alchemist/it.unibo.alchemist.model.biochemistry.reactions/BiochemicalReaction

BiochemicalReaction

class BiochemicalReaction : ChemicalReaction<T>

A biochemical Reaction.

Constructors

constructor(node: Node<Double>, timeDistribution: TimeDistribution<Double>, environment: Environment<Double, out Any>, randomGenerator: RandomGenerator)

Properties

node

val node: Node<T>

timeDistribution

val timeDistribution: TimeDistribution<T>

Functions

canExecute

abstract fun canExecute(): Boolean

open fun canExecute(): Boolean

The default implementation verifies if all the conditions are valid.

cloneOnNewNode

abstract fun cloneOnNewNode(node: Node<T>, currentTime: Time): Reaction<T>

This method allows to clone this reaction on a new node. It may result useful to support runtime creation of nodes with the same reaction programming, e.g. for morphogenesis.

open fun cloneOnNewNode(node: Node<Double>, currentTime: Time): BiochemicalReaction

This method allows to clone this reaction on a new node.

compareTo

fun compareTo(o: Actionable<T>): Int

abstract fun compareTo(p: T): Int

equals

fun equals(o: Any): Boolean

execute

abstract fun execute()

Executes the reactions.

open fun execute()

The default execution iterates all the actions in order and executes them.

getActions

abstract fun getActions(): List<Action<T>>

The list of Actions of the Reaction. Please be careful when you modify this list.

open fun getActions(): List<Action<T>>

Override only if you need to implement extremely tricky behaviours.

getConditions

abstract fun getConditions(): List<Condition<T>>

The list of Conditions of the Reaction. Please be careful when you modify this list.

open fun getConditions(): List<Condition<T>>

Override only if you need to implement extremely tricky behaviours.

getInboundDependencies

abstract fun getInboundDependencies(): NonExistentClass

fun getInboundDependencies(): ListSet<Dependency>

getInputContext

abstract fun getInputContext(): Context

The widest Context among Conditions, namely the smallest Context in which the Reaction can read informations.

fun getInputContext(): Context

The widest Context among Conditions, namely the smallest Context in which the Reaction can read informations.

getNode

abstract fun getNode(): Node<T>

getOutboundDependencies

abstract fun getOutboundDependencies(): NonExistentClass

fun getOutboundDependencies(): ListSet<Dependency>

getOutputContext

abstract fun getOutputContext(): Context

The widest Context among Actions, namely the smallest context in which the Reaction can do modifications.

fun getOutputContext(): Context

The widest Context among Actions, namely the smallest context in which the Reaction can do modifications.

getRate

open fun getRate(): Double

Returns the speed of this Reaction. It is an average number, and can potentially change during the simulation, depending on the implementation.

fun getRate(): Double

Returns the speed of this Reaction.

getTau

open fun getTau(): Time

fun getTau(): Time

getTimeDistribution

abstract fun getTimeDistribution(): TimeDistribution<T>

hashCode

fun hashCode(): Int

initializationComplete

abstract fun initializationComplete(atTime: Time, environment: Environment<T, out Any>)

This method is called when the environment has completed its initialization. Can be used by this reaction to compute its next execution time - in case such computation requires an inspection of the environment.

fun initializationComplete(atTime: Time, environment: Environment<T, out Any>)

This method is called when the environment has completed its initialization.

setActions

abstract fun setActions(<set-?>: List<out Action<T>>)

The list of Actions of the Reaction. Please be careful when you modify this list.

open fun setActions(actions: List<out Action<T>>)

This should get overridden only if very tricky behaviours are implemented, such that the default Alchemist action addition model is no longer usable.

setConditions

abstract fun setConditions(<set-?>: List<out Condition<T>>)

The list of Conditions of the Reaction. Please be careful when you modify this list.

open fun setConditions(conditions: List<out Condition<Double>>)

This should get overridden only if very tricky behaviours are implemented, such that the default Alchemist condition addition model is no longer usable.

toGraphQLReactionSurrogate

fun <T> Reaction<T>.toGraphQLReactionSurrogate(): ReactionSurrogate<T>

Converts a Reaction to a ReactionSurrogate.

toString

open fun toString(): String

update

abstract fun update(currentTime: Time, hasBeenExecuted: Boolean, environment: Environment<T, out Any>)

Updates the scheduling of this reaction.

fun update(currentTime: Time, hasBeenExecuted: Boolean, environment: Environment<T, out Any>)

Updates the scheduling of this reaction.