Simulator (Systems Biology Simulation Core Library (SBSCL) 2.1 API)

java.lang.Object
- fern.simulation.Simulator

Direct Known Subclasses:

GibsonBruckSimulator, GillespieEnhanced, GillespieSimple, HybridMaximalTimeStep
```
public abstract class Simulator
extends Object
```
Base class for stochastic simulators. Extending classes just have to implement performStep which gets invoked as long as the simulation is lasting. They also may override initialize but should in that case call super.initialize() to avoid unwished effects.
Simulators also should handle the special time theta: is is a moment in time when thetaEvent is supposed to be invoked (e.g. to measure species populations at this moment). Consider this, if you want to implement a simulator.
The fireReaction are supposed to be invoked when a simulator causes a reaction to fire.
If an extending class sticks to these conventions, it can take full benefit of the observer system: One or more Observer can be registered at a simulator and observe certain aspects of the simulation (see the Observers javadoc for more information).

Author:

Florian Erhard

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Simulator.FireType
Defines different types of a firing for reactions.

Nested Classes
Modifier and Type	Class and Description
`static class`	`Simulator.FireType` Defines different types of a firing for reactions.

Constructor Summary

Constructors
Constructor and Description

Simulator(Network net)
Creates a new simulator for the given network.

Constructors
Constructor and Description
`Simulator(Network net)` Creates a new simulator for the given network.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`Observer`	`addObserver(Observer observer)` Adds an observer to the list of observers.
`double`	`getAmount(int species)` Gets the amount of the given species.
`abstract String`	`getName()` Gets the name of the algorithm.
`Network`	`getNet()` Gets the simulation network.
`double`	`getNextThetaEvent()` Theta defines a moment, where the simulator has to invoke `theta` of a observer.
`double`	`getPropensity(int reaction)` Gets the current propensity for the given reaction.
`PropensityCalculator`	`getPropensityCalculator()` Gets the `PropensityCalculator`.
`double`	`getTime()` Gets the actual simulation time.
`double`	`getVolume()` Gets the volume of the reaction network.
`void`	`initialize()` Initializes the algorithm: set t=0reset the `AmountManager`recalculate the propensities Gets called at the very beginning of `start`
`void`	`initializePropensities()` Initializes the propensities.
`boolean`	`isInterpolateTheta()` Gets whether the amount values are returned interpolated for theta events.
`abstract void`	`performStep(SimulationController control)` Performs one simulation step.
`void`	`postRun()` Finalizes a simulation, i.e. call it, when this simulation will not be continued.
`void`	`preRun()` Initializes this simulator for the first run (or a further run starting from time 0).
`void`	`registerNewTheta(Observer obs, double theta)` Is called by `Observer.setTheta(double)`.
`abstract void`	`reinitialize()` Reset propensities when a event has been executed.
`void`	`run(SimulationController control)` Runs a simulation, after it's initialized by calling `preRun()` (allows to continue a simulation).
`void`	`setAmount(int species, long amount)` Sets the amount of the given species.
`void`	`setInterpolateTheta(boolean interpolateTheta)` Sets whether the amount values are returned interpolated for theta events.
`void`	`setStochasticSeed(long seed)` Sets the seed for a particular model.
`void`	`setVolume(double volume)` Sets the volume of the reaction network.
`void`	`start(double time)` Starts the simulation up to a given time.
`void`	`start(SimulationController control)` Start the simulation with the given `SimulationController`.

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - Simulator
```
public Simulator(Network net)
```
    Creates a new simulator for the given network.
    
    Parameters:
    
    net - the network to simulate
- Method Detail
  - start
```
public void start(double time)
```
    Starts the simulation up to a given time. It just uses a DefaultController and calls start(SimulationController).
    
    Parameters:
    
    time - simulation time
  - start
```
public void start(SimulationController control)
```
    Start the simulation with the given SimulationController. Basically calls preRun(),run(SimulationController) and postRun().
    
    Parameters:
    
    control - the SimulationController
  - preRun
```
public void preRun()
```
    Initializes this simulator for the first run (or a further run starting from time 0).
  - run
```
public void run(SimulationController control)
```
    Runs a simulation, after it's initialized by calling preRun() (allows to continue a simulation).
    
