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// The Computer Language Benchmarks Game
// http://benchmarksgame.alioth.debian.org/
//
// contributed by the Rust Project Developers
// Copyright (c) 2013-2014 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-pretty very bad with line comments
// ignore-android doesn't terminate?
#![feature(slicing_syntax)]
use std::iter::range_step;
use std::io::{stdin, stdout, File};
static LINE_LEN: uint = 60;
fn make_complements() -> [u8, ..256] {
let transforms = [
('A', 'T'), ('C', 'G'), ('G', 'C'), ('T', 'A'),
('U', 'A'), ('M', 'K'), ('R', 'Y'), ('W', 'W'),
('S', 'S'), ('Y', 'R'), ('K', 'M'), ('V', 'B'),
('H', 'D'), ('D', 'H'), ('B', 'V'), ('N', 'N'),
('\n', '\n')];
let mut complements: [u8, ..256] = [0, ..256];
for (i, c) in complements.iter_mut().enumerate() {
*c = i as u8;
}
let lower = 'A' as u8 - 'a' as u8;
for &(from, to) in transforms.iter() {
complements[from as uint] = to as u8;
complements[(from as u8 - lower) as uint] = to as u8;
}
complements
}
fn main() {
let complements = make_complements();
let data = if std::os::getenv("RUST_BENCH").is_some() {
File::open(&Path::new("shootout-k-nucleotide.data")).read_to_end()
} else {
stdin().read_to_end()
};
let mut data = data.unwrap();
for seq in data.as_mut_slice().split_mut(|c| *c == '>' as u8) {
// skip header and last \n
let begin = match seq.iter().position(|c| *c == '\n' as u8) {
None => continue,
Some(c) => c
};
let len = seq.len();
let seq = seq[mut begin+1..len-1];
// arrange line breaks
let len = seq.len();
let off = LINE_LEN - len % (LINE_LEN + 1);
for i in range_step(LINE_LEN, len, LINE_LEN + 1) {
for j in std::iter::count(i, -1).take(off) {
seq[j] = seq[j - 1];
}
seq[i - off] = '\n' as u8;
}
// reverse complement, as
// seq.reverse(); for c in seq.iter_mut() {*c = complements[*c]}
// but faster:
let mut it = seq.iter_mut();
loop {
match (it.next(), it.next_back()) {
(Some(front), Some(back)) => {
let tmp = complements[*front as uint];
*front = complements[*back as uint];
*back = tmp;
}
(Some(last), None) => *last = complements[*last as uint], // last element
_ => break // vector exhausted.
}
}
}
stdout().write(data.as_slice()).unwrap();
}
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