it.unibo.alchemist.core.implementations

Class Engine<T>

java.lang.Object

it.unibo.alchemist.core.implementations.Engine<T>

Type Parameters:

T -

All Implemented Interfaces:

it.unibo.alchemist.core.interfaces.Simulation<T>, java.lang.Runnable

public final class Engine<T>
extends java.lang.Object
implements it.unibo.alchemist.core.interfaces.Simulation<T>

This class implements a simulation. It offers a wide number of static factories to ease the creation process.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Engine.StateCommand<T> This class provides a flexible Builder to create a new Command whose aim is to change the status of a Engine.

Constructor Summary

Constructors

Constructor and Description
Engine(it.unibo.alchemist.model.interfaces.Environment<T> e, long maxSteps) Builds a simulation for a given environment.
Engine(it.unibo.alchemist.model.interfaces.Environment<T> e, long maxSteps, it.unibo.alchemist.model.interfaces.Time t) Builds a simulation for a given environment.
Engine(it.unibo.alchemist.model.interfaces.Environment<T> e, it.unibo.alchemist.model.interfaces.Time t) Builds a simulation for a given environment.

Method Summary

Modifier and Type	Method and Description
void	addCommand(it.unibo.alchemist.core.interfaces.Command<T> comm)
static <T> void	addOutputMonitor(it.unibo.alchemist.model.interfaces.Environment<T> env, it.unibo.alchemist.boundary.interfaces.OutputMonitor<T> monitor) Statically searches for the simulation running some environment, and adds an OutputMonitor to it.
void	addOutputMonitor(it.unibo.alchemist.boundary.interfaces.OutputMonitor<T> op)
static <T> Engine<T>	buildSimulation(it.unibo.alchemist.model.interfaces.Environment<T> env)
static <T> Engine<T>	buildSimulation(it.unibo.alchemist.model.interfaces.Environment<T> env, long steps)
static <T> Engine<T>	buildSimulation(it.unibo.alchemist.model.interfaces.Environment<T> env, long steps, it.unibo.alchemist.model.interfaces.Time t)
static <T> Engine<T>	buildSimulation(it.unibo.alchemist.model.interfaces.Environment<T> env, it.unibo.alchemist.model.interfaces.Time t)
static <T> Engine<T>	fromEnvironment(it.unibo.alchemist.model.interfaces.Environment<T> env) Given an environment, returns the corresponding simulation.
it.unibo.alchemist.core.interfaces.DependencyGraph<T>	getDependencyGraph()
it.unibo.alchemist.model.interfaces.Environment<T>	getEnvironment()
java.lang.Throwable	getError()
long	getFinalStep()
it.unibo.alchemist.model.interfaces.Time	getFinalTime()
it.unibo.alchemist.core.interfaces.ReactionManager<T>	getReactionManager()
it.unibo.alchemist.core.interfaces.Status	getStatus()
long	getStep()
it.unibo.alchemist.model.interfaces.Time	getTime()
static <T> void	neighborAdded(it.unibo.alchemist.model.interfaces.Environment<T> env, it.unibo.alchemist.model.interfaces.Node<T> node, it.unibo.alchemist.model.interfaces.Node<T> n)
static <T> void	neighborRemoved(it.unibo.alchemist.model.interfaces.Environment<T> env, it.unibo.alchemist.model.interfaces.Node<T> node, it.unibo.alchemist.model.interfaces.Node<T> n)
static <T> void	nodeAdded(it.unibo.alchemist.model.interfaces.Environment<T> env, it.unibo.alchemist.model.interfaces.Node<T> node) This method provide a facility for adding all the reactions of a node to the current simulation, creating also the dependencies.
static <T> void	nodeMoved(it.unibo.alchemist.model.interfaces.Environment<T> env, it.unibo.alchemist.model.interfaces.Node<T> node)
static <T> void	nodeRemoved(it.unibo.alchemist.model.interfaces.Environment<T> env, it.unibo.alchemist.model.interfaces.Node<T> node, it.unibo.alchemist.model.interfaces.Neighborhood<T> oldNeighborhood) This method provide a facility for removing all the reactions of a node from the current simulation, along with their dependencies.
void	removeOutputMonitor(it.unibo.alchemist.boundary.interfaces.OutputMonitor<T> op)
static <T> void	removeReaction(it.unibo.alchemist.model.interfaces.Environment<T> env, it.unibo.alchemist.model.interfaces.Reaction<T> r)
void	run()
java.lang.String	toString()
it.unibo.alchemist.core.interfaces.Status	waitFor(it.unibo.alchemist.core.interfaces.Status s, long timeout, java.util.concurrent.TimeUnit tu)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Engine

public Engine(it.unibo.alchemist.model.interfaces.Environment<T> e,
              it.unibo.alchemist.model.interfaces.Time t)

