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

A

AbstractDeltaFunction<FunctionReturnType> - Class in bio.singa.simulation.model.modules.concentration.functions

Delta Functions are used to calculate updates for Updatables during simulation.

accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.AdditionExpressionNode

Implementation of the visitor design pattern.

accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.ConstantExpressionNode

Implementation of the visitor design pattern.

accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.ExponentiationExpressionNode

Implementation of the visitor design pattern.

accept(ExpressionNodeVisitor) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNode

Method needed for the visitor design pattern

accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.FunctionExpressionNode

Implementation of the visitor design pattern.

accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode

Implementation of the visitor design pattern.

accept(ExpressionNodeVisitor) - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode

Implementation of the visitor design pattern.

acceptValue(String, double) - Method in class bio.singa.simulation.model.rules.AppliedExpression

Replaces a value for the parameter with the given identifier.

ActinBoostVelocity - Class in bio.singa.simulation.features.endocytosis

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

ActinBoostVelocity(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.ActinBoostVelocity

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

addAssociatedNode(AutomatonNode, Quantity<Area>) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

addCellRegion(CellRegion) - Method in class bio.singa.simulation.model.graphs.AutomatonGraph

Adds a cell section to this graph but does not associate any node to it.

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

Adds a delta function to the module.

addDeltaFunction(EntityDeltaFunction) - Method in class bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific

addDeltaFunction(SectionDeltaFunction) - Method in class bio.singa.simulation.model.modules.concentration.specifity.SectionSpecific

addDeltaFunction(UpdatableDeltaFunction) - Method in class bio.singa.simulation.model.modules.concentration.specifity.UpdatableSpecific

addDeltaFunction(DeltaFunctionType) - Method in interface bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity

Adds the implementation of a AbstractDeltaFunction to be calculated during simulation.

addDeltaFunction(Function<Vesicle, DisplacementDelta>, Predicate<Vesicle>) - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

addEdgeBetween(int, AutomatonNode, AutomatonNode) - Method in class bio.singa.simulation.model.graphs.AutomatonGraph

addEdgeBetween(AutomatonNode, AutomatonNode) - Method in class bio.singa.simulation.model.graphs.AutomatonGraph

addFilament(Vector2D, Vector2D) - Method in class bio.singa.simulation.model.agents.filaments.FilamentLayer

addGraphUpdateListener(UpdateEventListener<GraphUpdatedEvent>) - Method in class bio.singa.simulation.model.simulation.SimulationManager

Adds a new listener for graph based events.

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.

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

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

addMembrane(Membrane) - Method in class bio.singa.simulation.model.agents.membranes.MembraneLayer

addMembraneCargo(Quantity<Area>, double, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.displacement.implementations.ClathrinMediatedEndocytosis

addMembraneCargo(Quantity<Area>, double, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis

addMembranes(Collection<Membrane>) - Method in class bio.singa.simulation.model.agents.membranes.MembraneLayer

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

addMembraneSegment(MembraneSegment) - Method in class bio.singa.simulation.model.modules.displacement.implementations.ClathrinMediatedEndocytosis

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

addMicrotubuleSegment(SkeletalFilament, Vector2D) - Method in class bio.singa.simulation.model.graphs.AutomatonNode

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

References the module and referenced entities to the referenced simulation.

addNodeToObserve(AutomatonNode) - Method in class bio.singa.simulation.events.EpochUpdateWriter

Initializes a node that will be observed during simulation.

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

Adds a new listener for node based events.

addPotentialDelta(ConcentrationDelta) - Method in class bio.singa.simulation.model.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 class bio.singa.simulation.model.modules.displacement.Vesicle

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.modules.displacement.Vesicle

addProduct(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

addProduct(ChemicalEntity, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

addReferencedEntities(Collection<? extends ChemicalEntity>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Adds multiple referenced chemical entities.

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

Adds a referenced chemical entity.

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

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

addStochiometricReactant(StoichiometricReactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

addSubSection(CellTopology, CellSubsection) - Method in class bio.singa.simulation.model.sections.CellRegion

addSubsectionRepresentation(CellSubsection, Polygon) - Method in class bio.singa.simulation.model.graphs.AutomatonNode

addSubstrate(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

addSubstrate(ChemicalEntity, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

addSubstrate(ChemicalEntity, double, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

addVesicle(Vesicle) - Method in class bio.singa.simulation.model.modules.displacement.VesicleLayer

AppliedExpression - Class in bio.singa.simulation.model.rules

Applied expressions encapsulate formulas in given in String form.

AppliedExpression(String, Unit<?>) - Constructor for class bio.singa.simulation.model.rules.AppliedExpression

Creates an expression from the given string.

AppliedScale - Class in bio.singa.simulation.features.scale

AppliedScale(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.scale.AppliedScale

AppliedScale() - Constructor for class bio.singa.simulation.features.scale.AppliedScale

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

Apply all referenced assignment rules.

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

Applies all final deltas and clears the delta list.

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

Applies all final deltas and clears the delta list.

applyDeltas() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

applyDeltas() - Method in class bio.singa.simulation.model.modules.displacement.VesicleLayer

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

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

AssignmentRule - Class in bio.singa.simulation.model.rules

AssignmentRule(ChemicalEntity, AppliedExpression) - Constructor for class bio.singa.simulation.model.rules.AssignmentRule

AssignmentRules - Class in bio.singa.simulation.model.rules

AttachmentDistance - Class in bio.singa.simulation.features.endocytosis

AttachmentDistance(ComparableQuantity<Length>, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.AttachmentDistance

AttachmentDistance(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.AttachmentDistance

AutomatonEdge - Class in bio.singa.simulation.model.graphs

AutomatonEdge(int) - Constructor for class bio.singa.simulation.model.graphs.AutomatonEdge

AutomatonGraph - Class in bio.singa.simulation.model.graphs

The Automaton graph class is the underlying graph of cellular graph automaton Simulations.

AutomatonGraph(int, int) - Constructor for class bio.singa.simulation.model.graphs.AutomatonGraph

Creates a new empty graph, initialized with node and edge capacity.

AutomatonGraphRenderer - Class in bio.singa.simulation.renderer

AutomatonGraphRenderer(AutomatonGraph) - Constructor for class bio.singa.simulation.renderer.AutomatonGraphRenderer

AutomatonGraphRenderer() - Constructor for class bio.singa.simulation.renderer.AutomatonGraphRenderer

AutomatonGraphs - Class in bio.singa.simulation.model.graphs

AutomatonNode - Class in bio.singa.simulation.model.graphs

A node of the AutomatonGraph.

AutomatonNode(RectangularCoordinate) - Constructor for class bio.singa.simulation.model.graphs.AutomatonNode

AutomatonNode(int, int) - Constructor for class bio.singa.simulation.model.graphs.AutomatonNode

availableFeatures - Static variable in class bio.singa.simulation.model.modules.displacement.Vesicle

B

backwardsRateConstant(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.Builder

BindingBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder

bio.singa.simulation - package bio.singa.simulation

The simulations allows for the definition of models and simulations based on modules, that define cellular processes.

bio.singa.simulation.events - package bio.singa.simulation.events

bio.singa.simulation.exceptions - package bio.singa.simulation.exceptions

bio.singa.simulation.features - package bio.singa.simulation.features

bio.singa.simulation.features.endocytosis - package bio.singa.simulation.features.endocytosis

bio.singa.simulation.features.permeability - package bio.singa.simulation.features.permeability

bio.singa.simulation.features.scale - package bio.singa.simulation.features.scale

bio.singa.simulation.model.agents - package bio.singa.simulation.model.agents

bio.singa.simulation.model.agents.filaments - package bio.singa.simulation.model.agents.filaments

bio.singa.simulation.model.agents.membranes - package bio.singa.simulation.model.agents.membranes

bio.singa.simulation.model.agents.organelles - package bio.singa.simulation.model.agents.organelles

bio.singa.simulation.model.graphs - package bio.singa.simulation.model.graphs

bio.singa.simulation.model.modules - package bio.singa.simulation.model.modules

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

bio.singa.simulation.model.modules.concentration.functions - package bio.singa.simulation.model.modules.concentration.functions

