fun <T> Environment<T, *>.allShortestPaths(computeDistance: (Node<T>, Node<T>) -> Double = neighborDistanceMetric { n1, n2 -> getDistanceBetweenNodes(n1, n2) }): Map<Environments.UndirectedEdge<T>, Double>

Computes all the minimum distances with the provided metric using the Floyd–Warshall algorithm.

allSubNetworks

fun <T> Environment<T, *>.allSubNetworks(computeDistance: (Node<T>, Node<T>) -> Double = environmentMetricDistance()): Set<Network<T>>

Computes the diameter of all subnetworks in the environment. The diameter is the longest shortest path between any two nodes. Returns a Set containing the SubNetworks.

allSubNetworksByNode

fun <T> Environment<T, *>.allSubNetworksByNode(computeDistance: (Node<T>, Node<T>) -> Double = environmentMetricDistance()): Map<Node<T>, Network<T>>

Computes the diameter of all subnetworks in the environment. The diameter is the longest shortest path between any two nodes. Returns a Set containing the SubNetworks.

allSubNetworksByNodeWithHopDistance

fun <T> Environment<T, *>.allSubNetworksByNodeWithHopDistance(): Map<Node<T>, Network<T>>

Computes the diameter of all subnetworks in the environment. The diameter is the longest shortest path between any two nodes, evaluated using the allShortestHopPaths method. Returns a Set containing the SubNetworks.

allSubNetworksWithHopDistance

fun <T> Environment<T, *>.allSubNetworksWithHopDistance(): Set<Network<T>>

forEach

fun forEach(action: Consumer<in Node<T>>)

getDimensions

abstract fun getDimensions(): Int

The number of dimensions of this environment.

getDistanceBetweenNodes

fun getDistanceBetweenNodes(n1: Node<T>, n2: Node<T>): Double

Measures the distance between two nodes (n1, n2) in the environment.

getGlobalReactions

abstract fun getGlobalReactions(): NonExistentClass

Get the Environment's GlobalReactions.

getIncarnation

abstract fun getIncarnation(): Incarnation<T, P>

Return the Incarnation used to initialize the entities of this Environment, if it has been set.

getLayer

fun getLayer(molecule: Molecule): Layer<T, P>

Get the Layer associate to the given molecule.

getLayers

fun getLayers(): ListSet<Layer<T, P>>

Return all the Layers in this Environment.

getLinkingRule

abstract fun getLinkingRule(): LinkingRule<T, P>

Returns the current LinkingRule.

getNeighborhood

fun getNeighborhood(node: Node<T>): Neighborhood<T>

Given a node, this method returns its neighborhood.

getNodeByID

fun getNodeByID(id: Int): Node<T>

Allows accessing a Node in this Environment known its id.

getNodeCount

fun getNodeCount(): Int

Returns the number of Nodes currently in the Environment.

getNodes

abstract fun getNodes(): NonExistentClass

Returns all the Nodes that exist in current Environment.

getNodesWithinRange

fun getNodesWithinRange(position: P, range: Double): ListSet<Node<T>>

Given a position this method returns a list of all the surrounding nodes within the given range.

fun getNodesWithinRange(node: Node<T>, range: Double): ListSet<Node<T>>

Given a node this method returns a list of all the surrounding nodes within the given range.

getOffset

abstract fun getOffset(): Array<Double>

This method allows to know which are the smallest coordinates represented. Return an array of length dimensions containing the smallest coordinates for each dimension.

getPosition

fun getPosition(node: Node<T>): P

Calculates the position of a node.

getSimulation

abstract fun getSimulation(): Simulation<T, P>

Return the current Simulation, if present, or throws an IllegalStateException otherwise.

getSimulationOrNull

open fun getSimulationOrNull(): Simulation<T, P>

Return the current Simulation, if present, or null otherwise.

getSize

abstract fun getSize(): Array<Double>

The size of the environment as an array of length getDimensions(). This method must return distance measured with the same unit used by the positions. No non-euclidean distance metrics are allowed.

getSizeInDistanceUnits

open fun getSizeInDistanceUnits(): Array<Double>

Override this method if units measuring distance do not match with units used for coordinates.

isNetworkSegmented

fun <T> Environment<T, *>.isNetworkSegmented(): Boolean

Returns true the network is segmented, false otherwise.

isTerminated

fun isTerminated(): Boolean

Return true if all the terminators are true.

iterator

fun iterator(): Iterator<Node<T>>

makePosition

abstract fun makePosition(coordinates: Array<Number>): P

Given the coordinates of the point, returns a Position compatible with this environment.

moveNodeToPosition

abstract fun moveNodeToPosition(node: Node<T>, position: P)

This method moves a node in the environment to some position. If node movement is unsupported, it does nothing.

networkDiameter

fun Environment<*, *>.networkDiameter(): Double

Returns the diameter of the network in environment units if it is not segmented, and NaN otherwise.

networkDiameterByHopDistance

fun Environment<*, *>.networkDiameterByHopDistance(): Double

Returns the hop-distance diameter of the network if it is not segmented, and NaN otherwise.

fun <T> Environment<T, *>.networkDiameterByHopDistance(node: Node<T>): Double

Computes the network diameter of the segment containing node.

randomElement

fun <R> Iterable<R>.randomElement(randomGenerator: <Error class: unknown class>): R

Returns a random element of the Iterable using the provided randomGenerator.

removeGlobalReaction

open fun removeGlobalReaction(reaction: GlobalReaction<T>)

Remove a GlobalReaction from the Environment.

removeNode

fun removeNode(node: Node<T>)

Removes node.

setLinkingRule

abstract fun setLinkingRule(<set-?>: LinkingRule<T, P>)

Returns the current LinkingRule.

setSimulation

abstract fun setSimulation(<set-?>: Simulation<T, P>)

Return the current Simulation, if present, or throws an IllegalStateException otherwise.

shuffled

fun <R> Iterable<R>.shuffled(randomGenerator: <Error class: unknown class>): Iterable<R>

Fisher–Yates shuffle algorithm using a RandomGenerator. More information on Wikipedia.

spliterator

fun spliterator(): Spliterator<Node<T>>

subscriptionMonitor

fun <T, P : Position<out P>> Environment<T, P>.subscriptionMonitor(): EnvironmentSubscriptionMonitor<T, P>

Returns the EnvironmentSubscriptionMonitor of this Environment.

toEnvironmentSurrogate

fun <T, P : Position<out P>, TS : Any> Environment<T, P>.toEnvironmentSurrogate(toConcentrationSurrogate: (T) -> TS): EnvironmentSurrogate<TS, PositionSurrogate>

A function that maps an Environment to its surrogate class (EnvironmentSurrogate). Use the toSuitablePositionSurrogate strategy for PositionSurrogate mapping.

fun <T, P : Position<out P>, TS : Any, PS : PositionSurrogate> Environment<T, P>.toEnvironmentSurrogate(toConcentrationSurrogate: (T) -> TS, toPositionSurrogate: (P) -> PS): EnvironmentSurrogate<TS, PS>

A function that maps an Environment to its surrogate class (EnvironmentSurrogate).

toGraphQLEnvironmentSurrogate

fun <T, P : Position<out P>> Environment<T, P>.toGraphQLEnvironmentSurrogate(): EnvironmentSurrogate<T, P>

Converts an Environment to a EnvironmentSurrogate.

toString

open fun toString(): String

Not used internally.