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.

AbstractKineticLaw - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

AbstractKineticLaw(Reaction) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.AbstractKineticLaw

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 - Static variable in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

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>, List<Evidence>) - Constructor for class bio.singa.simulation.features.ActinBoostVelocity

ActinBoostVelocity(Quantity<Speed>, Evidence) - Constructor for class bio.singa.simulation.features.ActinBoostVelocity

ActinBoostVelocity(Quantity<Speed>) - Constructor for class bio.singa.simulation.features.ActinBoostVelocity

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

addAgent(VolumeLikeAgent) - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLayer

addAgents(Collection<VolumeLikeAgent>) - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLayer

addAll(Variation<?>...) - Method in class bio.singa.simulation.features.variation.VariationSet

addAssociatedNode(AutomatonNode, double) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

addCatalyst(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

addCatalyst(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addCatalyst(ChemicalEntity, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addCatalyst(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addCatalyst(ChemicalEntity, CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addCatalyst(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

addCatalyst(ChemicalEntity, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

addCatalyst(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

addCatalyst(ChemicalEntity, CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

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.

addCompositionCondition(EntityCompositionCondition) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

addCompositionCondition(EntityCompositionCondition) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity.Builder

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

addDynamicProduct(String, ComplexModification) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

addDynamicProduct(String, List<ComplexModification>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

addDynamicSubstrate(DynamicChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

addEdgeBetween(int, ReactionGraphNode, ReactionGraphNode) - Method in class bio.singa.simulation.export.reactiongraph.ReactionGraph

addEdgeBetween(ReactionGraphNode, ReactionGraphNode) - Method in class bio.singa.simulation.export.reactiongraph.ReactionGraph

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

addFilaments(Collection<LineLikeAgent>) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

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

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

addModule(UpdateModule) - Method in class bio.singa.simulation.model.simulation.Simulation

addModule(UpdateModule) - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

addNode(ChemicalEntity) - Method in class bio.singa.simulation.export.reactiongraph.ReactionGraph

addNodeUpdateListener(UpdateEventListener<UpdatableUpdatedEvent>) - Method in class bio.singa.simulation.model.simulation.SimulationManager

Adds a new listener for node based events.

addPossibleTopology(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

addPossibleTopology(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity.Builder

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(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

addProduct(DynamicChemicalEntity, ComplexModification) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addProduct(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addProduct(ChemicalEntity, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addProduct(ChemicalEntity, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addProduct(ChemicalEntity, CellTopology, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addProduct(DynamicChemicalEntity, ComplexModification) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addProduct(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addProduct(ChemicalEntity, CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addProduct(ChemicalEntity, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addProduct(ChemicalEntity, CellTopology, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addProduct(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

addProduct(ChemicalEntity, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

addProduct(ChemicalEntity, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

addProduct(ChemicalEntity, CellTopology, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

addProduct(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

addProduct(ChemicalEntity, CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

addProduct(ChemicalEntity, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

addProduct(ChemicalEntity, CellTopology, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

addReactant(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

addReactant(Reactant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantBehavior

addReactant(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

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

addRow(ReactionTable.ReactionTableRow) - Method in class bio.singa.simulation.export.reactiontable.ReactionTable

addSegment(AutomatonNode, LineSegment) - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane

addState(String) - Static method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry

addStaticCatalyst(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

addStaticProduct(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

addStaticSubstrate(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

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(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

addSubstrate(DynamicChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addSubstrate(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addSubstrate(ChemicalEntity, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addSubstrate(ChemicalEntity, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addSubstrate(ChemicalEntity, CellTopology, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

addSubstrate(DynamicChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addSubstrate(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addSubstrate(ChemicalEntity, CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addSubstrate(ChemicalEntity, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addSubstrate(ChemicalEntity, CellTopology, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

addSubstrate(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

addSubstrate(ChemicalEntity, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

addSubstrate(ChemicalEntity, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

addSubstrate(ChemicalEntity, CellTopology, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

addSubstrate(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

addSubstrate(ChemicalEntity, CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

addSubstrate(ChemicalEntity, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

addSubstrate(ChemicalEntity, CellTopology, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

addTargetTopology(ChemicalEntity, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

addTrajectoryData(Double, TrajectoryData) - Method in class bio.singa.simulation.trajectories.nested.Trajectories

addUpdatableToObserve(Updatable) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder

Initializes a updatable that will be observed during simulation.

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

addVesicles(Collection<Vesicle>) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer

AffectedRegion - Class in bio.singa.simulation.features

AffectedRegion(CellRegion, List<Evidence>) - Constructor for class bio.singa.simulation.features.AffectedRegion

AffectedRegion(CellRegion, Evidence) - Constructor for class bio.singa.simulation.features.AffectedRegion

AffectedRegion(CellRegion) - Constructor for class bio.singa.simulation.features.AffectedRegion

appendTimestampedFolder(Path) - Static method in class bio.singa.simulation.trajectories.Recorders

AppliedVesicleState - Class in bio.singa.simulation.features

AppliedVesicleState(String, List<Evidence>) - Constructor for class bio.singa.simulation.features.AppliedVesicleState

AppliedVesicleState(String, Evidence) - Constructor for class bio.singa.simulation.features.AppliedVesicleState

AppliedVesicleState(String) - Constructor for class bio.singa.simulation.features.AppliedVesicleState

apply(Collection<ChemicalEntity>, EntityCompositionCondition...) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.EntityReducer

apply(Collection<ChemicalEntity>, Collection<EntityCompositionCondition>) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.EntityReducer

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.VesicleLayer

applyDeltas() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

Applies all final deltas and clears the delta list.

applyParameters(Simulation, List<?>) - Static method in class bio.singa.simulation.features.variation.VariationSet

applyRule(AutomatonNode) - Method in class bio.singa.simulation.model.rules.AssignmentRule

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

associationRate(RateConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ComplexBuildingReactionStep

associationRate(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

AttachedFilament - Class in bio.singa.simulation.features

AttachedFilament(String, List<Evidence>) - Constructor for class bio.singa.simulation.features.AttachedFilament

AttachedFilament(String, Evidence) - Constructor for class bio.singa.simulation.features.AttachedFilament

AttachedFilament(String) - Constructor for class bio.singa.simulation.features.AttachedFilament

AttachedMotor - Class in bio.singa.simulation.features

AttachedMotor(ChemicalEntity, List<Evidence>) - Constructor for class bio.singa.simulation.features.AttachedMotor

AttachedMotor(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.AttachedMotor

AttachedMotor(ChemicalEntity) - Constructor for class bio.singa.simulation.features.AttachedMotor

AttachmentDistance - Class in bio.singa.simulation.features

AttachmentDistance(Quantity<Length>, List<Evidence>) - Constructor for class bio.singa.simulation.features.AttachmentDistance

AttachmentDistance(Quantity<Length>, Evidence) - Constructor for class bio.singa.simulation.features.AttachmentDistance

AttachmentDistance(Quantity<Length>) - 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.

