SunSpider/tests/sunspider-0.9/string-fasta.js
author Dremov Kirill (Nokia-D-MSW/Tampere) <kirill.dremov@nokia.com>
Mon, 04 Oct 2010 01:32:07 +0300
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permissions -rw-r--r--
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// The Great Computer Language Shootout
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//  http://shootout.alioth.debian.org
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//
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//  Contributed by Ian Osgood
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var last = 42, A = 3877, C = 29573, M = 139968;
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function rand(max) {
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  last = (last * A + C) % M;
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  return max * last / M;
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}
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var ALU =
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  "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
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  "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
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  "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
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  "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
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  "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
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  "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
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  "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
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var IUB = {
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  a:0.27, c:0.12, g:0.12, t:0.27,
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  B:0.02, D:0.02, H:0.02, K:0.02,
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  M:0.02, N:0.02, R:0.02, S:0.02,
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  V:0.02, W:0.02, Y:0.02
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}
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var HomoSap = {
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  a: 0.3029549426680,
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  c: 0.1979883004921,
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  g: 0.1975473066391,
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  t: 0.3015094502008
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}
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function makeCumulative(table) {
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  var last = null;
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  for (var c in table) {
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    if (last) table[c] += table[last];
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    last = c;
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  }
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}
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function fastaRepeat(n, seq) {
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  var seqi = 0, lenOut = 60;
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  while (n>0) {
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    if (n<lenOut) lenOut = n;
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    if (seqi + lenOut < seq.length) {
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      ret = seq.substring(seqi, seqi+lenOut);
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      seqi += lenOut;
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    } else {
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      var s = seq.substring(seqi);
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      seqi = lenOut - s.length;
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      ret = s + seq.substring(0, seqi);
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    }
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    n -= lenOut;
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  }
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}
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function fastaRandom(n, table) {
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  var line = new Array(60);
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  makeCumulative(table);
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  while (n>0) {
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    if (n<line.length) line = new Array(n);
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    for (var i=0; i<line.length; i++) {
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      var r = rand(1);
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      for (var c in table) {
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        if (r < table[c]) {
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          line[i] = c;
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          break;
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        }
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      }
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    }
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    ret = line.join('');
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    n -= line.length;
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  }
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}
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var ret;
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var count = 7;
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ret = fastaRepeat(2*count*100000, ALU);
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ret = fastaRandom(3*count*1000, IUB);
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ret = fastaRandom(5*count*1000, HomoSap);
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