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

AbstractComplexEntityModification - Class in bio.singa.simulation.reactions.modifications

AbstractComplexEntityModification(BindingSite) - Constructor for class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

AbstractConcentrationCondition - Class in bio.singa.simulation.model.concentrations

AbstractConcentrationCondition(int) - Constructor for class bio.singa.simulation.model.concentrations.AbstractConcentrationCondition

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

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

AbstractGraphComplexReactor - Class in bio.singa.simulation.reactions.reactors

AbstractGraphComplexReactor() - Constructor for class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

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

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

AbstractReactorBuilder() - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

AbstractUpdateModule - Class in bio.singa.simulation.model.modules

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

acceleratingEntity(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.AccelerationStep

acceleratingEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder

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

Implementation of the visitor design pattern.

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

Implementation of the visitor design pattern.

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

Implementation of the visitor design pattern.

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

Method needed for the visitor design pattern

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

Implementation of the visitor design pattern.

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

Implementation of the visitor design pattern.

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

Implementation of the visitor design pattern.

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

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

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

ActinBoostVelocity - Class in bio.singa.simulation.features

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

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

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

add(BindingSite, ChemicalEntity) - Static method in class bio.singa.simulation.reactions.modifications.ComplexEntityModificationBuilder

add(BindingSite, ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

add(BindingSite, ChemicalEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder

add(BindingSite, ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReactorChoiceStep

add(ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

add(ChemicalEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder

add(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReactorChoiceStep

add(ChemicalEntity, BindingSite) - Method in class bio.singa.simulation.entities.ComplexEntity

add(ReactionChain) - Method in class bio.singa.simulation.reactions.ReactionNetworkGenerator

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

add(String, Parameter) - Static method in class bio.singa.simulation.model.parameters.ParameterStorage

add(ExpressionNode, boolean) - Method in class uk.co.cogitolearning.cogpar.SequenceExpressionNode

Add another term to the sequence

addActin(Vector2D, Vector2D) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

addAdditionalIdentifier(Identifier) - Method in class bio.singa.simulation.entities.SimpleEntity

addAdditionalIdentifiers(Collection<Identifier>) - Method in class bio.singa.simulation.entities.SimpleEntity

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

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

addAreaMapping(CellSubsection, AutomatonNode.AreaMapping) - Method in class bio.singa.simulation.model.graphs.AutomatonNode

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

addBindingSite(BindingSite) - Method in class bio.singa.simulation.entities.GraphComplexNode

addBindingSite(ChemicalEntity, BindingSite) - Method in class bio.singa.simulation.entities.ComplexEntity

addCandidate(ComplexEntity) - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

addCandidate(ComplexEntity) - Method in interface bio.singa.simulation.reactions.modifications.ComplexEntityModification

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

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

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

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

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

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.

addConcentration(ChemicalEntity, double) - Method in class bio.singa.simulation.trajectories.nested.TrajectoryDataPoint.SubsectionDataPoint

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

addCondition(ConcentrationCondition) - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

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

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 class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Adds a delta function to the module.

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, GraphComplexNode, GraphComplexNode) - Method in class bio.singa.simulation.entities.ComplexEntity

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

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

addEdgeBetween(GraphComplexNode, GraphComplexNode) - Method in class bio.singa.simulation.entities.ComplexEntity

addEdgeBetween(GraphComplexNode, GraphComplexNode, BindingSite) - Method in class bio.singa.simulation.entities.ComplexEntity

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

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

addEvidence(Evidence) - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

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

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

addFullDelta(ConcentrationDeltaIdentifier, ConcentrationDelta) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

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

Adds a new listener for graph based events.

addHalfDelta(ConcentrationDeltaIdentifier, ConcentrationDelta) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

addInformation(long, String) - Method in class bio.singa.simulation.trajectories.errors.DebugRecorder

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

Node id for addition nodes

additionalIdentifier(Identifier) - Method in class bio.singa.simulation.entities.SimpleEntity.SimpleEntityBuilder

additionalIdentifiers(Collection<Identifier>) - Method in class bio.singa.simulation.entities.SimpleEntity.SimpleEntityBuilder

AdditionExpressionNode - Class in uk.co.cogitolearning.cogpar

An ExpressionNode that handles additions and subtractions.

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

Constructor to create an addition with the first term already added.

addLineLikeAgentSegment(LineLikeAgent, Vector2D) - Method in class bio.singa.simulation.model.graphs.AutomatonNode

addListener(UpdateEventListener<ErrorManager.Reason>) - Static method in class bio.singa.simulation.model.simulation.error.TimeStepManager

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

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

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

addMicrotubule(Vector2D, Vector2D) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

AddModification - Class in bio.singa.simulation.reactions.modifications

AddModification(BindingSite, ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.modifications.AddModification

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

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

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

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

Adds a new listener for node based events.

addPosition(Vector2D) - Method in class bio.singa.simulation.trajectories.nested.TrajectoryDataPoint.SubsectionDataPoint

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

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

Adds a potential delta to this node.

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

Adds a potential delta to this updatable.

addPotentialDelta(ConcentrationDelta) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

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

Adds a displacement delta.

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

addPreReaction(ReactionChain) - Method in class bio.singa.simulation.reactions.ReactionNetworkGenerator

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

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

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

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

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

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

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

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

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

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

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

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

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

AddReactionChainBuilder(BindingSite, ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactionChainBuilder

AddReactionChainBuilder(ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactionChainBuilder

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

Adds multiple referenced chemical entities.

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

Adds a referenced chemical entity.

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

addRow(ModuleTableRow) - Method in class bio.singa.simulation.export.modules.ModuleTable

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

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

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

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.reactions.ReactionBuilder.StaticBuilder

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

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

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

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

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

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

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

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

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

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

Initializes a updatable that will be observed during simulation.

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

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

AffectedRegion - Class in bio.singa.simulation.features

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

AffectedRegion.Builder - Class in bio.singa.simulation.features

AffectedSection - Class in bio.singa.simulation.features

AffectedSection(CellSubsection) - Constructor for class bio.singa.simulation.features.AffectedSection

AffectedSection.Builder - Class in bio.singa.simulation.features

allErrorsAreSafe() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

allWith(String...) - Static method in class bio.singa.simulation.entities.EntityRegistry

and() - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

and() - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ConnectorStep

append(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

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

AppliedVesicleState - Class in bio.singa.simulation.features

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

AppliedVesicleState.Builder - Class in bio.singa.simulation.features

apply() - Method in class bio.singa.simulation.reactions.modifications.AddModification

apply() - Method in class bio.singa.simulation.reactions.modifications.BindModification

apply() - Method in interface bio.singa.simulation.reactions.modifications.ComplexEntityModification

apply() - Method in class bio.singa.simulation.reactions.modifications.ReleaseModification

apply() - Method in class bio.singa.simulation.reactions.modifications.RemoveModification

apply() - Method in interface bio.singa.simulation.reactions.reactors.ComplexReactor

apply() - Method in class bio.singa.simulation.reactions.reactors.OneToOneReactor

apply() - Method in class bio.singa.simulation.reactions.reactors.OneToTwoReactor

apply() - Method in class bio.singa.simulation.reactions.reactors.TwoToOneReactor

apply(ComplexEntity) - Method in class bio.singa.simulation.reactions.modifications.AddModification

apply(ComplexEntity) - Method in class bio.singa.simulation.reactions.modifications.ReleaseModification

apply(ComplexEntity) - Method in class bio.singa.simulation.reactions.modifications.RemoveModification

apply(ComplexEntity, ComplexEntity) - Method in class bio.singa.simulation.reactions.modifications.BindModification

apply(Simulation) - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

apply(Updatable) - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

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

Apply all referenced assignment rules.

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

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

Applies all final deltas and clears the delta list.

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

AreaCondition - Class in bio.singa.simulation.model.concentrations

AreaCondition(Polygon) - Constructor for class bio.singa.simulation.model.concentrations.AreaCondition

AreaMapping(AutomatonNode, AutomatonNode, CellSubsection, double) - Constructor for class bio.singa.simulation.model.graphs.AutomatonNode.AreaMapping

assembleRowsSet(int) - Method in class bio.singa.simulation.export.modules.ReactionTableRow

assignFeature(Feature) - Method in class bio.singa.simulation.entities.SimpleEntity.SimpleEntityBuilder

assignFeature(Class<? extends Feature>) - Method in class bio.singa.simulation.entities.SimpleEntity.SimpleEntityBuilder

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

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

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

associateInGraph(AutomatonGraph) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

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

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

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

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

attachBindingSites(Map<ChemicalEntity, Set<BindingSite>>, Map.Entry<BindingSite, Pair<ChemicalEntity>>) - Static method in class bio.singa.simulation.entities.ComplexEntityBuilder

AttachedFilament - Class in bio.singa.simulation.features

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

AttachedFilament.Builder - Class in bio.singa.simulation.features

AttachedMotor - Class in bio.singa.simulation.features

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

AttachedMotor.Builder - Class in bio.singa.simulation.features

AttachmentDistance - Class in bio.singa.simulation.features

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

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

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

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

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

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

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

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

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

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

A node of the AutomatonGraph.

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

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

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

availableFeatures - Static variable in class bio.singa.simulation.entities.ComplexEntity

availableFeatures - Static variable in class bio.singa.simulation.entities.SimpleEntity

availableFeatures - Static variable in class bio.singa.simulation.model.agents.pointlike.Vesicle

B

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

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

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

bind(BindingSite) - Static method in class bio.singa.simulation.reactions.modifications.ComplexEntityModificationBuilder

bind(BindingSite, ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

bind(BindingSite, ChemicalEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder

bind(BindingSite, ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReactorChoiceStep

bind(ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

bind(ChemicalEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder

bind(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReactorChoiceStep

bind(ComplexEntity, BindingSite) - Method in class bio.singa.simulation.entities.ComplexEntity

bindingSite - Variable in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

BindingSite - Class in bio.singa.simulation.entities

BindModification - Class in bio.singa.simulation.reactions.modifications

BindModification(BindingSite) - Constructor for class bio.singa.simulation.reactions.modifications.BindModification

BindReactionChainBuilder(BindingSite, ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactionChainBuilder

BindReactionChainBuilder(ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactionChainBuilder

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

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

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

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

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

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

bio.singa.simulation.export.modules - package bio.singa.simulation.export.modules

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

bio.singa.simulation.reactions.conditions - package bio.singa.simulation.reactions.conditions

bio.singa.simulation.reactions.modifications - package bio.singa.simulation.reactions.modifications

bio.singa.simulation.reactions.reactors - package bio.singa.simulation.reactions.reactors

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

bio.singa.simulation.trajectories.errors - package bio.singa.simulation.trajectories.errors

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

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

BlackListVesicleStates - Class in bio.singa.simulation.features

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

BlackListVesicleStates.Builder - Class in bio.singa.simulation.features

BoostMediatingEntity - Class in bio.singa.simulation.features

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

BoostMediatingEntity.Builder - Class in bio.singa.simulation.features

build() - Method in interface bio.singa.simulation.entities.ComplexEntityBuilder.CombineStep

build() - Method in class bio.singa.simulation.entities.ComplexEntityBuilder.ComplexEntityCombiner

build() - Method in class bio.singa.simulation.entities.SimpleEntity.SimpleEntityBuilder

build() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.BuildStep

build() - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

build() - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

build() - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ConnectorStep

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

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

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

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

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

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

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

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

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

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

Builder(CellSubsection) - Constructor for class bio.singa.simulation.features.AffectedSection.Builder

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

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

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

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

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

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

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

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

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

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

Builder(List<InitialConcentration>) - Constructor for class bio.singa.simulation.features.InitialConcentrations.Builder

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

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

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

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

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

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

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

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

Builder(Quantity<Length>) - Constructor for class bio.singa.simulation.features.MembraneTickness.Builder

Builder(Quantity<Length>) - Constructor for class bio.singa.simulation.features.VesicleRadius.Builder

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

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

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

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

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

C

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

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

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

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

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

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

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

Calculates the total displacement resulting from the potential deltas and sets the result as the next position.

calculateUpdates() - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

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.qualitative.implementations.ClathrinMediatedEndocytosis

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

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

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

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

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

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

CandidateCondition - Interface in bio.singa.simulation.reactions.conditions

CandidateConditionBuilder - Class in bio.singa.simulation.reactions.conditions

CandidateConditionBuilder() - Constructor for class bio.singa.simulation.reactions.conditions.CandidateConditionBuilder

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

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

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

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

cargo(Cargo) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.FeatureStep

cargo(Cargo) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.PorousDiffusionBuilder

cargo(Cargoes) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder

cargo(Cargoes) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EntityStep

Cargo - Class in bio.singa.simulation.features

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

Cargo.Builder - Class in bio.singa.simulation.features

cargoAdditionRate(CargoAdditionRate) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder

cargoAdditionRate(CargoAdditionRate) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.RateStep

CargoAdditionRate - Class in bio.singa.simulation.features

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

CargoAdditionRate.Builder - Class in bio.singa.simulation.features

Cargoes - Class in bio.singa.simulation.features

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

Cargoes.Builder - Class in bio.singa.simulation.features

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

CELL - bio.singa.simulation.model.agents.organelles.OrganelleTypes

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

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

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

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

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

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

CellRegion(String, GoTerm) - Constructor for class bio.singa.simulation.model.sections.CellRegion

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

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

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

A cell subsection organizes the contents of a Updatable.

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

Creates a new cell subsection with the given identifier and dynamic preferred concentration unit.

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

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

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

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

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

The cell topology defines how the subsections are spatially organized.

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

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

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

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

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

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

checkSkipping() - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

ChemicalEntities - Class in bio.singa.simulation.entities

ChemicalEntity - Interface in bio.singa.simulation.entities

Chemical Entity is an abstract class that provides the common features of all chemical substances on a descriptive level.

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

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

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

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

clear() - Static method in class bio.singa.simulation.model.parameters.ParameterStorage

clear() - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

clear() - Method in interface bio.singa.simulation.reactions.modifications.ComplexEntityModification

clear() - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

clear() - Method in interface bio.singa.simulation.reactions.reactors.ComplexReactor

clear() - Method in class bio.singa.simulation.reactions.reactors.OneToTwoReactor

clear() - Method in class bio.singa.simulation.reactions.reactors.TwoToOneReactor

clear() - Method in class bio.singa.simulation.trajectories.errors.DebugRecorder

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

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

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

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

Clears all full end half deltas.

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

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

Clears the list of potential deltas.

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

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

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

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

Clears all concentration deltas that may be assigned by this module

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

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

Clears all potential displacement deltas.

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

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

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

Token id for closing brackets

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

Close all associated writers.

collectCandidates(List<ComplexEntity>) - Method in interface bio.singa.simulation.reactions.reactors.ComplexReactor

collectCandidates(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.OneToOneReactor

collectCandidates(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.OneToTwoReactor

collectCandidates(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.TwoToOneReactor

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

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

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

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

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

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

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

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

COLUMN_END_BREAKING - Static variable in class bio.singa.simulation.export.TeXFormat

COLUMN_END_NON_BREAKING - Static variable in class bio.singa.simulation.export.TeXFormat

COLUMN_SEPERATOR - Static variable in class bio.singa.simulation.export.TeXFormat

COLUMN_SEPERATOR_SPACED - Static variable in class bio.singa.simulation.export.TeXFormat

combine(ChemicalEntity, ChemicalEntity) - Method in interface bio.singa.simulation.entities.ComplexEntityBuilder.CombineStep

combine(ChemicalEntity, ChemicalEntity) - Method in class bio.singa.simulation.entities.ComplexEntityBuilder.ComplexEntityCombiner

combine(ChemicalEntity, ChemicalEntity, BindingSite) - Method in interface bio.singa.simulation.entities.ComplexEntityBuilder.CombineStep

combine(ChemicalEntity, ChemicalEntity, BindingSite) - Method in class bio.singa.simulation.entities.ComplexEntityBuilder.ComplexEntityCombiner

combine(GraphComplexNode, GraphComplexNode, ComplexEntity, BindingSite) - Method in class bio.singa.simulation.entities.ComplexEntity

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

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

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

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

ComplexEntity - Class in bio.singa.simulation.entities

ComplexEntity() - Constructor for class bio.singa.simulation.entities.ComplexEntity

ComplexEntityBuilder - Class in bio.singa.simulation.entities

ComplexEntityBuilder() - Constructor for class bio.singa.simulation.entities.ComplexEntityBuilder

ComplexEntityBuilder.CombineStep - Interface in bio.singa.simulation.entities

ComplexEntityBuilder.ComplexEntityCombiner - Class in bio.singa.simulation.entities

ComplexEntityCombiner() - Constructor for class bio.singa.simulation.entities.ComplexEntityBuilder.ComplexEntityCombiner

ComplexEntityModification - Interface in bio.singa.simulation.reactions.modifications

ComplexEntityModificationBuilder - Class in bio.singa.simulation.reactions.modifications

ComplexEntityModificationBuilder() - Constructor for class bio.singa.simulation.reactions.modifications.ComplexEntityModificationBuilder

ComplexReactor - Interface in bio.singa.simulation.reactions.reactors

concentration(Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

concentration(Quantity<MolarConcentration>) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationStep

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

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

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.