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

backupConcentrations() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

backwardReactionRate(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

backwardReactionRate(RateConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ReversibleReactionStep

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.export.format - package bio.singa.simulation.export.format

bio.singa.simulation.export.reactiongraph - package bio.singa.simulation.export.reactiongraph

bio.singa.simulation.export.reactiontable - package bio.singa.simulation.export.reactiontable

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.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.reactions - package bio.singa.simulation.model.modules.concentration.imlementations.reactions

bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas - package bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas

bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws - package bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants - package bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

bio.singa.simulation.model.modules.concentration.imlementations.transport - package bio.singa.simulation.model.modules.concentration.imlementations.transport

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.trajectories - package bio.singa.simulation.trajectories

bio.singa.simulation.trajectories.flat - package bio.singa.simulation.trajectories.flat

bio.singa.simulation.trajectories.nested - package bio.singa.simulation.trajectories.nested

BlackListVesicleStates - Class in bio.singa.simulation.features

BlackListVesicleStates(List<String>, List<Evidence>) - Constructor for class bio.singa.simulation.features.BlackListVesicleStates

BlackListVesicleStates(List<String>, Evidence) - Constructor for class bio.singa.simulation.features.BlackListVesicleStates

BlackListVesicleStates(List<String>) - Constructor for class bio.singa.simulation.features.BlackListVesicleStates

BoostMediatingEntity - Class in bio.singa.simulation.features

BoostMediatingEntity(ChemicalEntity, List<Evidence>) - Constructor for class bio.singa.simulation.features.BoostMediatingEntity

BoostMediatingEntity(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.BoostMediatingEntity

BoostMediatingEntity(ChemicalEntity) - Constructor for class bio.singa.simulation.features.BoostMediatingEntity

build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.FinalStep

build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.BuildStep

build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.DiffusionBuilder

build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.BuildStep

build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.MembraneDiffusionBuilder

build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.BuildStep

build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder

build() - Method in interface bio.singa.simulation.model.modules.concentration.ModuleBuilder

build() - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.BuildStep

build() - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.ConcentrationUnitStep

build() - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

build() - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.TimeUnitStep

Builder(SimpleStringIdentifier) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity.Builder

Builder(String) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity.Builder

C

cachedFeature - Variable in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.AbstractKineticLaw

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

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.ActinCortexDiffusivityScaling

calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis

calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationStateChange

calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.DiffusivityScaling

calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment

calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentDetachment

calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion

calculateUpdates() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VolumeLikeAgentContainment

calculateUpdates() - Method in interface bio.singa.simulation.model.modules.UpdateModule

Cargo - Class in bio.singa.simulation.features

Cargo(ChemicalEntity, List<Evidence>) - Constructor for class bio.singa.simulation.features.Cargo

Cargo(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.Cargo

Cargo(ChemicalEntity) - Constructor for class bio.singa.simulation.features.Cargo

cargo(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.CargoStep

cargo(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.MembraneDiffusionBuilder

cargo(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.CargoStep

cargo(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder

CargoAdditionRate - Class in bio.singa.simulation.features

CargoAdditionRate(Quantity<FirstOrderRate>, List<Evidence>) - Constructor for class bio.singa.simulation.features.CargoAdditionRate

CargoAdditionRate(Quantity<FirstOrderRate>, Evidence) - Constructor for class bio.singa.simulation.features.CargoAdditionRate

CargoAdditionRate(Quantity<FirstOrderRate>) - Constructor for class bio.singa.simulation.features.CargoAdditionRate

Cargoes - Class in bio.singa.simulation.features

Cargoes(List<ChemicalEntity>, Evidence) - Constructor for class bio.singa.simulation.features.Cargoes

Cargoes(List<ChemicalEntity>) - Constructor for class bio.singa.simulation.features.Cargoes

Cargoes(ChemicalEntity...) - Constructor for class bio.singa.simulation.features.Cargoes

CELL_CORTEX - Static variable in class bio.singa.simulation.model.sections.CellRegions

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.transport.Diffusion

checkFeatures() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

checkFeatures() - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleConfinedDiffusion

checkFeatures() - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleCytoplasmDiffusion

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

clearAttachmentInformation() - 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.

clearPotentialDeltas() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

Clears the list of potential deltas.

clearPotentialDeltas() - Method in class bio.singa.simulation.model.modules.concentration.scope.DependentUpdate

clearPotentialDeltas() - Method in class bio.singa.simulation.model.modules.concentration.scope.IndependentUpdate

clearPotentialDeltas() - Method in class bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate

clearPotentialDeltas() - Method in interface bio.singa.simulation.model.modules.concentration.scope.UpdateScope

Clears all concentration deltas that may be assigned by this module

clearPotentialDeltasBut(UpdateModule) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

Clears the list of potential deltas retaining updates from a specific module.

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.trajectories.flat.FlatUpdateRecorder

Close all associated writers.

collectCatalysts() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

collectDeltas(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

collectProducts() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

collectReactants(Collection<Reactant>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

collectReactants(Collection<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.NodeBehavior

collectReactants(Collection<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.VesicleBehavior

collectSubstrates() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

collectUpdatables() - Method in class bio.singa.simulation.model.simulation.Simulation

complexBuilding() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

complexBuilding() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

complexBuilding() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

complexBuilding() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

Complex building reactions classically require two substrates that react to build one complex.

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.

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, double) - 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(GeneralConcentrationFormatter) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.ConcentrationUnitStep

concentrationFormat(GeneralConcentrationFormatter) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.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.

ConcentrationStateChange - Class in bio.singa.simulation.model.modules.qualitative.implementations

ConcentrationStateChange() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationStateChange

concentrationUnit(Unit<MolarConcentration>) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.ConcentrationUnitStep

concentrationUnit(Unit<MolarConcentration>) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

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.

