color.php

<?php

namespace Equidea\Engine;

// Base phenotypes

define('COLOR_BLACK', 1);
define('COLOR_SEALBROWN', 2);

define('COLOR_BAY', 3);
define('COLOR_WILDBAY', 4);

define('COLOR_CHESTNUT', 5);
define('COLOR_FLAXEN_CHESTNUT', 6);

// Single cream phenotypes

define('COLOR_SMOKY_BLACK', 7);
define('COLOR_SMOKY_BROWN', 8);

define('COLOR_BUCKSKIN', 9);
define('COLOR_WILD_BUCKSKIN', 10);

define('COLOR_PALOMINO', 11);

// Double cream phenotypes

define('COLOR_SMOKY_CREAM', 12);
define('COLOR_SEALBROWN_CREAM', 13);

define('COLOR_PERLINO', 14);
define('COLOR_CREMELLO', 15);

/**
 * An object representation of a full horse color genome.
 *
 * A genome contains many different locuses, which are the places where genetic
 * information about color mutations and manipulation of molecules such as
 * eumelanin and pheomelanin are stored.
 *
 * @see https://en.wikipedia.org/wiki/Equine_coat_color_genetics
 *
 * @author      Lisa Saalfrank <lisa.saalfrank@web.de>
 * @copyright   2020 Lisa Saalfrank
 * @package     Equidea\Engine
 * @version     0.1.0
 */
class ColorDna
{
    public const GENE_CHECK_HOMOZYGOUS = true;
    public const GENE_CHECK_HETEROZYGOUS = false;

    // Agouti

    public const AGOUTI_INACTIVE = 'a';
    public const AGOUTI_SEALBROWN = 'at';
    public const AGOUTI_BAY = 'A';
    public const AGOUTI_WILDBAY = 'A+';

    // Extension

    public const EXTENSION_INACTIVE = 'e';
    public const EXTENSION_ACTIVE = 'E';

    // Flaxen

    public const FLAXEN_INACTIVE = 'F';
    public const FLAXEN_ACTIVE = 'f';

    // Cream

    public const CREAM_INACTIVE = 'cr'
    public const CREAM_ACTIVE = 'Cr';

    protected array $agouti = [
        self::AGOUTI_INACTIVE,
        self::AGOUTI_INACTIVE
    ];

    protected array $extension = [
       self::EXTENSION_INACTIVE,
       self::EXTENSION_INACTIVE
    ];

    protected array $flaxen = [
        self::FLAXEN_INACTIVE,
        self::FLAXEN_INACTIVE
    ];

    protected array $cream = [
        self::CREAM_INACTIVE,
        self::CREAM_INACTIVE
    ];

    public function getAgouti() : array {
        return $this->agouti;
    }

    public function getExtension() : array {
        return $this->extension;
    }

    public function getFlaxen() : array {
        return $this->flaxen;
    }

    public function getCream() : array {
        return $this->cream;
    }

    public function agoutiHas(string $gene) : bool {
        return in_array($gene, $this->agouti);
    }

    public function extensionHas(string $gene) : bool {
        return in_array($gene, $this->extension);
    }

    public function flaxenHas(string $gene) : bool {
        return in_array($gene, $this->flaxen);
    }

    public function creamHas(string $gene, bool $type = false) : bool
    {
        if ($type == true) {
            return $this->cream[0] == $gene && $this->cream[1] == $gene;
        }

        return in_array($gene, $this->cream);
    }

    public function setAllAlleles(array $dna) : void
    {
        $this->agouti = $dna['agouti'];
        $this->extension = $dna['extension'];
        $this->flaxen = $dna['flaxen'];
        $this->cream = $dna['cream'];
    }

    public function getAllAlleles() : array
    {
        return [
            'agouti' => $this->agouti,
            'extension' => $this->extension,
            'flaxen' => $this->flaxen,
            'cream' => $this->cream
        ];
    }

    public function importJson(array $jsonDna) : void
    {
        $this->agouti = json_decode($jsonDna['agouti']);
        $this->extension = json_decode($jsonDna['extension']);
        $this->flaxen = json_decode($jsonDna['flaxen']);
        $this->cream = json_decode($jsonDna['cream']);
    }

    public function exportJson() : array
    {
        return [
            'agouti' => json_encode($this->agouti),
            'extension' => json_encode($this->extension),
            'flaxen' => json_encode($this->flaxen),
            'cream' => json_encode($this->cream)
        ];
    }
}

// Color inheritance

function inheritColorDna(ColorDna $mother, ColorDna $father) : ColorDna
{
    $randomGene = function(array $genes) : string {
        return $genes[array_rand($genes)];
    };

    $motherAlleles = $mother->getAllAlleles();
    $fatherAlleles = $father->getAllAlleles();