ConcentrationBuilder - Class in bio.singa.simulation.model.concentrations

ConcentrationBuilder() - Constructor for class bio.singa.simulation.model.concentrations.ConcentrationBuilder

ConcentrationBuilder.AdditionalConditionsStep - Interface in bio.singa.simulation.model.concentrations

ConcentrationBuilder.BuildStep - Interface in bio.singa.simulation.model.concentrations

ConcentrationBuilder.ConcentrationBuilderImpl - Class in bio.singa.simulation.model.concentrations

ConcentrationBuilder.ConcentrationStep - Interface in bio.singa.simulation.model.concentrations

ConcentrationBuilder.ConcentrationUnitStep - Interface in bio.singa.simulation.model.concentrations

ConcentrationBuilder.EntityStep - Interface in bio.singa.simulation.model.concentrations

ConcentrationBuilder.PoolStep - Interface in bio.singa.simulation.model.concentrations

ConcentrationBuilder.TimedUnitStep - Interface in bio.singa.simulation.model.concentrations

ConcentrationBuilderImpl() - Constructor for class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

ConcentrationBuilderImpl(Simulation) - Constructor for class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

ConcentrationCondition - Interface in bio.singa.simulation.model.concentrations

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

The concentration container manages the concentrations of one updatable.

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

Creates a new concentration container.

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

The delta object manages the change that will be applied to the concentration of a specific ChemicalEntity in a CellSubsection.

ConcentrationDelta(UpdateModule, CellSubsection, ChemicalEntity, double) - Constructor for class bio.singa.simulation.model.modules.concentration.ConcentrationDelta

Creates a new concentration delta.

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

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

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

Creates a new DeltaIdentifier.

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

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

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

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

Creates a new Concentration Delta Manager.

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

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

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

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

The concentration pool manages the MolarConcentration of ChemicalEntitys in CellSubsections.

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

Creates a new, empty concentration pool.

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

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

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

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

concentrationValue(double) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

concentrationValue(double) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationStep

concerns(BindingSite) - Method in interface bio.singa.simulation.reactions.conditions.CandidateCondition

concerns(BindingSite) - Method in class bio.singa.simulation.reactions.conditions.HasAnyNumberOfEntities

concerns(BindingSite) - Method in class bio.singa.simulation.reactions.conditions.HasNoMoreThanNumberOfPartners

concerns(BindingSite) - Method in class bio.singa.simulation.reactions.conditions.HasNumberOfEntities

concerns(BindingSite) - Method in class bio.singa.simulation.reactions.conditions.HasOccupiedBindingSite

concerns(BindingSite) - Method in class bio.singa.simulation.reactions.conditions.HasUnoccupiedBindingSite

concerns(BindingSite) - Method in class bio.singa.simulation.reactions.conditions.IsOnlyBoundAt

concerns(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.conditions.CandidateCondition

concerns(ChemicalEntity) - Method in class bio.singa.simulation.reactions.conditions.HasAnyNumberOfEntities

concerns(ChemicalEntity) - Method in class bio.singa.simulation.reactions.conditions.HasNoMoreThanNumberOfPartners

concerns(ChemicalEntity) - Method in class bio.singa.simulation.reactions.conditions.HasNumberOfEntities

concerns(ChemicalEntity) - Method in class bio.singa.simulation.reactions.conditions.HasOccupiedBindingSite

concerns(ChemicalEntity) - Method in class bio.singa.simulation.reactions.conditions.HasUnoccupiedBindingSite

concerns(ChemicalEntity) - Method in class bio.singa.simulation.reactions.conditions.IsOnlyBoundAt

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

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

condition(CandidateCondition) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactionChainBuilder

condition(CandidateCondition) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactorPrimaryConditionStep

condition(CandidateCondition) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactionChainBuilder

condition(CandidateCondition) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactorPrimaryConditionStep

condition(CandidateCondition) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactionChainBuilder

condition(CandidateCondition) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactorPrimaryConditionStep

considerInversion - Variable in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

considerInversion() - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

considerInversion() - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ConnectorStep

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

Node id for constant nodes

ConstantExpressionNode - Class in uk.co.cogitolearning.cogpar

An ExpressionNode that stores a constant value

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

Construct with the fixed value.

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

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

ContainmentRegion - Class in bio.singa.simulation.features

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

ContainmentRegion.Builder - Class in bio.singa.simulation.features

contains(String) - Static method in class bio.singa.simulation.entities.EntityRegistry

containsEntity(ChemicalEntity) - Method in class bio.singa.simulation.entities.ComplexEntity

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

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

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

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

convert(Simulation) - Static method in class bio.singa.simulation.export.modules.ModuleTableConverter

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

countParts(ChemicalEntity) - Method in class bio.singa.simulation.entities.ComplexEntity

create() - Static method in class bio.singa.simulation.entities.ComplexEntityBuilder

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

create() - Static method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder

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

create(Simulation) - Static method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder

create(String) - Static method in class bio.singa.simulation.entities.SimpleEntity

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

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

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

createInitialEntities(Map<ChemicalEntity, Set<BindingSite>>) - Method in class bio.singa.simulation.reactions.ReactionNetworkGenerator

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

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

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

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

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

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

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

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

createNamed(String) - Static method in class bio.singa.simulation.entities.BindingSite

createObject(ChemicalEntity) - Method in class bio.singa.simulation.features.AttachedMotor.Builder

createObject(ChemicalEntity) - Method in class bio.singa.simulation.features.BoostMediatingEntity.Builder

createObject(ChemicalEntity) - Method in class bio.singa.simulation.features.Cargo.Builder

createObject(ChemicalEntity) - Method in class bio.singa.simulation.features.Transporter.Builder

createObject(CellRegion) - Method in class bio.singa.simulation.features.AffectedRegion.Builder

createObject(CellRegion) - Method in class bio.singa.simulation.features.ContainmentRegion.Builder

createObject(CellSubsection) - Method in class bio.singa.simulation.features.AffectedSection.Builder

createObject(String) - Method in class bio.singa.simulation.features.AppliedVesicleState.Builder

createObject(String) - Method in class bio.singa.simulation.features.AttachedFilament.Builder

createObject(String) - Method in class bio.singa.simulation.features.MotorPullDirection.Builder

createObject(String) - Method in class bio.singa.simulation.features.RequiredVesicleState.Builder

createObject(List<ChemicalEntity>) - Method in class bio.singa.simulation.features.Cargoes.Builder

createObject(List<ChemicalEntity>) - Method in class bio.singa.simulation.features.MatchingQSnares.Builder

createObject(List<ChemicalEntity>) - Method in class bio.singa.simulation.features.MatchingRSnares.Builder

createObject(List<ChemicalEntity>) - Method in class bio.singa.simulation.features.PrimaryCargoes.Builder

createObject(List<ChemicalEntity>) - Method in class bio.singa.simulation.features.ScalingEntities.Builder

createObject(List<ChemicalEntity>) - Method in class bio.singa.simulation.features.Solutes.Builder

createObject(List<InitialConcentration>) - Method in class bio.singa.simulation.features.InitialConcentrations.Builder

createObject(List<String>) - Method in class bio.singa.simulation.features.BlackListVesicleStates.Builder

createObject(List<String>) - Method in class bio.singa.simulation.features.WhiteListVesicleStates.Builder

createObject(Quantity<FirstOrderRate>) - Method in class bio.singa.simulation.features.CargoAdditionRate.Builder

createObject(Quantity<MolarConcentration>) - Method in class bio.singa.simulation.features.EndocytosisCheckpointConcentration.Builder

createObject(Quantity<SpawnRate>) - Method in class bio.singa.simulation.features.PitFormationRate.Builder

createObject(Quantity<Dimensionless>) - Method in class bio.singa.simulation.features.Ratio.Builder

createObject(Quantity<Dimensionless>) - Method in class bio.singa.simulation.features.SNAREFusionPairs.Builder

createObject(Quantity<Length>) - Method in class bio.singa.simulation.features.AttachmentDistance.Builder

createObject(Quantity<Length>) - Method in class bio.singa.simulation.features.MembraneTickness.Builder

createObject(Quantity<Length>) - Method in class bio.singa.simulation.features.VesicleRadius.Builder

createObject(Quantity<Speed>) - Method in class bio.singa.simulation.features.ActinBoostVelocity.Builder

createObject(Quantity<Speed>) - Method in class bio.singa.simulation.features.MotorMovementVelocity.Builder

createObject(Quantity<Time>) - Method in class bio.singa.simulation.features.EndocytosisCheckpointTime.Builder

createObject(Quantity<Time>) - Method in class bio.singa.simulation.features.FusionTime.Builder

createObject(Quantity<Time>) - Method in class bio.singa.simulation.features.MaturationTime.Builder

createOneToOne(ComplexEntity, ComplexEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionElement

createOneToTwo(ComplexEntity, ComplexEntity, ComplexEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionElement

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

createTopology() - Method in class bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder

createTwoToOne(ComplexEntity, ComplexEntity, ComplexEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionElement

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

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

D

DebugRecorder - Class in bio.singa.simulation.trajectories.errors

DebugRecorder() - Constructor for class bio.singa.simulation.trajectories.errors.DebugRecorder

decreaseTimeStep(ErrorManager.Reason) - Static method in class bio.singa.simulation.model.simulation.error.TimeStepManager

DEFAULT_VESICLE_DIFFUSIVITY - Static variable in class bio.singa.simulation.model.agents.pointlike.Vesicle

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

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

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

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.

determineBindingSites() - Method in class bio.singa.simulation.reactions.ReactionNetworkGenerator

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

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

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

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

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

Determines all deltas for a Concentration container.

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

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

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

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

determineSpawnPosition(Membrane, Membrane) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

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

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

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

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

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

deviationIsAcceptable() - Method in class bio.singa.simulation.model.simulation.error.GlobalDisplacementDeviationManager

deviationIsCritical() - Method in class bio.singa.simulation.model.simulation.error.GlobalDisplacementDeviationManager

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Creates a new Displacement Delta Manager.

DisplacementDeviation - Class in bio.singa.simulation.model.simulation.error

DisplacementDeviation(Vesicle, double) - Constructor for class bio.singa.simulation.model.simulation.error.DisplacementDeviation

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

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

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

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

E

EARLY_ENDOSOME - bio.singa.simulation.model.agents.organelles.OrganelleTypes

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

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

emitNodeEvent(Simulation, Updatable) - Method in class bio.singa.simulation.model.simulation.SimulationManager

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

Returns a empty copy of this container, keeping subsections and cell topologies associated.

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

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

EndocytosisCheckpointConcentration - Class in bio.singa.simulation.features

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

EndocytosisCheckpointConcentration.Builder - Class in bio.singa.simulation.features

EndocytosisCheckpointTime - Class in bio.singa.simulation.features

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

EndocytosisCheckpointTime.Builder - Class in bio.singa.simulation.features

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

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

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

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

EndocytoticPitAbsorption.AccelerationStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

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

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

EndocytoticPitAbsorption.EntityStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

EndocytoticPitAbsorption.InhibitionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

EndocytoticPitAbsorption.RateStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

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

entity(ChemicalEntity) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

entity(ChemicalEntity) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.EntityStep

ENTITY_SPECIFIC - bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity

References EntitySpecific.

EntityDeltaFunction - Class in bio.singa.simulation.model.modules.concentration.functions

Entity delta functions are AbstractDeltaFunctions which return only one concentration delta.

EntityDeltaFunction(Function<ConcentrationContainer, ConcentrationDelta>, Predicate<ConcentrationContainer>) - Constructor for class bio.singa.simulation.model.modules.concentration.functions.EntityDeltaFunction

Creates a new entity delta function with the specified condition and function.

EntityFeature - Class in bio.singa.simulation.features.model

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

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

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

EntityRegistry - Class in bio.singa.simulation.entities

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

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

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

Initializes the update specificity for the corresponding module.

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

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

Token id for the epsilon terminal

equals(Object) - Method in class bio.singa.simulation.entities.BindingSite

equals(Object) - Method in class bio.singa.simulation.entities.ComplexEntity

equals(Object) - Method in class bio.singa.simulation.entities.SimpleEntity

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

equals(Object) - Method in class bio.singa.simulation.model.graphs.AutomatonNode.AreaMapping

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

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

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

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

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

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

equals(Object) - Method in class bio.singa.simulation.reactions.reactors.ReactionElement

ERRORED - bio.singa.simulation.model.modules.concentration.ModuleState

Some error has occurred during calculation.

errorIsAcceptable() - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

errorIsCritical() - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

errorIsNegligible() - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

ErrorManager - Class in bio.singa.simulation.model.simulation.error

ErrorManager(UpdateScheduler) - Constructor for class bio.singa.simulation.model.simulation.error.ErrorManager

ErrorManager.CalculationStage - Enum in bio.singa.simulation.model.simulation.error

ErrorManager.Reason - Enum in bio.singa.simulation.model.simulation.error

evaluateDeviation() - Method in class bio.singa.simulation.model.simulation.error.GlobalDisplacementDeviationManager

evaluateError() - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

evaluateGlobalDeviation() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

evaluateGlobalError() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

EVALUATION_STAGE - bio.singa.simulation.model.simulation.error.ErrorManager.CalculationStage

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.

evidence(Evidence) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.BuildStep

evidence(Evidence) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

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

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

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

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

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

Node id for exponentiation nodes

ExponentiationExpressionNode - Class in uk.co.cogitolearning.cogpar

An ExpressionNode that handles exponentiation.

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

Construct the ExponentiationExpressionNode with base and exponent

expression - Variable in class uk.co.cogitolearning.cogpar.SequenceExpressionNode.Term

the expression node

ExpressionNode - Interface in uk.co.cogitolearning.cogpar

An interface for expression nodes.

ExpressionNodeVisitor - Interface in uk.co.cogitolearning.cogpar

An interface for the visitor design pattern.

ExpressionParser - Class in uk.co.cogitolearning.cogpar

A parser for mathematical expressions.

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

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

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

F

FeatureManager - Class in bio.singa.simulation.model.parameters

FeatureManager() - Constructor for class bio.singa.simulation.model.parameters.FeatureManager

FeatureRandomizer - Class in bio.singa.simulation.features

FeatureRandomizer() - Constructor for class bio.singa.simulation.features.FeatureRandomizer

features - Variable in class bio.singa.simulation.model.agents.pointlike.Vesicle

FeatureTable - Class in bio.singa.simulation.export.features

FeatureTable() - Constructor for class bio.singa.simulation.export.features.FeatureTable

FeatureTableRow - Class in bio.singa.simulation.export.features

FeatureTableRow() - Constructor for class bio.singa.simulation.export.features.FeatureTableRow

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

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

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

filterCandidates(List<ComplexEntity>, List<CandidateCondition>) - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

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

fixed() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

fixed() - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

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

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

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

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

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

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

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

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

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

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

FOLLOW - bio.singa.simulation.model.agents.linelike.LineLikeAgent.GrowthBehaviour

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

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

forAllEntities(ChemicalEntity...) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder

forAllEntities(ChemicalEntity...) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EntityStep

forAllEntities(ChemicalEntity...) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.EntityLimitationStep

forAllEntities(ChemicalEntity...) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.LateralMembraneDiffusionBuilder

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

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

forAllEntities(Collection<ChemicalEntity>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder

forAllEntities(Collection<ChemicalEntity>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EntityStep

forAllEntities(Collection<ChemicalEntity>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.EntityLimitationStep

forAllEntities(Collection<ChemicalEntity>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.LateralMembraneDiffusionBuilder

forAllMembranes() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.LateralMembraneDiffusionBuilder

forAllMembranes() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.SectionLimitationStep

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

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

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

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

forEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder

forEntity(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EntityStep

forEntity(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.EntityLimitationStep

forEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.LateralMembraneDiffusionBuilder

forIdentifier(String) - Static method in class bio.singa.simulation.model.concentrations.NodeIdentifierCondition

forIdentifiers(String...) - Static method in class bio.singa.simulation.model.concentrations.NodeIdentifierCondition

forIdentifiers(List<String>) - Static method in class bio.singa.simulation.model.concentrations.NodeIdentifierCondition

formatAllEvidence(Feature) - Static method in class bio.singa.simulation.export.format.FormatFeature

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

formatASCII(List<Reactant>, List<Reactant>, List<Reactant>, KineticLaw) - Static method in class bio.singa.simulation.export.format.FormatReactionEquation

formatCompoundFeature(Feature<?>, String, List<String>) - Static method in class bio.singa.simulation.export.features.FeatureTableRow

formatEvidence(Object) - Static method in class bio.singa.simulation.export.format.FormatFeature

formatEvidence(List<Evidence>) - Static method in class bio.singa.simulation.export.features.FeatureTableRow

formatFeature(Feature<?>) - Static method in class bio.singa.simulation.export.features.FeatureTableRow

formatFeature(Feature<?>, String) - Static method in class bio.singa.simulation.export.features.FeatureTableRow

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

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

formatFeatures(UpdateModule) - Static method in class bio.singa.simulation.export.format.FormatFeature

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

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

formatNumber(double) - Static method in class bio.singa.simulation.export.TeXFormat

formatRates(Reaction) - Static method in class bio.singa.simulation.export.format.FormatFeature

map: key: feature - value: list: evidence

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

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

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

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

formatStates(String) - Static method in class bio.singa.simulation.export.features.FeatureTableRow

formatTableMultiColumn(String, int) - Static method in class bio.singa.simulation.export.TeXFormat

formatTableNumberColumnValue(String) - Static method in class bio.singa.simulation.export.TeXFormat

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

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

forMembrane(CellRegion) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.LateralMembraneDiffusionBuilder

forMembrane(CellRegion) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.SectionLimitationStep

forPair(Pair<ChemicalEntity>) - Static method in class bio.singa.simulation.entities.BindingSite

forPair(ChemicalEntity, ChemicalEntity) - Static method in class bio.singa.simulation.entities.BindingSite

forRegion(CellRegion) - Static method in class bio.singa.simulation.model.concentrations.AreaCondition

forRegion(CellRegion) - Static method in class bio.singa.simulation.model.concentrations.RegionCondition

forRegions(CellRegion...) - Static method in class bio.singa.simulation.model.concentrations.RegionCondition

forRegions(List<CellRegion>) - Static method in class bio.singa.simulation.model.concentrations.RegionCondition

forSection(CellSubsection) - Static method in class bio.singa.simulation.model.concentrations.SectionCondition

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

forSection(CellSubsection) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.SectionLimitationStep

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

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

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

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

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

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

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

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

from(ChemicalEntity) - Static method in class bio.singa.simulation.entities.ComplexEntity

from(ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactionChainBuilder

from(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep

from(ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactionChainBuilder

from(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactorSecondarySubstrateStep

from(ChemicalEntity, BindingSite) - Static method in class bio.singa.simulation.entities.ComplexEntity

from(ChemicalEntity, ChemicalEntity) - Static method in class bio.singa.simulation.entities.ComplexEntity

from(ChemicalEntity, Collection<BindingSite>) - Static method in class bio.singa.simulation.entities.ComplexEntity

from(FeatureTable) - Static method in class bio.singa.simulation.export.features.VariationTable

from(UpdateModule) - Static method in class bio.singa.simulation.export.modules.GeneralModuleRow

from(Simulation) - Static method in class bio.singa.simulation.export.features.ModuleSummaryTable

fromSimulation(Simulation) - Static method in class bio.singa.simulation.export.features.FeatureTable

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.

fullSpace - Static variable in interface bio.singa.simulation.export.modules.ModuleTableRow

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

Token id for function names

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

Node id for function nodes

FunctionExpressionNode - Class in uk.co.cogitolearning.cogpar

An ExpressionNode that handles mathematical functions.

