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// 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.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
// FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
// COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
// (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
// HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
// STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
// 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()
}
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