91 lines
2.8 KiB
Rust
91 lines
2.8 KiB
Rust
// The Computer Language Benchmarks Game
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// https://benchmarksgame-team.pages.debian.net/benchmarksgame/
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//
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// contributed by the Rust Project Developers
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// contributed by TeXitoi
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// contributed by BurntSushi
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// This technically solves the problem posed in the `regex-dna` benchmark, but
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// it cheats by combining all of the replacements into a single regex and
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// replacing them with a single linear scan. i.e., it re-implements
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// `replace_all`. As a result, this is around 25% faster. ---AG
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use std::io::{self, Read};
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use std::sync::Arc;
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use std::thread;
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macro_rules! regex {
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($re:expr) => {
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::regex::Regex::new($re).unwrap()
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};
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}
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fn main() {
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let mut seq = String::with_capacity(50 * (1 << 20));
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io::stdin().read_to_string(&mut seq).unwrap();
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let ilen = seq.len();
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seq = regex!(">[^\n]*\n|\n").replace_all(&seq, "").into_owned();
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let clen = seq.len();
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let seq_arc = Arc::new(seq.clone());
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let variants = vec![
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regex!("agggtaaa|tttaccct"),
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regex!("[cgt]gggtaaa|tttaccc[acg]"),
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regex!("a[act]ggtaaa|tttacc[agt]t"),
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regex!("ag[act]gtaaa|tttac[agt]ct"),
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regex!("agg[act]taaa|ttta[agt]cct"),
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regex!("aggg[acg]aaa|ttt[cgt]ccct"),
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regex!("agggt[cgt]aa|tt[acg]accct"),
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regex!("agggta[cgt]a|t[acg]taccct"),
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regex!("agggtaa[cgt]|[acg]ttaccct"),
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];
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let mut counts = vec![];
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for variant in variants {
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let seq = seq_arc.clone();
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let restr = variant.to_string();
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let future = thread::spawn(move || variant.find_iter(&seq).count());
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counts.push((restr, future));
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}
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let substs = vec![
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(b'B', "(c|g|t)"),
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(b'D', "(a|g|t)"),
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(b'H', "(a|c|t)"),
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(b'K', "(g|t)"),
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(b'M', "(a|c)"),
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(b'N', "(a|c|g|t)"),
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(b'R', "(a|g)"),
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(b'S', "(c|g)"),
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(b'V', "(a|c|g)"),
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(b'W', "(a|t)"),
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(b'Y', "(c|t)"),
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]; // combined into one regex in `replace_all`
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let seq = replace_all(&seq, substs);
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for (variant, count) in counts {
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println!("{} {}", variant, count.join().unwrap());
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}
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println!("\n{}\n{}\n{}", ilen, clen, seq.len());
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}
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fn replace_all(text: &str, substs: Vec<(u8, &str)>) -> String {
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let mut replacements = vec![""; 256];
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let mut alternates = vec![];
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for (re, replacement) in substs {
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replacements[re as usize] = replacement;
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alternates.push((re as char).to_string());
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}
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let re = regex!(&alternates.join("|"));
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let mut new = String::with_capacity(text.len());
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let mut last_match = 0;
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for m in re.find_iter(text) {
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new.push_str(&text[last_match..m.start()]);
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new.push_str(replacements[text.as_bytes()[m.start()] as usize]);
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last_match = m.end();
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}
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new.push_str(&text[last_match..]);
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new
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}
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