source code
// The Computer Language Benchmarks Game
// http://benchmarksgame.alioth.debian.org/
//
// contributed by the Rust Project Developers
// contributed by Cristi Cobzarenco (@cristicbz)
// contributed by TeXitoi
// Rust #4 modified to use same get_seq as Rust #3
// modified by Tung Duong
#![allow(non_snake_case)]
extern crate rayon;
extern crate ordermap;
use std::sync::Arc;
use std::hash::{Hasher, BuildHasherDefault};
use rayon::prelude::*;
use Item::*;
use ordermap::OrderMap;
struct NaiveHasher(u64);
impl Default for NaiveHasher {
fn default() -> Self {
NaiveHasher(0)
}
}
impl Hasher for NaiveHasher {
fn finish(&self) -> u64 {
self.0
}
fn write(&mut self, _: &[u8]) {
unimplemented!()
}
fn write_u64(&mut self, i: u64) {
self.0 = i ^ i >> 7;
}
}
type NaiveBuildHasher = BuildHasherDefault<NaiveHasher>;
type NaiveHashMap<K, V> = OrderMap<K, V, NaiveBuildHasher>;
type Map = NaiveHashMap<Code, u32>;
#[derive(Hash, PartialEq, PartialOrd, Ord, Eq, Clone, Copy)]
struct Code(u64);
impl Code {
fn push(&mut self, c: u8, mask: u64) {
self.0 <<= 2;
self.0 |= c as u64;
self.0 &= mask;
}
fn from_str(s: &str) -> Code {
let mask = Code::make_mask(s.len());
let mut res = Code(0);
for c in s.as_bytes() {
res.push(Code::encode(*c), mask);
}
res
}
fn to_string(&self, frame: usize) -> String {
let mut res = vec![];
let mut code = self.0;
for _ in 0..frame {
let c = match code as u8 & 0b11 {
c if c == Code::encode(b'A') => b'A',
c if c == Code::encode(b'T') => b'T',
c if c == Code::encode(b'G') => b'G',
c if c == Code::encode(b'C') => b'C',
_ => unreachable!(),
};
res.push(c);
code >>= 2;
}
res.reverse();
String::from_utf8(res).unwrap()
}
fn make_mask(frame: usize) -> u64 {
(1u64 << (2 * frame)) - 1
}
fn encode(c: u8) -> u8 {
(c & 0b110) >> 1
}
}
struct Iter<'a> {
iter: std::slice::Iter<'a, u8>,
code: Code,
mask: u64,
}
impl<'a> Iter<'a> {
fn new(input: &[u8], frame: usize) -> Iter {
let mut iter = input.iter();
let mut code = Code(0);
let mask = Code::make_mask(frame);
for c in iter.by_ref().take(frame - 1) {
code.push(*c, mask);
}
Iter {
iter: iter,
code: code,
mask: mask,
}
}
}
impl<'a> Iterator for Iter<'a> {
type Item = Code;
fn next(&mut self) -> Option<Self::Item> {
self.iter.next().map(|&c| {
self.code.push(c, self.mask);
self.code
})
}
}
fn gen_freq(input: &[u8], frame: usize) -> Map {
let mut freq = Map::default();
for code in Iter::new(input, frame) {
*freq.entry(code).or_insert(0) += 1;
}
freq
}
#[derive(Clone, Copy)]
enum Item {
Freq(usize),
Occ(&'static str),
}
impl Item {
fn print(&self, freq: &Map) {
match *self {
Freq(frame) => {
let mut v: Vec<_> = freq.iter().map(|(&code, &count)| (count, code)).collect();
v.sort();
let total = v.iter().map(|&(count, _)| count).sum::<u32>() as f32;
for &(count, key) in v.iter().rev() {
println!("{} {:.3}", key.to_string(frame), (count as f32 * 100.) / total);
}
println!("");
}
Occ(occ) => {
let count = if freq.contains_key(&Code::from_str(occ)){
freq[&Code::from_str(occ)]
}else { 0 };
println!("{}\t{}", count , occ);
},
}
}
fn gen_freq(&self, input: &[u8]) -> Map {
match *self {
Freq(frame) => gen_freq(input, frame),
Occ(occ) => gen_freq(input, occ.len()),
}
}
}
fn get_seq<R: std::io::BufRead>(r: R, key: &str) -> Vec<u8> {
let mut res = Vec::new();
for l in r.lines().map(|l| l.unwrap()).skip_while(|l| !l.starts_with(key)).skip(1) {
res.extend(l.trim().as_bytes().iter().cloned().map(Code::encode));
}
res
}
fn main() {
let ITEMS = vec![
Freq(1),
Freq(2),
Occ("GGT"),
Occ("GGTA"),
Occ("GGTATT"),
Occ("GGTATTTTAATT"),
Occ("GGTATTTTAATTTATAGT"),
];
let stdin = std::io::stdin();
let input = get_seq(stdin.lock(), ">THREE");
let input = Arc::new(input);
// In reverse to spawn big tasks first
let items: Vec<_> = ITEMS.into_par_iter().rev().map(|item| {
let input = input.clone();
(item, item.gen_freq(&input))
}).collect();
for (item, freq) in items.into_iter().rev() {
item.print(&freq);
}
}