Method in class bio.singa.simulation.features.DecayingEntity
getSymbol() - Method in class bio.singa.simulation.features.EndocytosisCheckpointTime
getSymbol() - Method in class bio.singa.simulation.features.EndocytosisCkeckpointConcentration
getSymbol() - Method in class bio.singa.simulation.features.FusionPairs
getSymbol() - Method in class bio.singa.simulation.features.MatchingQSnares
getSymbol() - Method in class bio.singa.simulation.features.MatchingRSnares
getSymbol() - Method in class bio.singa.simulation.features.MaturationTime
getSymbol() - Method in class bio.singa.simulation.features.MaximalConcentration
getSymbol() - Method in class bio.singa.simulation.features.MotorMovementVelocity
getSymbol() - Method in class bio.singa.simulation.features.MotorPullDirection
getSymbol() - Method in class bio.singa.simulation.features.PitFormationRate
getSymbol() - Method in class bio.singa.simulation.features.Solutes
getSymbol() - Method in class bio.singa.simulation.features.TetheringTime
getSymbol() - Method in class bio.singa.simulation.features.Transporter
getSymbol() - Method in class bio.singa.simulation.features.VesicleRadius
getTargetDirection() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getTargetEntity() - Method in class bio.singa.simulation.model.rules.AssignmentRule
getTetheredVesicles() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion
getTime() - Method in class bio.singa.simulation.events.UpdatableUpdatedEvent: Returns the time the event was emitted.
getTimeUnit() - Method in class bio.singa.simulation.trajectories.Trajectories
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.
getTrajectories() - Method in class bio.singa.simulation.trajectories.TrajectoryObserver
getTrajectoryData() - Method in class bio.singa.simulation.trajectories.Trajectories
getType() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
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
getUpdatable() - Method in class bio.singa.simulation.events.UpdatableUpdatedEvent: Returns the updatable
getUpdatable() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier: Returns the object the delta is assigned to.
getUpdatable() - Method in class bio.singa.simulation.model.modules.concentration.LocalError: Returns the node where the error occurred.
getUpdatables() - Method in class bio.singa.simulation.model.simulation.Simulation
getUpdateManager() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
getValue() - Method in class bio.singa.simulation.model.modules.concentration.LocalError: Returns the actual value of the error.
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
getVariations() - Method in class bio.singa.simulation.features.variation.Variation
getVariations() - Method in class bio.singa.simulation.features.variation.VariationSet
getVesicleLayer() - Method in class bio.singa.simulation.model.simulation.Simulation
getVesicles() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
getVesicleState() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getVolume() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
getVolumeLayer() - Method in class bio.singa.simulation.model.simulation.Simulation
getWorkspaceFolder() - Method in class bio.singa.simulation.events.EpochUpdateWriter
GraphEventEmitter - Class in bio.singa.simulation.events: The implementation of an UpdateEventEmitter emitting updates of the graph to all listeners.
GraphEventEmitter() - Constructor for class bio.singa.simulation.events.GraphEventEmitter: Creates a new GraphEventEmitter.
GraphImageWriter - Class in bio.singa.simulation.events
GraphImageWriter(Path, Path, List<ChemicalEntity>) - Constructor for class bio.singa.simulation.events.GraphImageWriter
GraphUpdatedEvent - Class in bio.singa.simulation.events: The Event that is emitted from the GraphEventEmitter, encapsulating a graph.
GraphUpdatedEvent(AutomatonGraph, Quantity<Time>) - Constructor for class bio.singa.simulation.events.GraphUpdatedEvent: Creates a new GraphUpdatedEvent.

H

halfScaledQuantity - Variable in class bio.singa.simulation.model.parameters.Parameter
handleDelta(ConcentrationDeltaIdentifier, ConcentrationDelta) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Handles a delta based on the current state of the calculation.
hasDeltas() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
hasDeltas() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
hasDeltas() - Method in interface bio.singa.simulation.model.simulation.Updatable
hasFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
hasFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.parameters.FeatureManager
hasGrowingFilaments() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
hashCode() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry.VesicleState
hashCode() - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
hashCode() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier
hashCode() - Method in class bio.singa.simulation.model.sections.CellRegion
hashCode() - Method in class bio.singa.simulation.model.sections.CellSubsection
hashCode() - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
hashCode() - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
hasMembrane() - Method in class bio.singa.simulation.model.sections.CellRegion

I

identifier(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSelection
identifier(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
identifier(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.DiffusionBuilder
identifier(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.SelectionStep
identifier(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
identifier(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.KineticLawStep
identifier(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
in(CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSectionSelection
in(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
increaseTimeStep() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler
IndependentUpdate - Class in bio.singa.simulation.model.modules.concentration.scope: Independent Updatable ConcentrationBasedModules require the integer state of the currently calculated Updatable.
IndependentUpdate(ConcentrationBasedModule) - Constructor for class bio.singa.simulation.model.modules.concentration.scope.IndependentUpdate: Initializes the update scope for the corresponding module.
InitialConcentration - Interface in bio.singa.simulation.model.sections.concentration
initialize() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
initialize() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
initialize() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion
initialize() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction
initialize() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction
initialize() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction
initialize() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction
initialize(Simulation) - Method in class bio.singa.simulation.model.sections.concentration.ConcentrationInitializer
initialize(Simulation) - Method in interface bio.singa.simulation.model.sections.concentration.InitialConcentration
initialize(Simulation) - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
initialize(Simulation) - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
initialize(CellSubsection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer
initialize(CellTopology, ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer
initializeActin() - Method in class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre
initializeComplexes() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion
initializeGraph() - Method in class bio.singa.simulation.model.simulation.Simulation
initializeGroup(int, String, String) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
initializeGroup(int, CellRegion) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
initializeGroup(CellRegion) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
initializeMicrotubules() - Method in class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre
initializeSpatialRepresentations() - Method in class bio.singa.simulation.model.simulation.Simulation
initializeSpeciesWithConcentration(ChemicalEntity, double) - Method in class bio.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 bio.singa.simulation.model.graphs.AutomatonGraph: Initializes the concentration of the given chemical entity of every node in this graph.
initializeSubsection(CellSubsection, CellTopology) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Initializes a new concentration pool for the corresponding subsection and topology.
inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion
inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion
inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction
inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction
inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction
inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport
isCatalyst() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant
isConcentrationFixed() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
isConcentrationFixed() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Returns true if the concentration is fixed - no deltas are applied.
isElementary() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction: Returns true if this Reaction is considered elementary and false otherwise.
isGrouped() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
isObserved() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle: Returns true if this node is observed.
isObserved() - Method in class bio.singa.simulation.model.graphs.AutomatonNode: Returns true if this node is observed.
isObserved() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Returns true if the concentrations are observed.
isObserved() - Method in interface bio.singa.simulation.model.simulation.Updatable
isProduct() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant: Returns true if this reactant is a product.
isStrutCalculation() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Returns the current state of calculations.
isSubstrate() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant: Returns true if this reactant is a substrate.

