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Major refactoring and performance improvements.
Overview of changes: * Instruction set has been redesigned to be smaller, mostly by collapsing empty-width matches into one instruction type. In addition to moving instruction-matching out of the matching engine, this makes matching engine code much simpler. * Rewrote input handling to use an inline representation of `Option<char>` and clearer position handling with the `Input` trait. * Added a new bounded backtracking matching engine that is invoked for small regexes/inputs. It's about twice as fast as the full NFA matching engine. * Implemented caching for both the NFA and backtracking engines. This avoids costly allocations on subsequent uses of the regex. * Overhauled prefix handling at both discovery and matching. Namely, sets of prefix literals can now be extracted from regexes. Depending on what the prefixes look like, an Aho-Corasick DFA is built from them. (This adds a dependency on the `aho-corasick` crate.) * When appropriate, use `memchr` to jump around in the input when there is a single common byte prefix. (This adds a dependency on the `memchr` crate.) * Bring the `regex!` macro up to date. Unfortunately, it still implements the full NFA matching engine and doesn't yet have access to the new prefix DFA handling. Thus, its performance has gotten *worse* than the dynamic implementation in most cases. The docs have been updated to reflect this change. Surprisingly, all of this required exactly one new application of `unsafe`, which is isolated in the `memchr` crate. (Aho-Corasick has no `unsafe` either!) There should be *no* breaking changes in this commit. The only public facing change is the addition of a method to the `Replacer` trait, but it comes with a default implementation so that existing implementors won't break. (Its purpose is to serve as a hint as to whether or not replacement strings need to be expanded. This is crucial to speeding up simple replacements.) Closes #21.
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Original file line number | Diff line number | Diff line change |
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agggtaaa|tttaccct 0 | ||
[cgt]gggtaaa|tttaccc[acg] 3 | ||
a[act]ggtaaa|tttacc[agt]t 9 | ||
ag[act]gtaaa|tttac[agt]ct 8 | ||
agg[act]taaa|ttta[agt]cct 10 | ||
aggg[acg]aaa|ttt[cgt]ccct 3 | ||
agggt[cgt]aa|tt[acg]accct 4 | ||
agggta[cgt]a|t[acg]taccct 3 | ||
agggtaa[cgt]|[acg]ttaccct 5 | ||
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||
101745 | ||
100000 | ||
133640 |
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Original file line number | Diff line number | Diff line change |
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// The Computer Language Benchmarks Game | ||
// http://benchmarksgame.alioth.debian.org/ | ||
// | ||
// contributed by the Rust Project Developers | ||
// contributed by TeXitoi | ||
// contributed by BurntSushi | ||
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extern crate regex; | ||
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use std::io::{self, Read}; | ||
use std::sync::Arc; | ||
use std::thread; | ||
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macro_rules! regex { ($re:expr) => { ::regex::Regex::new($re).unwrap() } } | ||
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fn main() { | ||
let mut seq = String::with_capacity(10 * (1 << 20)); | ||
io::stdin().read_to_string(&mut seq).unwrap(); | ||
let ilen = seq.len(); | ||
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seq = regex!(">[^\n]*\n|\n").replace_all(&seq, ""); | ||
let clen = seq.len(); | ||
let seq_arc = Arc::new(seq.clone()); | ||
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let variants = vec![ | ||
regex!("agggtaaa|tttaccct"), | ||
regex!("[cgt]gggtaaa|tttaccc[acg]"), | ||
regex!("a[act]ggtaaa|tttacc[agt]t"), | ||
regex!("ag[act]gtaaa|tttac[agt]ct"), | ||
regex!("agg[act]taaa|ttta[agt]cct"), | ||
regex!("aggg[acg]aaa|ttt[cgt]ccct"), | ||
regex!("agggt[cgt]aa|tt[acg]accct"), | ||
regex!("agggta[cgt]a|t[acg]taccct"), | ||
regex!("agggtaa[cgt]|[acg]ttaccct"), | ||
]; | ||
let mut counts = vec![]; | ||
for variant in variants { | ||
let seq = seq_arc.clone(); | ||
let restr = variant.to_string(); | ||
let future = thread::spawn(move || variant.find_iter(&seq).count()); | ||
counts.push((restr, future)); | ||
} | ||
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let substs = vec![ | ||
(regex!("B"), "(c|g|t)"), | ||
(regex!("D"), "(a|g|t)"), | ||
(regex!("H"), "(a|c|t)"), | ||
(regex!("K"), "(g|t)"), | ||
(regex!("M"), "(a|c)"), | ||
(regex!("N"), "(a|c|g|t)"), | ||
(regex!("R"), "(a|g)"), | ||
(regex!("S"), "(c|g)"), | ||
(regex!("V"), "(a|c|g)"), | ||
(regex!("W"), "(a|t)"), | ||
(regex!("Y"), "(c|t)"), | ||
]; | ||
let mut seq = seq; | ||
for (re, replacement) in substs.into_iter() { | ||
seq = re.replace_all(&seq, replacement); | ||
} | ||
let rlen = seq.len(); | ||
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for (variant, count) in counts { | ||
println!("{} {}", variant, count.join().unwrap()); | ||
} | ||
println!("\n{}\n{}\n{}", ilen, clen, rlen); | ||
} |
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