Builds a simulation for a given environment. By default it uses a DependencyGraph and an IndexedPriorityQueue internally. If you want to use your own implementations of DependencyGraph and ReactionManager interfaces, don't use this constructor.

Parameters:

e - the environment at the initial time

t - the maximum time to reach

Engine

public Engine(it.unibo.alchemist.model.interfaces.Environment<T> e,
              long maxSteps)

Builds a simulation for a given environment. By default it uses a DependencyGraph and an IndexedPriorityQueue internally. If you want to use your own implementations of DependencyGraph and ReactionManager interfaces, don't use this constructor.

Parameters:

e - the environment at the initial time

maxSteps - the maximum number of steps to do

Engine

public Engine(it.unibo.alchemist.model.interfaces.Environment<T> e,
              long maxSteps,
              it.unibo.alchemist.model.interfaces.Time t)

Builds a simulation for a given environment. By default it uses a DependencyGraph and an IndexedPriorityQueue internally. If you want to use your own implementations of DependencyGraph and ReactionManager interfaces, don't use this constructor.

Parameters:

e - the environment at the initial time

maxSteps - the maximum number of steps to do

t - the maximum time to reach

Method Detail

addOutputMonitor

public static <T> void addOutputMonitor(it.unibo.alchemist.model.interfaces.Environment<T> env,
                                        it.unibo.alchemist.boundary.interfaces.OutputMonitor<T> monitor)

Statically searches for the simulation running some environment, and adds an OutputMonitor to it.

Type Parameters:

T - The format of the concentrations

Parameters:

env - The current environment

monitor - The monitor to add

buildSimulation

public static <T> Engine<T> buildSimulation(it.unibo.alchemist.model.interfaces.Environment<T> env)

Type Parameters:

T - The format of the concentrations

Parameters:

env - The environment to be simulated

Returns:

A simulation ready to be run, the environment structures get updated coherently

buildSimulation

public static <T> Engine<T> buildSimulation(it.unibo.alchemist.model.interfaces.Environment<T> env,
                                            it.unibo.alchemist.model.interfaces.Time t)

Type Parameters:

T - The format of the concentrations

Parameters:

env - The environment to be simulated

t - The final simulation time to reach

Returns:

A simulation ready to be run, the environment structures get updated coherently

buildSimulation

public static <T> Engine<T> buildSimulation(it.unibo.alchemist.model.interfaces.Environment<T> env,
                                            long steps)

Type Parameters:

T - The format of the concentrations

Parameters:

env - The environment to be simulated

steps - The number of steps to run

Returns:

A simulation ready to be run, the environment structures get updated coherently

buildSimulation

public static <T> Engine<T> buildSimulation(it.unibo.alchemist.model.interfaces.Environment<T> env,
                                            long steps,
                                            it.unibo.alchemist.model.interfaces.Time t)

Type Parameters:

T - The format of the concentrations

Parameters:

env - The environment to be simulated

steps - The number of steps to run

t - The final simulation time to reach

Returns:

A simulation ready to be run, the environment structures get updated coherently

fromEnvironment

public static <T> Engine<T> fromEnvironment(it.unibo.alchemist.model.interfaces.Environment<T> env)

Given an environment, returns the corresponding simulation.