J

JHA2015 - Static variable in class bio.singa.simulation.features.DefaultFeatureSources

K

keepPlatformOpen() - Method in class bio.singa.simulation.model.simulation.SimulationManager
kineticLaw(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
kineticLaw(KineticLaw) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
kineticLaw(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.KineticLawStep
kineticLaw(KineticLaw) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.KineticLawStep
KineticLaw - Class in bio.singa.simulation.model.modules.concentration.reactants: Dynamic kinetic laws allow for the definition of reaction kinetics based on equations.
KineticLaw(String) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw

L

LANG2000 - Static variable in class bio.singa.simulation.features.DefaultFeatureSources
LineLikeAgent - Class in bio.singa.simulation.model.agents.linelike
LineLikeAgent(LineLikeAgent.FilamentType) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgent
LineLikeAgent(LineLikeAgent.FilamentType, Vector2D, Vector2D, AutomatonGraph) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgent
LineLikeAgent(LineLikeAgent.FilamentType, List<Vector2D>, NeumannRectangularDirection) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgent
LineLikeAgent.FilamentType - Enum in bio.singa.simulation.model.agents.linelike
LineLikeAgent.GrowthBehaviour - Enum in bio.singa.simulation.model.agents.linelike
LineLikeAgentAttachment - Class in bio.singa.simulation.model.modules.qualitative.implementations
LineLikeAgentAttachment() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment
LineLikeAgentLayer - Class in bio.singa.simulation.model.agents.linelike
LineLikeAgentLayer(Simulation, MembraneLayer) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
LineLikeAgentTemplate - Class in bio.singa.simulation.model.agents.linelike
LineLikeAgentTemplate(List<LineLikeAgent>, Quantity<Length>) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate
LocalError - Class in bio.singa.simulation.model.modules.concentration: The LocalError object stores the error as an result of the currently applied time step.
LocalError(Updatable, ChemicalEntity, double) - Constructor for class bio.singa.simulation.model.modules.concentration.LocalError: Creates a new LocalError.

M

MacroscopicLayerPlayground - Class in bio.singa.simulation.model.agents
MacroscopicLayerPlayground() - Constructor for class bio.singa.simulation.model.agents.MacroscopicLayerPlayground
main(String[]) - Static method in class bio.singa.simulation.features.variation.VariationSet
main(String[]) - Static method in class bio.singa.simulation.model.agents.EndocytosisPlayground
main(String[]) - Static method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground
main(String[]) - Static method in class bio.singa.simulation.model.agents.pointlike.VesiclePlayground
mapToSystemExtend() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate
mapToSystemExtend() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
MatchingQSnares - Class in bio.singa.simulation.features
MatchingQSnares(Set<ChemicalEntity>, Evidence) - Constructor for class bio.singa.simulation.features.MatchingQSnares
MatchingRSnares - Class in bio.singa.simulation.features
MatchingRSnares(Set<ChemicalEntity>, Evidence) - Constructor for class bio.singa.simulation.features.MatchingRSnares
MaturationTime - Class in bio.singa.simulation.features
MaturationTime(Quantity<Time>, Evidence) - Constructor for class bio.singa.simulation.features.MaturationTime
MaturationTime(double, Evidence) - Constructor for class bio.singa.simulation.features.MaturationTime
MaximalConcentration - Class in bio.singa.simulation.features
MaximalConcentration(Quantity<MolarConcentration>, Evidence) - Constructor for class bio.singa.simulation.features.MaximalConcentration
Membrane - Class in bio.singa.simulation.model.agents.surfacelike
Membrane(String) - Constructor for class bio.singa.simulation.model.agents.surfacelike.Membrane
MEMBRANE - Static variable in class bio.singa.simulation.model.sections.CellRegion
MEMBRANE - Static variable in class bio.singa.simulation.model.sections.CellSubsection: A general membrane subsection.
MEMBRANE_TETHERED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
MembraneConcentration - Class in bio.singa.simulation.model.sections.concentration
MembraneConcentration(CellRegion, ChemicalEntity, Quantity<Area>, double, Evidence) - Constructor for class bio.singa.simulation.model.sections.concentration.MembraneConcentration
MembraneDiffusion - Class in bio.singa.simulation.model.modules.concentration.imlementations: The membrane diffusion module describes the movement of chemical entities across Membranes driven by the MembranePermeability of the cargo.
MembraneDiffusion() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion
MembraneDiffusion.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
MembraneDiffusion.CargoStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
MembraneDiffusion.MembraneDiffusionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations
MembraneDiffusionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion.MembraneDiffusionBuilder
MembraneFactory - Class in bio.singa.simulation.model.agents.surfacelike
MembraneFactory(Collection<Vector2D>, AutomatonGraph, Map<Vector2D, CellRegion>) - Constructor for class bio.singa.simulation.model.agents.surfacelike.MembraneFactory
MembraneLayer - Class in bio.singa.simulation.model.agents.surfacelike
MembraneLayer() - Constructor for class bio.singa.simulation.model.agents.surfacelike.MembraneLayer
MembraneSegment - Class in bio.singa.simulation.model.agents.surfacelike
MembraneSegment(AutomatonNode, LineSegment) - Constructor for class bio.singa.simulation.model.agents.surfacelike.MembraneSegment
MembraneTracer - Class in bio.singa.simulation.model.agents.surfacelike
MembraneTracer(AutomatonGraph) - Constructor for class bio.singa.simulation.model.agents.surfacelike.MembraneTracer
MERRIFIELD2005 - Static variable in class bio.singa.simulation.features.DefaultFeatureSources
MichaelisMentenReaction - Class in bio.singa.simulation.model.modules.concentration.imlementations
MichaelisMentenReaction() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction
MichaelisMentenReaction.MichaelisMentenReactionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations
MichaelisMentenReactionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction.MichaelisMentenReactionBuilder
MICROTUBULE_ATTACHED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
MicrotubuleOrganizingCentre - Class in bio.singa.simulation.model.agents.linelike
MicrotubuleOrganizingCentre(Simulation, MembraneLayer, Circle, int) - Constructor for class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre
MINIMAL_EMPTY_ERROR - Static variable in class bio.singa.simulation.model.modules.concentration.LocalError: The minimal possible error not assigned to any node or chemical entity.
ModuleBuilder<ModuleType extends ConcentrationBasedModule> - Interface in bio.singa.simulation.model.modules.concentration
ModuleCalculationException - Exception in bio.singa.simulation.exceptions
ModuleCalculationException(String) - Constructor for exception bio.singa.simulation.exceptions.ModuleCalculationException
ModuleFactory - Class in bio.singa.simulation.model.modules.concentration: Handles module creation with certain UpdateScope and UpdateSpecificity.
ModuleFactory() - Constructor for class bio.singa.simulation.model.modules.concentration.ModuleFactory
ModuleFactory.Scope - Enum in bio.singa.simulation.model.modules.concentration: The type of UpdateScope.
ModuleFactory.Specificity - Enum in bio.singa.simulation.model.modules.concentration: The type of UpdateSpecificity.
ModuleFeatureVariation<FeatureType> - Class in bio.singa.simulation.features.variation
ModuleFeatureVariation(UpdateModule, Class<? extends Feature<FeatureType>>) - Constructor for class bio.singa.simulation.features.variation.ModuleFeatureVariation
ModuleFeatureVariationEntry - Class in bio.singa.simulation.features.variation
ModuleFeatureVariationEntry(UpdateModule, Feature<?>) - Constructor for class bio.singa.simulation.features.variation.ModuleFeatureVariationEntry
modules(Set<ConcentrationBasedModule>) - Method in class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
modules(Set<ConcentrationBasedModule>) - Method in interface bio.singa.simulation.events.EpochUpdateWriter.ModulesStep
ModuleState - Enum in bio.singa.simulation.model.modules.concentration: The state of the module is used to schedule the processing of modules in the UpdateScheduler.
MotorMovementVelocity - Class in bio.singa.simulation.features
MotorMovementVelocity(Quantity<Speed>, Evidence) - Constructor for class bio.singa.simulation.features.MotorMovementVelocity
MotorMovementVelocity(double, Evidence) - Constructor for class bio.singa.simulation.features.MotorMovementVelocity
MotorPullDirection - Class in bio.singa.simulation.features
MotorPullDirection(MotorPullDirection.Direction, Evidence) - Constructor for class bio.singa.simulation.features.MotorPullDirection
MotorPullDirection.Direction - Enum in bio.singa.simulation.features
move(Vector2D) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
MULTDIV - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for multiplication or division
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 bio.singa.simulation.model.modules.concentration.ConcentrationDelta: Multiplies (modifies) this delta with the given multiplicand.