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

bio.singa.simulation.model.modules.concentration.reactants - package bio.singa.simulation.model.modules.concentration.reactants

bio.singa.simulation.model.modules.concentration.scope - package bio.singa.simulation.model.modules.concentration.scope

bio.singa.simulation.model.modules.concentration.specifity - package bio.singa.simulation.model.modules.concentration.specifity

bio.singa.simulation.model.modules.displacement - package bio.singa.simulation.model.modules.displacement

bio.singa.simulation.model.modules.displacement.implementations - package bio.singa.simulation.model.modules.displacement.implementations

bio.singa.simulation.model.modules.qualitative - package bio.singa.simulation.model.modules.qualitative

bio.singa.simulation.model.modules.qualitative.implementations - package bio.singa.simulation.model.modules.qualitative.implementations

bio.singa.simulation.model.parameters - package bio.singa.simulation.model.parameters

bio.singa.simulation.model.rules - package bio.singa.simulation.model.rules

bio.singa.simulation.model.sections - package bio.singa.simulation.model.sections

bio.singa.simulation.model.simulation - package bio.singa.simulation.model.simulation

bio.singa.simulation.parser.organelles - package bio.singa.simulation.parser.organelles

bio.singa.simulation.parser.sbml - package bio.singa.simulation.parser.sbml

bio.singa.simulation.parser.sbml.converter - package bio.singa.simulation.parser.sbml.converter

bio.singa.simulation.renderer - package bio.singa.simulation.renderer

BioGraphRenderOptions - Class in bio.singa.simulation.renderer

BioGraphRenderOptions() - Constructor for class bio.singa.simulation.renderer.BioGraphRenderOptions

BIOMODELS_FETCH_URL - Static variable in class bio.singa.simulation.parser.sbml.BioModelsParserService

BioModelsParserService - Class in bio.singa.simulation.parser.sbml

BioModelsParserService() - Constructor for class bio.singa.simulation.parser.sbml.BioModelsParserService

BuddingRate - Class in bio.singa.simulation.features.endocytosis

BuddingRate(Quantity<SpawnRate>, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.BuddingRate

BuddingRate(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.BuddingRate

build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder

build() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BuilderStep

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

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

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

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

build() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

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

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

Builder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction.Builder

Builder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction.Builder

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

Builder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.Builder

builderObject - Variable in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

by(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BinderSelection

by(ChemicalEntity, RateConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BinderSelection

by(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder

by(ChemicalEntity, RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder

C

calculateDeltas(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

Calculates all deltas for all reactants for the reaction.

calculateDisplacement(Vesicle) - Method in class bio.singa.simulation.model.modules.displacement.implementations.EndocytosisActinBoost

calculateDisplacement(Vesicle) - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleDiffusion

calculateDisplacement(Vesicle) - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleTransport

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.

calculateTotalDisplacement() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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.ClathrinMediatedEndocytosis

calculateUpdates() - Method in class bio.singa.simulation.model.modules.displacement.implementations.EndocytosisActinBoost

calculateUpdates() - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleDiffusion

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

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

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

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

calculateVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction

calculateVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction

calculateVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction

calculateVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

Calculates the reaction velocity, depending on the kinetic law.

calculateVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction

calculateVelocity(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw

Calculates the velocity of the reaction based on the entities in the concentration container.

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

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

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

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

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

CatalyticReactant - Class in bio.singa.simulation.model.modules.concentration.reactants

CatalyticReactants are Reactants that are not consumed or produced during Reactions, but influence its velocity (reaction rate).

CatalyticReactant(ChemicalEntity, ReactantRole) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.CatalyticReactant

Creates a new catalytic reactant.

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

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

CellSubsection(String, boolean) - Constructor for class bio.singa.simulation.model.sections.CellSubsection

Creates a new cell subsection.

CellSubsections - Class in bio.singa.simulation.model.sections

CellSubsections() - Constructor for class bio.singa.simulation.model.sections.CellSubsections

CellTopology - Enum in bio.singa.simulation.model.sections

The cell topology defines how the subsections are spatially organized.

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

checkFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction

checkFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction

checkFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction

checkFeatures() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction

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

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

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

ClathrinMediatedEndocytosis() - Constructor for class bio.singa.simulation.model.modules.displacement.implementations.ClathrinMediatedEndocytosis

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

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

clearAssociatedNodes() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

Clears all full end half deltas.

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

Clears the list of potential deltas.

clearPotentialConcentrationDeltas() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

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

Clears the list of potential deltas.

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

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

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

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

Clears all concentration deltas that may be assigned to the given updatable.

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

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

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

clearPotentialDeltasBut(UpdateModule) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

clearPotentialDisplacementDeltas() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager

Clears all potential displacement deltas.

clearPotentialDisplacementDeltas() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

clearUpdates() - Method in class bio.singa.simulation.model.modules.displacement.VesicleLayer

ClippingPlayground - Class in bio.singa.simulation.model.agents

ClippingPlayground() - Constructor for class bio.singa.simulation.model.agents.ClippingPlayground

CLOSE_BRACKET - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for closing brackets

closeWriters() - Method in class bio.singa.simulation.events.EpochUpdateWriter

Close all associated writers.

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

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

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

combineToGif() - Method in class bio.singa.simulation.events.GraphImageWriter

CompartmentHandler - Class in bio.singa.simulation.parser.sbml.converter

CompartmentHandler() - Constructor for class bio.singa.simulation.parser.sbml.converter.CompartmentHandler

ComplexBuildingReaction - Class in bio.singa.simulation.model.modules.concentration.imlementations

Complex building or breaking reactions are a special kind of ReversibleReaction.

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

ComplexBuildingReaction.BindeeSectionSelection - Interface in bio.singa.simulation.model.modules.concentration.imlementations

ComplexBuildingReaction.BindeeSelection - Interface in bio.singa.simulation.model.modules.concentration.imlementations

ComplexBuildingReaction.BinderSectionSelection - Interface in bio.singa.simulation.model.modules.concentration.imlementations

ComplexBuildingReaction.BinderSelection - Interface in bio.singa.simulation.model.modules.concentration.imlementations

ComplexBuildingReaction.BindingBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations

ComplexBuildingReaction.BuilderStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations

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, Quantity<MolarConcentration>) - Constructor for class bio.singa.simulation.model.modules.concentration.ConcentrationDelta

Creates a new concentration delta.

ConcentrationDeltaIdentifier - Class in bio.singa.simulation.model.modules.concentration

Used to identify changes to concentrations (ConcentrationDeltas) (mostly in maps).

ConcentrationDeltaIdentifier(Updatable, CellSubsection, ChemicalEntity) - Constructor for class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier

Creates a new DeltaIdentifier.

ConcentrationDeltaManager - Class in bio.singa.simulation.model.modules.concentration

The ConcentrationDeltaManager handles current concentrations of an updatable and the updates to those concentrations that should be applied during simulation.

ConcentrationDeltaManager(ConcentrationContainer) - Constructor for class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

Creates a new Concentration Delta Manager.

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.

CONSTANT_NODE - Static variable in interface uk.co.cogitolearning.cogpar.ExpressionNode

Node id for constant nodes

ConstantExpressionNode - Class in uk.co.cogitolearning.cogpar

An ExpressionNode that stores a constant value

ConstantExpressionNode(double) - Constructor for class uk.co.cogitolearning.cogpar.ConstantExpressionNode

Construct with the fixed value.

ConstantExpressionNode(String) - Constructor for class uk.co.cogitolearning.cogpar.ConstantExpressionNode

Convenience constructor that takes a string and converts it to a double before storing the value.

convertAssignmentRule(AssignmentRule) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLAssignmentRuleConverter

convertKineticLaw(KineticLaw) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLKineticLawConverter

convertLocalParameter(LocalParameter) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLParameterConverter

convertRawExpression(ASTNode, ListOf<LocalParameter>, Unit<?>) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLExpressionConverter

convertRawExpression(ASTNode, Unit<?>) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLExpressionConverter

convertReaction(Reaction) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLReactionConverter

convertReactions(ListOf<Reaction>) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLReactionConverter

convertSimulationParameter(Parameter) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLParameterConverter

convertSimulationParameters(ListOf<Parameter>) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLParameterConverter

convertUnit(UnitDefinition) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLUnitConverter

convertUnits(ListOf<UnitDefinition>) - Method in class bio.singa.simulation.parser.sbml.converter.SBMLUnitConverter

create() - Method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes

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

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

This simulation simulates the thermal decomposition of dinitrogen pentaoxide.

createDiffusionModuleExample(int, Quantity<Time>) - Static method in class bio.singa.simulation.model.simulation.SimulationExamples

This simulation simulates a diffusion of small molecules in a rectangular gird graph.

