alchemist/it.unibo.alchemist.model.biochemistry.environments/BioRect2DEnvironmentNoOverlap

BioRect2DEnvironmentNoOverlap

class BioRect2DEnvironmentNoOverlap : BioRect2DEnvironment, EnvironmentSupportingDeformableCells<P>

Implements a limited environment supporting cells with a defined shape, avoiding any overlapping among them.

Constructors

constructor(incarnation: BiochemistryIncarnation)

Returns an infinite BioRect2DEnvironment.

constructor(incarnation: BiochemistryIncarnation, minX: Double, maxX: Double, minY: Double, maxY: Double)

Returns a limited rectangular BioRect2DEnvironment.

Properties

globalReactions

val globalReactions: ListSet<GlobalReaction<T>>

incarnation

open val incarnation: Incarnation<T, P>

nodes

val nodes: ListSet<Node<T>>

shapeFactory

val shapeFactory: Euclidean2DShapeFactory

simulation

open var simulation: Simulation<T, P>

Functions

addGlobalReaction

open fun addGlobalReaction(p: GlobalReaction<T>)

addLayer

fun addLayer(p: Molecule, p1: Layer<T, P>)

addNode

fun addNode(p: Node<T>, p1: P): Boolean

addTerminator

fun addTerminator(p: Predicate<Environment<T, P>>)

farthestPositionReachable

abstract fun farthestPositionReachable(p: Node<T>, p1: P, p2: Double): P

open fun farthestPositionReachable(p: Node<T>, p1: Euclidean2DPosition, p2: Double): Euclidean2DPosition

forEach

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

getDimensions

fun getDimensions(): Int

getDistanceBetweenNodes

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

getHeading

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

open fun getHeading(p: Node<T>): Euclidean2DPosition

getLayer

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

getLayers

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

getLinkingRule

fun getLinkingRule(): LinkingRule<T, P>

getMaxDiameterAmongCircularDeformableCells

open fun getMaxDiameterAmongCircularDeformableCells(): Double

getNeighborhood

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

getNodeByID

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

getNodeCount

fun getNodeCount(): Int

getNodesWithin

open fun getNodesWithin(p: Shape<Euclidean2DPosition, Euclidean2DTransformation>): List<Node<T>>

getNodesWithinRange

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

getOffset

fun getOffset(): Array<Double>

getOrigin

open fun getOrigin(): P

open fun getOrigin(): Euclidean2DPosition

getPosition

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

getShape

abstract fun getShape(p: Node<T>): Shape<P, A>

open fun getShape(p: Node<T>): Shape<Euclidean2DPosition, Euclidean2DTransformation>

getShapeFactory

abstract fun getShapeFactory(): F

getSize

fun getSize(): Array<Double>

getSizeInDistanceUnits

open fun getSizeInDistanceUnits(): Array<Double>

isTerminated

fun isTerminated(): Boolean

iterator

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

abstract fun iterator(): Iterator<T>

makePosition

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

open fun makePosition(p: Array<Number>): Euclidean2DPosition

moveNode

open fun moveNode(p: Node<T>, p1: P)

fun moveNode(node: Node<Double>, @Nonnull direction: Euclidean2DPosition)

moveNodeToPosition

open fun moveNodeToPosition(@Nonnull node: Node<Double>, newPos: Euclidean2DPosition)

removeGlobalReaction

open fun removeGlobalReaction(p: GlobalReaction<T>)

removeNode

fun removeNode(p: Node<T>)

setHeading

open fun setHeading(p: Node<T>, p1: Euclidean2DPosition)

setLinkingRule

fun setLinkingRule(p: LinkingRule<T, P>)

spliterator

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

open fun spliterator(): Spliterator<T>

subscriptionMonitor

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

Returns the EnvironmentSubscriptionMonitor of this Environment.

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