FusionTime - Class in bio.singa.simulation.features

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

FusionTime.Builder - Class in bio.singa.simulation.features

G

GeneralModuleRow - Class in bio.singa.simulation.export.modules

GeneralModuleRow(UpdateModule) - Constructor for class bio.singa.simulation.export.modules.GeneralModuleRow

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

generate() - Method in class bio.singa.simulation.reactions.ReactionNetworkGenerator

generate(Simulation) - Method in class bio.singa.simulation.export.features.FeatureTable

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

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

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

generateFeatureString(Map<String, List<String>>) - Method in interface bio.singa.simulation.export.modules.ModuleTableRow

generateHeader(String) - Method in interface bio.singa.simulation.export.modules.ModuleTableRow

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.

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

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

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

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

Returns the concentration of a entity.

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(String) - Static method in class bio.singa.simulation.entities.EntityRegistry

get(String) - Static method in class bio.singa.simulation.model.parameters.ParameterStorage

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

getAll() - Static method in class bio.singa.simulation.entities.EntityRegistry

getAll() - Static method in class bio.singa.simulation.model.parameters.ParameterStorage

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

getAllIdentifiers() - Method in interface bio.singa.simulation.entities.ChemicalEntity

getAllIdentifiers() - Method in class bio.singa.simulation.entities.ComplexEntity

getAllIdentifiers() - Method in class bio.singa.simulation.entities.SimpleEntity

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

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

Returns all referenced sections in this node.

getAllReferencedSections() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

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

Returns the application condition for this module.The module is only evaluated if the updatable fulfills the given predicate.

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

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

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

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

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

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

getAssociatedNode() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

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

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

getAvailableFeatures() - Method in class bio.singa.simulation.entities.ComplexEntity

getAvailableFeatures() - Method in class bio.singa.simulation.entities.SimpleEntity

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

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

getBindingSite() - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

getBindingSite() - Method in interface bio.singa.simulation.reactions.modifications.ComplexEntityModification

getBindingSite() - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

getBindingSite() - Method in interface bio.singa.simulation.reactions.reactors.ComplexReactor

getBindingSites() - Method in class bio.singa.simulation.entities.GraphComplexNode

getBuilder() - Method in class bio.singa.simulation.features.ActinBoostVelocity.Builder

getBuilder() - Method in class bio.singa.simulation.features.AffectedRegion.Builder

getBuilder() - Method in class bio.singa.simulation.features.AffectedSection.Builder

getBuilder() - Method in class bio.singa.simulation.features.AppliedVesicleState.Builder

getBuilder() - Method in class bio.singa.simulation.features.AttachedFilament.Builder

getBuilder() - Method in class bio.singa.simulation.features.AttachedMotor.Builder

getBuilder() - Method in class bio.singa.simulation.features.AttachmentDistance.Builder

getBuilder() - Method in class bio.singa.simulation.features.BlackListVesicleStates.Builder

getBuilder() - Method in class bio.singa.simulation.features.BoostMediatingEntity.Builder

getBuilder() - Method in class bio.singa.simulation.features.Cargo.Builder

getBuilder() - Method in class bio.singa.simulation.features.CargoAdditionRate.Builder

getBuilder() - Method in class bio.singa.simulation.features.Cargoes.Builder

getBuilder() - Method in class bio.singa.simulation.features.ContainmentRegion.Builder

getBuilder() - Method in class bio.singa.simulation.features.EndocytosisCheckpointConcentration.Builder

getBuilder() - Method in class bio.singa.simulation.features.EndocytosisCheckpointTime.Builder

getBuilder() - Method in class bio.singa.simulation.features.FusionTime.Builder

getBuilder() - Method in class bio.singa.simulation.features.InitialConcentrations.Builder

getBuilder() - Method in class bio.singa.simulation.features.MatchingQSnares.Builder

getBuilder() - Method in class bio.singa.simulation.features.MatchingRSnares.Builder

getBuilder() - Method in class bio.singa.simulation.features.MaturationTime.Builder

getBuilder() - Method in class bio.singa.simulation.features.MembraneTickness.Builder

getBuilder() - Method in class bio.singa.simulation.features.MotorMovementVelocity.Builder

getBuilder() - Method in class bio.singa.simulation.features.MotorPullDirection.Builder

getBuilder() - Method in class bio.singa.simulation.features.PitFormationRate.Builder

getBuilder() - Method in class bio.singa.simulation.features.PrimaryCargoes.Builder

getBuilder() - Method in class bio.singa.simulation.features.Ratio.Builder

getBuilder() - Method in class bio.singa.simulation.features.RequiredVesicleState.Builder

getBuilder() - Method in class bio.singa.simulation.features.ScalingEntities.Builder

getBuilder() - Method in class bio.singa.simulation.features.SNAREFusionPairs.Builder

getBuilder() - Method in class bio.singa.simulation.features.Solutes.Builder

getBuilder() - Method in class bio.singa.simulation.features.Transporter.Builder

getBuilder() - Method in class bio.singa.simulation.features.VesicleRadius.Builder

getBuilder() - Method in class bio.singa.simulation.features.WhiteListVesicleStates.Builder

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

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

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

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

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

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

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

getCandidates() - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

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

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

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

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

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

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

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

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

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

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

getCellRegion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

getCellRegion(String) - Method in class bio.singa.simulation.model.graphs.AutomatonGraph

Return the cell section with the given identifier.

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

Returns all CellSubsections referenced in this graph.

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

Returns the subsection.

getCheckpointTime() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

Returns the chemical entities.

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

Returns the chemical entity.

getChemicalEntity() - Method in class bio.singa.simulation.model.simulation.error.NumericalError

Returns the chemical entity where the error occurred.

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

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

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

getConcentration() - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

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

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

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

Returns the ConcentrationContainer used by this node.

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

Returns the current concentration container.

getConcentrationContainer() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

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

getConcentrationDeltaManager() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

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

getConcentrationManager() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

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

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

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

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

getConcentrations() - Method in class bio.singa.simulation.trajectories.nested.TrajectoryDataPoint.SubsectionDataPoint

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

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

Returns the application condition.

getConditions() - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

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

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

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

getConnectedSite() - Method in class bio.singa.simulation.entities.GraphComplexEdge

getCopy() - Method in class bio.singa.simulation.entities.ComplexEntity

getCopy() - Method in class bio.singa.simulation.entities.GraphComplexEdge

getCopy() - Method in class bio.singa.simulation.entities.GraphComplexNode

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

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

getCopy(int) - Method in class bio.singa.simulation.entities.GraphComplexEdge

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

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

Returns the current chemical entity.

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

Returns all currently available full deltas.

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

Returns all currently available half deltas.

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

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

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

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

Returns the current position.

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

Returns the current subsection.

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

Returns the current updatable.

getDebugDirectory() - Method in class bio.singa.simulation.trajectories.errors.DebugRecorder

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

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

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

getDeviation() - Method in class bio.singa.simulation.model.simulation.error.GlobalDisplacementDeviationManager

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

getDisplacementLowerThreshold() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getDisplacementReferenceFactor() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getDisplacementReferenceLength() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getDisplacementUpperThreshold() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

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

getElapsedTime() - Static method in class bio.singa.simulation.model.simulation.error.TimeStepManager

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

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

getEntity() - Method in class bio.singa.simulation.entities.GraphComplexNode

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

getEntity() - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

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

Returns the chemical entity the delta is assigned to.

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

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

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

getEquations() - Method in class bio.singa.simulation.export.modules.ReactionTableRow

getError() - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

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

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

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

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

getEvidence() - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

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

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

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

A static method that returns a tokenizer for mathematical expressions

getFeature(Class<FeatureType>) - Method in class bio.singa.simulation.entities.ComplexEntity

getFeature(Class<FeatureType>) - Method in class bio.singa.simulation.entities.SimpleEntity

getFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

getFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

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

getFeatureIdentifierMap() - Method in class bio.singa.simulation.export.features.FeatureTable

getFeatureManager() - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

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

getFeatures() - Method in class bio.singa.simulation.entities.ComplexEntity

getFeatures() - Method in class bio.singa.simulation.entities.SimpleEntity

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

getFeatures() - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

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

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

getFeatureTable() - Method in class bio.singa.simulation.export.features.ModuleSummaryTable

getFeatureTable() - Method in class bio.singa.simulation.export.features.VariationTable

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

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

getFilaments(Path, String, NeumannRectangularDirection) - Static method in class bio.singa.simulation.model.agents.organelles.OrganelleImageParser

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

Returns all deltas that are going to be applied to this node.

getFirst() - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

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

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.

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

getGlobalDisplacementDeviation() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getGlobalNumericalError() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getGlobalNumericalTolerance() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

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

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

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

Returns the encapsulated graph.

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

getGraph() - Method in class bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder

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

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

getGrid() - Method in class bio.singa.simulation.model.agents.surfacelike.GridImageReader

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

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

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

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

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

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

Return the half step concentration of a node after the full update has been calculated for the full step and the resulting delta is known.

getIdentifier() - Method in interface bio.singa.simulation.entities.ChemicalEntity

getIdentifier() - Method in class bio.singa.simulation.entities.ComplexEntity

getIdentifier() - Method in class bio.singa.simulation.entities.SimpleEntity

getIdentifier() - Method in class bio.singa.simulation.export.modules.ReactionTableRow

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

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

Returns the identifier of this module.

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

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

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

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

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

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

Returns the identifier.

getIdentifier() - Method in class bio.singa.simulation.reactions.reactors.ReactionChain

getIdentifiers() - Method in class bio.singa.simulation.model.concentrations.NodeIdentifierCondition

getIndex() - Method in enum bio.singa.simulation.model.sections.CellTopology

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

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

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

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

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

Returns the inner subsection.

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

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

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

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

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

Returns the largest error as of yet.

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

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

getLast() - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

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

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

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

getListeners() - Method in class bio.singa.simulation.model.simulation.error.TimeStepManager

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

getLocalDisplacementDeviation() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getLocalDisplacementDeviationModule() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

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

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

getLocalNumericalError() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getLocalNumericalErrorModule() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getLocalNumericalErrorUpdate() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getLocalNumericalTolerance() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getLocation() - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

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

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

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

getMembraneMapping() - Method in class bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder

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

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

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

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

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

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

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

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

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

Returns the membrane subsection.

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

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

Overrides RuntimeException.getMessage to add the token information into the error message.

getMicrotubuleOrganizingCentre() - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneLayer

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

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

getModification() - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

getModification() - Method in interface bio.singa.simulation.reactions.reactors.ComplexReactor

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

Returns the module, that calculated this delta.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

getNegligibility() - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

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

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

Returns the next position.

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

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

Returns all currently registered node event listeners.

getNodesWithUnoccupiedBindingSite(BindingSite) - Method in class bio.singa.simulation.entities.ComplexEntity

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

getNodeWithUnoccupiedBindingSite(BindingSite) - Method in class bio.singa.simulation.entities.ComplexEntity

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

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

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

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

getNumericalInstabilityCutoff() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

getNumericalNegligenceCutoff() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

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

getOrganelleTemplate(String) - Static method in class bio.singa.simulation.model.agents.organelles.OrganelleImageParser

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

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

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

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

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

Returns the outer subsection.

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

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

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

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

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

getPolygon() - Method in class bio.singa.simulation.model.concentrations.AreaCondition

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

Returns the topology and concentration pool for the subsection.

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

Returns the subsection and concentration pool for the topology.

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

Returns all concentration pools in this container.

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

getPosition() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

getPositions() - Method in class bio.singa.simulation.trajectories.nested.TrajectoryDataPoint.SubsectionDataPoint

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

Returns all potential deltas that should be applied.

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

Returns a specific delta applied by the given module.

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

Returns the potential displacement deltas.

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

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

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

getPrimaryCandidateConditions() - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

getPrimaryEntity() - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

getPrimaryEntity() - Method in interface bio.singa.simulation.reactions.modifications.ComplexEntityModification

getPrimaryProducts() - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

getPrimarySubstrates() - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

getPriority() - Method in class bio.singa.simulation.model.concentrations.AbstractConcentrationCondition

getPriority() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationCondition

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

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

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

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

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

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

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

getProducts() - Method in interface bio.singa.simulation.reactions.reactors.ComplexReactor

getProducts() - Method in class bio.singa.simulation.reactions.reactors.OneToOneReactor

getProducts() - Method in class bio.singa.simulation.reactions.reactors.OneToTwoReactor

getProducts() - Method in class bio.singa.simulation.reactions.reactors.ReactionElement

getProducts() - Method in class bio.singa.simulation.reactions.reactors.TwoToOneReactor

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

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

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

getRadius() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

getRates() - Method in class bio.singa.simulation.export.modules.ReactionTableRow

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

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

getReactantElements() - Method in class bio.singa.simulation.reactions.reactors.ReactionChain

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

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

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

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

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

Returns the reaction order.

getReactors() - Method in class bio.singa.simulation.reactions.reactors.ReactionChain

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

getReferencedChemicalEntities() - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

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

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

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

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

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

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

Returns all entities referenced in any concentration pool.

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

Returns all entities referenced in this map.

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

Returns all subsections, referenced in this container.

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

getRegion(Vector2D) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

getRegion(Map<CellRegion, Set<Vector2D>>, Vector2D) - Static method in class bio.singa.simulation.model.agents.surfacelike.MembraneTracer

Deprecated.

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

getRegionMapping() - Method in class bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder

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

getRegions() - Method in class bio.singa.simulation.model.concentrations.RegionCondition

getRelation() - Method in class bio.singa.simulation.model.concentrations.TimedCondition

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

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

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

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

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

getResults() - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

getResults() - Method in interface bio.singa.simulation.reactions.modifications.ComplexEntityModification

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

Gets the role of this reactant.

getRows() - Method in class bio.singa.simulation.export.modules.ModuleTable

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

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

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

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

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

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

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

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

Returns the scope of this module.

getSecondaryEntity() - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

getSecondaryEntity() - Method in interface bio.singa.simulation.reactions.modifications.ComplexEntityModification

getSecondaryProducts() - Method in class bio.singa.simulation.reactions.reactors.OneToTwoReactor

getSecondarySubstrates() - Method in class bio.singa.simulation.reactions.reactors.TwoToOneReactor

getSecondCandidateConditions() - Method in class bio.singa.simulation.reactions.reactors.TwoToOneReactor

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

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

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

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

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

Returns the referenced simulation.

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

Returns the simulation.

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

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

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

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

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

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

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

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

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

getSpawnSite() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

Returns the specificity of this module.

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

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

getState() - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

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

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

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

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

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

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

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

getStringIdentifier() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

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

getSubsection() - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

getSubsection() - Method in class bio.singa.simulation.model.concentrations.SectionCondition

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

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.

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

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

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

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

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

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

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

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

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

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

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

getSubstrates() - Method in class bio.singa.simulation.reactions.reactors.ReactionElement

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

Returns the field supplier.

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

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

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

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

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

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

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

getTexString() - Method in class bio.singa.simulation.export.features.VariationTable

getTeXString() - Method in class bio.singa.simulation.export.features.FeatureTable

getTeXString() - Method in class bio.singa.simulation.export.features.ModuleSummaryTable

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

Returns the time the event was emitted.

getTime() - Method in class bio.singa.simulation.model.concentrations.TimedCondition

getTimeStepsDecreased() - Static method in class bio.singa.simulation.model.simulation.error.TimeStepManager

getTimeStepsIncreased() - Static method in class bio.singa.simulation.model.simulation.error.TimeStepManager

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

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

Get the token.

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

Get the tokens generated in the last call to tokenize.

getTolerance() - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

getTopology() - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

getTopology() - Method in class bio.singa.simulation.model.concentrations.TopologyCondition

getTopology(int) - Static method in enum bio.singa.simulation.model.sections.CellTopology

getTrack() - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

getTracks() - Method in class bio.singa.simulation.reactions.reactors.ReactionChain

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

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

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

getType() - Method in class bio.singa.simulation.model.concentrations.NodeTypeCondition

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

getUniqueColors() - Method in class bio.singa.simulation.model.agents.surfacelike.GridImageReader

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.simulation.error.NumericalError

Returns the node where the error occurred.

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

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

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

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

Returns the value of the change.

getValue() - Method in class bio.singa.simulation.model.simulation.error.DisplacementDeviation

getValue() - Method in class bio.singa.simulation.model.simulation.error.NumericalError

Returns the actual value of the error.