N

NANOMETRE_PER_SECOND - Static variable in class bio.singa.simulation.features.ActinBoostVelocity
nextEpoch() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
nextEpoch() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
nextEpoch() - Method in class bio.singa.simulation.model.simulation.Simulation: Calculates the next epoch.
nextEpoch() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler
NodeEventEmitter - Class in bio.singa.simulation.events: The implementation of an UpdateEventEmitter emitting updates of specific nodes to all listeners.
NodeEventEmitter() - Constructor for class bio.singa.simulation.events.NodeEventEmitter: Creates a new NodeEventEmitter.
NthOrderReaction - Class in bio.singa.simulation.model.modules.concentration.imlementations
NthOrderReaction() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction
NthOrderReaction.NthOrderReactionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations
NthOrderReactionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction.NthOrderReactionBuilder
NUCLEAR_MEMBRANE - Static variable in class bio.singa.simulation.model.sections.CellSubsections
NUCLEOPLASM - Static variable in class bio.singa.simulation.model.sections.CellSubsections
NUMBER - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for numbers
NumericalInstabilityException - Exception in bio.singa.simulation.exceptions
NumericalInstabilityException(String) - Constructor for exception bio.singa.simulation.exceptions.NumericalInstabilityException

O

observeNode(Updatable) - Method in class bio.singa.simulation.model.simulation.Simulation
of(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSelection
of(ChemicalEntity, RateConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSelection
of(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
of(ChemicalEntity, RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
of(Updatable, Unit<MolarConcentration>) - Static method in class bio.singa.simulation.trajectories.ConcentrationData
of(Collection<AutomatonNode>, Unit<MolarConcentration>) - Static method in class bio.singa.simulation.trajectories.TrajectoryData
onCompletion() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
onCompletion() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexAttachment
onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexDiffusivityScaling
onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment
onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion
onCompletion() - Method in interface bio.singa.simulation.model.modules.UpdateModule
onEventReceived(UpdatableUpdatedEvent) - Method in class bio.singa.simulation.events.EpochUpdateWriter
onEventReceived(GraphUpdatedEvent) - Method in class bio.singa.simulation.events.GraphImageWriter
onEventReceived(GraphUpdatedEvent) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer
onEventReceived(GraphUpdatedEvent) - Method in class bio.singa.simulation.trajectories.TrajectoryObserver
onlyFor(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.DiffusionBuilder
onlyFor(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.Diffusion.SelectionStep
onReset() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
onReset() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexAttachment
onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexDiffusivityScaling
onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment
onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion
onReset() - Method in interface bio.singa.simulation.model.modules.UpdateModule
OPEN_BRACKET - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for opening brackets
optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexAttachment
optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ActinCortexDiffusivityScaling
optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment
optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion
optimizeTimeStep() - Method in interface bio.singa.simulation.model.modules.UpdateModule
OrganelleImageParser - Class in bio.singa.simulation.model.agents.organelles
OrganelleImageParser(BufferedImage) - Constructor for class bio.singa.simulation.model.agents.organelles.OrganelleImageParser
OrganelleTemplate - Class in bio.singa.simulation.model.agents.organelles
OrganelleTemplate(Quantity<Length>, Polygon, Map<Integer, Set<Vector2D>>) - Constructor for class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
OrganelleTypes - Enum in bio.singa.simulation.model.agents.organelles