    $childAlleles = [];

    foreach (array_keys($motherAlleles) as $allele)
    {
        $childAlleles[$allele] = [
            $randomGene($motherAlleles[$allele]),
            $randomGene($fatherAlleles[$allele])
        ];
    }

    $child = new ColorDna();
    $child->setAllAlleles($childAlleles);
    return $child;
}

// Color calculation

function findBasePhenotype(ColorDna $dna) : int
{
    if ($dna->extensionHas(ColorDna::EXTENSION_ACTIVE))
    {
        if ($dna->agoutiHas(ColorDna::AGOUTI_WILDBAY)) {
            return COLOR_WILDBAY;
        }

        if ($dna->agoutiHas(ColorDna::AGOUTI_BAY)) {
            return COLOR_BAY;
        }

        if ($dna->agoutiHas(ColorDna::AGOUTI_SEALBROWN)) {
            return COLOR_SEALBROWN;
        }

        return COLOR_BLACK;
    } else
    {
        if (!$dna->flaxenHas(ColorDna::FLAXEN_INACTIVE)) {
            return COLOR_FLAXEN_CHESTNUT;
        }

        return COLOR_CHESTNUT;
    }
}

function hasDoubleCreamPhenotype(ColorDna $dna) : bool
{
    return $dna->creamHas(
        ColorDna::CREAM_ACTIVE,
        ColorDna::GENE_CHECK_HOMOZYGOUS
    );
}

function findSingleCreamPhenotype(int $base) : int
{
    switch ($base)
    {
        case COLOR_BLACK: return COLOR_SMOKY_BLACK;
        case COLOR_SEALBROWN: return COLOR_SMOKY_BROWN;

        case COLOR_BAY: return COLOR_BUCKSKIN;
        case COLOR_WILDBAY: return COLOR_WILD_BUCKSKIN;

        case COLOR_CHESTNUT:
        case COLOR_FLAXEN_CHESTNUT: return COLOR_PALOMINO;
    }
}

function findDoubleCreamPhenotype(int $base) : int
{
    switch ($base)
    {
        case COLOR_BLACK: return COLOR_SMOKY_CREAM;
        case COLOR_SEALBROWN: return COLOR_SEALBROWN_CREAM;

        case COLOR_BAY:
        case COLOR_WILDBAY: return COLOR_PERLINO;

        case COLOR_CHESTNUT:
        case COLOR_FLAXEN_CHESTNUT: return COLOR_CREMELLO;
    }
}

function findBirthPhenotype(ColorDna $dna) : int
{
    $base = findBasePhenotype($dna);

    if ($dna->creamHas(ColorDna::CREAM_ACTIVE))
    {
        if (hasDoubleCreamPhenotype($dna)) {
            return findDoubleCreamPhenotype($base);
        }

        return findSingleCreamPhenotype($base);
    }

    return $base;
}




function hasGreyPhenotype(ColorDna $dna) : bool
{
    return !$dna->greyHas(
        ColorDna::GREY_INACTIVE,
        ColorDna::GENE_CHECK_HOMOZYGOUS
    );
}

function findIntermediateGreyPhenotype(int $base) : int
{
    switch ($base)
    {
        case COLOR_BLACK: return COLOR_BLACK_GREY;
        case COLOR_SEALBROWN: return COLOR_SEALBROWN_GREY;

        case COLOR_BAY: return COLOR_BAY_GREY;
        case COLOR_WILDBAY: return COLOR_WILDBAY_GREY;

        case COLOR_CHESTNUT: return COLOR_FLAXEN_CHESTNUT_GREY;
        case COLOR_FLAXEN_CHESTNUT: return COLOR_FLAXEN_CHESTNUT_GREY;

        case COLOR_SMOKY_BLACK: return COLOR_SMOKY_BLACK_GREY;
        case COLOR_SMOKY_BROWN: return COLOR_SMOKY_BROWN_GREY;

        case COLOR_BUCKSKIN: return COLOR_BUCKSKIN_GREY;
        case COLOR_WILD_BUCKSKIN: return COLOR_WILD_BUCKSKIN_GREY;

        case COLOR_PALOMINO: return COLOR_PALOMINO_GREY;
    }
}

function findFinalGreyPhenotype(ColorDna $dna) : int
{
    if ($dna->greyHas(ColorDna::GREY_NORMAL))
    {
        $isNormalHomozygous = $dna->greyHas(
            ColorDna::GREY_NORMAL,
            ColorDna::GENE_CHECK_HOMOZYGOUS
        );

        if ($isNormalHomozygous == true) {
            return COLOR_SOLID_GREY;
        }

        return COLOR_FLEABITTEN_GREY;
    }

    return COLOR_DAPPLE_GREY;
}