testing/performance/talos/page_load_test/jss/real-fasta-8.html

   1 <html><head>
   2 <!-- MOZ_INSERT_CONTENT_HOOK -->
   3 <script src = runner.js></script>
   4 <script>
   5 var onlyName = 'IUB ambiguity codes', onlyNum = 8;
   6 function thisTest() {
   7
   8 // The Great Computer Language Shootout
   9 //  http://shootout.alioth.debian.org
  10 //
  11 //  Contributed by Ian Osgood
  12
  13 var last = 42, A = 3877, C = 29573, M = 139968;
  14
  15 function rand(max) {
  16   last = (last * A + C) % M;
  17   return max * last / M;
  18 }
  19
  20 var ALU =
  21   "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
  22   "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
  23   "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
  24   "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
  25   "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
  26   "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
  27   "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
  28
  29 var IUB = {
  30   a:0.27, c:0.12, g:0.12, t:0.27,
  31   B:0.02, D:0.02, H:0.02, K:0.02,
  32   M:0.02, N:0.02, R:0.02, S:0.02,
  33   V:0.02, W:0.02, Y:0.02
  34 }
  35
  36 var HomoSap = {
  37   a: 0.3029549426680,
  38   c: 0.1979883004921,
  39   g: 0.1975473066391,
  40   t: 0.3015094502008
  41 }
  42
  43 function makeCumulative(table) {
  44   var last = null;
  45   for (var c in table) {
  46     if (last) table[c] += table[last];
  47     last = c;
  48   }
  49 }
  50
  51 function fastaRepeat(n, seq) {
  52   var seqi = 0, lenOut = 60;
  53   while (n>0) {
  54     if (n<lenOut) lenOut = n;
  55     if (seqi + lenOut < seq.length) {
  56       ret = seq.substring(seqi, seqi+lenOut);
  57       seqi += lenOut;
  58     } else {
  59       var s = seq.substring(seqi);
  60       seqi = lenOut - s.length;
  61       ret = s + seq.substring(0, seqi);
  62     }
  63     n -= lenOut;
  64   }
  65 }
  66
  67 function fastaRandom(n, table) {
  68   var line = new Array(60);
  69   makeCumulative(table);
  70   while (n>0) {
  71     if (n<line.length) line = new Array(n);
  72     for (var i=0; i<line.length; i++) {
  73       var r = rand(1);
  74       for (var c in table) {
  75         if (r < table[c]) {
  76           line[i] = c;
  77           break;
  78         }
  79       }
  80     }
  81     ret = line.join('');
  82     n -= line.length;
  83   }
  84 }
  85
  86 startTest("real-fasta");
  87
  88 var ret;
  89
  90 for ( var n = 2; n <= 16; n *= 2 ) (function(n){
  91         test( "Homo sapiens alu", n, function(){
  92                 ret = fastaRepeat(2*n*100000, ALU);
  93         });
  94
  95         test( "IUB ambiguity codes", n, function(){
  96                 ret = fastaRandom(3*n*1000, IUB);
  97         });
  98
  99         test( "Homo sapiens frequenc", n, function(){
 100                 ret = fastaRandom(5*n*1000, HomoSap);
 101         });
 102 })(n);
 103
 104 endTest();
 105 }
 106 </script>
 107 <body onload="thisTest()"></body></html>