DNA framework

/* ===
 
This code is licensed under Creative Commons Attribution-ShareAlike, if anyone is interested.
 
*/
 
class DNA {
    private $sequence = array();
    private $symbols = array();
 
    public function __construct($length = 10, $symbols=array('G','T','C', 'A')) {
        if (!empty($symbols) && IntVal($length)>0) {
            for($i=0;$i<=$length;$i++){
                $this->sequence[] = $symbols[0];
            }
            $this->symbols = $symbols;
            $this->length = count($this->sequence);
        }
    }
 
    public function inscribe($seq, $length) {
        if(strlen($seq) == 1 && isset($length) && in_array($seq, $this->symbols)) {
 
            // Clear the sequence
            $this->sequence = array();
 
            for($i=0;$i<=$length;$i++){
                $this->sequence[] = $seq;
            }
            return true;
        }
 
        if(is_string($seq) || is_array($seq)) {
 
            // Clear the sequence
            $this->sequence = array();
 
            if (is_string($seq)) {
                // Danger, memory leak here
                $seq = preg_split('//', $seq, -1, PREG_SPLIT_NO_EMPTY);
            }
 
            foreach($seq as $char) {
 
                // Checking allowed symbols
                if (in_array($char, $this->symbols)) {
                    $this->sequence[] = $char;
                }
 
            }
 
            return true;
        }
    }
 
    /**
    * @desc Mutates the sequence. Random symbols get replaced.
    * 
    * @param $count Number of replaced symbols
    * 
    * @param $probability Probability of replacement
    */
    public function mutate($count = 1, $probability = 100) {
        for($i=0;$i<=IntVal($count);$i++){
            $prob = rand(0,100);
            $random = rand(0, count($this->sequence) - 1);
            $target = rand(0, count($this->symbols) - 1);
 
            // We cannot mutate 'A' to 'A'
            while($this->sequence[$random] == $this->symbols[$target]) {
                $target = rand(0, count($this->symbols) - 1);
            }
 
            if ($prob <= $probability)
                $this->sequence[$random] = $this->symbols[$target];
        }
 
    }
 
 
    public function get_sequence() {
        return $this->sequence;
    }
 
    public function append($char) {
        if(in_array($char, $this->symbols)) {
            $this->sequence[] = $char;
        } else {
            echo $char . ' not in set: ' . implode($this->symbols) . '<br/>';
        }
    }
 
    public function clear() {
        $this->sequence = array();
    }
 
    function crossover($partner) {
        // Sequences must be of equal length
        if (count($this->sequence)) {
 
            //$partner = preg_split('//', $partner, -1, PREG_SPLIT_NO_EMPTY);
            $partner_genes = $partner->get_sequence();
            $child = new DNA(count($this->sequence), $this->symbols);
            $child->clear();
 
            $cut_place = rand(0, count($this->sequence) - 1);
 
            for($i=0;$i<$cut_place;$i++){
                $child->append($this->sequence[$i]);
            }
 
            for($i=$cut_place;$i<=(count($this->sequence) - 1);$i++){
                $child->append($partner_genes[$i]);
            }
 
            return $child;
        }
    }
 
    public function fitness() {
        $fit = 0;
        foreach($this->sequence AS $char) {
            if ($char == $this->symbols[0]) $fit++;
        }
        return $fit;
    }
 
    function __toString() {
        return implode($this->sequence);
    }
 
 
 
  }