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

Returns the value of the sub-expression that is rooted at this node.

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

Returns the value of the constant

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

Returns the value of the sub-expression that is rooted at this node.

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

Calculates and returns the value of the sub-expression represented by the node.

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

Returns the value of the sub-expression that is rooted at this node.

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

Returns the value of the sub-expression that is rooted at this node.

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

Returns the value of the variable but throws an exception if the value has not been set

getVesicle() - Method in class bio.singa.simulation.model.simulation.error.DisplacementDeviation

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

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

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

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

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

GLOBAL_DEVIATION - bio.singa.simulation.model.simulation.error.ErrorManager.Reason

GLOBAL_ERROR - bio.singa.simulation.model.simulation.error.ErrorManager.Reason

globalDeviationIsAcceptable() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

globalDeviationIsCritical() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

GlobalDisplacementDeviationManager - Class in bio.singa.simulation.model.simulation.error

GlobalDisplacementDeviationManager(UpdateScheduler) - Constructor for class bio.singa.simulation.model.simulation.error.GlobalDisplacementDeviationManager

globalErrorIsAcceptable() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

globalNumericalErrorIsCritical() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

GlobalNumericalErrorManager - Class in bio.singa.simulation.model.simulation.error

GlobalNumericalErrorManager(UpdateScheduler) - Constructor for class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

GraphComplexEdge - Class in bio.singa.simulation.entities

GraphComplexEdge(int) - Constructor for class bio.singa.simulation.entities.GraphComplexEdge

GraphComplexEdge(GraphComplexEdge, int) - Constructor for class bio.singa.simulation.entities.GraphComplexEdge

GraphComplexNode - Class in bio.singa.simulation.entities

GraphComplexNode(Integer) - Constructor for class bio.singa.simulation.entities.GraphComplexNode

GraphComplexNode(Integer, Vector2D) - Constructor for class bio.singa.simulation.entities.GraphComplexNode

GraphEventEmitter - Class in bio.singa.simulation.events

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

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

Creates a new GraphEventEmitter.

GraphUpdatedEvent - Class in bio.singa.simulation.events

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

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

Creates a new GraphUpdatedEvent.

GREATER - bio.singa.simulation.model.concentrations.TimedCondition.Relation

GREATER_EQUALS - bio.singa.simulation.model.concentrations.TimedCondition.Relation

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

GridImageReader(BufferedImage) - Constructor for class bio.singa.simulation.model.agents.surfacelike.GridImageReader

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

GridMembraneBuilder(int[][]) - Constructor for class bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder

GROW - bio.singa.simulation.model.agents.linelike.LineLikeAgent.GrowthBehaviour

H

halfScaledQuantity - Variable in class bio.singa.simulation.model.parameters.Parameter

handleDelta(ConcentrationDeltaIdentifier, ConcentrationDelta) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Handles a delta based on the current state of the calculation.

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

HasAnyNumberOfEntities - Class in bio.singa.simulation.reactions.conditions

HasAnyNumberOfEntities(ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.conditions.HasAnyNumberOfEntities

hasAnyOfEntity(ChemicalEntity) - Static method in class bio.singa.simulation.reactions.conditions.CandidateConditionBuilder

hasBindingSite(BindingSite) - Method in class bio.singa.simulation.entities.GraphComplexNode

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

hasFeature(Class<FeatureType>) - Method in class bio.singa.simulation.entities.ComplexEntity

hasFeature(Class<FeatureType>) - Method in class bio.singa.simulation.entities.SimpleEntity

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

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

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

hashCode() - Method in class bio.singa.simulation.entities.BindingSite

hashCode() - Method in class bio.singa.simulation.entities.ComplexEntity

hashCode() - Method in class bio.singa.simulation.entities.SimpleEntity

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

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

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

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

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

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

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

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

hashCode() - Method in class bio.singa.simulation.reactions.reactors.ReactionElement

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

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

hasNoMoreThanNumberOfPartners(ChemicalEntity, int) - Static method in class bio.singa.simulation.reactions.conditions.CandidateConditionBuilder

HasNoMoreThanNumberOfPartners - Class in bio.singa.simulation.reactions.conditions

HasNoMoreThanNumberOfPartners(ChemicalEntity, int) - Constructor for class bio.singa.simulation.reactions.conditions.HasNoMoreThanNumberOfPartners

hasNoneOfEntity(ChemicalEntity) - Static method in class bio.singa.simulation.reactions.conditions.CandidateConditionBuilder

hasNotNumberOfEntity(ChemicalEntity, int) - Static method in class bio.singa.simulation.reactions.conditions.CandidateConditionBuilder

HasNumberOfEntities - Class in bio.singa.simulation.reactions.conditions

HasNumberOfEntities(ChemicalEntity, int) - Constructor for class bio.singa.simulation.reactions.conditions.HasNumberOfEntities

hasNumberOfEntity(ChemicalEntity, int) - Static method in class bio.singa.simulation.reactions.conditions.CandidateConditionBuilder

hasOccupiedBindingSite(BindingSite) - Static method in class bio.singa.simulation.reactions.conditions.CandidateConditionBuilder

HasOccupiedBindingSite - Class in bio.singa.simulation.reactions.conditions

HasOccupiedBindingSite(BindingSite) - Constructor for class bio.singa.simulation.reactions.conditions.HasOccupiedBindingSite

hasOneOfEntity(ChemicalEntity) - Static method in class bio.singa.simulation.reactions.conditions.CandidateConditionBuilder

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

hasUnoccupiedBindingSite(BindingSite) - Static method in class bio.singa.simulation.reactions.conditions.CandidateConditionBuilder

HasUnoccupiedBindingSite - Class in bio.singa.simulation.reactions.conditions

HasUnoccupiedBindingSite(BindingSite) - Constructor for class bio.singa.simulation.reactions.conditions.HasUnoccupiedBindingSite

HOLT2004 - Static variable in class bio.singa.simulation.model.agents.pointlike.Vesicle

I

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

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

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

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

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

identifier(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EntityStep

identifier(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.EntityLimitationStep

identifier(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.LateralMembraneDiffusionBuilder

identifier(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.FeatureStep

identifier(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.PorousDiffusionBuilder

identifier(String) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

identifier(String) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ConnectorStep

IN_PERINUCLEAR_STORAGE - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry

inArea(Polygon) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

inArea(Polygon) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

inBetweenHalfSteps() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

inBetweenHalfSteps() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion

INCREASE - bio.singa.simulation.model.simulation.error.ErrorManager.Reason

increaseTimeStep() - Static method in class bio.singa.simulation.model.simulation.error.TimeStepManager

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.

inhibitingEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder

inhibitingEntity(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.InhibitionStep

InitialConcentration - Class in bio.singa.simulation.model.concentrations

InitialConcentration() - Constructor for class bio.singa.simulation.model.concentrations.InitialConcentration

InitialConcentration(Quantity<MolarConcentration>) - Constructor for class bio.singa.simulation.model.concentrations.InitialConcentration

InitialConcentration(Quantity<MolarConcentration>, Evidence) - Constructor for class bio.singa.simulation.model.concentrations.InitialConcentration

InitialConcentration(Quantity<MolarConcentration>, List<Evidence>) - Constructor for class bio.singa.simulation.model.concentrations.InitialConcentration

InitialConcentrations - Class in bio.singa.simulation.features

InitialConcentrations(List<InitialConcentration>) - Constructor for class bio.singa.simulation.features.InitialConcentrations

InitialConcentrations.Builder - Class in bio.singa.simulation.features

initialize() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

initialize() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport

initialize() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

initialize() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis

initialize() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion

initialize() - Method in class bio.singa.simulation.model.modules.qualitative.QualitativeModule

initialize() - Method in interface bio.singa.simulation.model.modules.UpdateModule

initialize() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

initialize() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

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

initialize(UpdateScheduler) - Static method in class bio.singa.simulation.model.simulation.error.TimeStepManager

initializeActin(LineLikeAgentLayer, CellRegion, int) - Method in class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre

initializeDiffusiveReduction(AutomatonNode, Polygon, Ratio) - Static method in class bio.singa.simulation.model.graphs.NeighborhoodMappingManager

initializeGroup(int, CellRegion) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

initializeGroup(int, String, String) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

initializeGroup(CellRegion) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

initializeMembraneToMembraneMicrotubules(Membrane, Membrane, int) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

initializeMicrotubules(LineLikeAgentLayer, CellRegion, int) - Method in class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre

initializeNeighborhoodForGraph(AutomatonGraph) - Static method in class bio.singa.simulation.model.graphs.NeighborhoodMappingManager

initializeSpatialRepresentations() - Method in class bio.singa.simulation.model.simulation.Simulation

initializeSubsection(CellSubsection, CellTopology) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

Initializes a new concentration pool for the corresponding subsection and topology.

INNER - bio.singa.simulation.model.sections.CellTopology

A membrane is enclosing this subsection.

inPolygon(Polygon) - Static method in class bio.singa.simulation.model.concentrations.AreaCondition

inRegionArea(CellRegion) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

inRegionArea(CellRegion) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion

inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption

inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion

inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion

inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion

inSimulation(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport

interrupt() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

Returns true if the calling module was the first to call the method, therefore being allowed to optimize the time step.

INTERRUPTED - bio.singa.simulation.model.modules.concentration.ModuleState

Interrupted by another calculation

invert() - Method in class bio.singa.simulation.reactions.modifications.AddModification

invert() - Method in class bio.singa.simulation.reactions.modifications.BindModification

invert() - Method in interface bio.singa.simulation.reactions.modifications.ComplexEntityModification

invert() - Method in class bio.singa.simulation.reactions.modifications.ReleaseModification

invert() - Method in class bio.singa.simulation.reactions.modifications.RemoveModification

invert() - Method in interface bio.singa.simulation.reactions.reactors.ComplexReactor

invert() - Method in class bio.singa.simulation.reactions.reactors.OneToOneReactor

invert() - Method in class bio.singa.simulation.reactions.reactors.OneToTwoReactor

invert() - Method in class bio.singa.simulation.reactions.reactors.TwoToOneReactor

irreversible() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

irreversible() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.KineticStep

IrreversibleKineticLaw - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

IrreversibleKineticLaw(Reaction) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.IrreversibleKineticLaw

isCached() - Method in class bio.singa.simulation.model.graphs.AutomatonNode.AreaMapping

isCatalyst() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

isCollecting() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

isConsiderInversion() - Method in class bio.singa.simulation.reactions.reactors.ReactionChain

isDebug() - Method in class bio.singa.simulation.model.simulation.Simulation

isEntity(ChemicalEntity) - Method in class bio.singa.simulation.entities.GraphComplexNode

isFix() - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

isGrouped() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

isInner() - Static method in class bio.singa.simulation.model.concentrations.TopologyCondition

isInverse() - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

isLargerThan(NumericalError) - Method in class bio.singa.simulation.model.simulation.error.NumericalError

isMembrane() - Static method in class bio.singa.simulation.model.concentrations.TopologyCondition

isMembrane() - Method in class bio.singa.simulation.model.sections.CellSubsection

isMembraneBound() - Method in interface bio.singa.simulation.entities.ChemicalEntity

isMembraneBound() - Method in class bio.singa.simulation.entities.ComplexEntity

isMembraneBound() - Method in class bio.singa.simulation.entities.SimpleEntity

isNode() - Static method in class bio.singa.simulation.model.concentrations.NodeTypeCondition

isObserved() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

Returns true if this node is observed.

isObserved() - Method in class bio.singa.simulation.model.graphs.AutomatonNode

Returns true if this node is observed.

isObserved() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

Returns true if the concentrations are observed.

isOnlyBoundAt(BindingSite) - Static method in class bio.singa.simulation.reactions.conditions.CandidateConditionBuilder

IsOnlyBoundAt - Class in bio.singa.simulation.reactions.conditions

IsOnlyBoundAt(BindingSite) - Constructor for class bio.singa.simulation.reactions.conditions.IsOnlyBoundAt

isOuter() - Static method in class bio.singa.simulation.model.concentrations.TopologyCondition

isProduct() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Returns true if this reactant is a product.

isSealed() - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

isSkipDisplacementChecks() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

isSmall() - Method in interface bio.singa.simulation.entities.ChemicalEntity

isSmall() - Method in class bio.singa.simulation.entities.ComplexEntity

isSmall() - Method in class bio.singa.simulation.entities.SimpleEntity

isSmallerThan(NumericalError) - Method in class bio.singa.simulation.model.simulation.error.NumericalError

isStrutCalculation() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Returns the current state of calculations.

isSubstrate() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Returns true if this reactant is a substrate.

isTargetedGrowth() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

isTimeStepRescaled() - Static method in class bio.singa.simulation.model.simulation.error.TimeStepManager

isTopology(CellTopology) - Static method in class bio.singa.simulation.model.concentrations.TopologyCondition

isUseContinuousIndex() - Method in class bio.singa.simulation.export.features.FeatureTable

isVesicle() - Static method in class bio.singa.simulation.model.concentrations.NodeTypeCondition

isWritingAliveFile() - Method in class bio.singa.simulation.model.simulation.SimulationManager

K

keepPlatformOpen() - Method in class bio.singa.simulation.model.simulation.SimulationManager

kineticLaw(String) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

kineticLaw(String) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.KineticStep

KineticLaw - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

L

LateralMembraneDiffusion - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

LateralMembraneDiffusion() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion

LateralMembraneDiffusion.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

LateralMembraneDiffusion.EntityLimitationStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

LateralMembraneDiffusion.LateralMembraneDiffusionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

LateralMembraneDiffusion.SectionLimitationStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

LateralMembraneDiffusionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.LateralMembraneDiffusion.LateralMembraneDiffusionBuilder

LESS - bio.singa.simulation.model.concentrations.TimedCondition.Relation

LESS_EQUALS - bio.singa.simulation.model.concentrations.TimedCondition.Relation

LineLikeAgent - Class in bio.singa.simulation.model.agents.linelike

LineLikeAgent(String) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgent

LineLikeAgent(String, Vector2D, Vector2D, AutomatonGraph) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgent

LineLikeAgent(String, List<Vector2D>, NeumannRectangularDirection) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgent

LineLikeAgent.GrowthBehaviour - Enum in bio.singa.simulation.model.agents.linelike

LineLikeAgentAttachment - Class in bio.singa.simulation.model.modules.qualitative.implementations

LineLikeAgentAttachment() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment

LineLikeAgentLayer - Class in bio.singa.simulation.model.agents.linelike

LineLikeAgentLayer(Simulation, MembraneLayer) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

LineLikeAgentTemplate - Class in bio.singa.simulation.model.agents.linelike

LineLikeAgentTemplate(List<LineLikeAgent>, Quantity<Length>) - Constructor for class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate

listEntities() - Static method in class bio.singa.simulation.entities.EntityRegistry

LOCAL_DEVIATION - bio.singa.simulation.model.simulation.error.ErrorManager.Reason

LOCAL_ERROR - bio.singa.simulation.model.simulation.error.ErrorManager.Reason

localDisplacementDeviationIsCritical() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

localErrorIsAcceptable(NumericalError) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

localNumericalErrorIsCritical() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

logger - Static variable in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

logger - Static variable in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

M

mapRegionGrid(RectangularGrid<Integer>) - Method in class bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder

mapToSystemExtend() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate

mapToSystemExtend() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

matchExactly(String...) - Static method in class bio.singa.simulation.entities.EntityRegistry

MatchingQSnares - Class in bio.singa.simulation.features

MatchingQSnares(List<ChemicalEntity>) - Constructor for class bio.singa.simulation.features.MatchingQSnares

MatchingQSnares.Builder - Class in bio.singa.simulation.features

MatchingRSnares - Class in bio.singa.simulation.features

MatchingRSnares(List<ChemicalEntity>) - Constructor for class bio.singa.simulation.features.MatchingRSnares

MatchingRSnares.Builder - Class in bio.singa.simulation.features

MaturationTime - Class in bio.singa.simulation.features

MaturationTime(Quantity<Time>) - Constructor for class bio.singa.simulation.features.MaturationTime

MaturationTime.Builder - Class in bio.singa.simulation.features

MAXIMAL_NEGATIVE_DEVIATION - Static variable in class bio.singa.simulation.model.simulation.error.DisplacementDeviation

If reference value is larger then current displacement, the deviation is small (below zero).

MAXIMAL_POSITIVE_DEVIATION - Static variable in class bio.singa.simulation.model.simulation.error.DisplacementDeviation

If reference value is smaller then current displacement, the deviation is large (above zero).

Membrane - Class in bio.singa.simulation.model.agents.surfacelike

Membrane(String) - Constructor for class bio.singa.simulation.model.agents.surfacelike.Membrane

MEMBRANE - bio.singa.simulation.model.sections.CellTopology

The membrane separating inner and outer subsections.

MEMBRANE_TETHERED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry

membraneBound() - Method in class bio.singa.simulation.entities.SimpleEntity.SimpleEntityBuilder

MembraneDiffusion - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

The membrane diffusion module describes the movement of chemical entities across Membranes driven by the MembranePermeability of the cargo.

MembraneDiffusion() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion

MembraneDiffusion.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

MembraneDiffusion.CargoStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

MembraneDiffusion.MembraneDiffusionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

MembraneDiffusionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion.MembraneDiffusionBuilder

MembraneLayer - Class in bio.singa.simulation.model.agents.surfacelike

MembraneLayer() - Constructor for class bio.singa.simulation.model.agents.surfacelike.MembraneLayer

MembraneRestrictedBehavior - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas

MembraneRestrictedBehavior(ReactionEvent) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.MembraneRestrictedBehavior

MembraneSegment - Class in bio.singa.simulation.model.agents.surfacelike

MembraneSegment(AutomatonNode, LineSegment) - Constructor for class bio.singa.simulation.model.agents.surfacelike.MembraneSegment

membraneThickness(MembraneTickness) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.FeatureStep

membraneThickness(MembraneTickness) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.PorousDiffusionBuilder

MembraneTickness - Class in bio.singa.simulation.features

MembraneTickness(Quantity<Length>) - Constructor for class bio.singa.simulation.features.MembraneTickness

MembraneTickness.Builder - Class in bio.singa.simulation.features

MembraneTracer - Class in bio.singa.simulation.model.agents.surfacelike

Deprecated.

