Smith–Waterman for string in PHP?

Question

i need smith-waterman in php, do you know if there is already an implementation?

I need this algo for proxmity searches ( Function that returns affinity between text

Answer 1

I reverse engineered the SimMetrics java code for SmithWatermanGotoh - I found that SmithWatermanGotoh is more efficient than SmithWaterman with very similar results:

class SmithWatermanGotoh 
{
    private $gapValue;
    private $substitution;

    /**
     * Constructs a new Smith Waterman metric.
     * 
     * @param gapValue
     *            a non-positive gap penalty
     * @param substitution
     *            a substitution function
     */
    public function __construct($gapValue=-0.5, 
                $substitution=null) 
    {
        if($gapValue > 0.0) throw new Exception("gapValue must be <= 0");
        //if(empty($substitution)) throw new Exception("substitution is required");
        if (empty($substitution)) $this->substitution = new SmithWatermanMatchMismatch(1.0, -2.0);
        else $this->substitution = $substitution;
        $this->gapValue = $gapValue;
    }

    public function compare($a, $b) 
    {
        if (empty($a) && empty($b)) {
            return 1.0;
        }

        if (empty($a) || empty($b)) {
            return 0.0;
        }

        $maxDistance = min(mb_strlen($a), mb_strlen($b))
                * max($this->substitution->max(), $this->gapValue);
        return $this->smithWatermanGotoh($a, $b) / $maxDistance;
    }

    private function smithWatermanGotoh($s, $t) 
    {   
        $v0 = [];
        $v1 = [];
        $t_len = mb_strlen($t);
        $max = $v0[0] = max(0, $this->gapValue, $this->substitution->compare($s, 0, $t, 0));

        for ($j = 1; $j < $t_len; $j++) {
            $v0[$j] = max(0, $v0[$j - 1] + $this->gapValue,
                    $this->substitution->compare($s, 0, $t, $j));

            $max = max($max, $v0[$j]);
        }

        // Find max
        for ($i = 1; $i < mb_strlen($s); $i++) {
            $v1[0] = max(0, $v0[0] + $this->gapValue, $this->substitution->compare($s, $i, $t, 0));

            $max = max($max, $v1[0]);

            for ($j = 1; $j < $t_len; $j++) {
                $v1[$j] = max(0, $v0[$j] + $this->gapValue, $v1[$j - 1] + $this->gapValue,
                        $v0[$j - 1] + $this->substitution->compare($s, $i, $t, $j));

                $max = max($max, $v1[$j]);
            }

            for ($j = 0; $j < $t_len; $j++) {
                $v0[$j] = $v1[$j];
            }
        }

        return $max;
    }
}

class SmithWatermanMatchMismatch
{
    private $matchValue;
    private $mismatchValue;

    /**
     * Constructs a new match-mismatch substitution function. When two
     * characters are equal a score of <code>matchValue</code> is assigned. In
     * case of a mismatch a score of <code>mismatchValue</code>. The
     * <code>matchValue</code> must be strictly greater then
     * <code>mismatchValue</code>
     * 
     * @param matchValue
     *            value when characters are equal
     * @param mismatchValue
     *            value when characters are not equal
     */
    public function __construct($matchValue, $mismatchValue) {
        if($matchValue <= $mismatchValue) throw new Exception("matchValue must be > matchValue");

        $this->matchValue = $matchValue;
        $this->mismatchValue = $mismatchValue;
    }

    public function compare($a, $aIndex, $b, $bIndex) {
        return ($a[$aIndex] === $b[$bIndex] ? $this->matchValue
                : $this->mismatchValue);
    }

    public function max() {
        return $this->matchValue;
    }

    public function min() {
        return $this->mismatchValue;
    }
}

$str1 = "COELACANTH";
$str2 = "PELICAN";
$o = new SmithWatermanGotoh();
echo $o->compare($str1, $str2);

Answer 2

There is this "BioStor" project that has an implementation of the Smith-Waterman algorithm in PHP.