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

This simulation simulates a equilibrium reaction.

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

This simulation simulates a multiple reactions involving iodine.

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

This simulation simulates a MichaelisMentenReaction, where D-Fructose 1-phosphate is convertet to glycerone phosphate and D-glyceraldehyde using fructose bisphosphate aldolase.

createObject(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction.Builder

createObject(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction.Builder

createObject(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

createObject(Simulation) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.Builder

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

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

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

This simulation simulates the synthesis of 1,3,5-octatriene (C8H12) from Buta-1,3-diene (C4H6).

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

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_ACTIN_VELOCITY - Static variable in class bio.singa.simulation.features.endocytosis.ActinBoostVelocity

Average lateral displacement velocity after scission for 11 seconds.

DEFAULT_BUDDING_RATE - Static variable in class bio.singa.simulation.features.endocytosis.BuddingRate

About three events per 10^8 nm^2 s^-1, developing into actual vesicles.

DEFAULT_CLATHRIN_DEPOLYMERIZATION_RATE - Static variable in class bio.singa.simulation.model.modules.displacement.implementations.EndocytosisActinBoost

Average vesicle with a radius of 50 nm was coated by 60 clathrins.

DEFAULT_DYNEIN_ATTACHMENT_DISTANCE - Static variable in class bio.singa.simulation.features.endocytosis.AttachmentDistance

Size of the dynein complex fom vesicle surface to microtubule.

DEFAULT_MATURATION_TIME - Static variable in class bio.singa.simulation.features.endocytosis.MaturationTime

Average maturation time is 100 seconds.

DEFAULT_MOTOR_VELOCITY - Static variable in class bio.singa.simulation.features.endocytosis.MotorMovementVelocity

Average lateral displacement velocity after scission for 11 seconds.

DEFAULT_TETHERING_TIME - Static variable in class bio.singa.simulation.features.endocytosis.TetheringTime

Average maturation time is 100 seconds.

DEFAULT_VESICLE_RADIUS - Static variable in class bio.singa.simulation.features.endocytosis.VesicleRadius

DefautFeatureSources - Class in bio.singa.simulation.features

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

Returns true if the delta is valid, i.e.

deltasAreBelowDisplacementCutoff() - Method in class bio.singa.simulation.model.modules.displacement.VesicleLayer

DependentUpdate - Class in bio.singa.simulation.model.modules.concentration.scope

Dependent Updatable ConcentrationBasedModules require an integer state of basically all updatables in a simulation.

DependentUpdate(ConcentrationBasedModule<?>) - Constructor for class bio.singa.simulation.model.modules.concentration.scope.DependentUpdate

Initializes the update scope for the corresponding module.

determineDeltas(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific

determineDeltas(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.specifity.SectionSpecific

determineDeltas(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.specifity.UpdatableSpecific

determineDeltas(ConcentrationContainer) - Method in interface bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity

Determines all deltas for a Concentration container.

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

determineEffectiveConcentration(ConcentrationContainer, ReactantRole) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

Determines the concentration of reactants that influence the velocity of the reaction.

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

The local error is calculated and the largest local error of the current epoch resulting from the executing module is returned.

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

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

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

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

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

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

DisplacementBasedModule - Class in bio.singa.simulation.model.modules.displacement

DisplacementBasedModule() - Constructor for class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

DisplacementDelta - Class in bio.singa.simulation.model.modules.displacement

DisplacementDelta(DisplacementBasedModule, Vector2D) - Constructor for class bio.singa.simulation.model.modules.displacement.DisplacementDelta

DisplacementDeltaManager - Class in bio.singa.simulation.model.modules.displacement

The DisplacementDeltaManager handles the current position an updatable amd the updates to this position during simulation.

DisplacementDeltaManager(Vector2D) - Constructor for class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager

Creates a new Displacement Delta Manager.

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

drawEdge(AutomatonEdge) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer

drawNode(AutomatonNode) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer

DynamicReaction - Class in bio.singa.simulation.model.modules.concentration.imlementations

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

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.DefautFeatureSources

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

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.

EntitySpecific - Class in bio.singa.simulation.model.modules.concentration.specifity

Entity specific ConcentrationBasedModules calculate their AbstractDeltaFunction for every chemical entity and every subsection of an updatable.

EntitySpecific(ConcentrationBasedModule<EntityDeltaFunction>) - Constructor for class bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific

Initializes the update specificity for the corresponding module.

enzyme(Enzyme) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction.Builder

EpochUpdateWriter - Class in bio.singa.simulation.events

This class can be used to write the concentration of chemical entities of a node and the changes applied to the node to a file.

EpochUpdateWriter(Path, Path, Set<ChemicalEntity>, Set<ConcentrationBasedModule>) - Constructor for class bio.singa.simulation.events.EpochUpdateWriter

Creates a new EpochUpdateWriter.

EpochUpdateWriter(Path, Path, Set<ChemicalEntity>, Set<ConcentrationBasedModule>, boolean) - Constructor for class bio.singa.simulation.events.EpochUpdateWriter

Creates a new EpochUpdateWriter.

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.membranes.Membrane

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

equals(Object) - Method in class bio.singa.simulation.model.sections.CellRegion

equals(Object) - Method in class bio.singa.simulation.model.sections.CellSubsection

evaluate() - Method in class bio.singa.simulation.model.rules.AppliedExpression

Evaluates the expression and returns the result.

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

evaluateModuleState() - Method in class bio.singa.simulation.model.modules.displacement.implementations.ClathrinMediatedEndocytosis

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

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

features - Variable in class bio.singa.simulation.model.modules.displacement.Vesicle

FieldSupplier - Class in bio.singa.simulation.model.modules.concentration

The field supplier manages all files required for different behaviours of a module.

FilamentLayer - Class in bio.singa.simulation.model.agents.filaments

FilamentLayer(Simulation, MembraneLayer) - Constructor for class bio.singa.simulation.model.agents.filaments.FilamentLayer

fillRegion(AutomatonGraph, CellRegion, RectangularCoordinate, int) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs

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

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

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

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

formingComplex(ComplexedChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder

formingComplex(ComplexedChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BuilderStep

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

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

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

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

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

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

forVesicle(String) - Static method in class bio.singa.simulation.model.sections.CellRegion

forwardsRateConstant(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.Builder

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.

FunctionReference - Class in bio.singa.simulation.parser.sbml

FunctionReference(String, String, List<String>) - Constructor for class bio.singa.simulation.parser.sbml.FunctionReference

FunctionReference(String, String) - Constructor for class bio.singa.simulation.parser.sbml.FunctionReference

G

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

Creates and returns a map that contains all chemical entities that are present in the given graph as values and with the name of the entity as key.

get(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.

getAllFeatures() - Method in class bio.singa.simulation.model.parameters.FeatureManager

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

Returns all referenced sections in this node.

getAllReferencedSections() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

getAnnotations() - Method in class bio.singa.simulation.model.parameters.SimulationParameter

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.modules.displacement.Vesicle

getAssignmentRules() - Method in class bio.singa.simulation.parser.sbml.SBMLParser

getAssociatedNodes() - Method in class bio.singa.simulation.model.agents.filaments.SkeletalFilament

getAssociatedNodes() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

getAttachedFilament() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

getAttachmentState() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

getAvailableFeatures() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

getAvailableFeatures() - Method in class bio.singa.simulation.model.parameters.FeatureManager

getBioRenderingOptions() - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer

getBuilder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction.Builder

getBuilder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction.Builder

getBuilder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

getBuilder() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction.Builder

getCatalyticReactants() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction

Returns the catalytic reactants.

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 class bio.singa.simulation.model.modules.displacement.Vesicle

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.

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

Returns the chemical entities.

getChemicalEntities() - Method in class bio.singa.simulation.parser.sbml.SBMLParser

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.modules.displacement.Vesicle

getColor(GoTerm) - Static method in class bio.singa.simulation.model.sections.CellSubsections

getColor(CellSubsection) - Static method in class bio.singa.simulation.model.sections.CellSubsections

getColor(CellRegion) - Static method in class bio.singa.simulation.model.sections.CellSubsections

getColorForUpdatable(Updatable) - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions

getCompartments() - Method in class bio.singa.simulation.parser.sbml.SBMLParser

getComplex() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction

getConcentration(CellSubsection, ChemicalEntity) - Method in class bio.singa.simulation.model.graphs.AutomatonNode

Returns the concentration of the given chemical entity in the given compartment.

getConcentration(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

getConcentration(CellSubsection, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

getConcentration(CellSubsection, ChemicalEntity) - Method in interface bio.singa.simulation.model.simulation.Updatable

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 class bio.singa.simulation.model.modules.displacement.Vesicle

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

getConcentrationFormatter() - Method in class bio.singa.simulation.events.EpochUpdateWriter

getConcentrations() - Method in class bio.singa.simulation.model.sections.ConcentrationPool

getCondition() - Method in class bio.singa.simulation.model.modules.concentration.functions.AbstractDeltaFunction

Returns the application condition.