MembraneTracer(AutomatonGraph) - Constructor for class bio.singa.simulation.model.agents.surfacelike.MembraneTracer

Deprecated.

michaelisConstant(MichaelisConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

michaelisConstant(MichaelisConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.MichaelisMentenReactionStep

michaelisMenten() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

michaelisMenten() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.KineticStep

MichaelisMentenKineticLaw - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

MichaelisMentenKineticLaw(Reaction) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.MichaelisMentenKineticLaw

microMolar() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationUnitStep

MICROTUBULE - Static variable in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

MICROTUBULE_ATTACHED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry

MicrotubuleOrganizingCentre - Class in bio.singa.simulation.model.agents.linelike

MicrotubuleOrganizingCentre(MembraneLayer, Circle) - Constructor for class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre

milliMolar() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationUnitStep

milliSeconds() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.TimedUnitStep

MINIMAL_DEVIATION - Static variable in class bio.singa.simulation.model.simulation.error.DisplacementDeviation

If reference value is equal to the current displacement, the deviation is zero.

MINIMAL_EMPTY_ERROR - Static variable in class bio.singa.simulation.model.simulation.error.NumericalError

The minimal possible error not assigned to any node or chemical entity.

MINUS - Static variable in class bio.singa.simulation.features.MotorPullDirection

minutes() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.TimedUnitStep

modification - Variable in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

ModuleBuilder<ModuleType extends ConcentrationBasedModule> - Interface in bio.singa.simulation.model.modules.concentration

ModuleCalculationException - Exception in bio.singa.simulation.exceptions

ModuleCalculationException(String) - Constructor for exception bio.singa.simulation.exceptions.ModuleCalculationException

ModuleFactory - Class in bio.singa.simulation.model.modules.concentration

Handles module creation with certain UpdateScope and UpdateSpecificity.

ModuleFactory() - Constructor for class bio.singa.simulation.model.modules.concentration.ModuleFactory

ModuleFactory.Scope - Enum in bio.singa.simulation.model.modules.concentration

The type of UpdateScope.

ModuleFactory.Specificity - Enum in bio.singa.simulation.model.modules.concentration

The type of UpdateSpecificity.

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.

ModuleSummaryTable - Class in bio.singa.simulation.export.features

ModuleSummaryTable(FeatureTable) - Constructor for class bio.singa.simulation.export.features.ModuleSummaryTable

ModuleTable - Class in bio.singa.simulation.export.modules

ModuleTable() - Constructor for class bio.singa.simulation.export.modules.ModuleTable

ModuleTableConverter - Class in bio.singa.simulation.export.modules

ModuleTableRow - Interface in bio.singa.simulation.export.modules

molecules(double) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

molecules(double) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationStep

MotorMovementVelocity - Class in bio.singa.simulation.features

MotorMovementVelocity(Quantity<Speed>) - Constructor for class bio.singa.simulation.features.MotorMovementVelocity

MotorMovementVelocity.Builder - Class in bio.singa.simulation.features

MotorPullDirection - Class in bio.singa.simulation.features

MotorPullDirection(String) - Constructor for class bio.singa.simulation.features.MotorPullDirection

MotorPullDirection.Builder - Class in bio.singa.simulation.features

move(Vector2D) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

MULTDIV - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for multiplication or division

MultiEntityFeature - Class in bio.singa.simulation.features.model

MultiEntityFeature(List<ChemicalEntity>) - Constructor for class bio.singa.simulation.features.model.MultiEntityFeature

MultiEntityFeature(List<ChemicalEntity>, Evidence) - Constructor for class bio.singa.simulation.features.model.MultiEntityFeature

MultiEntityFeature(List<ChemicalEntity>, List<Evidence>) - Constructor for class bio.singa.simulation.features.model.MultiEntityFeature

MULTIPLICATION_NODE - Static variable in interface uk.co.cogitolearning.cogpar.ExpressionNode

Node id for multiplication nodes

MultiplicationExpressionNode - Class in uk.co.cogitolearning.cogpar

An ExpressionNode that handles multiplications and divisions.

MultiplicationExpressionNode() - Constructor for class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode

Default constructor.

MultiplicationExpressionNode(ExpressionNode, boolean) - Constructor for class uk.co.cogitolearning.cogpar.MultiplicationExpressionNode

Constructor to create a multiplication with the first term already added.

multiply(double) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDelta

Multiplies (modifies) this delta with the given multiplicand.

multiply(List<ReactantConcentration>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.AbstractKineticLaw

MultiStringFeature - Class in bio.singa.simulation.features.model

MultiStringFeature(List<String>) - Constructor for class bio.singa.simulation.features.model.MultiStringFeature

MultiStringFeature(List<String>, Evidence) - Constructor for class bio.singa.simulation.features.model.MultiStringFeature

MultiStringFeature(List<String>, List<Evidence>) - Constructor for class bio.singa.simulation.features.model.MultiStringFeature

N

NANOMETRE_PER_SECOND - Static variable in class bio.singa.simulation.features.ActinBoostVelocity

nanoMolar() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationUnitStep

NEGATIVE_CONCENTRATIONS - bio.singa.simulation.model.simulation.error.ErrorManager.Reason

NeighborhoodMappingManager - Class in bio.singa.simulation.model.graphs

NeighborhoodMappingManager() - Constructor for class bio.singa.simulation.model.graphs.NeighborhoodMappingManager

NEIGHBOURHOOD_DEPENDENT - bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope

References DependentUpdate.

NEIGHBOURHOOD_INDEPENDENT - bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope

References IndependentUpdate.

NestedUpdateRecorder - Class in bio.singa.simulation.trajectories.nested

NestedUpdateRecorder(Simulation) - Constructor for class bio.singa.simulation.trajectories.nested.NestedUpdateRecorder

NestedUpdateRecorder(Simulation, Unit<Time>, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.trajectories.nested.NestedUpdateRecorder

nextEdgeIdentifier() - Method in class bio.singa.simulation.entities.ComplexEntity

nextEpoch() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

nextEpoch() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

nextEpoch() - Method in class bio.singa.simulation.model.simulation.Simulation

Calculates the next epoch.

nextEpoch() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

nextNodeIdentifier() - Method in class bio.singa.simulation.entities.ComplexEntity

NodeBehavior - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas

NodeBehavior(ReactionEvent) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.NodeBehavior

NodeEventEmitter - Class in bio.singa.simulation.events

The implementation of an UpdateEventEmitter emitting updates of specific nodes to all listeners.

NodeEventEmitter() - Constructor for class bio.singa.simulation.events.NodeEventEmitter

Creates a new NodeEventEmitter.

NodeIdentifierCondition - Class in bio.singa.simulation.model.concentrations

NodeTypeCondition - Class in bio.singa.simulation.model.concentrations

NUCLEAR_MEMBRANE - Static variable in class bio.singa.simulation.model.sections.CellSubsections

NUCLEOPLASM - Static variable in class bio.singa.simulation.model.sections.CellSubsections

NUCLEUS - bio.singa.simulation.model.agents.organelles.OrganelleTypes

NUMBER - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for numbers

NumericalError - Class in bio.singa.simulation.model.simulation.error

The LocalError object stores the error as an result of the currently applied time step.

NumericalError(Updatable, ChemicalEntity, double) - Constructor for class bio.singa.simulation.model.simulation.error.NumericalError

Creates a new LocalError.

NumericalInstabilityException - Exception in bio.singa.simulation.exceptions

NumericalInstabilityException(String) - Constructor for exception bio.singa.simulation.exceptions.NumericalInstabilityException

O

of(double) - Static method in class bio.singa.simulation.features.Ratio

of(double) - Static method in class bio.singa.simulation.features.SNAREFusionPairs

of(double, Unit<FirstOrderRate>) - Static method in class bio.singa.simulation.features.CargoAdditionRate

of(double, Unit<MolarConcentration>) - Static method in class bio.singa.simulation.features.EndocytosisCheckpointConcentration

of(double, Unit<SpawnRate>) - Static method in class bio.singa.simulation.features.PitFormationRate

of(double, Unit<Length>) - Static method in class bio.singa.simulation.features.AttachmentDistance

of(double, Unit<Length>) - Static method in class bio.singa.simulation.features.MembraneTickness

of(double, Unit<Length>) - Static method in class bio.singa.simulation.features.VesicleRadius

of(double, Unit<Speed>) - Static method in class bio.singa.simulation.features.ActinBoostVelocity

of(double, Unit<Speed>) - Static method in class bio.singa.simulation.features.MotorMovementVelocity

of(double, Unit<Time>) - Static method in class bio.singa.simulation.features.EndocytosisCheckpointTime

of(double, Unit<Time>) - Static method in class bio.singa.simulation.features.FusionTime

of(double, Unit<Time>) - Static method in class bio.singa.simulation.features.MaturationTime

of(ChemicalEntity) - Static method in class bio.singa.simulation.features.AttachedMotor

of(ChemicalEntity) - Static method in class bio.singa.simulation.features.BoostMediatingEntity

of(ChemicalEntity) - Static method in class bio.singa.simulation.features.Cargo

of(ChemicalEntity) - Static method in class bio.singa.simulation.features.Transporter

of(ChemicalEntity...) - Static method in class bio.singa.simulation.features.Cargoes

of(ChemicalEntity...) - Static method in class bio.singa.simulation.features.MatchingQSnares

of(ChemicalEntity...) - Static method in class bio.singa.simulation.features.MatchingRSnares

of(ChemicalEntity...) - Static method in class bio.singa.simulation.features.PrimaryCargoes

of(ChemicalEntity...) - Static method in class bio.singa.simulation.features.ScalingEntities

of(ChemicalEntity...) - Static method in class bio.singa.simulation.features.Solutes

of(InitialConcentration...) - Static method in class bio.singa.simulation.features.InitialConcentrations

of(TimedCondition.Relation, ComparableQuantity<Time>) - Static method in class bio.singa.simulation.model.concentrations.TimedCondition

of(CellRegion) - Static method in class bio.singa.simulation.features.AffectedRegion

of(CellRegion) - Static method in class bio.singa.simulation.features.ContainmentRegion

of(CellSubsection) - Static method in class bio.singa.simulation.features.AffectedSection

of(Updatable, Unit<MolarConcentration>) - Static method in class bio.singa.simulation.trajectories.nested.TrajectoryDataPoint

of(String) - Static method in class bio.singa.simulation.features.AppliedVesicleState

of(String) - Static method in class bio.singa.simulation.features.AttachedFilament

of(String) - Static method in class bio.singa.simulation.features.MotorPullDirection

of(String) - Static method in class bio.singa.simulation.features.RequiredVesicleState

of(String...) - Static method in class bio.singa.simulation.features.BlackListVesicleStates

of(String...) - Static method in class bio.singa.simulation.features.WhiteListVesicleStates

of(Collection<ChemicalEntity>) - Static method in class bio.singa.simulation.features.Cargoes

of(Collection<Updatable>, Unit<MolarConcentration>) - Static method in class bio.singa.simulation.trajectories.nested.TrajectoryData

of(List<ChemicalEntity>) - Static method in class bio.singa.simulation.features.Cargoes

of(List<ChemicalEntity>) - Static method in class bio.singa.simulation.features.MatchingQSnares

of(List<ChemicalEntity>) - Static method in class bio.singa.simulation.features.MatchingRSnares

of(List<ChemicalEntity>) - Static method in class bio.singa.simulation.features.PrimaryCargoes

of(List<ChemicalEntity>) - Static method in class bio.singa.simulation.features.ScalingEntities

of(List<ChemicalEntity>) - Static method in class bio.singa.simulation.features.Solutes

of(List<InitialConcentration>) - Static method in class bio.singa.simulation.features.InitialConcentrations

of(List<String>) - Static method in class bio.singa.simulation.features.BlackListVesicleStates

of(List<String>) - Static method in class bio.singa.simulation.features.WhiteListVesicleStates

of(Quantity<FirstOrderRate>) - Static method in class bio.singa.simulation.features.CargoAdditionRate

of(Quantity<MolarConcentration>) - Static method in class bio.singa.simulation.features.EndocytosisCheckpointConcentration

of(Quantity<SpawnRate>) - Static method in class bio.singa.simulation.features.PitFormationRate

of(Quantity<Dimensionless>) - Static method in class bio.singa.simulation.features.Ratio

of(Quantity<Dimensionless>) - Static method in class bio.singa.simulation.features.SNAREFusionPairs

of(Quantity<Length>) - Static method in class bio.singa.simulation.features.AttachmentDistance

of(Quantity<Length>) - Static method in class bio.singa.simulation.features.MembraneTickness

of(Quantity<Length>) - Static method in class bio.singa.simulation.features.VesicleRadius

of(Quantity<Speed>) - Static method in class bio.singa.simulation.features.ActinBoostVelocity

of(Quantity<Speed>) - Static method in class bio.singa.simulation.features.MotorMovementVelocity

of(Quantity<Time>) - Static method in class bio.singa.simulation.features.EndocytosisCheckpointTime

of(Quantity<Time>) - Static method in class bio.singa.simulation.features.FusionTime

of(Quantity<Time>) - Static method in class bio.singa.simulation.features.MaturationTime

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.ConcentrationApplier

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationStateChange

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.DiffusivityScaling

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion

onCompletion() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VolumeLikeAgentContainment

onCompletion() - Method in interface bio.singa.simulation.model.modules.UpdateModule

oneToOneAssignment(ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

OneToOneReactor - Class in bio.singa.simulation.reactions.reactors

This is for add and remove modifications.

OneToOneReactor() - Constructor for class bio.singa.simulation.reactions.reactors.OneToOneReactor

OneToTwoReactor - Class in bio.singa.simulation.reactions.reactors

This is for release modifications.

OneToTwoReactor() - Constructor for class bio.singa.simulation.reactions.reactors.OneToTwoReactor

onEventReceived(GraphUpdatedEvent) - Method in class bio.singa.simulation.model.simulation.SimulationStatus

onEventReceived(GraphUpdatedEvent) - Method in class bio.singa.simulation.trajectories.errors.DebugRecorder

onEventReceived(GraphUpdatedEvent) - Method in class bio.singa.simulation.trajectories.nested.NestedUpdateRecorder

onEventReceived(UpdatableUpdatedEvent) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder

onEventReceived(ErrorManager.Reason) - Method in class bio.singa.simulation.model.simulation.error.GlobalDisplacementDeviationManager

onEventReceived(ErrorManager.Reason) - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

onlyNodes() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

onlyNodes() - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

onlyVesicles() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

onlyVesicles() - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

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.ConcentrationApplier

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationStateChange

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.DiffusivityScaling

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion

onReset() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VolumeLikeAgentContainment

onReset() - Method in interface bio.singa.simulation.model.modules.UpdateModule

OPEN_BRACKET - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for opening brackets

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ClathrinMediatedEndocytosis

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationApplier

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.ConcentrationStateChange

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.DiffusivityScaling

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.LineLikeAgentAttachment

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion

optimizeTimeStep() - Method in class bio.singa.simulation.model.modules.qualitative.implementations.VolumeLikeAgentContainment

OrganelleImageParser - Class in bio.singa.simulation.model.agents.organelles

OrganelleImageParser(BufferedImage) - Constructor for class bio.singa.simulation.model.agents.organelles.OrganelleImageParser

OrganelleTemplate - Class in bio.singa.simulation.model.agents.organelles

OrganelleTemplate(Quantity<Length>, Polygon, Map<Integer, Set<Vector2D>>) - Constructor for class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

OrganelleTypes - Enum in bio.singa.simulation.model.agents.organelles

OUTER - bio.singa.simulation.model.sections.CellTopology

A membrane is separating this subsection form the inner subsection.

P

Parameter<QuantityType extends javax.measure.Quantity<QuantityType>> - Class in bio.singa.simulation.model.parameters

Parameter(String) - Constructor for class bio.singa.simulation.model.parameters.Parameter

Parameter(String, Quantity<QuantityType>, Evidence) - Constructor for class bio.singa.simulation.model.parameters.Parameter

ParameterStorage - Class in bio.singa.simulation.model.parameters

parse(String) - Method in class uk.co.cogitolearning.cogpar.ExpressionParser

Parse a mathematical expression in a string and return an ExpressionNode.

parse(LinkedList<Token>) - Method in class uk.co.cogitolearning.cogpar.ExpressionParser

Parse a mathematical expression in contained in a list of tokens and return an ExpressionNode.

ParserException - Exception in uk.co.cogitolearning.cogpar

A simple subclass of RuntimeException that indicates errors when trying to parse the input to Parser.

ParserException(String) - Constructor for exception uk.co.cogitolearning.cogpar.ParserException

Construct the evaluation exception with a message.

ParserException(String, Token) - Constructor for exception uk.co.cogitolearning.cogpar.ParserException

Construct the evaluation exception with a message and a token.

PENDING - bio.singa.simulation.model.modules.concentration.ModuleState

Currently unprocessed module.

