src/test/bench/shootout-fasta.rs

   1 // The Computer Language Benchmarks Game
   2 // http://benchmarksgame.alioth.debian.org/
   3 //
   4 // contributed by the Rust Project Developers
   5
   6 // Copyright (c) 2012-2014 The Rust Project Developers
   7 //
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   9 //
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  11 // modification, are permitted provided that the following conditions
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  13 //
  14 // - Redistributions of source code must retain the above copyright
  15 //   notice, this list of conditions and the following disclaimer.
  16 //
  17 // - Redistributions in binary form must reproduce the above copyright
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  19 //   the documentation and/or other materials provided with the
  20 //   distribution.
  21 //
  22 // - Neither the name of "The Computer Language Benchmarks Game" nor
  23 //   the name of "The Computer Language Shootout Benchmarks" nor the
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  40
  41 #![feature(old_io, old_path, io, core)]
  42
  43 use std::cmp::min;
  44 use std::old_io::*;
  45 use std::old_io;
  46 use std::old_path::Path;
  47 use std::num::Float;
  48 use std::env;
  49
  50 const LINE_LENGTH: usize = 60;
  51 const IM: u32 = 139968;
  52
  53 struct MyRandom {
  54     last: u32
  55 }
  56 impl MyRandom {
  57     fn new() -> MyRandom { MyRandom { last: 42 } }
  58     fn normalize(p: f32) -> u32 {(p * IM as f32).floor() as u32}
  59     fn gen(&mut self) -> u32 {
  60         self.last = (self.last * 3877 + 29573) % IM;
  61         self.last
  62     }
  63 }
  64
  65 struct AAGen<'a> {
  66     rng: &'a mut MyRandom,
  67     data: Vec<(u32, u8)>
  68 }
  69 impl<'a> AAGen<'a> {
  70     fn new<'b>(rng: &'b mut MyRandom, aa: &[(char, f32)]) -> AAGen<'b> {
  71         let mut cum = 0.;
  72         let data = aa.iter()
  73             .map(|&(ch, p)| { cum += p; (MyRandom::normalize(cum), ch as u8) })
  74             .collect();
  75         AAGen { rng: rng, data: data }
  76     }
  77 }
  78 impl<'a> Iterator for AAGen<'a> {
  79     type Item = u8;
  80
  81     fn next(&mut self) -> Option<u8> {
  82         let r = self.rng.gen();
  83         self.data.iter()
  84             .skip_while(|pc| pc.0 < r)
  85             .map(|&(_, c)| c)
  86             .next()
  87     }
  88 }
  89
  90 fn make_fasta<W: Writer, I: Iterator<Item=u8>>(
  91     wr: &mut W, header: &str, mut it: I, mut n: usize)
  92     -> std::old_io::IoResult<()>
  93 {
  94     try!(wr.write(header.as_bytes()));
  95     let mut line = [0; LINE_LENGTH + 1];
  96     while n > 0 {
  97         let nb = min(LINE_LENGTH, n);
  98         for i in 0..nb {
  99             line[i] = it.next().unwrap();
 100         }
 101         n -= nb;
 102         line[nb] = '\n' as u8;
 103         try!(wr.write(&line[..nb+1]));
 104     }
 105     Ok(())
 106 }
 107
 108 fn run<W: Writer>(writer: &mut W) -> std::old_io::IoResult<()> {
 109     let mut args = env::args();
 110     let n = if env::var_os("RUST_BENCH").is_some() {
 111         25000000
 112     } else if args.len() <= 1 {
 113         1000
 114     } else {
 115         args.nth(1).unwrap().parse().unwrap()
 116     };
 117
 118     let rng = &mut MyRandom::new();
 119     let alu =
 120         "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG\
 121         GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA\
 122         CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT\
 123         ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA\
 124         GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG\
 125         AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC\
 126         AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
 127     let iub = &[('a', 0.27), ('c', 0.12), ('g', 0.12),
 128                 ('t', 0.27), ('B', 0.02), ('D', 0.02),
 129                 ('H', 0.02), ('K', 0.02), ('M', 0.02),
 130                 ('N', 0.02), ('R', 0.02), ('S', 0.02),
 131                 ('V', 0.02), ('W', 0.02), ('Y', 0.02)];
 132     let homosapiens = &[('a', 0.3029549426680),
 133                         ('c', 0.1979883004921),
 134                         ('g', 0.1975473066391),
 135                         ('t', 0.3015094502008)];
 136
 137     try!(make_fasta(writer, ">ONE Homo sapiens alu\n",
 138                     alu.as_bytes().iter().cycle().cloned(), n * 2));
 139     try!(make_fasta(writer, ">TWO IUB ambiguity codes\n",
 140                     AAGen::new(rng, iub), n * 3));
 141     try!(make_fasta(writer, ">THREE Homo sapiens frequency\n",
 142                     AAGen::new(rng, homosapiens), n * 5));
 143
 144     writer.flush()
 145 }
 146
 147 fn main() {
 148     let res = if env::var_os("RUST_BENCH").is_some() {
 149         let mut file = BufferedWriter::new(File::create(&Path::new("./shootout-fasta.data")));
 150         run(&mut file)
 151     } else {
 152         run(&mut old_io::stdout())
 153     };
 154     res.unwrap()
 155 }