function() {
    $.fitch = {
        score: function() {
            if ("DNA" == $.main.type) {
                void 0 == $.stage.stats && ($.stage.stats = {}), $.stage.stats.match = 0, $.stage.stats.mismatch = 0, $.stage.stats.open = 0, $.stage.stats.extend = 0, $.fitch.forwardBackward();
                var e = $.fitch.scoreRecurse($.stage.current);
                return e
            }
        },
        getLen: function() {
            return $.phylo.seqLen
        },
        forwardBackward: function() {
            for (var e = $.stage.current, t = $.fitch.getLen(), n = 0; t > n; n++) {
                var r = $.fitch.forward(e, n);
                $.phylo.tree[e].ancestor[n] = r.length < 1 ? "x" : 1 == r.length || 0 != r.indexOf("x") ? r[0] : r[1], $.phylo.tree[e].child >= 2 && $.fitch.backward($.phylo.tree[e].node1, $.phylo.tree[e].ancestor[n], n), $.phylo.tree[e].child >= 1 && $.fitch.backward($.phylo.tree[e].node2, $.phylo.tree[e].ancestor[n], n)
            }
        },
        forward: function(e, t) {
            if (0 == t && ($.phylo.tree[e].ancestor = [], $.phylo.tree[e].ancestorSet = []), 2 == $.phylo.tree[e].child) {
                for (var n = $.fitch.forward($.phylo.tree[e].node2, t), r = $.fitch.forward($.phylo.tree[e].node1, t), i = [], s = [], o = 0; o < n.length; o++) {
                    -1 == i.indexOf(n[o]) && i.push(n[o]);
                    for (var u = 0; u < r.length; u++) n[o] == r[u] && -1 == s.indexOf(n[o]) && s.push(n[o]), -1 == i.indexOf(r[u]) && i.push(r[u])
                }
                $.phylo.tree[e].ancestorSet[t] = s.length < 1 ? i : s
            } else if (1 == $.phylo.tree[e].child) {
                var n = $.fitch.forward($.phylo.tree[e].node2, t),
                    r = $.sequence.nuc($.sequence.track[$.phylo.tree[e].node1][t]);
                $.phylo.tree[e].ancestorSet[t] = n.indexOf(r) > -1 ? [r] : n.concat([r])
            } else {
                var n = $.sequence.nuc($.sequence.track[$.phylo.tree[e].node1][t]),
                    r = $.sequence.nuc($.sequence.track[$.phylo.tree[e].node2][t]);
                $.phylo.tree[e].ancestorSet[t] = r == n ? [n] : [n, r]
            }
            return $.phylo.tree[e].ancestorSet[t]
        },
        backward: function(e, t, n) {
            var r = $.phylo.tree[e].ancestorSet[n];
            $.phylo.tree[e].ancestor[n] = r.length < 1 ? "x" : 1 == r.length ? r[0] : r.indexOf(t) > -1 ? t : 0 != r.indexOf("x") ? r[0] : r[1], $.phylo.tree[e].child >= 2 && $.fitch.backward($.phylo.tree[e].node1, $.phylo.tree[e].ancestor[n], n), $.phylo.tree[e].child >= 1 && $.fitch.backward($.phylo.tree[e].node2, $.phylo.tree[e].ancestor[n], n)
        },
        forwardBackward2: function() {
            for (var e = $.stage.current, t = $.fitch.getLen(), n = $.fitch.forward2(e, r), r = 0; t > r; r++) $.phylo.tree[e].ancestor[r] = n[r].length < 1 ? "x" : 1 == n[r].length || 0 != n[r].indexOf("x") ? n[r][0] : n[r][1];
            $.phylo.tree[e].child >= 2 && $.fitch.backward2($.phylo.tree[e].node1, $.phylo.tree[e].ancestor), $.phylo.tree[e].child >= 1 && $.fitch.backward2($.phylo.tree[e].node2, $.phylo.tree[e].ancestor)
        },
        forward2: function(e) {
            var t = $.fitch.getLen();
            if ($.phylo.tree[e].ancestor = [], $.phylo.tree[e].ancestorSet = [], 2 == $.phylo.tree[e].child)
                for (var n = $.fitch.forward2($.phylo.tree[e].node2), r = $.fitch.forward2($.phylo.tree[e].node1), i = 0; t > i; i++) {
                    for (var s = [], o = [], u = 0; u < n[i].length; u++) {
                        -1 == s.indexOf(n[i][u]) && s.push(n[i][u]);