P

Parameter<QuantityType extends javax.measure.Quantity<QuantityType>> - Class in bio.singa.simulation.model.parameters
Parameter(String) - Constructor for class bio.singa.simulation.model.parameters.Parameter
Parameter(String, Quantity<QuantityType>, Evidence) - Constructor for class bio.singa.simulation.model.parameters.Parameter
ParameterStorage - Class in bio.singa.simulation.model.parameters
parse(String) - Method in class uk.co.cogitolearning.cogpar.ExpressionParser: Parse a mathematical expression in a string and return an ExpressionNode.
parse(LinkedList<Token>) - Method in class uk.co.cogitolearning.cogpar.ExpressionParser: Parse a mathematical expression in contained in a list of tokens and return an ExpressionNode.
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.
PER_SQUARE_NANOMETRE_PER_SECOND - Static variable in class bio.singa.simulation.features.PitFormationRate
Pit(Quantity<Time>, Vector2D, Quantity<Length>, ComparableQuantity<MolarConcentration>, AutomatonNode, ConcentrationDelta) - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit
PitFormationRate - Class in bio.singa.simulation.features
PitFormationRate(Quantity<SpawnRate>, Evidence) - Constructor for class bio.singa.simulation.features.PitFormationRate
PitFormationRate(double, Evidence) - Constructor for class bio.singa.simulation.features.PitFormationRate
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
processAllUpdatables(Collection<Updatable>) - Method in class bio.singa.simulation.model.modules.concentration.scope.DependentUpdate
processAllUpdatables(Collection<Updatable>) - Method in class bio.singa.simulation.model.modules.concentration.scope.IndependentUpdate
processAllUpdatables(Collection<Updatable>) - Method in class bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate
processAllUpdatables(Collection<Updatable>) - Method in interface bio.singa.simulation.model.modules.concentration.scope.UpdateScope: Processes all given updatables.
processAllVesicles(List<Vesicle>) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
processContainer(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific
processContainer(ConcentrationContainer, CellSubsection, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific
processContainer(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.specifity.SectionSpecific
processContainer(ConcentrationContainer, CellSubsection, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.specifity.SectionSpecific
processContainer(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.specifity.UpdatableSpecific
processContainer(ConcentrationContainer, CellSubsection, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.specifity.UpdatableSpecific
processContainer(ConcentrationContainer) - Method in interface bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity: Processes a concentration container.
processContainer(ConcentrationContainer, CellSubsection, ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity
processUpdatable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.DependentUpdate
processUpdatable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.IndependentUpdate
processUpdatable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate
processUpdatable(Updatable) - Method in interface bio.singa.simulation.model.modules.concentration.scope.UpdateScope: Calculates the given updatable.
putSubsectionPool(CellSubsection, CellTopology, ConcentrationPool) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Adds a concentration pool, referenced to the subsection and topology.

Q

QualitativeModule - Class in bio.singa.simulation.model.modules.qualitative
QualitativeModule() - Constructor for class bio.singa.simulation.model.modules.qualitative.QualitativeModule

R

RAISED - Static variable in class uk.co.cogitolearning.cogpar.Token: Token id for the exponentiation symbol
rateConstant(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction.NthOrderReactionBuilder
Reactant - Class in bio.singa.simulation.model.modules.concentration.reactants: A Reactant encapsulates a ChemicalEntity for the use in Reactions.
Reactant(ChemicalEntity, ReactantRole) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.Reactant: Creates a new reactant.
Reactant(ChemicalEntity, ReactantRole, CellTopology) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.Reactant
Reactant(ChemicalEntity, ReactantRole, double) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.Reactant
Reactant(ChemicalEntity, ReactantRole, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.Reactant
Reactant(ChemicalEntity, ReactantRole, CellTopology, double) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.Reactant
Reactant(ChemicalEntity, ReactantRole, CellTopology, double, double) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.Reactant
Reactant(ChemicalEntity, ReactantRole, double, double) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.Reactant
ReactantRole - Enum in bio.singa.simulation.model.modules.concentration.reactants: The role of the reactant: Increasing, for products and accelerating reactants and decreasing for substrates and inhibiting reactants.
Reaction - Class in bio.singa.simulation.model.modules.concentration.imlementations: Reactions in general are ConcentrationBasedModules following the laws of chemical kinetics.
Reaction() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.Reaction
Reaction.Builder<TopLevelType extends Reaction,BuilderType extends Reaction.Builder> - Class in bio.singa.simulation.model.modules.concentration.imlementations
reduce() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate
reduce() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
referenceChemicalEntityToParameter(String, ChemicalEntity) - Method in class bio.singa.simulation.model.rules.AssignmentRule
referenceConstant(String, double) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
referenceConstant(String, double, Evidence) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
referenceFeature(String, ScalableQuantityFeature) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
referenceFeature(ScalableQuantityFeature) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
referenceParameter(ScalableQuantityFeature<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
referenceParameter(String, ScalableQuantityFeature<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
referenceParameter(Parameter<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
referenceParameter(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
referenceParameter(String, Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
referenceParameter(String, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
referenceParameter(String, double, Evidence) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.DynamicReactionBuilder
referenceParameter(ScalableQuantityFeature<?>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.ParameterStep
referenceParameter(String, ScalableQuantityFeature<?>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.ParameterStep
referenceParameter(Reactant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.ParameterStep
referenceParameter(Parameter<?>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.ParameterStep
referenceParameter(String, Reactant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.ParameterStep
referenceParameter(String, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.ParameterStep
referenceParameter(String, double, Evidence) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction.ParameterStep
referenceParameter(Parameter<?>) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
referenceReactant(String, Reactant) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
referenceReactant(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
regionsToMembrane(AutomatonGraph) - Static method in class bio.singa.simulation.model.agents.surfacelike.MembraneTracer
reinitialize() - Static method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
removeSubsection(CellSubsection) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Removes a subsection, the corresponding topology and concentration pool from the container.
removeSubsection(CellTopology) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Removes a subsection, the given topology and concentration pool from the container.
removeVesicle(Vesicle) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
render() - Method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground
render(AutomatonGraph) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer
RenderingMode - Enum in bio.singa.simulation.renderer
renderVesicles() - Method in class bio.singa.simulation.model.agents.pointlike.VesiclePlayground
renderVoronoi(boolean) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer
rescaleColors(AutomatonGraph) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer
rescaleParameters() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler
resetError() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Resets the error to the minimal error.
resetNextPosition() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
resetNextPosition() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager: Resets the next position to the current position.
resetState() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
resetState() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
resetState() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
resetState() - Method in interface bio.singa.simulation.model.modules.UpdateModule
ReversibleReaction - Class in bio.singa.simulation.model.modules.concentration.imlementations: Reversible reactions are Reactions where the substrates form products, and products can also from substrates.
ReversibleReaction() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction
ReversibleReaction.ReversibleReactionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations
ReversibleReactionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.ReversibleReactionBuilder

