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Alchemist incarnation for biochemistry simulator

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/*
 * Copyright (C) 2010-2023, Danilo Pianini and contributors
 * listed, for each module, in the respective subproject's build.gradle.kts file.
 *
 * This file is part of Alchemist, and is distributed under the terms of the
 * GNU General Public License, with a linking exception,
 * as described in the file LICENSE in the Alchemist distribution's top directory.
 */

package it.unibo.alchemist.model.biochemistry.properties

import it.unibo.alchemist.model.Environment
import it.unibo.alchemist.model.Node
import it.unibo.alchemist.model.biochemistry.CellProperty
import it.unibo.alchemist.model.biochemistry.molecules.Junction
import it.unibo.alchemist.model.positions.Euclidean2DPosition
import it.unibo.alchemist.model.properties.AbstractNodeProperty
import org.apache.commons.math3.util.FastMath
import kotlin.math.nextDown
import kotlin.math.nextUp

/**
 * Base implementation of a [CellProperty].
 */
class Cell @JvmOverloads constructor(
    /**
     * The environment in which [node] is moving.
     */
    val environment: Environment,
    override val node: Node,
    override val junctions: MutableMap, Int>> = LinkedHashMap(),
) : AbstractNodeProperty(node), CellProperty {

    override var polarizationVersor: Euclidean2DPosition = Euclidean2DPosition.zero

    override fun addPolarizationVersor(versor: Euclidean2DPosition) {
        val tempCor = (polarizationVersor + versor.coordinates).coordinates
        val module = FastMath.hypot(tempCor[0], tempCor[1])
        polarizationVersor = when (module) {
            in 0.0.nextDown()..0.0.nextUp() -> Euclidean2DPosition.zero
            else -> Euclidean2DPosition(tempCor[0] / module, tempCor[1] / module)
        }
    }

    override fun cloneOnNewNode(node: Node) = Cell(environment, node)
}