ContainmentRegion - Class in bio.singa.simulation.features

ContainmentRegion(CellRegion, List<Evidence>) - Constructor for class bio.singa.simulation.features.ContainmentRegion

ContainmentRegion(CellRegion, Evidence) - Constructor for class bio.singa.simulation.features.ContainmentRegion

ContainmentRegion(CellRegion) - Constructor for class bio.singa.simulation.features.ContainmentRegion

containsEntity(CellTopology, ChemicalEntity) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

containsEntity(CellSubsection, ChemicalEntity) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

containsHiddenEntity(CellTopology, ChemicalEntity) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

containsSubstrates(ConcentrationContainer) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

convert(Simulation) - Static method in class bio.singa.simulation.export.reactiongraph.ReactionGraphConverter

convert(Simulation) - Static method in class bio.singa.simulation.export.reactiontable.ReactionTableConverter

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

create(String) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

create() - Static method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder

createCellCortex(Membrane, MooreRectangularDirection, Quantity<Length>, Quantity<Length>) - Static method in class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgentFactory

createCellCortex(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.

createDirectories(Path) - Static method in class bio.singa.simulation.trajectories.Recorders

createEquilibriumReactionExample() - Static method in class bio.singa.simulation.model.simulation.SimulationExamples

This simulation simulates a equilibrium reaction.

createFile(Path, String) - Static method in class bio.singa.simulation.trajectories.Recorders

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 Michaelis-Menten reaction, where D-Fructose 1-phosphate is converted to glycerone phosphate and D-glyceraldehyde using fructose bisphosphate aldolase.

createModule(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

createModule(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.DiffusionBuilder

createModule(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.MembraneDiffusionBuilder

createModule(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder

createModule(Simulation) - Method in interface bio.singa.simulation.model.modules.concentration.ModuleBuilder

createObject(SimpleStringIdentifier) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity.Builder

createRectangularAutomatonGraph(int, int) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs

CYTOPLASM - Static variable in class bio.singa.simulation.model.sections.CellSubsections

CYTOPLASM_REGION - Static variable in class bio.singa.simulation.model.sections.CellRegions

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

decreaseTimeStep() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

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_FUSION_TIME - Static variable in class bio.singa.simulation.features.FusionTime

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_VESICLE_RADIUS - Static variable in class bio.singa.simulation.features.VesicleRadius

DefaultFeatureSources - Class in bio.singa.simulation.features

DeltaBehavior - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas

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.

DetachmentProbability - Class in bio.singa.simulation.features

DetachmentProbability(Quantity<Frequency>, List<Evidence>) - Constructor for class bio.singa.simulation.features.DetachmentProbability

DetachmentProbability(Quantity<Frequency>, Evidence) - Constructor for class bio.singa.simulation.features.DetachmentProbability

DetachmentProbability(Quantity<Frequency>) - Constructor for class bio.singa.simulation.features.DetachmentProbability

determineComparisionConcentrations() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

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

determineGlobalNumericalError() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

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.

determineVelocity(ReactionEvent) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

determineVelocity(ReactionEvent) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.IrreversibleKineticLaw

determineVelocity(ReactionEvent) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.KineticLaw

determineVelocity(ReactionEvent) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.MichaelisMentenKineticLaw

determineVelocity(ReactionEvent) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.ReversibleKineticLaw

Diffusion - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

Diffusion is the fundamental force governing the random movement of molecules in cells.

Diffusion() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion

Diffusion.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

Diffusion.DiffusionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

Diffusion.SelectionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

DiffusionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.DiffusionBuilder

DiffusivityScaling - Class in bio.singa.simulation.model.modules.qualitative.implementations

DiffusivityScaling() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.DiffusivityScaling

directory(String, boolean) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.DirectoryStep

directory(String) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.DirectoryStep

directory(String, boolean) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

directory(String) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

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.

dissociationRate(RateConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ComplexBuildingReactionStep

dissociationRate(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

DONOVAN2015 - Static variable in class bio.singa.simulation.features.DefaultFeatureSources

DynamicBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

DynamicChemicalEntity - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

DynamicChemicalEntity(SimpleStringIdentifier) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

Creates a new Chemical Entity with the given identifier.

DynamicChemicalEntity(String) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

DynamicChemicalEntity.Builder - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

DynamicKineticLaw - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

DynamicKineticLaw(Reaction, String) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

DynamicReactantBehavior - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

DynamicReactantBehavior() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

dynamicReactants(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder

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

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

EndocytosisCheckpointConcentration - Class in bio.singa.simulation.features

EndocytosisCheckpointConcentration(Quantity<MolarConcentration>, List<Evidence>) - Constructor for class bio.singa.simulation.features.EndocytosisCheckpointConcentration

EndocytosisCheckpointConcentration(Quantity<MolarConcentration>, Evidence) - Constructor for class bio.singa.simulation.features.EndocytosisCheckpointConcentration

EndocytosisCheckpointConcentration(Quantity<MolarConcentration>) - Constructor for class bio.singa.simulation.features.EndocytosisCheckpointConcentration

EndocytosisCheckpointTime - Class in bio.singa.simulation.features

EndocytosisCheckpointTime(Quantity<Time>, List<Evidence>) - Constructor for class bio.singa.simulation.features.EndocytosisCheckpointTime

EndocytosisCheckpointTime(Quantity<Time>, Evidence) - Constructor for class bio.singa.simulation.features.EndocytosisCheckpointTime

EndocytosisCheckpointTime(Quantity<Time>) - Constructor for class bio.singa.simulation.features.EndocytosisCheckpointTime

EntityCompositionCondition - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

EntityCompositionCondition(String, ChemicalEntity, BiFunction<Collection<ChemicalEntity>, ChemicalEntity, List<ChemicalEntity>>) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.EntityCompositionCondition

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.

EntityFeature - Class in bio.singa.simulation.features

EntityFeature(ChemicalEntity, List<Evidence>) - Constructor for class bio.singa.simulation.features.EntityFeature

EntityFeature(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.EntityFeature

EntityFeature(ChemicalEntity) - Constructor for class bio.singa.simulation.features.EntityFeature

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

EntityReducer - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

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.

EpochUpdateWriterBuilder() - Constructor for class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.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.surfacelike.Membrane

equals(Object) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

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

evaluateGlobalNumericalAccuracy() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

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

FlatUpdateRecorder - Class in bio.singa.simulation.trajectories.flat

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.

FlatUpdateRecorder() - Constructor for class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder

FlatUpdateRecorder.BuildStep - Interface in bio.singa.simulation.trajectories.flat

FlatUpdateRecorder.ConcentrationUnitStep - Interface in bio.singa.simulation.trajectories.flat

FlatUpdateRecorder.DirectoryStep - Interface in bio.singa.simulation.trajectories.flat

FlatUpdateRecorder.EpochUpdateWriterBuilder - Class in bio.singa.simulation.trajectories.flat

FlatUpdateRecorder.SimulationStep - Interface in bio.singa.simulation.trajectories.flat

FlatUpdateRecorder.TimeUnitStep - Interface in bio.singa.simulation.trajectories.flat

FlatUpdateRecorder.WorkspaceStep - Interface in bio.singa.simulation.trajectories.flat

forAll(ChemicalEntity...) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.DiffusionBuilder

forAll(Collection<ChemicalEntity>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.DiffusionBuilder

forAll(ChemicalEntity...) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.SelectionStep

forAll(Collection<ChemicalEntity>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.SelectionStep

formatASCII(Reaction) - Static method in class bio.singa.simulation.export.format.FormatReactionEquation

FormatFeature - Class in bio.singa.simulation.export.format

FormatFeature() - Constructor for class bio.singa.simulation.export.format.FormatFeature

formatFeatures(List<Feature>) - Static method in class bio.singa.simulation.export.format.FormatFeature

formatRate(RateConstant) - Static method in class bio.singa.simulation.export.format.FormatFeature

FormatReactionEquation - Class in bio.singa.simulation.export.format

FormatReactionEquation() - Constructor for class bio.singa.simulation.export.format.FormatReactionEquation

FormatReactionKinetics - Class in bio.singa.simulation.export.format

FormatReactionKinetics() - Constructor for class bio.singa.simulation.export.format.FormatReactionKinetics

formatTex(Reaction) - Static method in class bio.singa.simulation.export.format.FormatReactionEquation

formatTex(Reaction) - Static method in class bio.singa.simulation.export.format.FormatReactionKinetics

forSolute(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder

forSolute(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SolutesStep

forSolutes(ChemicalEntity...) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder

forSolutes(Collection<ChemicalEntity>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder

forSolutes(ChemicalEntity...) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SolutesStep

forSolutes(Collection<ChemicalEntity>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SolutesStep

forwardReactionRate(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

forwardReactionRate(RateConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ReversibleReactionStep

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.