PER_SQUARE_MICRO_METRE_PER_SECOND - Static variable in interface bio.singa.simulation.features.SpawnRate

PER_SQUARE_NANOMETRE_PER_SECOND - Static variable in interface bio.singa.simulation.features.SpawnRate

PERINUCLEAR_REGION - Static variable in class bio.singa.simulation.model.sections.CellRegions

PIT_MEMBRANE - Static variable in class bio.singa.simulation.model.sections.CellSubsections

pitCounter - Static variable in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

PitFormationRate - Class in bio.singa.simulation.features

PitFormationRate(Quantity<SpawnRate>) - Constructor for class bio.singa.simulation.features.PitFormationRate

PitFormationRate.Builder - Class in bio.singa.simulation.features

PLUS - Static variable in class bio.singa.simulation.features.MotorPullDirection

PLUSMINUS - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for plus or minus

poreMembraneRatio(Ratio) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.FeatureStep

poreMembraneRatio(Ratio) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.PorousDiffusionBuilder

PorousDiffusion - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

Calculates diffusion through large pores (pore significantly larger than the cargo) in the membrane.

PorousDiffusion() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion

PorousDiffusion.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

PorousDiffusion.FeatureStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

PorousDiffusion.PorousDiffusionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

PorousDiffusionBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.PorousDiffusionBuilder

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

postConstruct() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption

prepare() - Method in class bio.singa.simulation.trajectories.errors.DebugRecorder

prepareReactionSets() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.RuleBasedReactantBehavior

preReaction(ReactionChain) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.RuleBasedBuilder

preReaction(ReactionChain) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.RuleBasedStep

primaryCandidateConditions - Variable in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

PrimaryCargoes - Class in bio.singa.simulation.features

PrimaryCargoes(List<ChemicalEntity>) - Constructor for class bio.singa.simulation.features.PrimaryCargoes

PrimaryCargoes.Builder - Class in bio.singa.simulation.features

primaryCondition(CandidateCondition) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactionChainBuilder

primaryCondition(CandidateCondition) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactorPrimaryConditionStep

primaryEntity - Variable in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

process(Collection<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.ReactionChain

processAllUpdatables(Collection<? extends Updatable>) - Method in class bio.singa.simulation.model.modules.concentration.scope.DependentUpdate

processAllUpdatables(Collection<? extends Updatable>) - Method in class bio.singa.simulation.model.modules.concentration.scope.IndependentUpdate

processAllUpdatables(Collection<? extends Updatable>) - Method in class bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate

processAllUpdatables(Collection<? extends Updatable>) - Method in interface bio.singa.simulation.model.modules.concentration.scope.UpdateScope

Processes all given updatables.

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.

processContainer(ConcentrationContainer, CellSubsection, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.specifity.EntitySpecific

processContainer(ConcentrationContainer, CellSubsection, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.specifity.SectionSpecific

processContainer(ConcentrationContainer, CellSubsection, ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.specifity.UpdatableSpecific

processContainer(ConcentrationContainer, CellSubsection, ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.specifity.UpdateSpecificity

processUpdatable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.DependentUpdate

processUpdatable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.IndependentUpdate

processUpdatable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate

processUpdatable(Updatable) - Method in interface bio.singa.simulation.model.modules.concentration.scope.UpdateScope

Calculates the given updatable.

PRODUCT - bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantRole

purgeMisguidedFilaments() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

put(ChemicalEntity) - Static method in class bio.singa.simulation.entities.EntityRegistry

put(CellSubsection, TrajectoryDataPoint.SubsectionDataPoint) - Method in class bio.singa.simulation.trajectories.nested.TrajectoryDataPoint

put(Updatable, TrajectoryDataPoint) - Method in class bio.singa.simulation.trajectories.nested.TrajectoryData

put(String, ChemicalEntity) - Static method in class bio.singa.simulation.entities.EntityRegistry

putSubsectionPool(CellSubsection, CellTopology, ConcentrationPool) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

Adds a concentration pool, referenced to the subsection and topology.

Q

QualitativeModule - Class in bio.singa.simulation.model.modules.qualitative

QualitativeModule() - Constructor for class bio.singa.simulation.model.modules.qualitative.QualitativeModule

R

RAISED - Static variable in class uk.co.cogitolearning.cogpar.Token

Token id for the exponentiation symbol

rate(RateConstant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

rate(RateConstant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.IrreversibleReactionStep

rate(Quantity<FirstOrderRate>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder

rate(Quantity<FirstOrderRate>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.RateStep

Ratio - Class in bio.singa.simulation.features

Ratio(double) - Constructor for class bio.singa.simulation.features.Ratio

Ratio(Quantity<Dimensionless>) - Constructor for class bio.singa.simulation.features.Ratio

Ratio.Builder - Class in bio.singa.simulation.features

Reactant - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

A Reactant encapsulates a ChemicalEntity for the use in Reactions.

Reactant(ChemicalEntity, ReactantRole) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Creates a new reactant.

Reactant(ChemicalEntity, ReactantRole, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, double, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, CellTopology) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, CellTopology, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, CellTopology, double, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, CellTopology, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Reactant(ChemicalEntity, ReactantRole, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

ReactantBehavior - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

ReactantConcentration - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas

ReactantConcentration(Reactant, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.ReactantConcentration

ReactantDelta - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas

ReactantDelta(ConcentrationDeltaIdentifier, double) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas.ReactantDelta

ReactantRole - Enum in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

The role of the reactant: Increasing, for products and accelerating reactants and decreasing for substrates and inhibiting reactants.

ReactantSet - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

ReactantSet(List<Reactant>, List<Reactant>) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantSet

ReactantSet(List<Reactant>, List<Reactant>, List<Reactant>) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantSet

reaction - Variable in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.AbstractKineticLaw

reaction - Variable in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

Reaction - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

Reaction() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.Reaction

ReactionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder

ReactionBuilder.ComplexBuildingReactionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.FinalStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.GeneralReactionBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.IrreversibleReactionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.KineticStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.MichaelisMentenReactionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.ParameterStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.ReversibleReactionStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.RuleBasedBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.RuleBasedStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.StaticBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionBuilder.StaticReactantStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionChain - Class in bio.singa.simulation.reactions.reactors

ReactionChain(List<ComplexReactor>) - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChain

ReactionChainBuilder - Class in bio.singa.simulation.reactions.reactors

ReactionChainBuilder() - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChainBuilder

ReactionChainBuilder.AbstractReactorBuilder - Class in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.AddReactionChainBuilder - Class in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.AddReactorPrimaryConditionStep - Interface in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.AddReactorSecondarySubstrateStep - Interface in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.BindReactionChainBuilder - Class in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.BindReactorPrimaryConditionStep - Interface in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.BindReactorSecondaryConditionStep - Interface in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.BindReactorSecondarySubstrateStep - Interface in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.ConnectorStep - Interface in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.ReactorChoiceStep - Interface in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.ReleaseReactionChainBuilder - Class in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.ReleaseReactorPrimaryConditionStep - Interface in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep - Interface in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.RemoveReactionChainBuilder - Class in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.RemoveReactorPrimaryConditionStep - Interface in bio.singa.simulation.reactions.reactors

ReactionChainBuilder.RemoveReactorSecondarySubstrateStep - Interface in bio.singa.simulation.reactions.reactors

ReactionElement - Class in bio.singa.simulation.reactions.reactors

ReactionElement() - Constructor for class bio.singa.simulation.reactions.reactors.ReactionElement

ReactionElement(List<ComplexEntity>, List<ComplexEntity>) - Constructor for class bio.singa.simulation.reactions.reactors.ReactionElement

ReactionEvent - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions

ReactionEvent(Reaction, ReactantSet) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

ReactionGraph - Class in bio.singa.simulation.export.reactiongraph

ReactionGraph() - Constructor for class bio.singa.simulation.export.reactiongraph.ReactionGraph

ReactionGraphConverter - Class in bio.singa.simulation.export.reactiongraph

ReactionGraphEdge - Class in bio.singa.simulation.export.reactiongraph

ReactionGraphEdge(int) - Constructor for class bio.singa.simulation.export.reactiongraph.ReactionGraphEdge

ReactionGraphEdge(int, double) - Constructor for class bio.singa.simulation.export.reactiongraph.ReactionGraphEdge

ReactionGraphNode - Class in bio.singa.simulation.export.reactiongraph

ReactionGraphNode(Integer) - Constructor for class bio.singa.simulation.export.reactiongraph.ReactionGraphNode

ReactionGraphNode(Integer, ChemicalEntity) - Constructor for class bio.singa.simulation.export.reactiongraph.ReactionGraphNode

ReactionNetworkGenerator - Class in bio.singa.simulation.reactions

ReactionNetworkGenerator() - Constructor for class bio.singa.simulation.reactions.ReactionNetworkGenerator

ReactionTableRow - Class in bio.singa.simulation.export.modules

ReactionTableRow(String, List<String>, List<String>, Map<String, List<String>>) - Constructor for class bio.singa.simulation.export.modules.ReactionTableRow

ReactionTrack - Class in bio.singa.simulation.reactions.reactors

ReactionTrack() - Constructor for class bio.singa.simulation.reactions.reactors.ReactionTrack

reactors - Variable in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

readTemplate(String) - Static method in class bio.singa.simulation.model.agents.surfacelike.GridImageReader

Recorders - Class in bio.singa.simulation.trajectories

reduce() - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate

reduce() - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

referenceChemicalEntityToParameter(String, ChemicalEntity) - Method in class bio.singa.simulation.model.rules.AssignmentRule

referenceConstant(String, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceConstant(String, double, Evidence) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceFeature(AbstractScalableQuantitativeFeature) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceFeature(String, AbstractScalableQuantitativeFeature) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceParameter(AbstractScalableQuantitativeFeature<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(AbstractScalableQuantitativeFeature<?>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(Reactant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(Parameter<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceParameter(Parameter<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(Parameter<?>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(String, double) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(String, double) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(String, double, Evidence) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(String, double, Evidence) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(String, AbstractScalableQuantitativeFeature<?>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(String, AbstractScalableQuantitativeFeature<?>) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceParameter(String, Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

referenceParameter(String, Reactant) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.ParameterStep

referenceReactant(Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

referenceReactant(String, Reactant) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

region(AffectedRegion) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.FeatureStep

region(AffectedRegion) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.PorousDiffusion.PorousDiffusionBuilder

region(CellRegion) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

region(CellRegion) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

RegionCondition - Class in bio.singa.simulation.model.concentrations

RegionCondition(List<CellRegion>) - Constructor for class bio.singa.simulation.model.concentrations.RegionCondition

RegionFeature - Class in bio.singa.simulation.features.model

RegionFeature(CellRegion) - Constructor for class bio.singa.simulation.features.model.RegionFeature

RegionFeature(CellRegion, Evidence) - Constructor for class bio.singa.simulation.features.model.RegionFeature

RegionFeature(CellRegion, List<Evidence>) - Constructor for class bio.singa.simulation.features.model.RegionFeature

regions(CellRegion...) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

regions(CellRegion...) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

regions(List<CellRegion>) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

regions(List<CellRegion>) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

regionsToMembrane(AutomatonGraph) - Static method in class bio.singa.simulation.model.agents.surfacelike.MembraneTracer

Deprecated.

reinitialize() - Static method in class bio.singa.simulation.entities.EntityRegistry

reinitialize() - Static method in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry

release(BindingSite) - Static method in class bio.singa.simulation.reactions.modifications.ComplexEntityModificationBuilder

release(BindingSite, ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

release(BindingSite, ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReactorChoiceStep

release(BindingSite, ChemicalEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder

release(ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

release(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReactorChoiceStep

release(ChemicalEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder

ReleaseModification - Class in bio.singa.simulation.reactions.modifications

ReleaseModification(BindingSite) - Constructor for class bio.singa.simulation.reactions.modifications.ReleaseModification

ReleaseReactionChainBuilder(BindingSite, ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactionChainBuilder

ReleaseReactionChainBuilder(ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReleaseReactionChainBuilder

remove(BindingSite, ChemicalEntity) - Static method in class bio.singa.simulation.reactions.modifications.ComplexEntityModificationBuilder

remove(BindingSite, ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

remove(BindingSite, ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReactorChoiceStep

remove(BindingSite, ChemicalEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder

remove(ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

remove(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.ReactorChoiceStep

remove(ChemicalEntity) - Static method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder

remove(ChemicalEntity, BindingSite) - Method in class bio.singa.simulation.entities.ComplexEntity

RemoveModification - Class in bio.singa.simulation.reactions.modifications

RemoveModification(BindingSite, ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.modifications.RemoveModification

RemoveReactionChainBuilder(BindingSite, ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactionChainBuilder

RemoveReactionChainBuilder(ChemicalEntity) - Constructor for class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.RemoveReactionChainBuilder

removeSubsection(CellSubsection) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

Removes a subsection, the corresponding topology and concentration pool from the container.

removeSubsection(CellTopology) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

Removes a subsection, the given topology and concentration pool from the container.

removeVesicle(Vesicle) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer

replaceTextMu(String) - Static method in class bio.singa.simulation.export.TeXFormat

RequiredVesicleState - Class in bio.singa.simulation.features

RequiredVesicleState(String) - Constructor for class bio.singa.simulation.features.RequiredVesicleState

RequiredVesicleState.Builder - Class in bio.singa.simulation.features

REQUIRING_RECALCULATION - bio.singa.simulation.model.modules.concentration.ModuleState

The calculation has finished but the numerical error was too large.

reset() - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

reset() - Method in interface bio.singa.simulation.model.modules.UpdateModule

reset() - Method in class bio.singa.simulation.model.simulation.error.GlobalDisplacementDeviationManager

reset() - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

resetAllErrors() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

resetDisplacementDeviations() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

resetError() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Resets the error to the minimal error.

resetGlobalDisplacementDeviation() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

resetGlobalNumericalError() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

resetLocalDisplacementDeviation() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

resetLocalErrors() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

resetLocalNumericalError() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

resetNextPosition() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

resetNextPosition() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager

Resets the next position to the current position.

resetNumericalErrors() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

resolveGlobalDeviationProblem() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

resolveGlobalErrorProblem() - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

resolveProblem() - Method in class bio.singa.simulation.model.simulation.error.GlobalDisplacementDeviationManager

resolveProblem() - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

restrictApplication() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

retrieveAreaAgent(Simulation) - Method in class bio.singa.simulation.features.ContainmentRegion

reversible() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

reversible() - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.KineticStep

Reversible reactions where the substrates form products, and products can also from substrates.

ReversibleKineticLaw - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws

ReversibleKineticLaw(Reaction) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.ReversibleKineticLaw

revertToOriginalConcentrations() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

ROTHMAN2016 - Static variable in class bio.singa.simulation.model.agents.pointlike.Vesicle

rule(ReactionChain) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.RuleBasedBuilder

rule(ReactionChain) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.RuleBasedStep

ruleBased(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder

RuleBasedBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.RuleBasedBuilder

RuleBasedReactantBehavior - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

RuleBasedReactantBehavior() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.RuleBasedReactantBehavior

RuleBasedReactantBehavior(ReactionChain) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.RuleBasedReactantBehavior

run() - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

run() - Method in class bio.singa.simulation.model.simulation.SimulationManager

S

scale() - Method in class bio.singa.simulation.features.AttachmentDistance

scale() - Method in class bio.singa.simulation.features.MotorMovementVelocity

scale() - Method in class bio.singa.simulation.features.VesicleRadius

scale() - Method in class bio.singa.simulation.model.parameters.Parameter

scale(double) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentTemplate

scale(double) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

scaledQuantity - Variable in class bio.singa.simulation.model.parameters.Parameter

scalingEntities(ScalingEntities) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.AccelerationStep

scalingEntities(ScalingEntities) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder

ScalingEntities - Class in bio.singa.simulation.features

ScalingEntities(List<ChemicalEntity>) - Constructor for class bio.singa.simulation.features.ScalingEntities

ScalingEntities.Builder - Class in bio.singa.simulation.features

seal() - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

secondaryCandidateConditions - Variable in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

secondaryCondition(CandidateCondition) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactionChainBuilder

secondaryCondition(CandidateCondition) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactorSecondaryConditionStep

secondaryEntity - Variable in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AbstractReactorBuilder

seconds() - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.TimedUnitStep

SECTION_SPECIFIC - bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity

References SectionSpecific.

SectionCondition - Class in bio.singa.simulation.model.concentrations

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.

SEMI_NEIGHBOURHOOD_DEPENDENT - bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope

References SemiDependentUpdate.

SemiDependentUpdate - Class in bio.singa.simulation.model.modules.concentration.scope

Semidependent Updatable ConcentrationBasedModules require the integer state of a subset of updatables.

SemiDependentUpdate(ConcentrationBasedModule) - Constructor for class bio.singa.simulation.model.modules.concentration.scope.SemiDependentUpdate

Initializes the update scope for the corresponding module.

sequence - Variable in class uk.co.cogitolearning.cogpar.Token

the string that the token was created from

SequenceExpressionNode - Class in uk.co.cogitolearning.cogpar

A base class for AdditionExpressionNode and MultiplicationExpressionNode.

SequenceExpressionNode() - Constructor for class uk.co.cogitolearning.cogpar.SequenceExpressionNode

Default constructor.

SequenceExpressionNode(ExpressionNode, boolean) - Constructor for class uk.co.cogitolearning.cogpar.SequenceExpressionNode

Constructor to create a sequence with the first term already added.

