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// The Computer Language Benchmarks Game
// http://benchmarksgame.alioth.debian.org/
//
// contributed by the Rust Project Developers
// Copyright (c) 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.
// ignore-stage1
// ignore-cross-compile #12102
#![feature(macro_rules, plugin, slicing_syntax)]
extern crate regex;
use std::io;
use regex::{NoExpand, Regex};
use std::sync::{Arc, Future};
macro_rules! regex {
($e:expr) => (Regex::new($e).unwrap())
}
fn count_matches(seq: &str, variant: &Regex) -> int {
let mut n = 0;
for _ in variant.find_iter(seq) {
n += 1;
}
n
}
fn main() {
let mut rdr = if std::os::getenv("RUST_BENCH").is_some() {
let fd = io::File::open(&Path::new("shootout-k-nucleotide.data"));
box io::BufferedReader::new(fd) as Box<io::Reader>
} else {
box io::stdin() as Box<io::Reader>
};
let mut seq = rdr.read_to_string().unwrap();
let ilen = seq.len();
seq = regex!(">[^\n]*\n|\n").replace_all(seq.as_slice(), NoExpand(""));
let seq_arc = Arc::new(seq.clone()); // copy before it moves
let clen = seq.len();
let mut seqlen = Future::spawn(move|| {
let substs = vec![
(regex!("B"), "(c|g|t)"),
(regex!("D"), "(a|g|t)"),
(regex!("H"), "(a|c|t)"),
(regex!("K"), "(g|t)"),
(regex!("M"), "(a|c)"),
(regex!("N"), "(a|c|g|t)"),
(regex!("R"), "(a|g)"),
(regex!("S"), "(c|g)"),
(regex!("V"), "(a|c|g)"),
(regex!("W"), "(a|t)"),
(regex!("Y"), "(c|t)"),
];
let mut seq = seq;
for (re, replacement) in substs.into_iter() {
seq = re.replace_all(seq.as_slice(), NoExpand(replacement));
}
seq.len()
});
let variants = vec![
regex!("agggtaaa|tttaccct"),
regex!("[cgt]gggtaaa|tttaccc[acg]"),
regex!("a[act]ggtaaa|tttacc[agt]t"),
regex!("ag[act]gtaaa|tttac[agt]ct"),
regex!("agg[act]taaa|ttta[agt]cct"),
regex!("aggg[acg]aaa|ttt[cgt]ccct"),
regex!("agggt[cgt]aa|tt[acg]accct"),
regex!("agggta[cgt]a|t[acg]taccct"),
regex!("agggtaa[cgt]|[acg]ttaccct"),
];
let (mut variant_strs, mut counts) = (vec!(), vec!());
for variant in variants.into_iter() {
let seq_arc_copy = seq_arc.clone();
variant_strs.push(variant.to_string());
counts.push(Future::spawn(move|| {
count_matches(seq_arc_copy.as_slice(), &variant)
}));
}
for (i, variant) in variant_strs.iter().enumerate() {
println!("{} {}", variant, counts[i].get());
}
println!("");
println!("{}", ilen);
println!("{}", clen);
println!("{}", seqlen.get());
}
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