FusionTime - Class in bio.singa.simulation.features

FusionTime(Quantity<Time>, List<Evidence>) - Constructor for class bio.singa.simulation.features.FusionTime

FusionTime(Quantity<Time>, Evidence) - Constructor for class bio.singa.simulation.features.FusionTime

FusionTime(Quantity<Time>) - Constructor for class bio.singa.simulation.features.FusionTime

G

GeneralReactionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

generateAllCombinations() - Method in class bio.singa.simulation.features.variation.VariationSet

generateDeltas(List<Reactant>, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

generateDeltas(List<Reactant>, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.NodeBehavior

generateDeltas(List<Reactant>, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.VesicleBehavior

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.

generateProductDeltas(double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

generateReactantSets(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

generateReactantSets(Updatable) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantBehavior

generateReactantSets(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

generateSubstrateDeltas(double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

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.

getAccuracyGain() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

getAccuracyGain() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

getAdditionDelta() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit

getAffectedParameters() - Method in class bio.singa.simulation.features.variation.VariationSet

getAgents() - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLayer

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

getBuilder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity.Builder

getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion

getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion

getBuilder(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport

getCargoConcentration() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit

getCatalysts() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

getCatalysts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.NodeBehavior

getCatalysts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.VesicleBehavior

getCatalysts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

getCatalysts() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantBehavior

getCatalysts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantSet

getCatalysts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

getCellRegion() - Method in class bio.singa.simulation.features.variation.ConcentrationVariation

getCellRegion() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

getCellRegion() - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent

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

getComposition() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

getConcentration() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.ReactantConcentration

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.nested.TrajectoryData

getConcentrationInitializer() - Method in class bio.singa.simulation.model.simulation.Simulation

getConcentrationManager() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

getConcentrationManager() - Method in class bio.singa.simulation.model.graphs.AutomatonNode

getConcentrationManager() - Method in interface bio.singa.simulation.model.simulation.Updatable

getConcentrationMap() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

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.nested.TrajactoryDataPoint

getConcentrationUnit() - Method in class bio.singa.simulation.trajectories.nested.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.export.reactiongraph.ReactionGraphNode

getCopy() - Method in class bio.singa.simulation.model.graphs.AutomatonNode

getCountDownLatch() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

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.

getCurrentNode() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

getCurrentNodeContainer() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

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.

getCurrentVesicle() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

getCurrentVesicleContainer() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

getDelta() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.ReactantDelta

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

getDynamicProducts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

getDynamicSubstrates() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

getElapsedTime() - Method in class bio.singa.simulation.events.GraphUpdatedEvent

getElapsedTime() - Method in class bio.singa.simulation.model.simulation.Simulation

getElapsedTime() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

getEndingPoint() - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment

getEntity() - Method in class bio.singa.simulation.export.reactiongraph.ReactionGraphNode

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.imlementations.reactions.behaviors.reactants.EntityCompositionCondition

getEntity() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.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

getEquation() - Method in class bio.singa.simulation.export.reactiontable.ReactionTable.ReactionTableRow

getErrorCutoff() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Returns the cutoff where numerical errors to be considered irretrievably unstable.

getEstimatedSpeed() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

getEstimatedTimeRemaining() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

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.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

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.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

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.

getFunction() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.EntityCompositionCondition

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

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.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.export.reactiontable.ReactionTable.ReactionTableRow

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.concentration.imlementations.reactions.behaviors.deltas.ReactantDelta

getIdentifier() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.EntityCompositionCondition

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

getInnerDirection() - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane

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.reactions.Reaction

getKinetics() - Method in class bio.singa.simulation.export.reactiontable.ReactionTable.ReactionTableRow

getLargestGlobalError() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

getLargestGlobalError() - 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.

getLargestLocalError() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

getLargestLocalError() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

getLargestLocalErrorUpdate() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

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

getLocalErrorModule() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

getLocalErrorUpdate() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

getMatchingEntities(Updatable, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

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.reactions.ReactionBuilder.GeneralReactionBuilder

getModule() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.DiffusionBuilder

getModule() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.MembraneDiffusionBuilder

getModule() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.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

getNodeListeners() - Method in class bio.singa.simulation.model.simulation.SimulationManager

Returns all currently registered node event listeners.

getNodeWithContent(ChemicalEntity) - Method in class bio.singa.simulation.export.reactiongraph.ReactionGraph

getNumberOfEpochsSinceLastUpdate() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

getNumberOfModules() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

getNumberOfMolecules() - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration

getNumberOfTimeStepDecreasesSinceLastUpdate() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

getNumberOfTimeStepIncreasesSinceLastUpdate() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

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

getOriginalConcentrations() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

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.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

getParameters() - Method in class bio.singa.simulation.export.reactiontable.ReactionTable.ReactionTableRow

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.

getPosition() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

getPosition() - Method in interface bio.singa.simulation.model.simulation.Updatable

getPosition() - Method in class bio.singa.simulation.trajectories.nested.TrajactoryDataPoint

getPossibleTopologies() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

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.imlementations.reactions.behaviors.reactants.Reactant

getPreferredTopology() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

getPreviousObservedDeltas(Updatable) - Method in class bio.singa.simulation.model.simulation.Simulation

getProducts() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

getProducts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.NodeBehavior

getProducts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.VesicleBehavior

getProducts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

getProducts() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantBehavior

getProducts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantSet

getProducts() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

getProgressInMilliSeconds() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

getQuantity() - Method in class bio.singa.simulation.model.parameters.Parameter

getRadius() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

getRate(Class<T>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.AbstractKineticLaw

getReactant() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.ReactantConcentration

getReactantBehavior() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.Reaction

getReactants() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

getReactionOrder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Returns the reaction order.