    Parameters:
    
    control -
  - postRun
```
public void postRun()
```
    Finalizes a simulation, i.e. call it, when this simulation will not be continued.
  - initialize
```
public void initialize()
```
    Initializes the algorithm:
    - set t=0
    - reset the AmountManager
    - recalculate the propensities
    Gets called at the very beginning of start
  - initializePropensities
```
public void initializePropensities()
```
    Initializes the propensities. Also, reinitialize them whenever any event is executed.
  - reinitialize
```
public abstract void reinitialize()
```
    Reset propensities when a event has been executed.
  - performStep
```
public abstract void performStep(SimulationController control)
```
    Performs one simulation step. Between steps the terminating condition is checked. The simulators controller is passed, if an extending class wants to check it within one step. Implementing algorithms cannot be sure that the propensities are correct at the beginning of a step (e.g. if the volume changed). They should override setAmount(int, long) and setVolume(double) if they need correct values!
    
    Parameters:
    
    control - the simulators controller
  - getName
```
public abstract String getName()
```
    Gets the name of the algorithm.
    
    Returns:
    
    name of the algorithm
  - getTime
```
public double getTime()
```
    Gets the actual simulation time.
    
    Returns:
    
    actual simulation time
  - registerNewTheta
```
public void registerNewTheta(Observer obs,
                             double theta)
```
    Is called by Observer.setTheta(double).
    
    Parameters:
    
    obs - the observer which is registering
    
    theta - the theta to register
  - getNextThetaEvent
```
public double getNextThetaEvent()
```
    Theta defines a moment, where the simulator has to invoke theta of a observer. It is used e.g. to determine the amounts of species at one moments. Extending class just have to call thetaEvent() which basically calls the observer.
    
    Returns:
    
    the theta
  - getAmount
```
public double getAmount(int species)
```
    Gets the amount of the given species.
    
    Parameters:
    
    species - species index
    
    Returns:
    
    amount of species
    
    See Also:
    
    AmountManager.getAmount(int)
  - setAmount
```
public void setAmount(int species,
                      long amount)
```
    Sets the amount of the given species. Propensities have to be recalculated!
    
    Parameters:
    
    species - species index
    
    amount - amount of species
    
    See Also:
    
    AmountManager.setAmount(int, long)
  - getPropensityCalculator
```
public PropensityCalculator getPropensityCalculator()
```
    Gets the PropensityCalculator.
    
    Returns:
    
    the PropensityCalculator
  - getNet
```
public Network getNet()
```
    Gets the simulation network.
    
    Returns:
    
    the network
  - addObserver
```
public Observer addObserver(Observer observer)
```
    Adds an observer to the list of observers.
    
    Parameters:
    
    observer - the observer to add
    
    Returns:
    
    the added observer
  - setStochasticSeed
```
public void setStochasticSeed(long seed)
```
    Sets the seed for a particular model.
    
    Parameters:
    
    seed -
  - getVolume
```
public double getVolume()
```
    Gets the volume of the reaction network.
    
    Returns:
    
    volume
  - setVolume
```
public void setVolume(double volume)
```
    Sets the volume of the reaction network.
    
    Parameters:
    
    volume - the volume
  - isInterpolateTheta
```
public boolean isInterpolateTheta()
```
    Gets whether the amount values are returned interpolated for theta events.
    
    Returns:
    
    interpolated
  - setInterpolateTheta
```
public void setInterpolateTheta(boolean interpolateTheta)
```
    Sets whether the amount values are returned interpolated for theta events.
  - getPropensity
```
public double getPropensity(int reaction)
```
    Gets the current propensity for the given reaction.
    
    Parameters:
    
    reaction - index of the reaction
    
    Returns:
    
    propensity for the reaction

Class Simulator

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Simulator

Method Detail

start

start

preRun

run

postRun

initialize

initializePropensities

reinitialize

performStep

getName

getTime

registerNewTheta

getNextThetaEvent

getAmount

setAmount

getPropensityCalculator

getNet

addObserver

setStochasticSeed

getVolume

setVolume

isInterpolateTheta

setInterpolateTheta

getPropensity