S

scale(double) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate
scale(double) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
scale() - Method in class bio.singa.simulation.model.parameters.Parameter
scaledQuantity - Variable in class bio.singa.simulation.model.parameters.Parameter
scaleScalableFeatures() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
scaleScalableFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction
scaleScalableFeatures() - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
scaleScalableFeatures() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
scaleScalableFeatures() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
scaleScalableFeatures() - Method in interface bio.singa.simulation.model.modules.UpdateModule
SECTION_A - Static variable in class bio.singa.simulation.model.sections.CellSubsection: A cellular subsection "A".
SECTION_B - Static variable in class bio.singa.simulation.model.sections.CellSubsection: A cellular subsection "B".
SectionConcentration - Class in bio.singa.simulation.model.sections.concentration
SectionConcentration(CellRegion, CellSubsection, ChemicalEntity, Quantity<MolarConcentration>) - Constructor for class bio.singa.simulation.model.sections.concentration.SectionConcentration
SectionConcentration(CellSubsection, ChemicalEntity, Quantity<MolarConcentration>) - Constructor for class bio.singa.simulation.model.sections.concentration.SectionConcentration
SectionDeltaFunction - Class in bio.singa.simulation.model.modules.concentration.functions: Section delta functions are AbstractDeltaFunctions which return a list of concentration deltas.
SectionDeltaFunction(Function<ConcentrationContainer, List<ConcentrationDelta>>, Predicate<ConcentrationContainer>) - Constructor for class bio.singa.simulation.model.modules.concentration.functions.SectionDeltaFunction: Creates a new section delta function with the specified condition and function.
SectionSpecific - Class in bio.singa.simulation.model.modules.concentration.specifity: Section specific ConcentrationBasedModules calculate their AbstractDeltaFunction for every subsection of an updatable.
SectionSpecific(ConcentrationBasedModule) - Constructor for class bio.singa.simulation.model.modules.concentration.specifity.SectionSpecific: Initializes the update specificity for the corresponding module.
SemiDependentUpdate - Class in bio.singa.simulation.model.modules.concentration.scope: Semidependent Updatable ConcentrationBasedModules require the integer state of a subset of updatables.
SemiDependentUpdate(ConcentrationBasedModule) - Constructor for class bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate: Initializes the update scope for the corresponding module.
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.
set(CellSubsection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Sets the concentration of the given entity in the given subsection.
set(CellTopology, ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Sets the concentration of the given entity in the given topology.
set(CellSubsection, ChemicalEntity, double) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Sets the concentration of the given entity in the given subsection.
set(CellTopology, ChemicalEntity, double) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer: Sets the concentration of the given entity in the subsection corresponding to the topological descriptor.
set(ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.ConcentrationPool: Sets the concentration of a entity.
setAdditionDelta(ConcentrationDelta) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit
setApplicationCondition(Predicate<Updatable>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Sets the application condition for this module.
setArea(Polygon) - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent
setArea(Quantity<Area>) - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
setAssignmentRules(List<AssignmentRule>) - Method in class bio.singa.simulation.model.simulation.Simulation: Adds a list of assignment rules, sorting them by their dependencies.
setAssociatedNodes(Set<AutomatonNode>) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
setAttachedFilament(LineLikeAgent) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
setBindee(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
setBindeeTopology(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
setBinder(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
setBinderTopology(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
setCargoConcentration(ComparableQuantity<MolarConcentration>) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit
setCellRegion(CellRegion) - Method in class bio.singa.simulation.model.graphs.AutomatonNode
setCheckpointTime(Quantity<Time>) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit
setComplex(ComplexedChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
setConcentration(Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
setConcentrationContainer(ConcentrationContainer) - Method in class bio.singa.simulation.model.graphs.AutomatonNode: Sets the ConcentrationContainer for this node.
setConcentrationContainer(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Sets the current concentration container.
setConcentrationFixed(boolean) - Method in class bio.singa.simulation.model.graphs.AutomatonNode
setConcentrationFixed(boolean) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Sets the concentration to be fixed - no deltas will be applied.
setConcentrationInitializer(ConcentrationInitializer) - Method in class bio.singa.simulation.model.simulation.Simulation
setConcentrationMap(Map<String, Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
setCortex(ActinCortex) - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLayer
setCurrentEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Sets the current chemical entity.
setCurrentSubsection(CellSubsection) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Sets the current subsection.
setCurrentUpdatable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Sets the current updatable.
setDeltaCutoff(double) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Sets the cutoff where deltas are validated to be effectively zero.
setDescription(String) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry.VesicleState
setDrawingHeight(double) - Method in class bio.singa.simulation.events.GraphImageWriter
setDrawingWidth(double) - Method in class bio.singa.simulation.events.GraphImageWriter
setElementary(boolean) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction: Sets this Reaction as elementary.
setEndingPoint(Vector2D) - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment
setEntity(ChemicalEntity) - Method in class bio.singa.simulation.features.variation.EntityFeatureVariationEntry
setEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant: Sets the entity representing this reactant.
setEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
setEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
setEntityReference(Map<ChemicalEntity, String>) - Method in class bio.singa.simulation.model.rules.AssignmentRule
setErrorCutoff(double) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Sets the cutoff where numerical errors to be considered irretrievably unstable.
setEvidence(Evidence) - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
setEvidence(Evidence) - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
setFeature(Feature<?>) - Method in class bio.singa.simulation.features.variation.VariationEntry
setFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
setFeature(FeatureType) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
setFeature(Feature<?>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Sets a feature.
setFeature(Feature<?>) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule: Sets a feature.
setFeature(Feature<?>) - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule: Sets a feature.
setFeature(Feature<?>) - Method in interface bio.singa.simulation.model.modules.UpdateModule
setFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.parameters.FeatureManager
setFeature(FeatureType) - Method in class bio.singa.simulation.model.parameters.FeatureManager
setFeatureMap(Map<String, ScalableQuantityFeature>) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
setFilaments(List<LineLikeAgent>) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
setGoTerm(GoTerm) - Method in class bio.singa.simulation.model.sections.CellSubsection
setGraph(AutomatonGraph) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
setGraph(AutomatonGraph) - Method in class bio.singa.simulation.model.simulation.Simulation
setGroups(Map<Integer, Set<Vector2D>>) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
setIdentifier(String) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry.VesicleState
setIdentifier(String) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Sets the identifier of this module.
setIdentifier(String) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
setIdentifier(String) - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
setIdentifier(String) - Method in class bio.singa.simulation.model.sections.CellSubsection
setInitialConcentrations(Set<InitialConcentration>) - Method in class bio.singa.simulation.model.sections.concentration.ConcentrationInitializer
setInnerRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
setInnerRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
setJfxShutdown(boolean) - Method in class bio.singa.simulation.events.GraphImageWriter
setKeepPlatformOpen(boolean) - Method in class bio.singa.simulation.model.simulation.SimulationManager
setKineticLaw(KineticLaw) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction: Sets the kinetic law.
setLargestLocalError(LocalError) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Sets the largest error as of yet.
setLineLayer(LineLikeAgentLayer) - Method in class bio.singa.simulation.model.simulation.Simulation
setMaximalTimeStep(Quantity<Time>) - Method in class bio.singa.simulation.model.simulation.Simulation
setMembraneLayer(MembraneLayer) - Method in class bio.singa.simulation.model.simulation.Simulation
setMembraneRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
setMembraneRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
setMembraneRegion(CellRegion) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
