michael@0: // The Great Computer Language Shootout
michael@0: //  http://shootout.alioth.debian.org
michael@0: //
michael@0: //  Contributed by Ian Osgood
michael@0: 
michael@0: var last = 42, A = 3877, C = 29573, M = 139968;
michael@0: 
michael@0: function rand(max) {
michael@0:   last = (last * A + C) % M;
michael@0:   return max * last / M;
michael@0: }
michael@0: 
michael@0: var ALU =
michael@0:   "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
michael@0:   "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
michael@0:   "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
michael@0:   "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
michael@0:   "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
michael@0:   "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
michael@0:   "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
michael@0: 
michael@0: var IUB = {
michael@0:   a:0.27, c:0.12, g:0.12, t:0.27,
michael@0:   B:0.02, D:0.02, H:0.02, K:0.02,
michael@0:   M:0.02, N:0.02, R:0.02, S:0.02,
michael@0:   V:0.02, W:0.02, Y:0.02
michael@0: }
michael@0: 
michael@0: var HomoSap = {
michael@0:   a: 0.3029549426680,
michael@0:   c: 0.1979883004921,
michael@0:   g: 0.1975473066391,
michael@0:   t: 0.3015094502008
michael@0: }
michael@0: 
michael@0: function makeCumulative(table) {
michael@0:   var last = null;
michael@0:   for (var c in table) {
michael@0:     if (last) table[c] += table[last];
michael@0:     last = c;
michael@0:   }
michael@0: }
michael@0: 
michael@0: function fastaRepeat(n, seq) {
michael@0:   var seqi = 0, lenOut = 60;
michael@0:   while (n>0) {
michael@0:     if (n<lenOut) lenOut = n;
michael@0:     if (seqi + lenOut < seq.length) {
michael@0:       ret = seq.substring(seqi, seqi+lenOut);
michael@0:       seqi += lenOut;
michael@0:     } else {
michael@0:       var s = seq.substring(seqi);
michael@0:       seqi = lenOut - s.length;
michael@0:       ret = s + seq.substring(0, seqi);
michael@0:     }
michael@0:     n -= lenOut;
michael@0:   }
michael@0:   return ret;
michael@0: }
michael@0: 
michael@0: function fastaRandom(n, table) {
michael@0:   var line = new Array(60);
michael@0:   makeCumulative(table);
michael@0:   while (n>0) {
michael@0:     if (n<line.length) line = new Array(n);
michael@0:     for (var i=0; i<line.length; i++) {
michael@0:       var r = rand(1);
michael@0:       for (var c in table) {
michael@0:         if (r < table[c]) {
michael@0:           line[i] = c;
michael@0:           break;
michael@0:         }
michael@0:       }
michael@0:     }
michael@0:     ret = line.join('');
michael@0:     n -= line.length;
michael@0:   }
michael@0:   return ret;
michael@0: }
michael@0: 
michael@0: var ret;
michael@0: 
michael@0: var count = 7;
michael@0: var actual1 = fastaRepeat(2*count*100000, ALU);
michael@0: var actual2 = fastaRandom(3*count*1000, IUB);
michael@0: var actual3 = fastaRandom(5*count*1000, HomoSap);
michael@0: 
michael@0: assertEq(actual1, "CAAAAAGGCCGGGCGCGGTG");
michael@0: assertEq(actual2, "VtttaDtKgcaaWaaaaatSccMcVatgtKgtaKgcgatatgtagtSaaaDttatacaaa");
michael@0: assertEq(actual3, "ttggctatatttatgttgga");