141 lines
4.7 KiB
Rust
141 lines
4.7 KiB
Rust
// Copyright 2012 The Rust Project Developers. See the COPYRIGHT
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// file at the top-level directory of this distribution and at
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// http://rust-lang.org/COPYRIGHT.
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//
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// Licensed under the Apache License, Version 2.0 <LICENSE-APACHE or
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// http://www.apache.org/licenses/LICENSE-2.0> or the MIT license
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// <LICENSE-MIT or http://opensource.org/licenses/MIT>, at your
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// option. This file may not be copied, modified, or distributed
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// except according to those terms.
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/* -*- mode: rust; indent-tabs-mode: nil -*-
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* Implementation of 'fasta' benchmark from
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* Computer Language Benchmarks Game
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* http://shootout.alioth.debian.org/
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*/
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extern mod std;
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use core::io::WriterUtil;
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fn LINE_LENGTH() -> uint { return 60u; }
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struct MyRandom {
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last: u32
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}
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fn myrandom_next(r: @mut MyRandom, mx: u32) -> u32 {
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r.last = (r.last * 3877u32 + 29573u32) % 139968u32;
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mx * r.last / 139968u32
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}
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struct AminoAcids {
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ch: char,
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prob: u32
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}
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fn make_cumulative(aa: ~[AminoAcids]) -> ~[AminoAcids] {
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let mut cp: u32 = 0u32;
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let mut ans: ~[AminoAcids] = ~[];
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for aa.each |a| {
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cp += a.prob;
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ans += ~[AminoAcids {ch: a.ch, prob: cp}];
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}
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return ans;
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}
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fn select_random(r: u32, genelist: ~[AminoAcids]) -> char {
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if r < genelist[0].prob { return genelist[0].ch; }
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fn bisect(v: ~[AminoAcids], lo: uint, hi: uint, target: u32) -> char {
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if hi > lo + 1u {
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let mid: uint = lo + (hi - lo) / 2u;
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if target < v[mid].prob {
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return bisect(v, lo, mid, target);
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} else { return bisect(v, mid, hi, target); }
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} else { return v[hi].ch; }
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}
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return bisect(copy genelist, 0, vec::len::<AminoAcids>(genelist) - 1, r);
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}
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fn make_random_fasta(wr: @io::Writer,
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id: ~str,
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desc: ~str,
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genelist: ~[AminoAcids],
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n: int) {
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wr.write_line(~">" + id + ~" " + desc);
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let rng = @mut MyRandom {last: rand::Rng().next()};
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let mut op: ~str = ~"";
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for uint::range(0u, n as uint) |_i| {
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str::push_char(&mut op, select_random(myrandom_next(rng, 100u32),
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copy genelist));
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if str::len(op) >= LINE_LENGTH() {
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wr.write_line(op);
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op = ~"";
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}
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}
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if str::len(op) > 0u { wr.write_line(op); }
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}
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fn make_repeat_fasta(wr: @io::Writer, id: ~str, desc: ~str, s: ~str, n: int) {
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unsafe {
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wr.write_line(~">" + id + ~" " + desc);
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let mut op: ~str = ~"";
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let sl: uint = str::len(s);
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for uint::range(0u, n as uint) |i| {
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str::raw::push_byte(&mut op, s[i % sl]);
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if str::len(op) >= LINE_LENGTH() {
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wr.write_line(op);
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op = ~"";
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}
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}
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if str::len(op) > 0u { wr.write_line(op); }
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}
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}
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fn acid(ch: char, prob: u32) -> AminoAcids {
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return AminoAcids {ch: ch, prob: prob};
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}
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fn main() {
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let args = os::args();
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let args = if os::getenv(~"RUST_BENCH").is_some() {
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// alioth tests k-nucleotide with this data at 25,000,000
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~[~"", ~"5000000"]
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} else if args.len() <= 1u {
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~[~"", ~"1000"]
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} else {
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args
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};
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let writer = if os::getenv(~"RUST_BENCH").is_some() {
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result::get(&io::file_writer(&Path("./shootout-fasta.data"),
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~[io::Truncate, io::Create]))
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} else {
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io::stdout()
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};
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let n = int::from_str(args[1]).get();
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let iub: ~[AminoAcids] =
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make_cumulative(~[acid('a', 27u32), acid('c', 12u32), acid('g', 12u32),
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acid('t', 27u32), acid('B', 2u32), acid('D', 2u32),
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acid('H', 2u32), acid('K', 2u32), acid('M', 2u32),
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acid('N', 2u32), acid('R', 2u32), acid('S', 2u32),
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acid('V', 2u32), acid('W', 2u32), acid('Y', 2u32)]);
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let homosapiens: ~[AminoAcids] =
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make_cumulative(~[acid('a', 30u32), acid('c', 20u32), acid('g', 20u32),
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acid('t', 30u32)]);
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let alu: ~str =
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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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make_repeat_fasta(writer, ~"ONE", ~"Homo sapiens alu", alu, n * 2);
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make_random_fasta(writer, ~"TWO", ~"IUB ambiguity codes", iub, n * 3);
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make_random_fasta(writer, ~"THREE",
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~"Homo sapiens frequency", homosapiens, n * 5);
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}
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