Type Parameters:

T - concentrations

Parameters:

env - the environment

Returns:

the simulation

neighborAdded

public static <T> void neighborAdded(it.unibo.alchemist.model.interfaces.Environment<T> env,
                                     it.unibo.alchemist.model.interfaces.Node<T> node,
                                     it.unibo.alchemist.model.interfaces.Node<T> n)

Type Parameters:

T - Type for concentrations

Parameters:

env - the environment

node - first node

n - second node

neighborRemoved

public static <T> void neighborRemoved(it.unibo.alchemist.model.interfaces.Environment<T> env,
                                       it.unibo.alchemist.model.interfaces.Node<T> node,
                                       it.unibo.alchemist.model.interfaces.Node<T> n)

Type Parameters:

T - Type for concentrations

Parameters:

env - the environment

node - first node

n - second node

nodeMoved

public static <T> void nodeMoved(it.unibo.alchemist.model.interfaces.Environment<T> env,
                                 it.unibo.alchemist.model.interfaces.Node<T> node)

Type Parameters:

T - Type for concentrations

Parameters:

env - the environment

node - the node

nodeAdded

public static <T> void nodeAdded(it.unibo.alchemist.model.interfaces.Environment<T> env,
                                 it.unibo.alchemist.model.interfaces.Node<T> node)

This method provide a facility for adding all the reactions of a node to the current simulation, creating also the dependencies. This method must be called only when it is possible for the environment to successfully compute the neighborhood for the new node.

Type Parameters:

T - Type for concentrations

Parameters:

env - the environment

node - the freshly added node

nodeRemoved

public static <T> void nodeRemoved(it.unibo.alchemist.model.interfaces.Environment<T> env,
                                   it.unibo.alchemist.model.interfaces.Node<T> node,
                                   it.unibo.alchemist.model.interfaces.Neighborhood<T> oldNeighborhood)

This method provide a facility for removing all the reactions of a node from the current simulation, along with their dependencies. This method must be called when it is still possible for the environment to successfully compute the neighborhood for the removed node.

Type Parameters:

T - Type for concentrations

Parameters:

env - the environment

node - the freshly removed node

oldNeighborhood - the neighborhood of the node as it was before it was removed (used to calculate reverse dependencies)

removeReaction

public static <T> void removeReaction(it.unibo.alchemist.model.interfaces.Environment<T> env,
                                      it.unibo.alchemist.model.interfaces.Reaction<T> r)

Type Parameters:

T - Type for concentrations

Parameters:

env - the environment

r - the removed reaction

addOutputMonitor

public void addOutputMonitor(it.unibo.alchemist.boundary.interfaces.OutputMonitor<T> op)

Specified by:

addOutputMonitor in interface it.unibo.alchemist.core.interfaces.Simulation<T>

removeOutputMonitor

public void removeOutputMonitor(it.unibo.alchemist.boundary.interfaces.OutputMonitor<T> op)

Specified by:

removeOutputMonitor in interface it.unibo.alchemist.core.interfaces.Simulation<T>

getDependencyGraph

public it.unibo.alchemist.core.interfaces.DependencyGraph<T> getDependencyGraph()

Returns:

the dependency graph

getEnvironment

public it.unibo.alchemist.model.interfaces.Environment<T> getEnvironment()

Specified by:

getEnvironment in interface it.unibo.alchemist.core.interfaces.Simulation<T>

getFinalStep

public long getFinalStep()

Specified by:

getFinalStep in interface it.unibo.alchemist.core.interfaces.Simulation<T>

getFinalTime

public it.unibo.alchemist.model.interfaces.Time getFinalTime()

Specified by:

getFinalTime in interface it.unibo.alchemist.core.interfaces.Simulation<T>

getReactionManager

public it.unibo.alchemist.core.interfaces.ReactionManager<T> getReactionManager()

Returns:

The IPQ

getStatus

public it.unibo.alchemist.core.interfaces.Status getStatus()

Specified by:

getStatus in interface it.unibo.alchemist.core.interfaces.Simulation<T>

getStep

public long getStep()

Specified by:

getStep in interface it.unibo.alchemist.core.interfaces.Simulation<T>

getTime

public it.unibo.alchemist.model.interfaces.Time getTime()

Specified by:

getTime in interface it.unibo.alchemist.core.interfaces.Simulation<T>

addCommand

public void addCommand(it.unibo.alchemist.core.interfaces.Command<T> comm)

Specified by:

addCommand in interface it.unibo.alchemist.core.interfaces.Simulation<T>

waitFor

public it.unibo.alchemist.core.interfaces.Status waitFor(it.unibo.alchemist.core.interfaces.Status s,
                                                         long timeout,
                                                         java.util.concurrent.TimeUnit tu)

Specified by:

waitFor in interface it.unibo.alchemist.core.interfaces.Simulation<T>

run

public void run()

Specified by:

run in interface java.lang.Runnable

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getError

public java.lang.Throwable getError()