src/test/bench/shootout-reverse-complement.rs

// The Computer Language Benchmarks Game
// http://benchmarksgame.alioth.debian.org/
//
// contributed by the Rust Project Developers

// Copyright (c) 2013-2014 The Rust Project Developers
//
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//
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//
// - Redistributions of source code must retain the above copyright
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//   the documentation and/or other materials provided with the
//   distribution.
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// - 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
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// ignore-android: FIXME(#10393) hangs without output

#![feature(libc)]

extern crate libc;

use std::io;
use std::io::prelude::*;
use std::ptr::copy;
use std::thread;

struct Tables {
    table8: Box<[u8; 1 << 8]>,
    table16: Box<[u16; 1 << 16]>,
}

impl Tables {
    fn new() -> Tables {
        let mut table8 = Box::new([0;1 << 8]);
        for (i, v) in table8.iter_mut().enumerate() {
            *v = Tables::computed_cpl8(i as u8);
        }
        let mut table16 = Box::new([0;1 << 16]);
        for (i, v) in table16.iter_mut().enumerate() {
            *v = (table8[i & 255] as u16) << 8 |
                 table8[i >> 8]  as u16;
        }
        Tables { table8: table8, table16: table16 }
    }

    fn computed_cpl8(c: u8) -> u8 {
        match c {
            b'A' | b'a' => b'T',
            b'C' | b'c' => b'G',
            b'G' | b'g' => b'C',
            b'T' | b't' => b'A',
            b'U' | b'u' => b'A',
            b'M' | b'm' => b'K',
            b'R' | b'r' => b'Y',
            b'W' | b'w' => b'W',
            b'S' | b's' => b'S',
            b'Y' | b'y' => b'R',
            b'K' | b'k' => b'M',
            b'V' | b'v' => b'B',
            b'H' | b'h' => b'D',
            b'D' | b'd' => b'H',
            b'B' | b'b' => b'V',
            b'N' | b'n' => b'N',
            i => i,
        }
    }

    /// Retrieves the complement for `i`.
    fn cpl8(&self, i: u8) -> u8 {
        self.table8[i as usize]
    }

    /// Retrieves the complement for `i`.
    fn cpl16(&self, i: u16) -> u16 {
        self.table16[i as usize]
    }
}

/// Finds the first position at which `b` occurs in `s`.
fn memchr(h: &[u8], n: u8) -> Option<usize> {
    use libc::{c_void, c_int, size_t};
    let res = unsafe {
        libc::memchr(h.as_ptr() as *const c_void, n as c_int, h.len() as size_t)
    };
    if res.is_null() {
        None
    } else {
        Some(res as usize - h.as_ptr() as usize)
    }
}

/// A mutable iterator over DNA sequences
struct MutDnaSeqs<'a> { s: &'a mut [u8] }
fn mut_dna_seqs<'a>(s: &'a mut [u8]) -> MutDnaSeqs<'a> {
    MutDnaSeqs { s: s }
}
impl<'a> Iterator for MutDnaSeqs<'a> {
    type Item = &'a mut [u8];

    fn next(&mut self) -> Option<&'a mut [u8]> {
        let tmp = std::mem::replace(&mut self.s, &mut []);
        let tmp = match memchr(tmp, b'\n') {
            Some(i) => &mut tmp[i + 1..],
            None => return None,
        };
        let (seq, tmp) = match memchr(tmp, b'>') {
            Some(i) => tmp.split_at_mut(i),
            None => {
                let len = tmp.len();
                tmp.split_at_mut(len)
            }
        };
        self.s = tmp;
        Some(seq)
    }
}

/// Length of a normal line without the terminating \n.
const LINE_LEN: usize = 60;

/// Compute the reverse complement.
fn reverse_complement(seq: &mut [u8], tables: &Tables) {
    let len = seq.len();
    let seq = &mut seq[..len - 1]; // Drop the last newline
    let len = seq.len();
    let off = LINE_LEN - len % (LINE_LEN + 1);
    let mut i = LINE_LEN;
    while i < len {
        unsafe {
            copy(seq.as_ptr().offset((i - off) as isize),
                 seq.as_mut_ptr().offset((i - off + 1) as isize), off);
            *seq.get_unchecked_mut(i - off) = b'\n';
        }
        i += LINE_LEN + 1;
    }

    let div = len / 4;
    let rem = len % 4;
    unsafe {
        let mut left = seq.as_mut_ptr() as *mut u16;
        // This is slow if len % 2 != 0 but still faster than bytewise operations.
        let mut right = seq.as_mut_ptr().offset(len as isize - 2) as *mut u16;
        let end = left.offset(div as isize);
        while left != end {
            let tmp = tables.cpl16(*left);
            *left = tables.cpl16(*right);
            *right = tmp;
            left = left.offset(1);
            right = right.offset(-1);
        }

        let end = end as *mut u8;
        match rem {
            1 => *end = tables.cpl8(*end),
            2 => {
                let tmp = tables.cpl8(*end);
                *end = tables.cpl8(*end.offset(1));
                *end.offset(1) = tmp;
            },
            3 => {
                *end.offset(1) = tables.cpl8(*end.offset(1));
                let tmp = tables.cpl8(*end);
                *end = tables.cpl8(*end.offset(2));
                *end.offset(2) = tmp;
            },
            _ => { },
        }
    }
}

/// Executes a closure in parallel over the given iterator over mutable slice.
/// The closure `f` is run in parallel with an element of `iter`.
// FIXME: replace with thread::scoped when it exists again
fn parallel<I: Iterator, F>(iter: I, ref f: F)
        where I::Item: Send,
              F: Fn(I::Item) + Sync, {
    iter.map(|x| {
        f(x)
    }).collect::<Vec<_>>();
}

fn main() {
    let mut data = Vec::with_capacity(1024 * 1024);
    io::stdin().read_to_end(&mut data).unwrap();
    let tables = &Tables::new();
    parallel(mut_dna_seqs(&mut data), |seq| reverse_complement(seq, tables));
    io::stdout().write_all(&data).unwrap();
}