setMicrotubuleOrganizingCentre(MicrotubuleOrganizingCentre) - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneLayer
setMinusEndBehaviour(LineLikeAgent.GrowthBehaviour) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
setModule(UpdateModule) - Method in class bio.singa.simulation.features.variation.ModuleFeatureVariationEntry
setNodeColorScale(ColorScale) - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions
setNodeHighlightEntity(ChemicalEntity) - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions
setNonElementary() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder
setNumberOfMolecules(double) - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
setObserved(boolean) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle: Sets the observed state of this node.
setObserved(boolean) - Method in class bio.singa.simulation.model.graphs.AutomatonNode: Sets the observed state of this node.
setObserved(boolean) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Sets the concentrations to be observed, this additional requires seting up a UpdateEventListener.
setObserved(boolean) - Method in interface bio.singa.simulation.model.simulation.Updatable
setOrigin(Evidence) - Method in class bio.singa.simulation.model.parameters.Parameter
setParameterMap(Map<String, Parameter>) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw
setPath(VectorPath) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
setPolygon(Polygon) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
setPreferredConcentrationUnit(Unit<MolarConcentration>) - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant
setPreferredTopology(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant
setQuantity(Quantity<QuantityType>) - Method in class bio.singa.simulation.model.parameters.Parameter
setRadius(Quantity<Length>) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
setRecalculationCutoff(double) - Method in class bio.singa.simulation.model.simulation.UpdateScheduler
setRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
setRegion(CellRegion) - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration
setRegion(CellRegion) - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
setRegionMap(Map<CellRegion, Set<Vector2D>>) - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane
setRenderingMode(RenderingMode) - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions
setRole(ReactantRole) - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant: Gets the role of this reactant.
setScale(Quantity<Length>) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate
setScheduler(UpdateScheduler) - Method in class bio.singa.simulation.model.simulation.Simulation
setSegmentIterator(ListIterator<Vector2D>) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
setSimulation(Simulation) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
setSimulation(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: References the simulation to this module.
setSimulation(Simulation) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
setSimulation(Simulation) - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
setSimulationRegion(Rectangle) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer
setSimulationRegion(Rectangle) - Method in class bio.singa.simulation.model.simulation.Simulation
setSimulationTerminationToEpochs(long) - Method in class bio.singa.simulation.model.simulation.SimulationManager: Schedules the termination of the simulation after the given number of epochs have passed.
setSimulationTerminationToTime(Quantity<Time>) - Method in class bio.singa.simulation.model.simulation.SimulationManager: Schedules the termination of the simulation after the given time (simulation time) has passed.
setSpatialRepresentation(Polygon) - Method in class bio.singa.simulation.model.graphs.AutomatonNode
setStartingPoint(Vector2D) - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment
setStrutCalculation(boolean) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier: Sets the current state of calculation.
setSubsection(CellSubsection) - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
setTargetDirection(MotorPullDirection.Direction) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
setTargetEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.rules.AssignmentRule
setTerminationCondition(Predicate<Simulation>) - Method in class bio.singa.simulation.model.simulation.SimulationManager: Sets a condition determining when the simulation should be terminated.
setTerminationLatch(CountDownLatch) - Method in class bio.singa.simulation.model.simulation.SimulationManager
setType(LineLikeAgent.FilamentType) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent
setUpConcentrationContainer() - Method in class bio.singa.simulation.model.sections.CellRegion
setUpdateEmissionCondition(Predicate<Simulation>) - Method in class bio.singa.simulation.model.simulation.SimulationManager: Sets a condition determining when events should be emitted.
setUpdateEmissionToTimePassed(Quantity<Time>) - Method in class bio.singa.simulation.model.simulation.SimulationManager: Schedules the emission of events after the given time (simulation time) has passed.
setUpdateManager(ConcentrationDeltaManager) - Method in class bio.singa.simulation.model.graphs.AutomatonNode
setupModule(Class<ModuleImplementation>, ModuleFactory.Scope, ModuleFactory.Specificity) - Static method in class bio.singa.simulation.model.modules.concentration.ModuleFactory: Creates a new module with the specified setup.
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
setVariations(Set<FeatureType>) - Method in class bio.singa.simulation.features.variation.Variation
setVariations(List<Variation<?>>) - Method in class bio.singa.simulation.features.variation.VariationSet
setVesicleLayer(VesicleLayer) - Method in class bio.singa.simulation.model.simulation.Simulation
setVesicleState(VesicleStateRegistry.VesicleState) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
setVolumeLayer(VolumeLayer) - Method in class bio.singa.simulation.model.simulation.Simulation
shiftDeltas() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
shiftDeltas() - Method in class bio.singa.simulation.model.graphs.AutomatonNode: Shifts the deltas from the potential delta list to the final delta list.
shiftDeltas() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager: Shifts the deltas from the potential delta list to the final delta list.
shiftDeltas() - Method in interface bio.singa.simulation.model.simulation.Updatable
shutDown() - Method in class bio.singa.simulation.events.GraphImageWriter
simulation(Simulation) - Method in class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
simulation(Simulation) - Method in interface bio.singa.simulation.events.EpochUpdateWriter.SimulationStep
simulation - Variable in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule: The simulation.
simulation - Variable in class bio.singa.simulation.model.modules.qualitative.QualitativeModule: The simulation.
Simulation - Class in bio.singa.simulation.model.simulation
Simulation() - Constructor for class bio.singa.simulation.model.simulation.Simulation: Creates a new plain simulation.
SimulationExamples - Class in bio.singa.simulation.model.simulation: A factory class that can be used to create different examples to test and explore certain aspects to the api.
SimulationExamples() - Constructor for class bio.singa.simulation.model.simulation.SimulationExamples
SimulationManager - Class in bio.singa.simulation.model.simulation: Changes in simulations can be observed by tagging AutomatonNodes of the AutomatonGraph.
SimulationManager(Simulation) - Constructor for class bio.singa.simulation.model.simulation.SimulationManager: Creates a new simulation manager for the given simulation.
SingleFileChannelMembraneTransport - Class in bio.singa.simulation.model.modules.concentration.imlementations: The single file channel transport describes the movement of cargo molecules through Transporter proteins, so called membrane channels.
SingleFileChannelMembraneTransport() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport
SingleFileChannelMembraneTransport.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
SingleFileChannelMembraneTransport.CargoStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations
SingleFileChannelMembraneTransport.SolutesStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
SingleFileChannelMembraneTransport.TransporterStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations
SingleFileChannelMembraneTransportBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder
singularGraph() - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs
Solutes - Class in bio.singa.simulation.features
Solutes(Set<ChemicalEntity>, Evidence) - Constructor for class bio.singa.simulation.features.Solutes
sortAssignmentRulesByPriority(List<AssignmentRule>) - Static method in class bio.singa.simulation.model.rules.AssignmentRules: It is possible, that AssignmentRules depend on each other.
spawnActinFilament(Membrane) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
spawnFilament(Membrane, Membrane) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
spawnHorizontalFilament(Membrane) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer
SpawnRate - Interface in bio.singa.simulation.features
splitRectangularGraphWithMembrane(AutomatonGraph, CellSubsection, CellSubsection, boolean) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs
SQUARE_NANOMETRE - Static variable in class bio.singa.simulation.features.PitFormationRate
start(Stage) - Method in class bio.singa.simulation.model.agents.EndocytosisPlayground
start(Stage) - Method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground
start(Stage) - Method in class bio.singa.simulation.model.agents.pointlike.VesiclePlayground
state - Variable in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
state - Variable in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
substratesAvailable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction
supplier - Variable in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule: Frequently required fields.
SYMBOL - Static variable in class bio.singa.simulation.features.ActinBoostVelocity
SYMBOL - Static variable in class bio.singa.simulation.features.AppliedScale
SYMBOL - Static variable in class bio.singa.simulation.features.CargoAdditionRate
SYMBOL - Static variable in class bio.singa.simulation.features.MotorMovementVelocity
SYMBOL - Static variable in class bio.singa.simulation.features.PitFormationRate

