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

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

open fun forEach(p: Consumer<in T>)

getDimensions

fun getDimensions(): Int

getDistanceBetweenNodes

abstract fun getDistanceBetweenNodes(p: Node<T>, p1: Node<T>): Double

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

getGlobalReactions

abstract fun getGlobalReactions(): ListSet<GlobalReaction<T>>

open fun getGlobalReactions(): ListSet<GlobalReaction<T>>

getIncarnation

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

getLayer

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

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

getLayers

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

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

getLinkingRule

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

getNeighborhood

abstract fun getNeighborhood(p: Node<T>): Neighborhood<T>

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

getNodeByID

abstract fun getNodeByID(p: Int): Node<T>

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

getNodeCount

abstract fun getNodeCount(): Int

fun getNodeCount(): Int

getNodes

abstract fun getNodes(): ListSet<Node<T>>

getNodesWithinRange

abstract fun getNodesWithinRange(p: Node<T>, p1: Double): ListSet<Node<T>>

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

getOffset

@Nonnull

fun getOffset(): Array<Double>

getPosition

abstract fun getPosition(p: Node<T>): P

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

getSimulation

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

fun getSimulation(): Simulation<T, P>

getSimulationOrNull

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

getSize

@Nonnull

fun getSize(): Array<Double>

getSizeInDistanceUnits

abstract fun getSizeInDistanceUnits(): Array<Double>

open fun getSizeInDistanceUnits(): Array<Double>

Override this property if units measuring distance do not match with units used for coordinates. For instance, if your space is non-Euclidean, or if you are using polar coordinates. A notable example is using geographical latitude-longitude as y-x coordinates and meters as distance measure.

isNetworkSegmented