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

getCurrentCellSection() - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw

Returns the current cell section the kinetic law is applied to.

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

Returns the current chemical entity.

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

Returns all currently available full deltas.

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

Returns all currently available half deltas.

getCurrentPosition() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager

Returns the current position.

getCurrentPosition() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

Returns the current subsection.

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

Returns the current updatable.

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

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

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

getDrawingHeight() - Method in class bio.singa.simulation.events.GraphImageWriter

getDrawingHeight() - Method in class bio.singa.simulation.model.agents.ClippingPlayground

getDrawingHeight() - Method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground

getDrawingHeight() - Method in class bio.singa.simulation.model.modules.displacement.VesiclePlayground

getDrawingWidth() - Method in class bio.singa.simulation.events.GraphImageWriter

getDrawingWidth() - Method in class bio.singa.simulation.model.agents.ClippingPlayground

getDrawingWidth() - Method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground

getDrawingWidth() - Method in class bio.singa.simulation.model.modules.displacement.VesiclePlayground

getEdgeColor(AutomatonEdge) - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions

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

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

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

getEntity() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier

Returns the chemical entity the delta is assigned to.

getEntity() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant

Gets the entity representing this reactant.

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

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

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

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

getExpression() - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw

Returns the actual expression use to calculate this kinetic law.

getExpressionString() - Method in class bio.singa.simulation.model.rules.AppliedExpression

Returns the expression string.

getExpressionTokenizer() - Static method in class uk.co.cogitolearning.cogpar.Tokenizer

A static method that returns a tokenizer for mathematical expressions

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.displacement.Vesicle

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

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.displacement.Vesicle

getFeatures() - Method in class bio.singa.simulation.model.parameters.FeatureManager

getFilaments() - Method in class bio.singa.simulation.model.agents.filaments.FilamentLayer

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.

getGlobalParameters() - Method in class bio.singa.simulation.parser.sbml.SBMLParser

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.simulation.Simulation

getGraphicsContext() - Method in class bio.singa.simulation.model.agents.ClippingPlayground

getGraphicsContext() - Method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground

getGraphicsContext() - Method in class bio.singa.simulation.model.modules.displacement.VesiclePlayground

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

getHalfScaledQuantity() - Method in class bio.singa.simulation.features.scale.AppliedScale

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.

getHead() - Method in class bio.singa.simulation.model.agents.filaments.SkeletalFilament

getIdentifier() - Method in class bio.singa.simulation.model.agents.membranes.Membrane

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

Returns the identifier of this module.

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

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

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

getIdentifier() - Method in class bio.singa.simulation.model.parameters.SimulationParameter

getIdentifier() - Method in class bio.singa.simulation.model.sections.CellRegion

getIdentifier() - Method in class bio.singa.simulation.model.sections.CellSubsection

Returns the identifier.

getInnerSubsection() - Method in class bio.singa.simulation.model.sections.CellRegion

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

Returns the inner subsection.

getInternalRegion() - Method in class bio.singa.simulation.model.agents.organelles.Organelle

getInternalRegion() - Method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes

getKineticLaw() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction

Returns the kinetic law.

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

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

Returns the largest error as of yet.

getListeners() - Method in class bio.singa.simulation.events.GraphEventEmitter

getListeners() - Method in class bio.singa.simulation.events.NodeEventEmitter

getMaturingVesicles() - Method in class bio.singa.simulation.model.modules.displacement.implementations.ClathrinMediatedEndocytosis

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

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.Organelle

getMembraneRegion() - Method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes

getMembranes() - Method in class bio.singa.simulation.model.agents.membranes.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.

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

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

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.displacement.DisplacementDelta

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

getName() - Method in class bio.singa.simulation.model.parameters.SimulationParameter

getName() - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode

getNextPosition() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager

Returns the next position.

getNextPosition() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

getNode() - Method in class bio.singa.simulation.model.agents.membranes.MembraneSegment

getNodeColorScale() - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions

getNodeHighlightEntity() - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions

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

Returns all currently registered node event listeners.

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

getOuterSubsection() - Method in class bio.singa.simulation.model.sections.CellRegion

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

Returns the outer subsection.

getParameters() - Method in class bio.singa.simulation.model.rules.AppliedExpression

Returns the parameters of the expression.

getPlusEndBehaviour() - Method in class bio.singa.simulation.model.agents.filaments.SkeletalFilament

getPolygon() - Method in class bio.singa.simulation.model.agents.organelles.Organelle

getPolygonTemplate(String) - Static method in class bio.singa.simulation.parser.organelles.OrganelleImageParser

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.

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.

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

getPotentialSpatialDeltas() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

getPreferredConcentrationUnit() - Method in class bio.singa.simulation.model.sections.CellSubsection

Returns the preferred concentration unit for this subsection.

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

Returns all products of this reaction.

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

Returns the quantity of the change.

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

getRadius() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

getReactionOrder() - Method in class bio.singa.simulation.model.modules.concentration.reactants.StoichiometricReactant

Returns the reaction order.

getReactions() - Method in class bio.singa.simulation.parser.sbml.SBMLParser

getReactionString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction

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

Returns a nicely formatted string representation of the reaction.

getReactionString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ReversibleReaction

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

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

Returns all chemical entities that might be accessed by this module.

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

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

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

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

Returns all entities referenced in any concentration pool.

getReferencedEntities() - Method in class bio.singa.simulation.model.sections.ConcentrationPool

Returns all entities referenced in this map.

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

Returns all subsections, referenced in this container.

getRenderingMode() - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions

getRepresentativeRegion() - Method in class bio.singa.simulation.model.agents.membranes.Membrane

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

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

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

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

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

getRequiredFeatures() - Method in class bio.singa.simulation.model.parameters.FeatureManager

getRole() - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant

Gets the role of this reactant.

getScaledFeature(Class<? extends ScalableFeature<FeatureContentType>>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

getScaledFeature(ChemicalEntity, Class<? extends ScalableFeature<FeatureContentType>>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Returns the requested feature of the given chemical entities, scaled according to the current time step and spatial scaling.

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

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

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

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

getScaledQuantity() - Method in class bio.singa.simulation.features.scale.AppliedScale

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.membranes.MembraneSegment

getSegmentIterator(Vector2D) - Method in class bio.singa.simulation.model.agents.filaments.SkeletalFilament

getSegmentIterator() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

getSegments() - Method in class bio.singa.simulation.model.agents.filaments.SkeletalFilament

getSegments() - Method in class bio.singa.simulation.model.agents.membranes.Membrane

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.VesicleLayer

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

Returns the simulation.

getSimulationArea() - Method in class bio.singa.simulation.model.modules.displacement.VesicleLayer

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

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

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

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

Returns the specificity of this module.

getStartingConcentrations() - Method in class bio.singa.simulation.parser.sbml.SBMLParser

getStartingPoint() - Method in class bio.singa.simulation.model.agents.membranes.MembraneSegment

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

getStoichiometricNumber() - Method in class bio.singa.simulation.model.modules.concentration.reactants.StoichiometricReactant

Returns the stoichiometric number (the number of molecules required for one reaction.).

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

Returns the list of reactants for this reaction.

getStrength() - Method in class bio.singa.simulation.model.modules.concentration.reactants.CatalyticReactant

Gets the strength of this Reactant.

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

getStringForProtocol() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction

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

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

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

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

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

getStringIdentifier() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

getSubsection() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier

Returns the cell section the delta is assigned to.

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 class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

Returns all substrates of this reaction.