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
TetheringTime - Class in bio.singa.simulation.features
TetheringTime(Quantity<Time>, Evidence) - Constructor for class bio.singa.simulation.features.TetheringTime
TetheringTime(double, Evidence) - Constructor for class bio.singa.simulation.features.TetheringTime
tieUpdateEmissionToFPS(int) - Method in class bio.singa.simulation.model.simulation.SimulationManager: Sets the emission of updates for a rending engine.
timeFormat(QuantityFormatter<Time>) - Method in class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
timeFormat(QuantityFormatter<Time>) - Method in interface bio.singa.simulation.events.EpochUpdateWriter.TimeUnitStep
timeStepWasRescaled() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler
to(CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BinderSectionSelection
to(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.ComplexBuildingReactionBuilder
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 bio.singa.simulation.features.variation.ConcentrationVariation
toString() - Method in class bio.singa.simulation.features.variation.EntityFeatureVariation
toString() - Method in class bio.singa.simulation.features.variation.EntityFeatureVariationEntry
toString() - Method in class bio.singa.simulation.features.variation.ModuleFeatureVariation
toString() - Method in class bio.singa.simulation.features.variation.ModuleFeatureVariationEntry
toString() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
toString() - Method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry.VesicleState
toString() - Method in class bio.singa.simulation.model.graphs.AutomatonNode
toString() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule
toString() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDelta
toString() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier
toString() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier
toString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction
toString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MembraneDiffusion
toString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction
toString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport
toString() - Method in class bio.singa.simulation.model.modules.concentration.LocalError
toString() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDelta
toString() - Method in class bio.singa.simulation.model.modules.displacement.implementations.EndocytosisActinBoost
toString() - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleCytoplasmDiffusion
toString() - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleTransport
toString() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis
toString() - Method in class bio.singa.simulation.model.parameters.Parameter
toString() - Method in class bio.singa.simulation.model.sections.CellRegion
toString() - Method in class bio.singa.simulation.model.sections.CellSubsection
toString() - Method in class bio.singa.simulation.model.sections.concentration.SectionConcentration
Trajectories - Class in bio.singa.simulation.trajectories
Trajectories() - Constructor for class bio.singa.simulation.trajectories.Trajectories
Trajectories(Unit<Time>, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.trajectories.Trajectories
TrajectoryData - Class in bio.singa.simulation.trajectories
TrajectoryObserver - Class in bio.singa.simulation.trajectories
TrajectoryObserver() - Constructor for class bio.singa.simulation.trajectories.TrajectoryObserver
TrajectoryObserver(Unit<Time>, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.trajectories.TrajectoryObserver
Transporter - Class in bio.singa.simulation.features
Transporter(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.Transporter
transporter(Protein) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder
transporter(Protein) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.SingleFileChannelMembraneTransport.TransporterStep

