bio.singa.simulation.model.modules

Interface UpdateModule

All Superinterfaces:

Runnable

All Known Implementing Classes:

ActinCortexDiffusivityScaling, ClathrinMediatedEndocytosis, ConcentrationBasedModule, ConcentrationStateChange, Diffusion, DiffusivityScaling, DisplacementBasedModule, EndocytosisActinBoost, LineLikeAgentAttachment, LineLikeAgentDetachment, MembraneDiffusion, QualitativeModule, Reaction, SingleFileChannelMembraneTransport, VesicleConfinedDiffusion, VesicleCytoplasmDiffusion, VesicleFusion, VesicleTransport, VolumeLikeAgentContainment

public interface UpdateModule
extends Runnable

Author:

cl

Method Summary

Modifier and Type	Method and Description
void	calculateUpdates()
void	checkFeatures()
Collection<bio.singa.features.model.Feature<?>>	getFeatures()
String	getIdentifier()
Set<ChemicalEntity>	getReferencedEntities()
Set<Class<? extends bio.singa.features.model.Feature>>	getRequiredFeatures()
double	getScaledFeature(Class<? extends bio.singa.features.model.ScalableQuantitativeFeature<?>> featureClass)
ModuleState	getState()
void	initialize()
void	onCompletion()
void	onReset()
void	optimizeTimeStep()
void	resetState()
void	setFeature(bio.singa.features.model.Feature<?> feature)
void	setSimulation(Simulation simulation)

Methods inherited from interface java.lang.Runnable

run

Method Detail

getIdentifier

String getIdentifier()

getReferencedEntities

Set<ChemicalEntity> getReferencedEntities()

setSimulation

void setSimulation(Simulation simulation)

getState

ModuleState getState()

resetState

void resetState()

getRequiredFeatures

Set<Class<? extends bio.singa.features.model.Feature>> getRequiredFeatures()

getFeatures

Collection<bio.singa.features.model.Feature<?>> getFeatures()

getScaledFeature

double getScaledFeature(Class<? extends bio.singa.features.model.ScalableQuantitativeFeature<?>> featureClass)

setFeature

void setFeature(bio.singa.features.model.Feature<?> feature)

checkFeatures

void checkFeatures()

initialize

void initialize()

calculateUpdates

void calculateUpdates()

optimizeTimeStep

void optimizeTimeStep()

onReset

void onReset()

onCompletion

void onCompletion()