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.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

getReferencedEntities() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantBehavior

getReferencedEntities() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

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

getRequiredFeatures() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

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.imlementations.reactions.behaviors.reactants.Reactant

Gets the role of this reactant.

getRows() - Method in class bio.singa.simulation.export.reactiontable.ReactionTable

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 ScalableQuantitativeFeature<?>>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

getScaledFeature(ChemicalEntity, Class<? extends ScalableQuantitativeFeature<?>>) - 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 ScalableQuantitativeFeature<?>>) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

getScaledFeature(ChemicalEntity, Class<? extends ScalableQuantitativeFeature<?>>) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

getScaledFeature(Class<? extends ScalableQuantitativeFeature<?>>) - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule

getScaledFeature(Class<? extends ScalableQuantitativeFeature<?>>) - Method in interface bio.singa.simulation.model.modules.UpdateModule

getScaledQuantity() - Method in class bio.singa.simulation.model.parameters.Parameter

getScaledRate(Class<? extends Feature>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.AbstractKineticLaw

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.modules.displacement.DisplacementBasedModule

getSimulation() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule

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

getSimulationStatus() - Method in class bio.singa.simulation.model.simulation.SimulationManager

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() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

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.imlementations.reactions.behaviors.reactants.Reactant

Returns the stoichiometric number (the number of molecules required for one 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

getSubstrates() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.DeltaBehavior

getSubstrates() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.NodeBehavior

getSubstrates() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.VesicleBehavior

getSubstrates() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

getSubstrates() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantBehavior

getSubstrates() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantSet

getSubstrates() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

getSupplier() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Returns the field supplier.

getTargetDirection() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

getTargetEntity() - Method in class bio.singa.simulation.model.rules.AssignmentRule

getTargetTopologies() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

getTerminationTime() - Method in class bio.singa.simulation.model.simulation.SimulationStatus

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.

getTimestepsDecreased() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

getTimestepsIncreased() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

getTimeUnit() - Method in class bio.singa.simulation.trajectories.nested.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.nested.NestedUpdateRecorder

getTrajectoryData() - Method in class bio.singa.simulation.trajectories.nested.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.

getUpdatableBehavior() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

getUpdatables() - Method in class bio.singa.simulation.model.simulation.Simulation

getValue() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDelta

Returns the value of the change.

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

getValueString(Object) - Static method in class bio.singa.simulation.features.variation.VariationSet

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

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.trajectories.flat.FlatUpdateRecorder

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.

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.modules.concentration.ConcentrationDeltaManager

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.surfacelike.Membrane

hashCode() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

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

hasNotPart(ChemicalEntity) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.EntityReducer

hasOnce(ChemicalEntity) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.EntityReducer

hasPart(ChemicalEntity) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.EntityReducer

hasTwice(ChemicalEntity) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.EntityReducer

I

identifier(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.FinalStep

identifier(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

identifier(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.DiffusionBuilder

identifier(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.SelectionStep

IN_STORAGE - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry

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.ConcentrationBasedModule

initialize() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport

initialize() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

initialize() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis

initialize() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion

initialize() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule

initialize() - Method in interface bio.singa.simulation.model.modules.UpdateModule

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(Updatable) - Method in interface bio.singa.simulation.model.sections.concentration.InitialConcentration

initialize(Updatable) - Method in class bio.singa.simulation.model.sections.concentration.MembraneConcentration

initialize(Updatable) - 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(LineLikeAgentLayer) - Method in class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre

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(LineLikeAgentLayer) - Method in class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre

initializeSpatialRepresentations() - Method in class bio.singa.simulation.model.simulation.Simulation

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.transport.Diffusion

inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion

inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport

interruptAllBut(Thread, UpdateModule) - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

Returns true if the calling module was the first to call the method, therefore being allowed to optimize the time step.

irreversible() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

irreversible() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

irreversible() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

IrreversibleKineticLaw - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

IrreversibleKineticLaw(Reaction) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.IrreversibleKineticLaw

isCatalyst() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

isConcentrationFixed() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

Returns true if the concentration is fixed - no deltas are applied.

isDynamicComplex() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

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.imlementations.reactions.behaviors.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.imlementations.reactions.behaviors.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 - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

kineticLaw(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

kineticLaw(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

kineticLaw(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

L

LANG2000 - Static variable in class bio.singa.simulation.features.DefaultFeatureSources

LineLikeAgent - Class in bio.singa.simulation.model.agents.linelike

LineLikeAgent(String) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgent

LineLikeAgent(String, Vector2D, Vector2D, AutomatonGraph) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgent

LineLikeAgent(String, List<Vector2D>, NeumannRectangularDirection) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgent

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

LineLikeAgentDetachment - Class in bio.singa.simulation.model.modules.qualitative.implementations

LineLikeAgentDetachment() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentDetachment

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

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(List<ChemicalEntity>, List<Evidence>) - Constructor for class bio.singa.simulation.features.MatchingQSnares

MatchingQSnares(List<ChemicalEntity>, Evidence) - Constructor for class bio.singa.simulation.features.MatchingQSnares

MatchingQSnares(List<ChemicalEntity>) - Constructor for class bio.singa.simulation.features.MatchingQSnares

MatchingQSnares(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.MatchingQSnares

MatchingQSnares(ChemicalEntity) - Constructor for class bio.singa.simulation.features.MatchingQSnares

MatchingRSnares - Class in bio.singa.simulation.features

MatchingRSnares(List<ChemicalEntity>, List<Evidence>) - Constructor for class bio.singa.simulation.features.MatchingRSnares

MatchingRSnares(List<ChemicalEntity>, Evidence) - Constructor for class bio.singa.simulation.features.MatchingRSnares

MatchingRSnares(List<ChemicalEntity>) - Constructor for class bio.singa.simulation.features.MatchingRSnares

MatchingRSnares(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.MatchingRSnares

MatchingRSnares(ChemicalEntity) - Constructor for class bio.singa.simulation.features.MatchingRSnares

MaturationTime - Class in bio.singa.simulation.features

MaturationTime(Quantity<Time>, List<Evidence>) - Constructor for class bio.singa.simulation.features.MaturationTime

MaturationTime(Quantity<Time>, Evidence) - Constructor for class bio.singa.simulation.features.MaturationTime

MaturationTime(Quantity<Time>) - Constructor for class bio.singa.simulation.features.MaturationTime

MaximalConcentration - Class in bio.singa.simulation.features

MaximalConcentration(Quantity<MolarConcentration>, List<Evidence>) - Constructor for class bio.singa.simulation.features.MaximalConcentration

MaximalConcentration(Quantity<MolarConcentration>, Evidence) - Constructor for class bio.singa.simulation.features.MaximalConcentration

MaximalConcentration(Quantity<MolarConcentration>) - 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.transport

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.transport.MembraneDiffusion

MembraneDiffusion.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

MembraneDiffusion.CargoStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

MembraneDiffusion.MembraneDiffusionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

MembraneDiffusionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.MembraneDiffusionBuilder

MembraneFactory - Class in bio.singa.simulation.model.agents.surfacelike

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

michaelisConstant(MichaelisConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

michaelisConstant(MichaelisConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.MichaelisMentenReactionStep

michaelisMenten() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

michaelisMenten() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

michaelisMenten() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

MichaelisMentenKineticLaw - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

MichaelisMentenKineticLaw(Reaction) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.MichaelisMentenKineticLaw

MICROTUBULE - Static variable in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

MICROTUBULE_ATTACHED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry

MicrotubuleOrganizingCentre - Class in bio.singa.simulation.model.agents.linelike

MicrotubuleOrganizingCentre(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.

