From 173d5ab7f37d75a7f85760b2b0a7de3ac863467a Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Wed, 19 Jun 2024 17:14:29 +0200
Subject: [PATCH] Cache the `Pipeline` used in `lightmotif::scan::Scanner`
---
lightmotif/src/scan.rs | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/lightmotif/src/scan.rs b/lightmotif/src/scan.rs
index 329824d..629a59b 100644
--- a/lightmotif/src/scan.rs
+++ b/lightmotif/src/scan.rs
@@ -66,6 +66,7 @@ pub struct Scanner<'a, A: Alphabet> {
block_size: usize,
row: usize,
hits: Vec<Hit>,
+ pipeline: Pipeline<A, Dispatch>,
}
impl<'a, A: Alphabet> Scanner<'a, A> {
@@ -79,6 +80,7 @@ impl<'a, A: Alphabet> Scanner<'a, A> {
block_size: 512,
row: 0,
hits: Vec::new(),
+ pipeline: Pipeline::dispatch(),
}
}
@@ -140,12 +142,12 @@ where
type Item = Hit;
fn next(&mut self) -> Option<Self::Item> {
while self.hits.is_empty() && self.row < self.seq.matrix().rows() {
- let pli = Pipeline::dispatch();
let end = (self.row + self.block_size)
.min(self.seq.matrix().rows().saturating_sub(self.seq.wrap()));
- pli.score_rows_into(&self.pssm, &self.seq, self.row..end, &mut self.scores);
+ self.pipeline
+ .score_rows_into(&self.pssm, &self.seq, self.row..end, &mut self.scores);
let matrix = self.scores.matrix();
- for c in pli.threshold(&self.scores, self.threshold) {
+ for c in self.pipeline.threshold(&self.scores, self.threshold) {
let index = c.col * (self.seq.matrix().rows() - self.seq.wrap()) + self.row + c.row;
self.hits.push(Hit::new(index, matrix[c]));
}
--
GitLab