rust/src/test/bench/shootout-fasta.rs

// The Computer Language Benchmarks Game
// http://benchmarksgame.alioth.debian.org/
//
// contributed by the Rust Project Developers

// Copyright (c) 2012-2014 The Rust Project Developers
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions
// are met:
//
// - Redistributions of source code must retain the above copyright
//   notice, this list of conditions and the following disclaimer.
//
// - Redistributions in binary form must reproduce the above copyright
//   notice, this list of conditions and the following disclaimer in
//   the documentation and/or other materials provided with the
//   distribution.
//
// - Neither the name of "The Computer Language Benchmarks Game" nor
//   the name of "The Computer Language Shootout Benchmarks" nor the
//   names of its contributors may be used to endorse or promote
//   products derived from this software without specific prior
//   written permission.
//
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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// OF THE POSSIBILITY OF SUCH DAMAGE.

#![feature(old_io, old_path, io, core)]

use std::cmp::min;
use std::old_io::*;
use std::old_io;
use std::old_path::Path;
use std::num::Float;
use std::env;

const LINE_LENGTH: usize = 60;
const IM: u32 = 139968;

struct MyRandom {
    last: u32
}
impl MyRandom {
    fn new() -> MyRandom { MyRandom { last: 42 } }
    fn normalize(p: f32) -> u32 {(p * IM as f32).floor() as u32}
    fn gen(&mut self) -> u32 {
        self.last = (self.last * 3877 + 29573) % IM;
        self.last
    }
}

struct AAGen<'a> {
    rng: &'a mut MyRandom,
    data: Vec<(u32, u8)>
}
impl<'a> AAGen<'a> {
    fn new<'b>(rng: &'b mut MyRandom, aa: &[(char, f32)]) -> AAGen<'b> {
        let mut cum = 0.;
        let data = aa.iter()
            .map(|&(ch, p)| { cum += p; (MyRandom::normalize(cum), ch as u8) })
            .collect();
        AAGen { rng: rng, data: data }
    }
}
impl<'a> Iterator for AAGen<'a> {
    type Item = u8;

    fn next(&mut self) -> Option<u8> {
        let r = self.rng.gen();
        self.data.iter()
            .skip_while(|pc| pc.0 < r)
            .map(|&(_, c)| c)
            .next()
    }
}

fn make_fasta<W: Writer, I: Iterator<Item=u8>>(
    wr: &mut W, header: &str, mut it: I, mut n: usize)
    -> std::old_io::IoResult<()>
{
    try!(wr.write(header.as_bytes()));
    let mut line = [0; LINE_LENGTH + 1];
    while n > 0 {
        let nb = min(LINE_LENGTH, n);
        for i in 0..nb {
            line[i] = it.next().unwrap();
        }
        n -= nb;
        line[nb] = '\n' as u8;
        try!(wr.write(&line[..nb+1]));
    }
    Ok(())
}

fn run<W: Writer>(writer: &mut W) -> std::old_io::IoResult<()> {
    let mut args = env::args();
    let n = if env::var_os("RUST_BENCH").is_some() {
        25000000
    } else if args.len() <= 1 {
        1000
    } else {
        args.nth(1).unwrap().parse().unwrap()
    };

    let rng = &mut MyRandom::new();
    let alu =
        "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG\
        GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA\
        CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT\
        ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA\
        GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG\
        AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC\
        AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
    let iub = &[('a', 0.27), ('c', 0.12), ('g', 0.12),
                ('t', 0.27), ('B', 0.02), ('D', 0.02),
                ('H', 0.02), ('K', 0.02), ('M', 0.02),
                ('N', 0.02), ('R', 0.02), ('S', 0.02),
                ('V', 0.02), ('W', 0.02), ('Y', 0.02)];
    let homosapiens = &[('a', 0.3029549426680),
                        ('c', 0.1979883004921),
                        ('g', 0.1975473066391),
                        ('t', 0.3015094502008)];

    try!(make_fasta(writer, ">ONE Homo sapiens alu\n",
                    alu.as_bytes().iter().cycle().cloned(), n * 2));
    try!(make_fasta(writer, ">TWO IUB ambiguity codes\n",
                    AAGen::new(rng, iub), n * 3));
    try!(make_fasta(writer, ">THREE Homo sapiens frequency\n",
                    AAGen::new(rng, homosapiens), n * 5));

    writer.flush()
}

fn main() {
    let res = if env::var_os("RUST_BENCH").is_some() {
        let mut file = BufferedWriter::new(File::create(&Path::new("./shootout-fasta.data")));
        run(&mut file)
    } else {
        run(&mut old_io::stdout())
    };
    res.unwrap()
}