MINUS - Static variable in class bio.singa.simulation.features.MotorPullDirection

ModifiedDiffusivity - Class in bio.singa.simulation.features

ModifiedDiffusivity(Quantity<Diffusivity>, List<Evidence>) - Constructor for class bio.singa.simulation.features.ModifiedDiffusivity

ModifiedDiffusivity(Quantity<Diffusivity>, Evidence) - Constructor for class bio.singa.simulation.features.ModifiedDiffusivity

ModifiedDiffusivity(Quantity<Diffusivity>) - Constructor for class bio.singa.simulation.features.ModifiedDiffusivity

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

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>, List<Evidence>) - Constructor for class bio.singa.simulation.features.MotorMovementVelocity

MotorMovementVelocity(Quantity<Speed>, Evidence) - Constructor for class bio.singa.simulation.features.MotorMovementVelocity

MotorMovementVelocity(Quantity<Speed>) - Constructor for class bio.singa.simulation.features.MotorMovementVelocity

MotorPullDirection - Class in bio.singa.simulation.features

MotorPullDirection(String, List<Evidence>) - Constructor for class bio.singa.simulation.features.MotorPullDirection

MotorPullDirection(String, Evidence) - Constructor for class bio.singa.simulation.features.MotorPullDirection

MotorPullDirection(String) - Constructor for class bio.singa.simulation.features.MotorPullDirection

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

MultiEntityFeature - Class in bio.singa.simulation.features

MultiEntityFeature(List<ChemicalEntity>, List<Evidence>) - Constructor for class bio.singa.simulation.features.MultiEntityFeature

MultiEntityFeature(List<ChemicalEntity>, Evidence) - Constructor for class bio.singa.simulation.features.MultiEntityFeature

MultiEntityFeature(List<ChemicalEntity>) - Constructor for class bio.singa.simulation.features.MultiEntityFeature

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.

multiply(List<ReactantConcentration>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.AbstractKineticLaw

MultiStringFeature - Class in bio.singa.simulation.features

MultiStringFeature(List<String>, List<Evidence>) - Constructor for class bio.singa.simulation.features.MultiStringFeature

MultiStringFeature(List<String>, Evidence) - Constructor for class bio.singa.simulation.features.MultiStringFeature

MultiStringFeature(List<String>) - Constructor for class bio.singa.simulation.features.MultiStringFeature

N

NANOMETRE_PER_SECOND - Static variable in class bio.singa.simulation.features.ActinBoostVelocity

NestedUpdateRecorder - Class in bio.singa.simulation.trajectories.nested

NestedUpdateRecorder(Simulation) - Constructor for class bio.singa.simulation.trajectories.nested.NestedUpdateRecorder

NestedUpdateRecorder(Simulation, Unit<Time>, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.trajectories.nested.NestedUpdateRecorder

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

NodeBehavior - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas

NodeBehavior(ReactionEvent) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.NodeBehavior

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.

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

observe(Updatable) - Method in class bio.singa.simulation.model.simulation.Simulation

of(Updatable, Unit<MolarConcentration>) - Static method in class bio.singa.simulation.trajectories.nested.TrajactoryDataPoint

of(Collection<Updatable>, Unit<MolarConcentration>) - Static method in class bio.singa.simulation.trajectories.nested.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.ActinCortexDiffusivityScaling

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationStateChange

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.DiffusivityScaling

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentDetachment

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VolumeLikeAgentContainment

onCompletion() - Method in interface bio.singa.simulation.model.modules.UpdateModule

onEventReceived(GraphUpdatedEvent) - Method in class bio.singa.simulation.model.simulation.SimulationStatus

onEventReceived(UpdatableUpdatedEvent) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder

onEventReceived(GraphUpdatedEvent) - Method in class bio.singa.simulation.trajectories.nested.NestedUpdateRecorder

onlyFor(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.DiffusionBuilder

onlyFor(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.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.ActinCortexDiffusivityScaling

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationStateChange

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.DiffusivityScaling

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentDetachment

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VolumeLikeAgentContainment

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.ActinCortexDiffusivityScaling

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationStateChange

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.DiffusivityScaling

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentDetachment

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VolumeLikeAgentContainment

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

OriginalDiffusivity - Class in bio.singa.simulation.features

OriginalDiffusivity(Quantity<Diffusivity>, List<Evidence>) - Constructor for class bio.singa.simulation.features.OriginalDiffusivity

OriginalDiffusivity(Quantity<Diffusivity>, Evidence) - Constructor for class bio.singa.simulation.features.OriginalDiffusivity

OriginalDiffusivity(Quantity<Diffusivity>) - Constructor for class bio.singa.simulation.features.OriginalDiffusivity

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 interface bio.singa.simulation.features.SpawnRate

PERINUCLEAR_REGION - Static variable in class bio.singa.simulation.model.sections.CellRegions

Pit(Quantity<Time>, Vector2D, Quantity<Length>, double, AutomatonNode, ConcentrationDelta) - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit

PitFormationRate - Class in bio.singa.simulation.features

PitFormationRate(Quantity<SpawnRate>, List<Evidence>) - Constructor for class bio.singa.simulation.features.PitFormationRate

PitFormationRate(Quantity<SpawnRate>, Evidence) - Constructor for class bio.singa.simulation.features.PitFormationRate

PitFormationRate(Quantity<SpawnRate>) - Constructor for class bio.singa.simulation.features.PitFormationRate

PLUS - Static variable in class bio.singa.simulation.features.MotorPullDirection

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

rate(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

rate(RateConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.IrreversibleReactionStep

Ratio - Class in bio.singa.simulation.features

Ratio(Quantity<Dimensionless>, List<Evidence>) - Constructor for class bio.singa.simulation.features.Ratio

Ratio(Quantity<Dimensionless>, Evidence) - Constructor for class bio.singa.simulation.features.Ratio

Ratio(Quantity<Dimensionless>) - Constructor for class bio.singa.simulation.features.Ratio

Ratio(double) - Constructor for class bio.singa.simulation.features.Ratio

Reactant - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

A Reactant encapsulates a ChemicalEntity for the use in Reactions.

Reactant(ChemicalEntity, ReactantRole) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Creates a new reactant.

Reactant(ChemicalEntity, ReactantRole, CellTopology) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, CellTopology, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, CellTopology, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, CellTopology, double, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, double, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

ReactantBehavior - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

ReactantConcentration - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas

ReactantConcentration(Reactant, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.ReactantConcentration

ReactantDelta - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas

ReactantDelta(ConcentrationDeltaIdentifier, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.ReactantDelta

ReactantRole - Enum in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

The role of the reactant: Increasing, for products and accelerating reactants and decreasing for substrates and inhibiting reactants.