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

Returns the field supplier.

getSymbol() - Method in class bio.singa.simulation.features.endocytosis.ActinBoostVelocity

getSymbol() - Method in class bio.singa.simulation.features.endocytosis.AttachmentDistance

getSymbol() - Method in class bio.singa.simulation.features.endocytosis.BuddingRate

getSymbol() - Method in class bio.singa.simulation.features.endocytosis.MaturationTime

getSymbol() - Method in class bio.singa.simulation.features.endocytosis.MotorMovementVelocity

getSymbol() - Method in class bio.singa.simulation.features.endocytosis.TetheringTime

getSymbol() - Method in class bio.singa.simulation.features.endocytosis.VesicleRadius

getSymbol() - Method in class bio.singa.simulation.features.permeability.MembraneEntry

getSymbol() - Method in class bio.singa.simulation.features.permeability.MembraneExit

getSymbol() - Method in class bio.singa.simulation.features.permeability.MembraneFlipFlop

getSymbol() - Method in class bio.singa.simulation.features.scale.AppliedScale

getTargetDirection() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

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

getTime() - Method in class bio.singa.simulation.events.UpdatableUpdatedEvent

Returns the time the event was emitted.

getTimeFormatter() - Method in class bio.singa.simulation.events.EpochUpdateWriter

getToken() - Method in exception uk.co.cogitolearning.cogpar.ParserException

Get the token.

getTokens() - Method in class uk.co.cogitolearning.cogpar.Tokenizer

Get the tokens generated in the last call to tokenize.

getType() - Method in class uk.co.cogitolearning.cogpar.AdditionExpressionNode

Returns the type of the node, in this case ExpressionNode.ADDITION_NODE

getType() - Method in class uk.co.cogitolearning.cogpar.ConstantExpressionNode

Returns the type of the node, in this case ExpressionNode.CONSTANT_NODE

getType() - Method in class uk.co.cogitolearning.cogpar.ExponentiationExpressionNode

Returns the type of the node, in this case ExpressionNode.EXPONENTIATION_NODE

getType() - Method in interface uk.co.cogitolearning.cogpar.ExpressionNode

Returns the type of the node.ExpressionNode Each class derived from ExpressionNode representing a specific role in the expression should return the type according to that role.

getType() - Method in class uk.co.cogitolearning.cogpar.FunctionExpressionNode

Returns the type of the node, in this case ExpressionNode.FUNCTION_NODE

getType() - Method in class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode

Returns the type of the node, in this case ExpressionNode.MULTIPLICATION_NODE

getType() - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode

Returns the type of the node, in this case ExpressionNode.VARIABLE_NODE

getUpdatable() - Method in class bio.singa.simulation.events.UpdatableUpdatedEvent

Returns the updatable

getUpdatable() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier

Returns the object the delta is assigned to.

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

Returns the node where the error occurred.

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

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

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

Returns the actual value of the error.

getValue() - Method in class bio.singa.simulation.model.parameters.SimulationParameter

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

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

getVesicles() - Method in class bio.singa.simulation.model.modules.displacement.VesicleLayer

getVolume() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

GraphEventEmitter - Class in bio.singa.simulation.events

The implementation of an UpdateEventEmitter emitting updates of the graph to all listeners.

GraphEventEmitter() - Constructor for class bio.singa.simulation.events.GraphEventEmitter

Creates a new GraphEventEmitter.

GraphImageWriter - Class in bio.singa.simulation.events

GraphImageWriter(Path, Path, List<ChemicalEntity>) - Constructor for class bio.singa.simulation.events.GraphImageWriter

GraphUpdatedEvent - Class in bio.singa.simulation.events

The Event that is emitted from the GraphEventEmitter, encapsulating a graph.

GraphUpdatedEvent(AutomatonGraph, Quantity<Time>) - Constructor for class bio.singa.simulation.events.GraphUpdatedEvent

Creates a new GraphUpdatedEvent.

H

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.graphs.AutomatonNode

hasDeltas() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

hasFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

hasFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.parameters.FeatureManager

hasGrowingFilaments() - Method in class bio.singa.simulation.model.agents.filaments.FilamentLayer

hashCode() - Method in class bio.singa.simulation.model.agents.membranes.Membrane

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

hashCode() - Method in class bio.singa.simulation.model.sections.CellRegion

hashCode() - Method in class bio.singa.simulation.model.sections.CellSubsection

hasMembrane() - Method in class bio.singa.simulation.model.sections.CellRegion

I

identifier(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSelection

identifier(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder

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

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

identifier(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

in(CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSectionSelection

in(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder

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.

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

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

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

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

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

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

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

initialize(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

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

initializeFilaments() - Method in class bio.singa.simulation.model.agents.organelles.MicrotubuleOrganizingCentre

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

initializeSpeciesWithConcentration(ChemicalEntity, double) - Method in class bio.singa.simulation.model.graphs.AutomatonGraph

Initializes the concentration of the given chemical entity of every node in this graph to to the given concentration in mol/l.

initializeSpeciesWithConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.graphs.AutomatonGraph

Initializes the concentration of the given chemical entity of every node in this graph.

initializeSubsection(CellSubsection, CellTopology) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

Initializes a new concentration pool for the corresponding subsection and topology.

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

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

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

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

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

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

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

isAccelerator() - Method in class bio.singa.simulation.model.modules.concentration.reactants.CatalyticReactant

Returns true if this Reactant is increasing the velocity of the associated reaction, and false otherwise.

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

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

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

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

Returns true if this Reaction is considered elementary and false otherwise.

isInhibitor() - Method in class bio.singa.simulation.model.modules.concentration.reactants.CatalyticReactant

Returns true if this Reactant is decreasing the velocity of the associated reaction, and false otherwise.

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 class bio.singa.simulation.model.modules.displacement.Vesicle

Returns true if this node is observed.

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

isProduct() - Method in class bio.singa.simulation.model.modules.concentration.reactants.StoichiometricReactant

Returns true if this reactant is a product.

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

Returns the current state of calculations.

isSubstrate() - Method in class bio.singa.simulation.model.modules.concentration.reactants.StoichiometricReactant

Returns true if this reactant is a substrate.

J

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

K

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

KineticLaw - Class in bio.singa.simulation.model.modules.concentration.reactants

Dynamic kinetic laws allow for the definition of reaction kinetics based on equations.

KineticLaw(AppliedExpression) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw

Creates a new dynamic kinetic law with the applied expression.

L

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

Returns a formatted string of the features of this module.

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

listFeatures(String) - Method in class bio.singa.simulation.model.parameters.FeatureManager

LocalError - Class in bio.singa.simulation.model.modules.concentration

The LocalError object stores the error as an result of the currently applied time step.

LocalError(Updatable, ChemicalEntity, double) - Constructor for class bio.singa.simulation.model.modules.concentration.LocalError

Creates a new LocalError.

M

MacroscopicLayerPlayground - Class in bio.singa.simulation.model.agents

MacroscopicLayerPlayground() - Constructor for class bio.singa.simulation.model.agents.MacroscopicLayerPlayground

main(String[]) - Static method in class bio.singa.simulation.model.agents.ClippingPlayground

main(String[]) - Static method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground

main(String[]) - Static method in class bio.singa.simulation.model.modules.displacement.VesiclePlayground

MaturationTime - Class in bio.singa.simulation.features.endocytosis

MaturationTime(ComparableQuantity<Time>, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.MaturationTime

MaturationTime(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.MaturationTime

Membrane - Class in bio.singa.simulation.model.agents.membranes

Membrane(String, CellRegion) - Constructor for class bio.singa.simulation.model.agents.membranes.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.

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

The membrane diffusion module describes the movement of chemical entities across Membranes driven by the MembranePermeability of the cargo.

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

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

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

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

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

MembraneEntry - Class in bio.singa.simulation.features.permeability

MembraneEntry(Quantity<Frequency>, FeatureOrigin) - Constructor for class bio.singa.simulation.features.permeability.MembraneEntry

MembraneEntry(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.permeability.MembraneEntry

MembraneExit - Class in bio.singa.simulation.features.permeability

MembraneExit(Quantity<Frequency>, FeatureOrigin) - Constructor for class bio.singa.simulation.features.permeability.MembraneExit

MembraneExit(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.permeability.MembraneExit

MembraneFlipFlop - Class in bio.singa.simulation.features.permeability

MembraneFlipFlop(Quantity<Frequency>, FeatureOrigin) - Constructor for class bio.singa.simulation.features.permeability.MembraneFlipFlop

MembraneFlipFlop(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.permeability.MembraneFlipFlop

MembraneLayer - Class in bio.singa.simulation.model.agents.membranes

MembraneLayer() - Constructor for class bio.singa.simulation.model.agents.membranes.MembraneLayer

MembraneSegment - Class in bio.singa.simulation.model.agents.membranes

MembraneSegment(AutomatonNode, LineSegment) - Constructor for class bio.singa.simulation.model.agents.membranes.MembraneSegment

membraneToRegion(Organelle, AutomatonGraph) - Static method in class bio.singa.simulation.model.agents.membranes.MembraneTracer

MembraneTracer - Class in bio.singa.simulation.model.agents.membranes

MembraneTracer(AutomatonGraph) - Constructor for class bio.singa.simulation.model.agents.membranes.MembraneTracer

MERRIFIELD2005 - Static variable in class bio.singa.simulation.features.DefautFeatureSources

MichaelisMentenReaction - Class in bio.singa.simulation.model.modules.concentration.imlementations

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

MichaelisMentenReaction.Builder - Class in bio.singa.simulation.model.modules.concentration.imlementations

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

MicrotubuleOrganizingCentre(Simulation, MembraneLayer, Circle, int) - Constructor for class bio.singa.simulation.model.agents.organelles.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.