U

uk.co.cogitolearning.cogpar - package uk.co.cogitolearning.cogpar
UNATTACHED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry
Updatable - Interface in bio.singa.simulation.model.simulation
UpdatableDeltaFunction - Class in bio.singa.simulation.model.modules.concentration.functions: Updatable delta functions are AbstractDeltaFunctions which return a map with ConcentrationDeltaIdentifiers mapping to to concentration deltas.
UpdatableDeltaFunction(Function<ConcentrationContainer, Map<ConcentrationDeltaIdentifier, ConcentrationDelta>>, Predicate<ConcentrationContainer>) - Constructor for class bio.singa.simulation.model.modules.concentration.functions.UpdatableDeltaFunction: Creates a new updatable delta function with the specified condition and function.
UpdatableSpecific - Class in bio.singa.simulation.model.modules.concentration.specifity: Updatable specific ConcentrationBasedModules calculate their AbstractDeltaFunction for every updatable.
UpdatableSpecific(ConcentrationBasedModule) - Constructor for class bio.singa.simulation.model.modules.concentration.specifity.UpdatableSpecific: Initializes the update specificity for the corresponding module.
UpdatableUpdatedEvent - Class in bio.singa.simulation.events: The Event that is emitted from the NodeEventEmitter, encapsulating a updatable.
UpdatableUpdatedEvent(Quantity<Time>, Updatable) - Constructor for class bio.singa.simulation.events.UpdatableUpdatedEvent: Creates a new NodeUpdatedEvent.
UpdateModule - Interface in bio.singa.simulation.model.modules
updatePosition() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle
updatePosition() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager: Sets the current position to the next position.
updateScheduler - Variable in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule
updateScheduler - Variable in class bio.singa.simulation.model.modules.qualitative.QualitativeModule
UpdateScheduler - Class in bio.singa.simulation.model.simulation
UpdateScheduler(Simulation) - Constructor for class bio.singa.simulation.model.simulation.UpdateScheduler
UpdateScope - Interface in bio.singa.simulation.model.modules.concentration.scope: The Update Scope determines the modules dependence on the rest of the simulation.
UpdateSpecificity<DeltaFunctionType extends AbstractDeltaFunction> - Interface in bio.singa.simulation.model.modules.concentration.specifity: Determines how fine-grained the updates need to be calculated.
useStructureFrom(GridGraph) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs: Copies the structure (nodes and edges) of an UndirectedGraph to a AutomatonGraph.

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valueOf(String) - Static method in enum bio.singa.simulation.features.MotorPullDirection.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bio.singa.simulation.model.agents.linelike.LineLikeAgent.FilamentType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bio.singa.simulation.model.agents.linelike.LineLikeAgent.GrowthBehaviour: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleState: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.reactants.ReactantRole: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bio.singa.simulation.model.sections.CellTopology: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum bio.singa.simulation.renderer.RenderingMode: Returns the enum constant of this type with the specified name.
values() - Static method in enum bio.singa.simulation.features.MotorPullDirection.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bio.singa.simulation.model.agents.linelike.LineLikeAgent.FilamentType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bio.singa.simulation.model.agents.linelike.LineLikeAgent.GrowthBehaviour: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleState: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bio.singa.simulation.model.modules.concentration.reactants.ReactantRole: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bio.singa.simulation.model.sections.CellTopology: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum bio.singa.simulation.renderer.RenderingMode: 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.
Variation<FeatureType> - Class in bio.singa.simulation.features.variation
Variation() - Constructor for class bio.singa.simulation.features.variation.Variation
VariationEntry - Class in bio.singa.simulation.features.variation
VariationEntry() - Constructor for class bio.singa.simulation.features.variation.VariationEntry
VariationSet - Class in bio.singa.simulation.features.variation
VariationSet() - Constructor for class bio.singa.simulation.features.variation.VariationSet
varyLength(Quantity<Length>) - Static method in class bio.singa.simulation.features.FeatureRandomizer
varyTime(Quantity<Time>) - Static method in class bio.singa.simulation.features.FeatureRandomizer
Vesicle - Class in bio.singa.simulation.model.agents.pointlike
Vesicle(String, Vector2D, Quantity<Length>) - Constructor for class bio.singa.simulation.model.agents.pointlike.Vesicle
Vesicle(Vector2D, Quantity<Length>) - Constructor for class bio.singa.simulation.model.agents.pointlike.Vesicle
VesicleConfinedDiffusion - Class in bio.singa.simulation.model.modules.displacement.implementations
VesicleConfinedDiffusion(VesicleStateRegistry.VesicleState, VolumeLikeAgent) - Constructor for class bio.singa.simulation.model.modules.displacement.implementations.VesicleConfinedDiffusion
VesicleCytoplasmDiffusion - Class in bio.singa.simulation.model.modules.displacement.implementations
VesicleCytoplasmDiffusion() - Constructor for class bio.singa.simulation.model.modules.displacement.implementations.VesicleCytoplasmDiffusion
VesicleFusion - Class in bio.singa.simulation.model.modules.qualitative.implementations
VesicleFusion() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion
VesicleLayer - Class in bio.singa.simulation.model.agents.pointlike
VesicleLayer(Simulation) - Constructor for class bio.singa.simulation.model.agents.pointlike.VesicleLayer
VesiclePlayground - Class in bio.singa.simulation.model.agents.pointlike
VesiclePlayground() - Constructor for class bio.singa.simulation.model.agents.pointlike.VesiclePlayground
VesicleRadius - Class in bio.singa.simulation.features
VesicleRadius(Quantity<Length>, Evidence) - Constructor for class bio.singa.simulation.features.VesicleRadius
VesicleRadius(double, Evidence) - Constructor for class bio.singa.simulation.features.VesicleRadius
VesicleState(String, String) - Constructor for class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry.VesicleState
VesicleStateRegistry - Class in bio.singa.simulation.model.agents.pointlike
VesicleStateRegistry.VesicleState - Class in bio.singa.simulation.model.agents.pointlike
VesicleTransport - Class in bio.singa.simulation.model.modules.displacement.implementations
VesicleTransport() - Constructor for class bio.singa.simulation.model.modules.displacement.implementations.VesicleTransport
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
VolumeLayer - Class in bio.singa.simulation.model.agents.volumelike
VolumeLayer() - Constructor for class bio.singa.simulation.model.agents.volumelike.VolumeLayer
VolumeLikeAgent - Class in bio.singa.simulation.model.agents.volumelike
VolumeLikeAgent(Polygon) - Constructor for class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent
VolumeLikeAgentFactory - Class in bio.singa.simulation.model.agents.volumelike

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workspace(Path) - Method in class bio.singa.simulation.events.EpochUpdateWriter.EpochUpdateWriterBuilder
workspace(Path) - Method in interface bio.singa.simulation.events.EpochUpdateWriter.WorkspaceStep

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