115 lines
4.1 KiB
Rust
115 lines
4.1 KiB
Rust
// The Computer Language Benchmarks Game
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// http://benchmarksgame.alioth.debian.org/
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//
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// contributed by the Rust Project Developers
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// Copyright (c) 2013-2014 The Rust Project Developers
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//
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions
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// are met:
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//
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// - Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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//
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// - Redistributions in binary form must reproduce the above copyright
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// notice, this list of conditions and the following disclaimer in
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// the documentation and/or other materials provided with the
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// distribution.
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//
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// - Neither the name of "The Computer Language Benchmarks Game" nor
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// the name of "The Computer Language Shootout Benchmarks" nor the
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// names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior
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// written permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
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// FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
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// COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
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// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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// (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
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// HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
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// STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
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// OF THE POSSIBILITY OF SUCH DAMAGE.
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// ignore-pretty very bad with line comments
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// ignore-android doesn't terminate?
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use std::iter::range_step;
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use std::io::{stdin, stdout, File};
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static LINE_LEN: uint = 60;
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fn make_complements() -> [u8, ..256] {
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let transforms = [
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('A', 'T'), ('C', 'G'), ('G', 'C'), ('T', 'A'),
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('U', 'A'), ('M', 'K'), ('R', 'Y'), ('W', 'W'),
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('S', 'S'), ('Y', 'R'), ('K', 'M'), ('V', 'B'),
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('H', 'D'), ('D', 'H'), ('B', 'V'), ('N', 'N'),
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('\n', '\n')];
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let mut complements: [u8, ..256] = [0, ..256];
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for (i, c) in complements.iter_mut().enumerate() {
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*c = i as u8;
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}
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let lower = 'A' as u8 - 'a' as u8;
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for &(from, to) in transforms.iter() {
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complements[from as uint] = to as u8;
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complements[(from as u8 - lower) as uint] = to as u8;
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}
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complements
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}
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fn main() {
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let complements = make_complements();
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let data = if std::os::getenv("RUST_BENCH").is_some() {
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File::open(&Path::new("shootout-k-nucleotide.data")).read_to_end()
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} else {
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stdin().read_to_end()
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};
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let mut data = data.unwrap();
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for seq in data.as_mut_slice().split_mut(|c| *c == '>' as u8) {
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// skip header and last \n
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let begin = match seq.iter().position(|c| *c == '\n' as u8) {
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None => continue,
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Some(c) => c
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};
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let len = seq.len();
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let seq = seq.slice_mut(begin + 1, len - 1);
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// arrange line breaks
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let len = seq.len();
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let off = LINE_LEN - len % (LINE_LEN + 1);
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for i in range_step(LINE_LEN, len, LINE_LEN + 1) {
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for j in std::iter::count(i, -1).take(off) {
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seq[j] = seq[j - 1];
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}
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seq[i - off] = '\n' as u8;
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}
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// reverse complement, as
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// seq.reverse(); for c in seq.iter_mut() {*c = complements[*c]}
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// but faster:
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let mut it = seq.iter_mut();
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loop {
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match (it.next(), it.next_back()) {
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(Some(front), Some(back)) => {
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let tmp = complements[*front as uint];
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*front = complements[*back as uint];
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*back = tmp;
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}
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(Some(last), None) => *last = complements[*last as uint], // last element
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_ => break // vector exhausted.
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}
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}
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}
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stdout().write(data.as_slice()).unwrap();
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}
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