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.

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.endocytosis

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

MotorMovementVelocity(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.MotorMovementVelocity

MULTDIV - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for multiplication or division

MULTIPLICATION_NODE - Static variable in interface uk.co.cogitolearning.cogpar.ExpressionNode

Node id for multiplication nodes

MultiplicationExpressionNode - Class in uk.co.cogitolearning.cogpar

An ExpressionNode that handles multiplications and divisions.

MultiplicationExpressionNode() - Constructor for class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode

Default constructor.

MultiplicationExpressionNode(ExpressionNode, boolean) - Constructor for class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode

Constructor to create a multiplication with the first term already added.

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

Multiplies (modifies) this delta with the given multiplicand.

N

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

nextEpoch() - Method in class bio.singa.simulation.model.agents.filaments.FilamentLayer

nextEpoch() - Method in class bio.singa.simulation.model.agents.filaments.SkeletalFilament

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

Calculates the next epoch.

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

NodeEventEmitter - Class in bio.singa.simulation.events

The implementation of an UpdateEventEmitter emitting updates of specific nodes to all listeners.

NodeEventEmitter() - Constructor for class bio.singa.simulation.events.NodeEventEmitter

Creates a new NodeEventEmitter.

NthOrderReaction - Class in bio.singa.simulation.model.modules.concentration.imlementations

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

NthOrderReaction.Builder - Class in bio.singa.simulation.model.modules.concentration.imlementations

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

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

NUMBER - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for numbers

NumericalInstabilityException - Exception in bio.singa.simulation.exceptions

NumericalInstabilityException(String) - Constructor for exception bio.singa.simulation.exceptions.NumericalInstabilityException

O

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

of(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSelection

of(ChemicalEntity, RateConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindeeSelection

of(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder

of(ChemicalEntity, RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder

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.ClathrinMediatedEndocytosis

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

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

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

onEventReceived(UpdatableUpdatedEvent) - Method in class bio.singa.simulation.events.EpochUpdateWriter

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

onEventReceived(GraphUpdatedEvent) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer

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

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

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

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

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

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

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

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

OPEN_BRACKET - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for opening brackets

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

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

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

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

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

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

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

Organelle - Class in bio.singa.simulation.model.agents.organelles

Organelle(CellRegion, CellRegion, Polygon, Quantity<Length>) - Constructor for class bio.singa.simulation.model.agents.organelles.Organelle

OrganelleImageParser - Class in bio.singa.simulation.parser.organelles

OrganelleImageParser(BufferedImage) - Constructor for class bio.singa.simulation.parser.organelles.OrganelleImageParser

OrganelleTypes - Enum in bio.singa.simulation.model.agents.organelles

P

parse() - Method in class bio.singa.simulation.parser.sbml.SabioRKParserService

parse() - Method in class bio.singa.simulation.parser.sbml.SBMLParser

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.

parseModelById(String) - Static method in class bio.singa.simulation.parser.sbml.BioModelsParserService

parseModelFromFile(String) - Static method in class bio.singa.simulation.parser.sbml.BioModelsParserService

parseModelFromStream(InputStream) - Static method in class bio.singa.simulation.parser.sbml.BioModelsParserService

ParserException - Exception in uk.co.cogitolearning.cogpar

A simple subclass of RuntimeException that indicates errors when trying to parse the input to Parser.

ParserException(String) - Constructor for exception uk.co.cogitolearning.cogpar.ParserException

Construct the evaluation exception with a message.

ParserException(String, Token) - Constructor for exception uk.co.cogitolearning.cogpar.ParserException

Construct the evaluation exception with a message and a token.

PER_SQUARE_NANOMETRE_PER_SECOND - Static variable in class bio.singa.simulation.features.endocytosis.BuddingRate

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) - 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) - Method in interface bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity

Processes a concentration container.

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

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

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

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

Calculates the given updatable.

putSubsectionPool(CellSubsection, CellTopology, ConcentrationPool) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

Adds a concentration pool, referenced to the subsection and topology.

Q

QualitativeModule - Class in bio.singa.simulation.model.modules.qualitative

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

R

RAISED - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for the exponentiation symbol

rateConstant(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.NthOrderReaction.Builder

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

A Reactant encapsulates a ChemicalEntity for the use in Reactions.

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

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

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

Reactions in general are ConcentrationBasedModules following the laws of chemical kinetics.

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

Reaction.Builder<TopLevelType extends Reaction,BuilderType extends Reaction.Builder> - Class in bio.singa.simulation.model.modules.concentration.imlementations

referenceChemicalEntityToParameter(String, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw

Assigns a parameter of the expression to the concentration of a chemical species.

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

regionsToMembrane(AutomatonGraph) - Static method in class bio.singa.simulation.model.agents.membranes.MembraneTracer

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.modules.displacement.VesicleLayer

render() - Method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground

render(AutomatonGraph) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer

RenderingMode - Enum in bio.singa.simulation.renderer

renderVesicles() - Method in class bio.singa.simulation.model.modules.displacement.VesiclePlayground

renderVoronoi(boolean) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer

replaceInEquation(String) - Method in class bio.singa.simulation.parser.sbml.FunctionReference

rescaleColors(AutomatonGraph) - Method in class bio.singa.simulation.renderer.AutomatonGraphRenderer

rescaleDiffusivity(Quantity<Diffusivity>, Quantity<Time>, Quantity<Length>) - Static method in class bio.singa.simulation.model.parameters.UnitScaler

Scales the diffusivity for the use with cellular graph automata.

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

rescaleReactionRate(Quantity<Frequency>, Quantity<Time>) - Static method in class bio.singa.simulation.model.parameters.UnitScaler

Scales the reaction rate for the use with cellular graph automata.

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.modules.displacement.DisplacementDeltaManager

Resets the next position to the current position.

resetNextPosition() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

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

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

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

ReversibleReaction - Class in bio.singa.simulation.model.modules.concentration.imlementations

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

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

ReversibleReaction.Builder - Class in bio.singa.simulation.model.modules.concentration.imlementations

S

SabioRKParserService - Class in bio.singa.simulation.parser.sbml

SabioRKParserService(String) - Constructor for class bio.singa.simulation.parser.sbml.SabioRKParserService

sampleNextEventTime(Quantity<Time>, Quantity<Frequency>) - Static method in class bio.singa.simulation.features.endocytosis.SpawnTimeSampler

sampleNextVesicleRadius(Quantity<Length>) - Static method in class bio.singa.simulation.features.endocytosis.SpawnTimeSampler

SBMLAssignmentRuleConverter - Class in bio.singa.simulation.parser.sbml.converter

SBMLAssignmentRuleConverter(Map<String, Unit<?>>, Map<String, ChemicalEntity>, Map<String, FunctionReference>, Map<String, SimulationParameter<?>>) - Constructor for class bio.singa.simulation.parser.sbml.converter.SBMLAssignmentRuleConverter

SBMLExpressionConverter - Class in bio.singa.simulation.parser.sbml.converter

SBMLExpressionConverter(Map<String, Unit<?>>, Map<String, FunctionReference>, Map<String, SimulationParameter<?>>) - Constructor for class bio.singa.simulation.parser.sbml.converter.SBMLExpressionConverter

SBMLKineticLawConverter - Class in bio.singa.simulation.parser.sbml.converter

Converts JSBML KineticLaws to SiNGA KineticLaws

SBMLKineticLawConverter(Map<String, Unit<?>>, Map<String, FunctionReference>, Map<String, SimulationParameter<?>>) - Constructor for class bio.singa.simulation.parser.sbml.converter.SBMLKineticLawConverter

SBMLParameterConverter - Class in bio.singa.simulation.parser.sbml.converter

Converts JSBML Parameters to SiNGA Parameters.