ReactantSet - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

ReactantSet(List<Reactant>, List<Reactant>, List<Reactant>) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantSet

ReactantSet(List<Reactant>, List<Reactant>) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantSet

reaction - Variable in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.AbstractKineticLaw

Reaction - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

Reaction() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.Reaction

reaction - Variable in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

ReactionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder

ReactionBuilder.ComplexBuildingReactionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.DynamicBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.DynamicReactantStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.FinalStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.GeneralReactionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.IrreversibleReactionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.MichaelisMentenReactionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.ParameterStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.ReversibleReactionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.StaticBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.StaticReactantStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionEvent - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionEvent(Reaction, ReactantSet) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

ReactionGraph - Class in bio.singa.simulation.export.reactiongraph

ReactionGraph() - Constructor for class bio.singa.simulation.export.reactiongraph.ReactionGraph

ReactionGraphConverter - Class in bio.singa.simulation.export.reactiongraph

ReactionGraphEdge - Class in bio.singa.simulation.export.reactiongraph

ReactionGraphEdge(int) - Constructor for class bio.singa.simulation.export.reactiongraph.ReactionGraphEdge

ReactionGraphEdge(int, double) - Constructor for class bio.singa.simulation.export.reactiongraph.ReactionGraphEdge

ReactionGraphNode - Class in bio.singa.simulation.export.reactiongraph

ReactionGraphNode(Integer) - Constructor for class bio.singa.simulation.export.reactiongraph.ReactionGraphNode

ReactionGraphNode(Integer, ChemicalEntity) - Constructor for class bio.singa.simulation.export.reactiongraph.ReactionGraphNode

ReactionTable - Class in bio.singa.simulation.export.reactiontable

ReactionTable() - Constructor for class bio.singa.simulation.export.reactiontable.ReactionTable

ReactionTable.ReactionTableRow - Class in bio.singa.simulation.export.reactiontable

ReactionTableConverter - Class in bio.singa.simulation.export.reactiontable

ReactionTableRow(String, String, String, String) - Constructor for class bio.singa.simulation.export.reactiontable.ReactionTable.ReactionTableRow

recalculationRequired() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

Recalculations are required if: the time step was rescaled during this calculation any module was interrupted during this calculation the global error was larger than the recalculation cutoff

Recorders - Class in bio.singa.simulation.trajectories

reduce() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate

reduce() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

reduce(Collection<ChemicalEntity>, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.EntityCompositionCondition

referenceChemicalEntityToParameter(String, ChemicalEntity) - Method in class bio.singa.simulation.model.rules.AssignmentRule

referenceConstant(String, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceConstant(String, double, Evidence) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceFeature(String, ScalableQuantitativeFeature) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceFeature(ScalableQuantitativeFeature) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceParameter(Parameter<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceParameter(ScalableQuantitativeFeature<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(String, ScalableQuantitativeFeature<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(Parameter<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(String, Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(String, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(String, double, Evidence) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(ScalableQuantitativeFeature<?>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(String, ScalableQuantitativeFeature<?>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(Reactant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(Parameter<?>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(String, Reactant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(String, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(String, double, Evidence) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceReactant(String, Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceReactant(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

RegionFeature - Class in bio.singa.simulation.features

RegionFeature(CellRegion, List<Evidence>) - Constructor for class bio.singa.simulation.features.RegionFeature

RegionFeature(CellRegion, Evidence) - Constructor for class bio.singa.simulation.features.RegionFeature

RegionFeature(CellRegion) - Constructor for class bio.singa.simulation.features.RegionFeature

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

RequiredVesicleState - Class in bio.singa.simulation.features

RequiredVesicleState(String, List<Evidence>) - Constructor for class bio.singa.simulation.features.RequiredVesicleState

RequiredVesicleState(String, Evidence) - Constructor for class bio.singa.simulation.features.RequiredVesicleState

RequiredVesicleState(String) - Constructor for class bio.singa.simulation.features.RequiredVesicleState

resetCalculation() - 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

reversible() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

reversible() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

reversible() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

Reversible reactions where the substrates form products, and products can also from substrates.

ReversibleKineticLaw - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

ReversibleKineticLaw(Reaction) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.ReversibleKineticLaw

revertToOriginalConcentrations() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

run() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

run() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

run() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule

run() - Method in class bio.singa.simulation.model.simulation.SimulationManager

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

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, 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 given topology.

set(ChemicalEntity, double) - 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

setCargoConcentration(double) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis.Pit

setCatalysts(List<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

setCellRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent

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

setComposition(List<EntityCompositionCondition>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

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.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

setConcentrationManager(ConcentrationDeltaManager) - Method in class bio.singa.simulation.model.graphs.AutomatonNode

setConcentrationMap(Map<String, Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

setCurrentEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Sets the current chemical entity.

setCurrentNode(AutomatonNode) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

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.

setCurrentVesicle(Vesicle) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

setDeltaCutoff(double) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Sets the cutoff where deltas are validated to be effectively zero.

setDynamicComplex(boolean) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

setDynamicSubstrates(List<DynamicChemicalEntity>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

setEndingPoint(Vector2D) - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment

setEntity(ChemicalEntity) - Method in class bio.singa.simulation.export.reactiongraph.ReactionGraphNode

setEntity(ChemicalEntity) - Method in class bio.singa.simulation.features.variation.EntityFeatureVariationEntry

setEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.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

setEquation(String) - Method in class bio.singa.simulation.export.reactiontable.ReactionTable.ReactionTableRow

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, ScalableQuantitativeFeature>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

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.export.reactiontable.ReactionTable.ReactionTableRow

setIdentifier(String) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

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

setInnerDirection(NeumannRectangularDirection) - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane

setInnerRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

setInnerRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane

setInterimAndUpdateCurrentConcentrations() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

setKeepPlatformOpen(boolean) - Method in class bio.singa.simulation.model.simulation.SimulationManager

setKineticLaw(KineticLaw) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.Reaction

setKinetics(String) - Method in class bio.singa.simulation.export.reactiontable.ReactionTable.ReactionTableRow

setLargestLocalError(LocalError) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Sets the largest error as of yet.

setLargestLocalError(LocalError, UpdateModule, double) - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

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

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.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

setParameters(String) - Method in class bio.singa.simulation.export.reactiontable.ReactionTable.ReactionTableRow

setPath(VectorPath) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

setPlusEndBehaviour(LineLikeAgent.GrowthBehaviour) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

setPolygon(Polygon) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

setPossibleTopologies(List<CellTopology>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicChemicalEntity

setPreferredConcentrationUnit(Unit<MolarConcentration>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

setPreferredTopology(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

setProducts(List<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

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

setReactantBehavior(ReactantBehavior) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.Reaction

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

setRole(ReactantRole) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Gets the role of this reactant.

setRows(List<ReactionTable.ReactionTableRow>) - Method in class bio.singa.simulation.export.reactiontable.ReactionTable

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

setSimulation(Simulation) - Method in interface bio.singa.simulation.model.modules.UpdateModule

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

setState(String) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

setStaticCatalysts(List<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

setStaticProducts(List<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

setStaticSubstrates(List<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.DynamicReactantBehavior

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

setSubstrates(List<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

setTargetDirection(String) - 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

setTerminationTime(Quantity<Time>) - Method in class bio.singa.simulation.model.simulation.SimulationStatus

setType(String) - 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.