SequenceExpressionNode.Term - Class in uk.co.cogitolearning.cogpar

An inner class that defines a pair containing an ExpressionNode and a boolean flag.

set(ChemicalEntity, double) - Method in class bio.singa.simulation.model.sections.ConcentrationPool

Sets the concentration of a entity.

set(CellSubsection, ChemicalEntity, double) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

Sets the concentration of the given entity in the given subsection.

set(CellTopology, ChemicalEntity, double) - Method in class bio.singa.simulation.model.sections.ConcentrationContainer

Sets the concentration of the given entity in the given topology.

setApplicationCondition(Predicate<Updatable>) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Sets the application condition for this module.

setArea(Polygon) - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent

setAreaRepresentation(Polygon) - Method in class bio.singa.simulation.model.sections.CellRegion

setAssignmentRules(List<AssignmentRule>) - Method in class bio.singa.simulation.model.simulation.Simulation

Adds a list of assignment rules, sorting them by their dependencies.

setAssociatedNodes(Set<AutomatonNode>) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

setAttachedFilament(LineLikeAgent) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

setBindingSite(BindingSite) - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

setBindingSites(List<BindingSite>) - Method in class bio.singa.simulation.entities.GraphComplexNode

setCache(double) - Method in class bio.singa.simulation.model.graphs.AutomatonNode.AreaMapping

setCandidates(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

setCatalysts(List<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

setCellRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent

setCellRegion(CellRegion) - Method in class bio.singa.simulation.model.graphs.AutomatonNode

setCellRegion(CellRegion) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

setCheckpointTime(Quantity<Time>) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

setCollecting(boolean) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

setConcentration(Quantity<MolarConcentration>) - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

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.

setConcentrationDeltaManager(ConcentrationDeltaManager) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

setConcentrationManager(ConcentrationDeltaManager) - Method in class bio.singa.simulation.model.graphs.AutomatonNode

setConcentrationMap(Map<String, Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

setConcentrations(List<InitialConcentration>) - Method in class bio.singa.simulation.model.simulation.Simulation

setConditions(TreeMap<Integer, ConcentrationCondition>) - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

setConditions(TreeMap<Integer, ConcentrationCondition>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.Reaction

setConnectedSite(BindingSite) - Method in class bio.singa.simulation.entities.GraphComplexEdge

setConsiderInversion(boolean) - Method in class bio.singa.simulation.reactions.reactors.ReactionChain

setCurrentEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Sets the current chemical entity.

setCurrentMembraneRestrictedUpdatable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

setCurrentNode(AutomatonNode) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionEvent

setCurrentSubsection(CellSubsection) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Sets the current subsection.

setCurrentUpdatable(Updatable) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Sets the current updatable.

setCursive(String) - Static method in class bio.singa.simulation.export.TeXFormat

setDebug(boolean) - Method in class bio.singa.simulation.model.simulation.Simulation

setDebugDirectory(Path) - Method in class bio.singa.simulation.trajectories.errors.DebugRecorder

setDebugRecorder(DebugRecorder) - Method in class bio.singa.simulation.model.simulation.Simulation

setDiffusiveRatio(double) - Method in class bio.singa.simulation.model.graphs.AutomatonNode.AreaMapping

setDisplacementLowerThreshold(double) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setDisplacementReferenceFactor(double) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setDisplacementReferenceLength(double) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setDisplacementUpperThreshold(double) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setEndingPoint(Vector2D) - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment

setEntity(ChemicalEntity) - Method in class bio.singa.simulation.entities.GraphComplexNode

setEntity(ChemicalEntity) - Method in class bio.singa.simulation.export.reactiongraph.ReactionGraphNode

setEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

setEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Sets the entity representing this reactant.

setEntityReference(Map<ChemicalEntity, String>) - Method in class bio.singa.simulation.model.rules.AssignmentRule

setEpochWithRescaledTimeStep(long) - Method in class bio.singa.simulation.model.simulation.Simulation

setEquations(List<String>) - Method in class bio.singa.simulation.export.modules.ReactionTableRow

setEvidence(List<Evidence>) - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

setFeature(Feature<?>) - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

Sets a feature.

setFeature(Feature<?>) - Method in interface bio.singa.simulation.model.modules.UpdateModule

setFeature(FeatureType) - Method in class bio.singa.simulation.entities.ComplexEntity

setFeature(FeatureType) - Method in class bio.singa.simulation.entities.SimpleEntity

setFeature(FeatureType) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

setFeature(FeatureType) - Method in class bio.singa.simulation.model.parameters.FeatureManager

setFeature(Class<FeatureType>) - Method in class bio.singa.simulation.entities.ComplexEntity

setFeature(Class<FeatureType>) - Method in class bio.singa.simulation.entities.SimpleEntity

setFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

setFeature(Class<FeatureType>) - Method in class bio.singa.simulation.model.parameters.FeatureManager

setFeatureIdentifierMap(Map<Feature<?>, String>) - Method in class bio.singa.simulation.export.features.FeatureTable

setFeatureManager(FeatureManager) - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

setFeatureMap(Map<String, AbstractScalableQuantitativeFeature>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

setFilaments(List<LineLikeAgent>) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

setFix(boolean) - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

setGlobalNumericalTolerance(double) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setGoTerm(GoTerm) - Method in class bio.singa.simulation.model.sections.CellSubsection

setGraph(AutomatonGraph) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

setGraph(AutomatonGraph) - Method in class bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder

setGraph(AutomatonGraph) - Method in class bio.singa.simulation.model.simulation.Simulation

setGroups(Map<Integer, Set<Vector2D>>) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

setIdentifier(int) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

setIdentifier(String) - Method in class bio.singa.simulation.export.modules.ReactionTableRow

setIdentifier(String) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

setIdentifier(String) - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

Sets the identifier of this module.

setIdentifier(String) - Method in class bio.singa.simulation.model.sections.CellSubsection

setIdentifier(String) - Method in class bio.singa.simulation.reactions.reactors.ReactionChain

setIndex(int) - Method in enum bio.singa.simulation.model.sections.CellTopology

setInnerRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

setInnerRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane

setInterimAndUpdateCurrentConcentrations() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

setInverse(boolean) - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

setKeepPlatformOpen(boolean) - Method in class bio.singa.simulation.model.simulation.SimulationManager

setKineticLaw(KineticLaw) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.Reaction

setKinetics(List<String>) - Method in class bio.singa.simulation.export.modules.ReactionTableRow

setLargestLocalDisplacementDeviation(DisplacementDeviation, UpdateModule) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setLargestLocalError(NumericalError) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Sets the largest error as of yet.

setLargestLocalNumericalError(NumericalError, UpdateModule, double) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setLineLayer(LineLikeAgentLayer) - Method in class bio.singa.simulation.model.simulation.Simulation

setLocalErrorModule(UpdateModule) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setLocalNumericalErrorUpdate(double) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setLocalNumericalTolerance(double) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setMaximalTimeStep(Quantity<Time>) - Method in class bio.singa.simulation.model.simulation.Simulation

setMembrane(boolean) - Method in class bio.singa.simulation.model.sections.CellSubsection

setMembraneBound(boolean) - Method in interface bio.singa.simulation.entities.ChemicalEntity

setMembraneBound(boolean) - Method in class bio.singa.simulation.entities.ComplexEntity

setMembraneBound(boolean) - Method in class bio.singa.simulation.entities.SimpleEntity

setMembraneLayer(MembraneLayer) - Method in class bio.singa.simulation.model.simulation.Simulation

setMembraneMapping(Map<Pair<Integer>, CellRegion>) - Method in class bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder

setMembraneRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

setMembraneRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.surfacelike.Membrane

setMembranes(Map<CellRegion, Membrane>) - Method in class bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder

setMicrotubuleOrganizingCentre(MicrotubuleOrganizingCentre) - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneLayer

setMinusEndBehaviour(LineLikeAgent.GrowthBehaviour) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

setModification(ComplexEntityModification) - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

setMonoSpace(String) - Static method in class bio.singa.simulation.export.TeXFormat

setNegligibility(double) - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

setNumericalInstabilityCutoff(double) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setNumericalNegligenceCutoff(double) - Method in class bio.singa.simulation.model.simulation.error.ErrorManager

setObserved(boolean) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

Sets the observed state of this node.

setObserved(boolean) - Method in class bio.singa.simulation.model.graphs.AutomatonNode

Sets the observed state of this node.

setObserved(boolean) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

Sets the concentrations to be observed, this additional requires seting up a UpdateEventListener.

setOrigin(Evidence) - Method in class bio.singa.simulation.model.parameters.Parameter

setOriginalConcentrations(ConcentrationContainer) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

setOutputFunction(Consumer<Trajectories>) - Method in class bio.singa.simulation.trajectories.nested.NestedUpdateRecorder

setParameterMap(Map<String, Parameter>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws.DynamicKineticLaw

setPath(VectorPath) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

setPlusEndBehaviour(LineLikeAgent.GrowthBehaviour) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

setPolygon(Polygon) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

setPreferredConcentrationUnit(Unit<MolarConcentration>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

setPreferredTopology(CellTopology) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

setPrimaryCandidateConditions(List<CandidateCondition>) - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

setPrimaryEntity(ChemicalEntity) - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

setPrimaryEntity(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.modifications.ComplexEntityModification

setPrimaryProducts(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

setPrimarySubstrates(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.AbstractGraphComplexReactor

setProducts(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.ReactionElement

setProducts(List<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

setQuantity(Quantity<QuantityType>) - Method in class bio.singa.simulation.model.parameters.Parameter

setRadius(Quantity<Length>) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

setRadius(Quantity<Length>) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

setRates(Map<String, List<String>>) - Method in class bio.singa.simulation.export.modules.ReactionTableRow

setReactantBehavior(ReactantBehavior) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.Reaction

setReactantSets(List<ReactantSet>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.RuleBasedReactantBehavior

setRegion(CellRegion) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

setRegionMapping(Map<Integer, CellRegion>) - Method in class bio.singa.simulation.model.agents.surfacelike.GridMembraneBuilder

setRestrictedSubsection(CellSubsection) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

setResults(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

setRole(ReactantRole) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

Gets the role of this reactant.

setRows(List<ModuleTableRow>) - Method in class bio.singa.simulation.export.modules.ModuleTable

setScale(Quantity<Length>) - Method in class bio.singa.simulation.model.agents.organelles.OrganelleTemplate

setScheduler(UpdateScheduler) - Method in class bio.singa.simulation.model.simulation.Simulation

setSealed(boolean) - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

setSecondaryEntity(ChemicalEntity) - Method in class bio.singa.simulation.reactions.modifications.AbstractComplexEntityModification

setSecondaryEntity(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.modifications.ComplexEntityModification

setSecondaryProducts(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.OneToTwoReactor

setSecondarySubstrates(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.TwoToOneReactor

setSecondCandidateConditions(List<CandidateCondition>) - Method in class bio.singa.simulation.reactions.reactors.TwoToOneReactor

setSegmentIterator(ListIterator<Vector2D>) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

setSimulation(Simulation) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer

setSimulation(Simulation) - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

References the simulation to this module.

setSimulation(Simulation) - Method in interface bio.singa.simulation.model.modules.UpdateModule

setSimulationHeight(double) - Method in class bio.singa.simulation.trajectories.nested.Trajectories

setSimulationRegion(Rectangle) - Method in class bio.singa.simulation.model.agents.pointlike.VesicleLayer

setSimulationRegion(Rectangle) - Method in class bio.singa.simulation.model.simulation.Simulation

setSimulationTerminationToEpochs(long) - Method in class bio.singa.simulation.model.simulation.SimulationManager

Schedules the termination of the simulation after the given number of epochs have passed.

setSimulationTerminationToTime(Quantity<Time>) - Method in class bio.singa.simulation.model.simulation.SimulationManager

Schedules the termination of the simulation after the given time (simulation time) has passed.

setSimulationWidth(double) - Method in class bio.singa.simulation.trajectories.nested.Trajectories

setSkipDisplacementChecks(boolean) - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

setSmall(boolean) - Method in class bio.singa.simulation.entities.SimpleEntity

setSpatialRepresentation(Polygon) - Method in class bio.singa.simulation.model.graphs.AutomatonNode

setSpawnSite(Vector2D) - Method in class bio.singa.simulation.model.modules.qualitative.implementations.EndocytoticPit

setStartingPoint(Vector2D) - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment

setState(ModuleState) - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

setState(String) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

setState(String) - Method in class bio.singa.simulation.trajectories.nested.TrajectoryDataPoint

setStrutCalculation(boolean) - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

Sets the current state of calculation.

setSubsection(CellSubsection) - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

setSubstrates(List<ComplexEntity>) - Method in class bio.singa.simulation.reactions.reactors.ReactionElement

setSubstrates(List<Reactant>) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

setTargetDirection(String) - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

setTargetedGrowth(boolean) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

setTargetEntity(ChemicalEntity) - Method in class bio.singa.simulation.model.rules.AssignmentRule

setTargetMembrane(CellRegion) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

setTargetPath(Path) - Method in class bio.singa.simulation.model.simulation.SimulationManager

setTerminationCondition(Predicate<Simulation>) - Method in class bio.singa.simulation.model.simulation.SimulationManager

Sets a condition determining when the simulation should be terminated.

setTerminationLatch(CountDownLatch) - Method in class bio.singa.simulation.model.simulation.SimulationManager

setTerminationTime(Quantity<Time>) - Method in class bio.singa.simulation.model.simulation.SimulationStatus

setTeXString(String) - Method in class bio.singa.simulation.export.features.FeatureTable

setTimeStepRescaled(boolean) - Static method in class bio.singa.simulation.model.simulation.error.TimeStepManager

setTolerance(double) - Method in class bio.singa.simulation.model.simulation.error.GlobalNumericalErrorManager

setTopology(CellTopology) - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

setTrack(Deque<List<ComplexEntity>>) - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

setTracks(List<ReactionTrack>) - Method in class bio.singa.simulation.reactions.reactors.ReactionChain

setType(String) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgent

SETUP_STAGE - bio.singa.simulation.model.simulation.error.ErrorManager.CalculationStage

setUpConcentrationContainer() - Method in class bio.singa.simulation.model.sections.CellRegion

setUpdatable(Updatable) - Method in class bio.singa.simulation.model.simulation.error.NumericalError

setUpdateEmissionCondition(Predicate<Simulation>) - Method in class bio.singa.simulation.model.simulation.SimulationManager

Sets a condition determining when events should be emitted.

setUpdateEmissionToTimePassed(Quantity<Time>) - Method in class bio.singa.simulation.model.simulation.SimulationManager

Schedules the emission of events after the given time (simulation time) has passed.

setupModule(Class<ModuleImplementation>, ModuleFactory.Scope, ModuleFactory.Specificity) - Static method in class bio.singa.simulation.model.modules.concentration.ModuleFactory

Creates a new module with the specified setup.

setUseContinuousIndex(boolean) - Method in class bio.singa.simulation.export.features.FeatureTable

setValue(double) - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDelta

setValue(double) - Method in class uk.co.cogitolearning.cogpar.VariableExpressionNode

Sets the value of the variable

SetVariable - Class in uk.co.cogitolearning.cogpar

A visitor that sets a variable with a specific name to a given value

SetVariable(String, double) - Constructor for class uk.co.cogitolearning.cogpar.SetVariable

Construct the visitor with the name and the value of the variable to set

setVesicleLayer(VesicleLayer) - Method in class bio.singa.simulation.model.simulation.Simulation

setVolumeLayer(VolumeLayer) - Method in class bio.singa.simulation.model.simulation.Simulation

setWriteAliveFile(boolean) - Method in class bio.singa.simulation.model.simulation.SimulationManager

shiftDeltas() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaManager

Shifts the deltas from the potential delta list to the final delta list.

SHRINK - bio.singa.simulation.model.agents.linelike.LineLikeAgent.GrowthBehaviour

shutdownExecutorService() - Method in class bio.singa.simulation.model.simulation.UpdateScheduler

SimpleEntity - Class in bio.singa.simulation.entities

SimpleEntity(String) - Constructor for class bio.singa.simulation.entities.SimpleEntity

Creates a new chemical entity with the given identifier.

SimpleEntity.SimpleEntityBuilder - Class in bio.singa.simulation.entities

SimpleEntityBuilder(String) - Constructor for class bio.singa.simulation.entities.SimpleEntity.SimpleEntityBuilder

simulation - Variable in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

simulation(Simulation) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

simulation(Simulation) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.SimulationStep

Simulation - Class in bio.singa.simulation.model.simulation

Simulation() - Constructor for class bio.singa.simulation.model.simulation.Simulation

Creates a new plain simulation.

SimulationManager - Class in bio.singa.simulation.model.simulation

Changes in simulations can be observed by tagging AutomatonNodes of the AutomatonGraph.

SimulationManager(Simulation) - Constructor for class bio.singa.simulation.model.simulation.SimulationManager

Creates a new simulation manager for the given simulation.

SimulationStatus - Class in bio.singa.simulation.model.simulation

SimulationStatus(Simulation) - Constructor for class bio.singa.simulation.model.simulation.SimulationStatus

SingleFileChannelMembraneTransport - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

The single file channel transport describes the movement of cargo molecules through Transporter proteins, so called membrane channels.