SBMLParameterConverter(Map<String, Unit<?>>) - Constructor for class bio.singa.simulation.parser.sbml.converter.SBMLParameterConverter

SBMLParser - Class in bio.singa.simulation.parser.sbml

SBMLParser(InputStream) - Constructor for class bio.singa.simulation.parser.sbml.SBMLParser

SBMLReactionConverter - Class in bio.singa.simulation.parser.sbml.converter

Converts JSBML Reactions to SiNGA Reactions

SBMLReactionConverter(Map<String, Unit<?>>, Map<String, ChemicalEntity>, Map<String, FunctionReference>, Map<String, SimulationParameter<?>>) - Constructor for class bio.singa.simulation.parser.sbml.converter.SBMLReactionConverter

SBMLUnitConverter - Class in bio.singa.simulation.parser.sbml.converter

Converts JSBML Units to UnitsOfMeasurement Units.

SBMLUnitConverter() - Constructor for class bio.singa.simulation.parser.sbml.converter.SBMLUnitConverter

scale(Quantity<Time>, Quantity<Length>) - Method in class bio.singa.simulation.features.endocytosis.ActinBoostVelocity

scale(Quantity<Time>, Quantity<Length>) - Method in class bio.singa.simulation.features.endocytosis.BuddingRate

scale(Quantity<Time>, Quantity<Length>) - Method in class bio.singa.simulation.features.endocytosis.MotorMovementVelocity

scale(Quantity<Time>, Quantity<Length>) - Method in class bio.singa.simulation.features.permeability.MembraneEntry

scale(Quantity<Time>, Quantity<Length>) - Method in class bio.singa.simulation.features.permeability.MembraneExit

scale(Quantity<Time>, Quantity<Length>) - Method in class bio.singa.simulation.features.permeability.MembraneFlipFlop

scale(Quantity<Time>, Quantity<Length>) - Method in class bio.singa.simulation.features.scale.AppliedScale

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

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

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

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

SECTION_A - Static variable in class bio.singa.simulation.model.sections.CellSubsection

A cellular subsection "A".

SECTION_B - Static variable in class bio.singa.simulation.model.sections.CellSubsection

A cellular subsection "B".

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

Independent Updatable ConcentrationBasedModules require the integer state of a subset of updatables.

SemiDependentUpdate(ConcentrationBasedModule) - Constructor for class bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate

Initializes the update scope for the corresponding module.

sequence - Variable in class uk.co.cogitolearning.cogpar.Token

the string that the token was created from

SequenceExpressionNode - Class in uk.co.cogitolearning.cogpar

A base class for AdditionExpressionNode and MultiplicationExpressionNode.

SequenceExpressionNode() - Constructor for class uk.co.cogitolearning.cogpar.SequenceExpressionNode

Default constructor.

SequenceExpressionNode(ExpressionNode, boolean) - Constructor for class uk.co.cogitolearning.cogpar.SequenceExpressionNode

Constructor to create a sequence with the first term already added.

SequenceExpressionNode.Term - Class in uk.co.cogitolearning.cogpar

An inner class that defines a pair containing an ExpressionNode and a boolean flag.

set(CellSubsection, ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

Sets the concentration of the given entity in the given subsection.

set(CellTopology, ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

Sets the concentration of the given entity in the given topology.

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

Sets the concentration of the given entity in the given subsection.

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

Sets the concentration of the given entity in the subsection corresponding to the topological descriptor.

set(ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.ConcentrationPool

Sets the concentration of a entity.

setApplicationCondition(Predicate<Updatable>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Sets the application condition for this module.

setAppliedScale(Double) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw

Sets the scaling factor that is applied to account for changes in the time step size.

setAssignmentRules(List<AssignmentRule>) - Method in class bio.singa.simulation.model.simulation.Simulation

Adds a list of assignment rules, sorting them by their dependencies.

setAttachedFilament(SkeletalFilament) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

setAttachmentState(Vesicle.AttachmentState) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

setCatalyticReactants(List<CatalyticReactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.DynamicReaction

Sets the catalytic reactants.

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

setConcentration(ChemicalEntity, Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

Sets the ConcentrationContainer for this node.

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

Sets the current concentration container.

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

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

Sets the concentration to be fixed - no deltas will be applied.

setConcentrationFormatter(QuantityFormatter<MolarConcentration>) - Method in class bio.singa.simulation.events.EpochUpdateWriter

setCurrentCellSection(CellSubsection) - Method in class bio.singa.simulation.model.modules.concentration.reactants.KineticLaw

Sets the current cell section the kinetic law is applied to.

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

Sets the current chemical entity.

setCurrentSubsection(CellSubsection) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Sets the current subsection.

setCurrentUpdatable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Sets the current updatable.

setDecayingEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.displacement.implementations.EndocytosisActinBoost

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

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

setDrawingHeight(double) - Method in class bio.singa.simulation.events.GraphImageWriter

setDrawingWidth(double) - Method in class bio.singa.simulation.events.GraphImageWriter

setElementary(boolean) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

Sets this Reaction as elementary.

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

setEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.reactants.Reactant

Sets the entity representing this reactant.

setEntityReference(Map<ChemicalEntity, String>) - Method in class bio.singa.simulation.model.rules.AssignmentRule

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

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

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

Sets a feature.

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

setFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

setFeature(FeatureType) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

setFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.parameters.FeatureManager

setFeature(FeatureType) - Method in class bio.singa.simulation.model.parameters.FeatureManager

setFilaments(List<SkeletalFilament>) - Method in class bio.singa.simulation.model.agents.filaments.FilamentLayer

setGoTerm(GoTerm) - Method in class bio.singa.simulation.model.sections.CellSubsection

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

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.sections.CellSubsection

setJfxShutdown(boolean) - Method in class bio.singa.simulation.events.GraphImageWriter

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

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

Sets the kinetic law.

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

Sets the largest error as of yet.

setMaximalTimeStep(Quantity<Time>) - Method in class bio.singa.simulation.model.simulation.Simulation

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

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

setNodeColorScale(ColorScale) - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions

setNodeHighlightEntity(ChemicalEntity) - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions

setNonElementary() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

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 class bio.singa.simulation.model.modules.displacement.Vesicle

Sets the observed state of this node.

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

setParameter(SimulationParameter) - Method in class bio.singa.simulation.model.rules.AppliedExpression

Sets a parameter of the expression.

setPreferredConcentrationUnit(Unit<MolarConcentration>) - Method in class bio.singa.simulation.model.sections.CellSubsection

Sets the preferred concentration unit for this subsection.

setQuantity(Quantity<QuantityType>) - Method in class bio.singa.simulation.model.parameters.SimulationParameter

setRadius(Quantity<Length>) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

setRenderingMode(RenderingMode) - Method in class bio.singa.simulation.renderer.BioGraphRenderOptions

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

Gets the role of this reactant.

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

setSegmentIterator(ListIterator<Vector2D>) - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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.displacement.VesicleLayer

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

setSimulationArea(Rectangle) - Method in class bio.singa.simulation.model.modules.displacement.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.membranes.MembraneSegment

setStoichiometricReactants(List<StoichiometricReactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

Sets the list of reactants for this reaction.

setStrength(double) - Method in class bio.singa.simulation.model.modules.concentration.reactants.CatalyticReactant

Sets the strength of this Reactant.

setStrutCalculation(boolean) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Sets the current state of calculation.

setTargetDirection(Vesicle.TargetDirection) - Method in class bio.singa.simulation.model.modules.displacement.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.

setTimeFormatter(QuantityFormatter<Time>) - Method in class bio.singa.simulation.events.EpochUpdateWriter

setUpConcentrationContainer() - Method in class bio.singa.simulation.model.sections.CellRegion

setUpdateEmissionCondition(Predicate<Simulation>) - Method in class bio.singa.simulation.model.simulation.SimulationManager

Sets a condition determining when events should be emitted.

setUpdateEmissionToTimePassed(Quantity<Time>) - Method in class bio.singa.simulation.model.simulation.SimulationManager

Schedules the emission of events after the given time (simulation time) has passed.