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 bio.singa.simulation.model.modules.concentration.ConcentrationDelta

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(List<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

setVolumeLayer(VolumeLayer) - Method in class bio.singa.simulation.model.simulation.Simulation

shiftDeltas() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

Shifts the deltas from the potential delta list to the final delta list.

simulation - Variable in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

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.

simulation(Simulation) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

simulation(Simulation) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.SimulationStep

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.

SimulationStatus - Class in bio.singa.simulation.model.simulation

SimulationStatus(Simulation) - Constructor for class bio.singa.simulation.model.simulation.SimulationStatus

SingleFileChannelMembraneTransport - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

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.transport.SingleFileChannelMembraneTransport

SingleFileChannelMembraneTransport.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

SingleFileChannelMembraneTransport.CargoStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

SingleFileChannelMembraneTransport.SolutesStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

SingleFileChannelMembraneTransport.TransporterStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

SingleFileChannelMembraneTransportBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder

singularGraph() - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs

singularGraph(CellRegion) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs

SNAREFusionPairs - Class in bio.singa.simulation.features

Snare pairs required for fusion event to trigger

SNAREFusionPairs(Quantity<Dimensionless>, List<Evidence>) - Constructor for class bio.singa.simulation.features.SNAREFusionPairs

SNAREFusionPairs(Quantity<Dimensionless>, Evidence) - Constructor for class bio.singa.simulation.features.SNAREFusionPairs

SNAREFusionPairs(Quantity<Dimensionless>) - Constructor for class bio.singa.simulation.features.SNAREFusionPairs

Solutes - Class in bio.singa.simulation.features

Solutes(List<ChemicalEntity>, List<Evidence>) - Constructor for class bio.singa.simulation.features.Solutes

Solutes(List<ChemicalEntity>, Evidence) - Constructor for class bio.singa.simulation.features.Solutes

Solutes(List<ChemicalEntity>) - 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 interface bio.singa.simulation.features.SpawnRate

state - Variable in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

state - Variable in class bio.singa.simulation.model.modules.qualitative.QualitativeModule

StaticBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

StaticReactantBehavior - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

StaticReactantBehavior() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

staticReactants(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder

sumOf(DynamicChemicalEntity) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

supplier - Variable in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Frequently required fields.

T

targetProductToTopology(ChemicalEntity, CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicBuilder

targetProductToTopology(ChemicalEntity, CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.DynamicReactantStep

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

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.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

timeFormat(QuantityFormatter<Time>) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.TimeUnitStep

timeStepWasAlteredInThisEpoch() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

timeStepWasRescaled() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

timeUnit(Unit<Time>) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

timeUnit(Unit<Time>) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.TimeUnitStep

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.features.variation.VariationSet

toString() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

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.reactions.behaviors.reactants.Reactant

toString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantSet

toString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion

toString() - Method in class bio.singa.simulation.model.modules.concentration.LocalError

toString() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

toString() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDelta

toString() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule

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

toTex() - Method in class bio.singa.simulation.export.reactiontable.ReactionTable

toTexTableRow() - Method in class bio.singa.simulation.export.reactiontable.ReactionTable.ReactionTableRow

TrajactoryDataPoint - Class in bio.singa.simulation.trajectories.nested

Trajectories - Class in bio.singa.simulation.trajectories.nested

Trajectories() - Constructor for class bio.singa.simulation.trajectories.nested.Trajectories

Trajectories(Unit<Time>, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.trajectories.nested.Trajectories

TrajectoryData - Class in bio.singa.simulation.trajectories.nested

Transporter - Class in bio.singa.simulation.features

Transporter(ChemicalEntity, List<Evidence>) - Constructor for class bio.singa.simulation.features.Transporter

Transporter(ChemicalEntity, Evidence) - Constructor for class bio.singa.simulation.features.Transporter

Transporter(ChemicalEntity) - Constructor for class bio.singa.simulation.features.Transporter

transporter(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder

transporter(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.TransporterStep

turnover(TurnoverNumber) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

turnover(TurnoverNumber) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.MichaelisMentenReactionStep

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.

V

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.imlementations.reactions.behaviors.reactants.ReactantRole

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.sections.CellTopology

Returns the enum constant of this type with the specified name.

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.imlementations.reactions.behaviors.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.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.sections.CellTopology

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(CellRegion, 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

VESICLE_LUMEN - Static variable in class bio.singa.simulation.model.sections.CellSubsections

VESICLE_MEMBRANE - Static variable in class bio.singa.simulation.model.sections.CellSubsections

VESICLE_REGION - Static variable in class bio.singa.simulation.model.sections.CellRegions

VesicleBehavior - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas

VesicleBehavior(ReactionEvent) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.VesicleBehavior

VesicleConfinedDiffusion - Class in bio.singa.simulation.model.modules.displacement.implementations

VesicleConfinedDiffusion() - Constructor for class bio.singa.simulation.model.modules.displacement.implementations.VesicleConfinedDiffusion

vesicleCounter - Static variable in class bio.singa.simulation.model.agents.pointlike.Vesicle

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

VesicleRadius - Class in bio.singa.simulation.features

VesicleRadius(Quantity<Length>, List<Evidence>) - Constructor for class bio.singa.simulation.features.VesicleRadius

VesicleRadius(Quantity<Length>, Evidence) - Constructor for class bio.singa.simulation.features.VesicleRadius

VesicleRadius(Quantity<Length>) - Constructor for class bio.singa.simulation.features.VesicleRadius

VesicleStateRegistry - 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

VolumeLikeAgent(Polygon, CellRegion) - Constructor for class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent

VolumeLikeAgentContainment - Class in bio.singa.simulation.model.modules.qualitative.implementations

For vesicles state changes upon entering certain regions represented by volume like agents

VolumeLikeAgentContainment() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.VolumeLikeAgentContainment

VolumeLikeAgentFactory - Class in bio.singa.simulation.model.agents.volumelike

W

workspace(Path) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

workspace(Path) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.WorkspaceStep

writeVariationLog(Path, List<?>) - Static method in class bio.singa.simulation.features.variation.VariationSet

writeVariationResults(Path, VariationSet, Map<String, Double>) - Static method in class bio.singa.simulation.features.variation.VariationSet

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