1.1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000
1.2 +++ b/js/src/devtools/jint/sunspider/string-fasta.js Wed Dec 31 06:09:35 2014 +0100
1.3 @@ -0,0 +1,95 @@
1.4 +// The Great Computer Language Shootout
1.5 +// http://shootout.alioth.debian.org
1.6 +//
1.7 +// Contributed by Ian Osgood
1.8 +
1.9 +var last = 42, A = 3877, C = 29573, M = 139968;
1.10 +
1.11 +function rand(max) {
1.12 + last = (last * A + C) % M;
1.13 + return max * last / M;
1.14 +}
1.15 +
1.16 +var ALU =
1.17 + "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
1.18 + "GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
1.19 + "CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
1.20 + "ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
1.21 + "GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
1.22 + "AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
1.23 + "AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
1.24 +
1.25 +var IUB = {
1.26 + a:0.27, c:0.12, g:0.12, t:0.27,
1.27 + B:0.02, D:0.02, H:0.02, K:0.02,
1.28 + M:0.02, N:0.02, R:0.02, S:0.02,
1.29 + V:0.02, W:0.02, Y:0.02
1.30 +}
1.31 +
1.32 +var HomoSap = {
1.33 + a: 0.3029549426680,
1.34 + c: 0.1979883004921,
1.35 + g: 0.1975473066391,
1.36 + t: 0.3015094502008
1.37 +}
1.38 +
1.39 +function makeCumulative(table) {
1.40 + var last = null;
1.41 + /* BEGIN LOOP */
1.42 + for (var c in table) {
1.43 + if (last) table[c] += table[last];
1.44 + last = c;
1.45 + }
1.46 + /* END LOOP */
1.47 +}
1.48 +
1.49 +function fastaRepeat(n, seq) {
1.50 + var seqi = 0, lenOut = 60;
1.51 + /* BEGIN LOOP */
1.52 + while (n>0) {
1.53 + if (n<lenOut) lenOut = n;
1.54 + if (seqi + lenOut < seq.length) {
1.55 + ret = seq.substring(seqi, seqi+lenOut);
1.56 + seqi += lenOut;
1.57 + } else {
1.58 + var s = seq.substring(seqi);
1.59 + seqi = lenOut - s.length;
1.60 + ret = s + seq.substring(0, seqi);
1.61 + }
1.62 + n -= lenOut;
1.63 + }
1.64 + /* END LOOP */
1.65 +}
1.66 +
1.67 +function fastaRandom(n, table) {
1.68 + var line = new Array(60);
1.69 + makeCumulative(table);
1.70 + /* BEGIN LOOP */
1.71 + while (n>0) {
1.72 + if (n<line.length) line = new Array(n);
1.73 + /* BEGIN LOOP */
1.74 + for (var i=0; i<line.length; i++) {
1.75 + var r = rand(1);
1.76 + /* BEGIN LOOP */
1.77 + for (var c in table) {
1.78 + if (r < table[c]) {
1.79 + line[i] = c;
1.80 + break;
1.81 + }
1.82 + }
1.83 + /* END LOOP */
1.84 + }
1.85 + /* END LOOP */
1.86 + ret = line.join('');
1.87 + n -= line.length;
1.88 + }
1.89 + /* END LOOP */
1.90 +}
1.91 +
1.92 +var ret;
1.93 +
1.94 +var count = 7;
1.95 +ret = fastaRepeat(2*count*100000, ALU);
1.96 +ret = fastaRandom(3*count*1000, IUB);
1.97 +ret = fastaRandom(5*count*1000, HomoSap);
1.98 +