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

setupModule(Class<ModuleImplementation>, ModuleFactory.Scope, ModuleFactory.Specificity) - Static method in class bio.singa.simulation.model.modules.concentration.ModuleFactory

Creates a new module with the specified setup.

setValue(double) - Method in class bio.singa.simulation.model.parameters.SimulationParameter

setValue(double) - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode

Sets the value of the variable

SetVariable - Class in uk.co.cogitolearning.cogpar

A visitor that sets a variable with a specific name to a given value

SetVariable(String, double) - Constructor for class uk.co.cogitolearning.cogpar.SetVariable

Construct the visitor with the name and the value of the variable to set

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

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

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

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

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

shiftDeltas() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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

shutDown() - Method in class bio.singa.simulation.events.GraphImageWriter

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

The simulation.

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

The simulation.

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

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

Creates a new plain simulation.

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

A factory class that can be used to create different examples to test and explore certain aspects to the api.

SimulationExamples() - Constructor for class bio.singa.simulation.model.simulation.SimulationExamples

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

Changes in simulations can be observed by tagging AutomatonNodes of the AutomatonGraph.

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

Creates a new simulation manager for the given simulation.

SimulationParameter<QuantityType extends javax.measure.Quantity<QuantityType>> - Class in bio.singa.simulation.model.parameters

SimulationParameter(String) - Constructor for class bio.singa.simulation.model.parameters.SimulationParameter

SimulationParameter(String, Quantity<QuantityType>) - Constructor for class bio.singa.simulation.model.parameters.SimulationParameter

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

The single file channel transport describes the movement of cargo molecules through Transporter proteins, so called membrane channels.

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

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

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

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

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

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

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

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

SkeletalFilament - Class in bio.singa.simulation.model.agents.filaments

Modified: Mirabet, Vincent, et al.

SkeletalFilament.FilamentBehaviour - Enum in bio.singa.simulation.model.agents.filaments

sortAssignmentRulesByPriority(List<AssignmentRule>) - Static method in class bio.singa.simulation.model.rules.AssignmentRules

It is possible, that AssignmentRules depend on each other.

spawnFilament(Membrane) - Method in class bio.singa.simulation.model.agents.filaments.FilamentLayer

spawnHorizontalFilament(Membrane) - Method in class bio.singa.simulation.model.agents.filaments.FilamentLayer

SpawnRate - Interface in bio.singa.simulation.features.endocytosis

SpawnTimeSampler - Class in bio.singa.simulation.features.endocytosis

SpawnTimeSampler() - Constructor for class bio.singa.simulation.features.endocytosis.SpawnTimeSampler

splitRectangularGraphWithMembrane(AutomatonGraph, CellSubsection, CellSubsection, boolean) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs

start(Stage) - Method in class bio.singa.simulation.model.agents.ClippingPlayground

start(Stage) - Method in class bio.singa.simulation.model.agents.MacroscopicLayerPlayground

start(Stage) - Method in class bio.singa.simulation.model.modules.displacement.VesiclePlayground

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

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

StoichiometricReactant - Class in bio.singa.simulation.model.modules.concentration.reactants

StoichiometricReactants are Reactants that are consumed or produced during the reaction.

StoichiometricReactant(ChemicalEntity, ReactantRole, double, double) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.StoichiometricReactant

Creates a new StoichiometricReactant.

StoichiometricReactant(ChemicalEntity, ReactantRole, double) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.StoichiometricReactant

Creates a new StoichiometricReactant.

StoichiometricReactant(ChemicalEntity, ReactantRole) - Constructor for class bio.singa.simulation.model.modules.concentration.reactants.StoichiometricReactant

Creates a new StoichiometricReactant.

stoichiometricReactants - Variable in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

The stoichiometric reactants.

substratesAvailable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

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

Frequently required fields.

SYMBOL - Static variable in class bio.singa.simulation.features.endocytosis.ActinBoostVelocity

SYMBOL - Static variable in class bio.singa.simulation.features.endocytosis.BuddingRate

SYMBOL - Static variable in class bio.singa.simulation.features.endocytosis.MotorMovementVelocity

SYMBOL - Static variable in class bio.singa.simulation.features.permeability.MembraneEntry

SYMBOL - Static variable in class bio.singa.simulation.features.permeability.MembraneExit

SYMBOL - Static variable in class bio.singa.simulation.features.permeability.MembraneFlipFlop

SYMBOL - Static variable in class bio.singa.simulation.features.scale.AppliedScale

T

Term(boolean, ExpressionNode) - Constructor for class uk.co.cogitolearning.cogpar.SequenceExpressionNode.Term

Construct the Term object with some values.

terms - Variable in class uk.co.cogitolearning.cogpar.SequenceExpressionNode

the list of terms in the sequence

TetheringTime - Class in bio.singa.simulation.features.endocytosis

TetheringTime(ComparableQuantity<Time>, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.TetheringTime

TetheringTime(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.TetheringTime

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

Sets the emission of updates for a rending engine.

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

to(CellTopology) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BinderSectionSelection

to(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction.BindingBuilder

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

topLevelObject - Variable in class bio.singa.simulation.model.modules.concentration.imlementations.Reaction.Builder

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

toString() - Method in class bio.singa.simulation.model.sections.CellRegion

toString() - Method in class bio.singa.simulation.model.sections.CellSubsection

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

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

U

uk.co.cogitolearning.cogpar - package uk.co.cogitolearning.cogpar

UnitScaler - Class in bio.singa.simulation.model.parameters

UnitScaler() - Constructor for class bio.singa.simulation.model.parameters.UnitScaler

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.

update(Observable, Object) - Method in class bio.singa.simulation.model.sections.CellSubsection

UpdateModule - Interface in bio.singa.simulation.model.modules

updatePosition() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager

Sets the current position to the next position.

updatePosition() - Method in class bio.singa.simulation.model.modules.displacement.Vesicle

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.

useEinsteinStrokesDiffusivity() - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleDiffusion

useLiteratureDiffusivity() - Method in class bio.singa.simulation.model.modules.displacement.implementations.VesicleDiffusion

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.filaments.SkeletalFilament.FilamentBehaviour

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

valueOf(String) - Static method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes

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

valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope

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

valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity

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

valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleState

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

valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.reactants.ReactantRole

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

valueOf(String) - Static method in enum bio.singa.simulation.model.modules.displacement.Vesicle.AttachmentState

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

valueOf(String) - Static method in enum bio.singa.simulation.model.modules.displacement.Vesicle.TargetDirection

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

valueOf(String) - Static method in enum bio.singa.simulation.model.sections.CellTopology

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

valueOf(String) - Static method in enum bio.singa.simulation.renderer.RenderingMode

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

values() - Static method in enum bio.singa.simulation.model.agents.filaments.SkeletalFilament.FilamentBehaviour

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.modules.concentration.reactants.ReactantRole

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.modules.displacement.Vesicle.AttachmentState

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.displacement.Vesicle.TargetDirection

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.sections.CellTopology

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.renderer.RenderingMode

Returns an array containing the constants of this enum type, in the order they are declared.

VARIABLE - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for variable names

VARIABLE_NODE - Static variable in interface uk.co.cogitolearning.cogpar.ExpressionNode

Node id for variable nodes

VariableExpressionNode - Class in uk.co.cogitolearning.cogpar

An ExpressionNode that stores a named variable

VariableExpressionNode(String) - Constructor for class uk.co.cogitolearning.cogpar.VariableExpressionNode

Construct with the name of the variable.

Vesicle - Class in bio.singa.simulation.model.modules.displacement

Vesicle(String, Vector2D, Quantity<Length>) - Constructor for class bio.singa.simulation.model.modules.displacement.Vesicle

Vesicle(Vector2D, Quantity<Length>) - Constructor for class bio.singa.simulation.model.modules.displacement.Vesicle

Vesicle.AttachmentState - Enum in bio.singa.simulation.model.modules.displacement

Vesicle.TargetDirection - Enum in bio.singa.simulation.model.modules.displacement

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

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

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

VesicleDiffusion() - Constructor for class bio.singa.simulation.model.modules.displacement.implementations.VesicleDiffusion

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.modules.displacement

VesicleLayer(Simulation) - Constructor for class bio.singa.simulation.model.modules.displacement.VesicleLayer

VesiclePlayground - Class in bio.singa.simulation.model.modules.displacement

VesiclePlayground() - Constructor for class bio.singa.simulation.model.modules.displacement.VesiclePlayground

VesicleRadius - Class in bio.singa.simulation.features.endocytosis

VesicleRadius(Quantity<Length>, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.VesicleRadius

VesicleRadius(double, FeatureOrigin) - Constructor for class bio.singa.simulation.features.endocytosis.VesicleRadius

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

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