<?php

namespace Equidea\Engine\Horse;

/**
 * An object representation of a full horse color genome.
 *
 * A genome contains many different locuses, which are the places for genetic information
 * about color mutations and manipulation of molecules such as eumelanin and pheomelanin.
 *
 * It provides methods for most common operations and supports JSON type array input
 * for allele locuses.
 *
 * @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 ColorGenome {

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

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

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

    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
    ];

    /**
     * Returns the allele on the agouti locus that controls the restriction of eumelanin
     * in the horses coat.
     *
     * There are for different variants of the gene:
     * - 'a' which results in black horses
     * - 'At' which results in seal brown horses
     * - 'A' which results in normal type bay horses
     * - 'A+' which results in wild type bay horses
     *
     * @see https://en.wikipedia.org/wiki/Equine_coat_color_genetics#Agouti_phenotypes
     *
     * @return  array   The agouti locus
     */
    public function getAgouti() : array {
        return $this->agouti;
    }

    /**
     * Returns the allele on the extension locus that controls whether a horses hair should
     * be black or red.
     *
     * There are two different variants of the gene:
     * - 'e' which will produce chestnut horses
     * - 'E' which produces black, seal brown, bay or wild bay horses
     *
     * @see https://en.wikipedia.org/wiki/Equine_coat_color_genetics#Extension_phenotypes
     *
     * @return  array   The extension locus
     */
    public function getExtension() : array {
        return $this->extension;
    }

    /**
     * Returns the allele on the flaxen locus that only affects chestnut based colors.
     * It controls whether the mane and tale are red or blond.
     *
     * There are two different variants of the gene:
     * - 'f' which causes the hair to turn blond, making the color flaxen chestnut
     * - 'F' Which causes th hair to turn red, making it a normal chestnut
     *
     * @see https://en.wikipedia.org/wiki/Flaxen_gene
     *
     * @return  array   The flaxen locus
     */
    public function getFlaxen() : array {
        return $this->flaxen;
    }

    /**
     * Checks whether either one or both of the two genes of the allele on the agouti locus
     * match the given single gene.
     *
     * @param   string  $gene   The gene to search for
     *
     * @return  bool    The result of the search
     */
    public function agoutiHas(string $gene) : bool {
        return in_array($gene, $this->agouti);
    }

    /**
     * Checks whether either one or both of the two genes of the allele on the extension
     * locus match the given single gene.
     *
     * @param   string  $gene   The gene to search for
     *
     * @return  bool    The result of the search
     */
    public function extensionHas(string $gene) : bool {
        return in_array($gene, $this->extension);
    }

    /**
     * Checks whether either one or both of the two genes of the allele on the flaxen locus
     * match the given single gene.
     *
     * @param   string  $gene   The gene to search for
     *
     * @return  bool    The result of the search
     */
    public function flaxenHas(string $gene) : bool {
        return in_array($gene, $this->flaxen);
    }

    /**
     * Fills all locuses with their allele pairs. Array must be a multi-dimensional
     * associative array with the keys for agouti, extension and flaxen.
     * The genes of an allele must be provided as an indexed array.
     *
     * Example:
     * [
     *  'agouti' => ['a', 'a'],
     *  'extension' => ['e', 'e'],
     *  'flaxen' => ['f', 'f']
     * ]
     *
     * @param   array   $dna    All color alleles for each locus of a genome
     *
     * @return  void
     */
    public function setAllAlleles(array $dna) : void
    {
        $this->agouti = $dna['agouti'];
        $this->extension = $dna['extension'];
        $this->flaxen = $dna['flaxen'];
    }

    /**
     * Retrieves all locuses with their allele pairs as a multi-dimensional
     * associative array with the keys for agouti, extension and flaxen.
     * The genes of an allele are provided as an indexed array.
     *
     * Example:
     * [
     *  'agouti' => ['a', 'a'],
     *  'extension' => ['e', 'e'],
     *  'flaxen' => ['f', 'f']
     * ]
     *
     * @return  array   All color alleles for each locus of a genome
     */
    public function getAllAlleles() : array
    {
        return [
            'agouti' => $this->agouti,
            'extension' => $this->extension,
            'flaxen' => $this->flaxen
        ];
    }

    /**
     * Receives an associative array of JSON-encoded allele pairs for each locus.
     * Decodes the JSON import to indexed arrays and stores them in the class. Must
     * contain the locuses agouti, extension and flaxen.
     *
     * Example:
     * [
     *  'agouti' => '["a","a"]',
     *  'extension' => '["e","e"]',
     *  'flaxen' => '["f","f"]'
     * ]
     *
     * @param   array   $jsonDna    All color alleles encoded as JSON
     *
     * @return  void
     */
    public function importJson(array $jsonDna) : void
    {
        $this->agouti = json_decode($jsonDna['agouti']);
        $this->extension = json_decode($jsonDna['extension']);
        $this->flaxen = json_decode($jsonDna['flaxen']);
    }

    /**
     * Returns an associative array of JSON-encoded allele pairs for each locus, which
     * are the locuses agouti, extension and flaxen. Note that only the alleles are
     * JSON encoded but not the associations with locuses.
     *
     * Example:
     * [
     *  'agouti' => '["a","a"]',
     *  'extension' => '["e","e"]',
     *  'flaxen' => '["f","f"]'
     * ]
     *
     * @return  All color alleles encoded as JSON
     */
    public function exportJson() : array
    {
        return [
            'agouti' => json_encode($this->agouti),
            'extension' => json_encode($this->extension),
            'flaxen' => json_encode($this->flaxen)
        ];
    }
}