1237530452
* Added `// no-pretty-expanded` to pretty-print a test, but not run it through the `expanded` variant. * Removed #[deriving] and other expanded attributes after they are expanded * Removed hacks around &str and &&str and friends (from both the parser and the pretty printer). * Un-ignored a bunch of tests
85 lines
2.8 KiB
Rust
85 lines
2.8 KiB
Rust
// Copyright 2013-2014 The Rust Project Developers. See the COPYRIGHT
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// file at the top-level directory of this distribution and at
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// http://rust-lang.org/COPYRIGHT.
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//
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// Licensed under the Apache License, Version 2.0 <LICENSE-APACHE or
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// http://www.apache.org/licenses/LICENSE-2.0> or the MIT license
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// <LICENSE-MIT or http://opensource.org/licenses/MIT>, at your
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// option. This file may not be copied, modified, or distributed
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// except according to those terms.
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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.mut_iter().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().mut_split(|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.mut_slice(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.mut_iter() {*c = complements[*c]}
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// but faster:
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let mut it = seq.mut_iter();
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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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