1 // The Computer Language Benchmarks Game
2 // http://benchmarksgame.alioth.debian.org/
4 // contributed by the Rust Project Developers
6 // Copyright (c) 2013-2014 The Rust Project Developers
8 // All rights reserved.
10 // Redistribution and use in source and binary forms, with or without
11 // modification, are permitted provided that the following conditions
14 // - Redistributions of source code must retain the above copyright
15 // notice, this list of conditions and the following disclaimer.
17 // - Redistributions in binary form must reproduce the above copyright
18 // notice, this list of conditions and the following disclaimer in
19 // the documentation and/or other materials provided with the
22 // - Neither the name of "The Computer Language Benchmarks Game" nor
23 // the name of "The Computer Language Shootout Benchmarks" nor the
24 // names of its contributors may be used to endorse or promote
25 // products derived from this software without specific prior
26 // written permission.
28 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
29 // "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
30 // LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
31 // FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
32 // COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
33 // INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
34 // (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
35 // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
36 // HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
37 // STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
38 // ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
39 // OF THE POSSIBILITY OF SUCH DAMAGE.
41 // ignore-pretty very bad with line comments
42 // ignore-android doesn't terminate?
44 use std::iter::range_step;
45 use std::io::{stdin, stdout, File};
47 static LINE_LEN: uint = 60;
49 fn make_complements() -> [u8, ..256] {
51 ('A', 'T'), ('C', 'G'), ('G', 'C'), ('T', 'A'),
52 ('U', 'A'), ('M', 'K'), ('R', 'Y'), ('W', 'W'),
53 ('S', 'S'), ('Y', 'R'), ('K', 'M'), ('V', 'B'),
54 ('H', 'D'), ('D', 'H'), ('B', 'V'), ('N', 'N'),
56 let mut complements: [u8, ..256] = [0, ..256];
57 for (i, c) in complements.mut_iter().enumerate() {
60 let lower = 'A' as u8 - 'a' as u8;
61 for &(from, to) in transforms.iter() {
62 complements[from as uint] = to as u8;
63 complements[(from as u8 - lower) as uint] = to as u8;
69 let complements = make_complements();
70 let data = if std::os::getenv("RUST_BENCH").is_some() {
71 File::open(&Path::new("shootout-k-nucleotide.data")).read_to_end()
75 let mut data = data.unwrap();
77 for seq in data.as_mut_slice().mut_split(|c| *c == '>' as u8) {
78 // skip header and last \n
79 let begin = match seq.iter().position(|c| *c == '\n' as u8) {
84 let seq = seq.mut_slice(begin + 1, len - 1);
86 // arrange line breaks
88 let off = LINE_LEN - len % (LINE_LEN + 1);
89 for i in range_step(LINE_LEN, len, LINE_LEN + 1) {
90 for j in std::iter::count(i, -1).take(off) {
93 seq[i - off] = '\n' as u8;
96 // reverse complement, as
97 // seq.reverse(); for c in seq.mut_iter() {*c = complements[*c]}
99 let mut it = seq.mut_iter();
101 match (it.next(), it.next_back()) {
102 (Some(front), Some(back)) => {
103 let tmp = complements[*front as uint];
104 *front = complements[*back as uint];
107 (Some(last), None) => *last = complements[*last as uint], // last element
108 _ => break // vector exhausted.
113 stdout().write(data.as_slice()).unwrap();