SingleFileChannelMembraneTransport() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport

SingleFileChannelMembraneTransport.BuildStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

SingleFileChannelMembraneTransport.CargoStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder - Class in bio.singa.simulation.model.modules.concentration.imlementations.transport

SingleFileChannelMembraneTransport.SolutesStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

SingleFileChannelMembraneTransport.TransporterStep - Interface in bio.singa.simulation.model.modules.concentration.imlementations.transport

SingleFileChannelMembraneTransportBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder

singularGraph() - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs

singularGraph(CellRegion) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs

SKIP - bio.singa.simulation.model.simulation.error.ErrorManager.CalculationStage

small() - Method in class bio.singa.simulation.entities.SimpleEntity.SimpleEntityBuilder

snapTo(ChemicalEntity, Set<BindingSite>) - Method in class bio.singa.simulation.entities.ComplexEntity

SNAREFusionPairs - Class in bio.singa.simulation.features

Snare pairs required for fusion event to trigger

SNAREFusionPairs(Quantity<Dimensionless>) - Constructor for class bio.singa.simulation.features.SNAREFusionPairs

SNAREFusionPairs.Builder - Class in bio.singa.simulation.features

Solutes - Class in bio.singa.simulation.features

Solutes(List<ChemicalEntity>) - Constructor for class bio.singa.simulation.features.Solutes

Solutes.Builder - Class in bio.singa.simulation.features

sortAssignmentRulesByPriority(List<AssignmentRule>) - Static method in class bio.singa.simulation.model.rules.AssignmentRules

It is possible, that AssignmentRules depend on each other.

sortByComplexDependencies(List<ChemicalEntity>) - Static method in class bio.singa.simulation.entities.ChemicalEntities

spawnActin(LineLikeAgentLayer) - Method in class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre

spawnActinFilament(Membrane) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

spawnHorizontalFilament(Membrane) - Method in class bio.singa.simulation.model.agents.linelike.LineLikeAgentLayer

spawnMicrotubule(LineLikeAgentLayer) - Method in class bio.singa.simulation.model.agents.linelike.MicrotubuleOrganizingCentre

SpawnRate - Interface in bio.singa.simulation.features

splitRectangularGraphWithMembrane(AutomatonGraph, CellSubsection, CellSubsection, boolean) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs

SQUARE_MICRO_METRE - Static variable in interface bio.singa.simulation.features.SpawnRate

SQUARE_NANOMETRE - Static variable in interface bio.singa.simulation.features.SpawnRate

STAGNANT - bio.singa.simulation.model.agents.linelike.LineLikeAgent.GrowthBehaviour

StaticBuilder(Simulation) - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

StaticReactantBehavior - Class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

StaticReactantBehavior() - Constructor for class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.StaticReactantBehavior

staticReactants(Simulation) - Static method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder

subsection(CellSubsection) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

subsection(CellSubsection) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.PoolStep

SubsectionDataPoint() - Constructor for class bio.singa.simulation.trajectories.nested.TrajectoryDataPoint.SubsectionDataPoint

SubsectionDataPoint(Map<ChemicalEntity, Double>, List<Vector2D>) - Constructor for class bio.singa.simulation.trajectories.nested.TrajectoryDataPoint.SubsectionDataPoint

SUBSTRATE - bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantRole

SUCCEEDED - bio.singa.simulation.model.modules.concentration.ModuleState

Calculation has completed with numerical error below the given threshold.

SUCCEEDED_WITH_PENDING_CHANGES - bio.singa.simulation.model.modules.concentration.ModuleState

The module has completed successfully but contains some changes to the simulation that should be applied at the very end of the time step.

supplier - Variable in class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

Frequently required fields.

T

TAGGED_FOR_EXOCYTOSIS - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry

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

test(ComplexEntity) - Method in interface bio.singa.simulation.reactions.conditions.CandidateCondition

test(ComplexEntity) - Method in class bio.singa.simulation.reactions.conditions.HasAnyNumberOfEntities

test(ComplexEntity) - Method in class bio.singa.simulation.reactions.conditions.HasNoMoreThanNumberOfPartners

test(ComplexEntity) - Method in class bio.singa.simulation.reactions.conditions.HasNumberOfEntities

test(ComplexEntity) - Method in class bio.singa.simulation.reactions.conditions.HasOccupiedBindingSite

test(ComplexEntity) - Method in class bio.singa.simulation.reactions.conditions.HasUnoccupiedBindingSite

test(ComplexEntity) - Method in class bio.singa.simulation.reactions.conditions.IsOnlyBoundAt

test(Updatable) - Method in class bio.singa.simulation.model.concentrations.AreaCondition

test(Updatable) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationCondition

test(Updatable) - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

test(Updatable) - Method in class bio.singa.simulation.model.concentrations.NodeIdentifierCondition

test(Updatable) - Method in class bio.singa.simulation.model.concentrations.NodeTypeCondition

test(Updatable) - Method in class bio.singa.simulation.model.concentrations.RegionCondition

test(Updatable) - Method in class bio.singa.simulation.model.concentrations.SectionCondition

test(Updatable) - Method in class bio.singa.simulation.model.concentrations.TimedCondition

test(Updatable) - Method in class bio.singa.simulation.model.concentrations.TopologyCondition

TETHERED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry

TeXFormat - Class in bio.singa.simulation.export

TeXFormat() - Constructor for class bio.singa.simulation.export.TeXFormat

tieUpdateEmissionToFPS(int) - Method in class bio.singa.simulation.model.simulation.SimulationManager

Sets the emission of updates for a rending engine.

TIME_STEP_RESCALED - bio.singa.simulation.model.simulation.error.ErrorManager.CalculationStage

timed(TimedCondition.Relation, double) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

timed(TimedCondition.Relation, double) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

timed(TimedCondition.Relation, ComparableQuantity<Time>) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

timed(TimedCondition.Relation, ComparableQuantity<Time>) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

TimedCondition - Class in bio.singa.simulation.model.concentrations

TimedCondition(TimedCondition.Relation, ComparableQuantity<Time>) - Constructor for class bio.singa.simulation.model.concentrations.TimedCondition

TimedCondition.Relation - Enum in bio.singa.simulation.model.concentrations

timeFormat(QuantityFormatter<Time>) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

timeFormat(QuantityFormatter<Time>) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.TimeUnitStep

TimeStepManager - Class in bio.singa.simulation.model.simulation.error

TimeStepManager(UpdateScheduler) - Constructor for class bio.singa.simulation.model.simulation.error.TimeStepManager

timeUnit(Unit<Time>) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

timeUnit(Unit<Time>) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.TimedUnitStep

timeUnit(Unit<Time>) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

timeUnit(Unit<Time>) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.TimeUnitStep

to(ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactionChainBuilder

to(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.AddReactorSecondarySubstrateStep

to(ChemicalEntity) - Method in class bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactionChainBuilder

to(ChemicalEntity) - Method in interface bio.singa.simulation.reactions.reactors.ReactionChainBuilder.BindReactorSecondarySubstrateStep

token - Variable in class uk.co.cogitolearning.cogpar.Token

the token identifier

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

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

topology(CellTopology) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

topology(CellTopology) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.PoolStep

TopologyCondition - Class in bio.singa.simulation.model.concentrations

toRow() - Method in class bio.singa.simulation.export.modules.GeneralModuleRow

toRow() - Method in interface bio.singa.simulation.export.modules.ModuleTableRow

toRow() - Method in class bio.singa.simulation.export.modules.ReactionTableRow

toString() - Method in class bio.singa.simulation.entities.BindingSite

toString() - Method in class bio.singa.simulation.entities.ComplexEntity

toString() - Method in class bio.singa.simulation.entities.GraphComplexNode

toString() - Method in class bio.singa.simulation.entities.SimpleEntity

toString() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

toString() - Method in class bio.singa.simulation.model.agents.surfacelike.MembraneSegment

toString() - Method in class bio.singa.simulation.model.concentrations.AreaCondition

toString() - Method in class bio.singa.simulation.model.concentrations.InitialConcentration

toString() - Method in class bio.singa.simulation.model.concentrations.NodeIdentifierCondition

toString() - Method in class bio.singa.simulation.model.concentrations.NodeTypeCondition

toString() - Method in class bio.singa.simulation.model.concentrations.RegionCondition

toString() - Method in class bio.singa.simulation.model.concentrations.SectionCondition

toString() - Method in class bio.singa.simulation.model.concentrations.TimedCondition

toString() - Method in class bio.singa.simulation.model.concentrations.TopologyCondition

toString() - Method in class bio.singa.simulation.model.graphs.AutomatonNode

toString() - Method in class bio.singa.simulation.model.modules.AbstractUpdateModule

toString() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDelta

toString() - Method in class bio.singa.simulation.model.modules.concentration.ConcentrationDeltaIdentifier

toString() - Method in class bio.singa.simulation.model.modules.concentration.FieldSupplier

toString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

toString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantSet

toString() - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.MembraneDiffusion

toString() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementBasedModule

toString() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDelta

toString() - Method in class bio.singa.simulation.model.parameters.Parameter

toString() - Method in class bio.singa.simulation.model.sections.CellRegion

toString() - Method in class bio.singa.simulation.model.sections.CellSubsection

toString() - Method in class bio.singa.simulation.model.simulation.error.DisplacementDeviation

toString() - Method in class bio.singa.simulation.model.simulation.error.NumericalError

toString() - Method in class bio.singa.simulation.reactions.modifications.AddModification

toString() - Method in class bio.singa.simulation.reactions.modifications.BindModification

toString() - Method in class bio.singa.simulation.reactions.modifications.ReleaseModification

toString() - Method in class bio.singa.simulation.reactions.modifications.RemoveModification

toString() - Method in class bio.singa.simulation.reactions.reactors.ReactionElement

toString() - Method in class bio.singa.simulation.reactions.reactors.ReactionTrack

toTex() - Method in class bio.singa.simulation.export.modules.ModuleTable

toTex(List<Feature<?>>) - Static method in class bio.singa.simulation.export.features.FeatureTable

Trajectories - Class in bio.singa.simulation.trajectories.nested

Trajectories() - Constructor for class bio.singa.simulation.trajectories.nested.Trajectories

Trajectories(Unit<Time>, Unit<MolarConcentration>) - Constructor for class bio.singa.simulation.trajectories.nested.Trajectories

TrajectoryData - Class in bio.singa.simulation.trajectories.nested

TrajectoryData() - Constructor for class bio.singa.simulation.trajectories.nested.TrajectoryData

TrajectoryDataPoint - Class in bio.singa.simulation.trajectories.nested

TrajectoryDataPoint() - Constructor for class bio.singa.simulation.trajectories.nested.TrajectoryDataPoint

TrajectoryDataPoint.SubsectionDataPoint - Class in bio.singa.simulation.trajectories.nested

transporter(ChemicalEntity) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder

transporter(ChemicalEntity) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.SingleFileChannelMembraneTransport.TransporterStep

Transporter - Class in bio.singa.simulation.features

Transporter(ChemicalEntity) - Constructor for class bio.singa.simulation.features.Transporter

Transporter.Builder - Class in bio.singa.simulation.features

turnover(TurnoverNumber) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

turnover(TurnoverNumber) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.MichaelisMentenReactionStep

TwoToOneReactor - Class in bio.singa.simulation.reactions.reactors

TwoToOneReactor() - Constructor for class bio.singa.simulation.reactions.reactors.TwoToOneReactor

U

uk.co.cogitolearning.cogpar - package uk.co.cogitolearning.cogpar

UNATTACHED - Static variable in class bio.singa.simulation.model.agents.pointlike.VesicleStateRegistry

unbind(BindingSite) - Method in class bio.singa.simulation.entities.ComplexEntity

unit(Unit<MolarConcentration>) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

unit(Unit<MolarConcentration>) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationUnitStep

Updatable - Interface in bio.singa.simulation.model.simulation

UPDATABLE_SPECIFIC - bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity

References UpdatableSpecific.

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.

updatableIdentifier(String) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

updatableIdentifier(String) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

updatableIdentifiers(String...) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

updatableIdentifiers(String...) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

updatableIdentifiers(List<String>) - Method in interface bio.singa.simulation.model.concentrations.ConcentrationBuilder.AdditionalConditionsStep

updatableIdentifiers(List<String>) - Method in class bio.singa.simulation.model.concentrations.ConcentrationBuilder.ConcentrationBuilderImpl

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() - Method in class bio.singa.simulation.entities.ComplexEntity

UpdateModule - Interface in bio.singa.simulation.model.modules

updatePosition() - Method in class bio.singa.simulation.model.agents.pointlike.Vesicle

updatePosition() - Method in class bio.singa.simulation.model.modules.displacement.DisplacementDeltaManager

Sets the current position to the next position.

UpdateScheduler - 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.

updateTime() - Static method in class bio.singa.simulation.model.simulation.error.TimeStepManager

useStructureFrom(GridGraph) - Static method in class bio.singa.simulation.model.graphs.AutomatonGraphs

Copies the structure (nodes and edges) of an UndirectedGraph to a AutomatonGraph.

V

valueOf(String) - Static method in enum bio.singa.simulation.model.agents.linelike.LineLikeAgent.GrowthBehaviour

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bio.singa.simulation.model.concentrations.TimedCondition.Relation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantRole

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleState

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bio.singa.simulation.model.sections.CellTopology

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bio.singa.simulation.model.simulation.error.ErrorManager.CalculationStage

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum bio.singa.simulation.model.simulation.error.ErrorManager.Reason

Returns the enum constant of this type with the specified name.

values() - Static method in enum bio.singa.simulation.model.agents.linelike.LineLikeAgent.GrowthBehaviour

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.agents.organelles.OrganelleTypes

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.concentrations.TimedCondition.Relation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.ReactantRole

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Scope

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleFactory.Specificity

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.modules.concentration.ModuleState

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.sections.CellTopology

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum bio.singa.simulation.model.simulation.error.ErrorManager.CalculationStage

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.simulation.error.ErrorManager.Reason

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.

VariationTable - Class in bio.singa.simulation.export.features

VariationTable(FeatureTable) - Constructor for class bio.singa.simulation.export.features.VariationTable

varyLength(Quantity<Length>) - Static method in class bio.singa.simulation.features.FeatureRandomizer

varyTime(Quantity<Time>) - Static method in class bio.singa.simulation.features.FeatureRandomizer

Vesicle - Class in bio.singa.simulation.model.agents.pointlike

Vesicle(Vector2D, Quantity<Length>) - Constructor for class bio.singa.simulation.model.agents.pointlike.Vesicle

Vesicle(CellRegion, Vector2D, Quantity<Length>) - Constructor for class bio.singa.simulation.model.agents.pointlike.Vesicle

VESICLE_LUMEN - Static variable in class bio.singa.simulation.model.sections.CellSubsections

VESICLE_MEMBRANE - Static variable in class bio.singa.simulation.model.sections.CellSubsections

VESICLE_REGION - Static variable in class bio.singa.simulation.model.sections.CellRegions

VesicleConfinedDiffusion - Class in bio.singa.simulation.model.modules.displacement.implementations

VesicleConfinedDiffusion() - Constructor for class bio.singa.simulation.model.modules.displacement.implementations.VesicleConfinedDiffusion

vesicleCounter - Static variable in class bio.singa.simulation.model.agents.pointlike.Vesicle

VesicleCytoplasmDiffusion - Class in bio.singa.simulation.model.modules.displacement.implementations

VesicleCytoplasmDiffusion() - Constructor for class bio.singa.simulation.model.modules.displacement.implementations.VesicleCytoplasmDiffusion

VesicleFusion - Class in bio.singa.simulation.model.modules.qualitative.implementations

VesicleFusion() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.VesicleFusion

VesicleLayer - Class in bio.singa.simulation.model.agents.pointlike

VesicleLayer(Simulation) - Constructor for class bio.singa.simulation.model.agents.pointlike.VesicleLayer

VesicleRadius - Class in bio.singa.simulation.features

VesicleRadius(Quantity<Length>) - Constructor for class bio.singa.simulation.features.VesicleRadius

VesicleRadius(Quantity<Length>, Evidence) - Constructor for class bio.singa.simulation.features.VesicleRadius

VesicleRadius(Quantity<Length>, List<Evidence>) - Constructor for class bio.singa.simulation.features.VesicleRadius

VesicleRadius.Builder - Class in bio.singa.simulation.features

VesicleStateRegistry - Class in bio.singa.simulation.model.agents.pointlike

VesicleTransport - Class in bio.singa.simulation.model.modules.displacement.implementations

VesicleTransport() - Constructor for class bio.singa.simulation.model.modules.displacement.implementations.VesicleTransport

visit(AdditionExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor

visit(AdditionExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable

Do nothing

visit(ConstantExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor

visit(ConstantExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable

Do nothing

visit(ExponentiationExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor

visit(ExponentiationExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable

Do nothing

visit(FunctionExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor

visit(FunctionExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable

Do nothing

visit(MultiplicationExpressionNode) - Method in interface uk.co.cogitolearning.cogpar.ExpressionNodeVisitor

visit(MultiplicationExpressionNode) - Method in class uk.co.cogitolearning.cogpar.SetVariable

Do nothing

visit(VariableExpressionNode) - 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

VolumeLayer - Class in bio.singa.simulation.model.agents.volumelike

VolumeLayer() - Constructor for class bio.singa.simulation.model.agents.volumelike.VolumeLayer

VolumeLikeAgent - Class in bio.singa.simulation.model.agents.volumelike

VolumeLikeAgent(Polygon, CellRegion) - Constructor for class bio.singa.simulation.model.agents.volumelike.VolumeLikeAgent

VolumeLikeAgentContainment - Class in bio.singa.simulation.model.modules.qualitative.implementations

For vesicles state changes upon entering certain regions represented by volume like agents

VolumeLikeAgentContainment() - Constructor for class bio.singa.simulation.model.modules.qualitative.implementations.VolumeLikeAgentContainment

VolumeLikeAgentFactory - Class in bio.singa.simulation.model.agents.volumelike

W

WhiteListVesicleStates - Class in bio.singa.simulation.features

WhiteListVesicleStates(List<String>) - Constructor for class bio.singa.simulation.features.WhiteListVesicleStates

WhiteListVesicleStates.Builder - Class in bio.singa.simulation.features

withReducedRatio(Ratio) - Method in class bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.DiffusionBuilder

withReducedRatio(Ratio) - Method in interface bio.singa.simulation.model.modules.concentration.imlementations.transport.Diffusion.SectionLimitationStep

workspace(Path) - Method in class bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.EpochUpdateWriterBuilder

workspace(Path) - Method in interface bio.singa.simulation.trajectories.flat.FlatUpdateRecorder.WorkspaceStep

writeStatus() - Method in class bio.singa.simulation.trajectories.nested.NestedUpdateRecorder

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