                        for (var a = 0; a < r.length; a++) n[i][u] == r[i][a] && -1 == o.indexOf(n[i][u]) && o.push(n[i][u]), -1 == s.indexOf(r[i][a]) && s.push(r[i][a])
                    }
                    $.phylo.tree[e].ancestorSet[i] = o.length < 1 ? s : o
                } else if (1 == $.phylo.tree[e].child)
                    for (var n = $.fitch.forward2($.phylo.tree[e].node2), r = $.sequence.nucArray($.sequence.track[$.phylo.tree[e].node1]), i = 0; t > i; i++) $.phylo.tree[e].ancestorSet[i] = n[i].indexOf(r[i]) > -1 ? [r[i]] : n[i].concat([r[i]]);
                else
                    for (var n = $.sequence.nucArray($.sequence.track[$.phylo.tree[e].node1]), r = $.sequence.nucArray($.sequence.track[$.phylo.tree[e].node2]), i = 0; t > i; i++) $.phylo.tree[e].ancestorSet[i] = r == n ? [n[i]] : [n[i], r[i]];
            return $.phylo.tree[e].ancestorSet
        },
        backward2: function(e, t) {
            for (var n = $.phylo.tree[e].ancestorSet, r = $.fitch.getLen(), i = 0; r > i; i++) $.phylo.tree[e].ancestor[i] = n[i].length < 1 ? "x" : 1 == n[i].length ? n[i][0] : n[i].indexOf(t[i]) > -1 ? t[i] : 0 != n[i].indexOf("x") ? n[i][0] : n[i][1];
            $.phylo.tree[e].child >= 2 && $.fitch.backward2($.phylo.tree[e].node1, $.phylo.tree[e].ancestor), $.phylo.tree[e].child >= 1 && $.fitch.backward2($.phylo.tree[e].node2, $.phylo.tree[e].ancestor)
        },
        scoreRecurse: function(e) {
            function t(e) {
                var t = {
                    match: 1,
                    mismatch: -1,
                    open: -4,
                    extend: -1
                };
                return e.match * t.match + e.mismatch * t.mismatch + e.open * t.open + e.extend * t.extend
            }

            function n(e, t) {
                function n(e) {
                    return "x" == e
                }
                for (var r = {
                    match: 0,
                    mismatch: 0,
                    open: 0,
                    extend: 0
                }, i = e.length - e.filter(n).length, s = t.length - t.filter(n).length, o = 0, u = 0, a = 0, f = 0; f < e.length; f++)("x" != e[f] || "x" != t[f]) && ("x" != e[f] && "x" != t[f] ? (t[f] == e[f] ? r.match++ : r.mismatch++, o++, u++, a = 0) : "x" != e[f] && "x" == t[f] ? (u > 0 && s > u && (1 == a ? r.extend++ : (r.open++, a = 1)), o++) : "x" == e[f] && "x" != t[f] && (o > 0 && i > o && (2 == a ? r.extend++ : (r.open++, a = 2)), u++));
                return r
            }
            if (0 == $.phylo.tree[e].child) var r = $.sequence.nucArray($.sequence.track[$.phylo.tree[e].node1]),
            i = $.sequence.nucArray($.sequence.track[$.phylo.tree[e].node2]);
            else if (1 == $.phylo.tree[e].child) var r = $.sequence.nucArray($.sequence.track[$.phylo.tree[e].node1]),
            i = $.phylo.tree[$.phylo.tree[e].node2].ancestor;
            else var r = $.phylo.tree[$.phylo.tree[e].node1].ancestor,
            i = $.phylo.tree[$.phylo.tree[e].node2].ancestor;
            var s = n($.phylo.tree[e].ancestor, r),
                o = n($.phylo.tree[e].ancestor, i),
                u = t(s) + t(o);
            return $.stage.stats.match += parseInt(s.match) + parseInt(o.match), $.stage.stats.mismatch += parseInt(s.mismatch) + parseInt(o.mismatch), $.stage.stats.open += parseInt(s.open) + parseInt(o.open), $.stage.stats.extend += parseInt(s.extend) + parseInt(o.extend), $.phylo.tree[e].child >= 2 && (u += $.fitch.scoreRecurse($.phylo.tree[e].node1)), $.phylo.tree[e].child >= 1 && (u += $.fitch.scoreRecurse($.phylo.tree[e].node2)), $.phylo.tree[e].score = u, u
        }
    }
}(),