From 04f013d6afdfffb2e3e034cbbd94279078966ccb Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 2 Sep 2024 20:40:48 +0200
Subject: [PATCH] Fix some Rust code issues in `lightmotif`
---
lightmotif-io/src/transfac/parse.rs | 8 +--
lightmotif/src/dense.rs | 5 +-
lightmotif/src/pli/mod.rs | 9 ++--
lightmotif/src/pli/platform/avx2.rs | 77 +++++++++++++++--------------
lightmotif/src/pli/platform/neon.rs | 4 +-
lightmotif/src/pli/platform/sse2.rs | 6 +--
lightmotif/src/pwm.rs | 10 +++-
lightmotif/src/scan.rs | 4 +-
lightmotif/src/seq.rs | 32 ++++++------
9 files changed, 80 insertions(+), 75 deletions(-)
diff --git a/lightmotif-io/src/transfac/parse.rs b/lightmotif-io/src/transfac/parse.rs
index 00e43bf..801a26e 100644
--- a/lightmotif-io/src/transfac/parse.rs
+++ b/lightmotif-io/src/transfac/parse.rs
@@ -186,10 +186,10 @@ pub fn parse_reference(mut input: &str) -> IResult<&str, Reference> {
pub fn parse_record<A: Alphabet>(mut input: &str) -> IResult<&str, Record<A>> {
let mut accession = None;
- let mut ba = None;
+ let mut _ba = None;
let mut name = None;
let mut id = None;
- let mut copyright = None;
+ let mut _copyright = None;
let mut description = None;
let mut dates = Vec::new();
let mut references = Vec::new();
@@ -207,7 +207,7 @@ pub fn parse_record<A: Alphabet>(mut input: &str) -> IResult<&str, Record<A>> {
}
"BA" => {
let (rest, line) = preceded(tag("BA"), parse_line)(input)?;
- ba = Some(line.trim().to_string()); // FIXME: check uniqueness?
+ _ba = Some(line.trim().to_string()); // FIXME: check uniqueness?
input = rest;
}
"BS" => {
@@ -227,7 +227,7 @@ pub fn parse_record<A: Alphabet>(mut input: &str) -> IResult<&str, Record<A>> {
}
"CO" => {
let (rest, line) = preceded(tag("CO"), parse_line)(input)?;
- copyright = Some(line.trim().to_string()); // FIXME: check uniqueness?
+ _copyright = Some(line.trim().to_string()); // FIXME: check uniqueness?
input = rest;
}
"DE" => {
diff --git a/lightmotif/src/dense.rs b/lightmotif/src/dense.rs
index 376a20d..66b8977 100644
--- a/lightmotif/src/dense.rs
+++ b/lightmotif/src/dense.rs
@@ -8,8 +8,6 @@ use std::ops::Index;
use std::ops::IndexMut;
use std::ops::Range;
-use crate::abc::Alphabet;
-use crate::abc::Symbol;
use crate::num::ArrayLength;
// --- MatrixElement -----------------------------------------------------------
@@ -60,6 +58,7 @@ impl<T: MatrixElement, C: ArrayLength> DenseMatrix<T, C> {
}
/// Create a new *uninitialized* matrix with the given number of rows.
+ #[allow(clippy::uninit_vec)]
pub unsafe fn uninitialized(rows: usize) -> Self {
let mut m = Self::new(0);
m.data.reserve(rows);
@@ -219,7 +218,7 @@ impl<'a, T: MatrixElement, C: ArrayLength> IntoIterator for &'a mut DenseMatrix<
}
}
-impl<'a, T: MatrixElement + PartialEq, C: ArrayLength> PartialEq for DenseMatrix<T, C> {
+impl<T: MatrixElement + PartialEq, C: ArrayLength> PartialEq for DenseMatrix<T, C> {
fn eq(&self, other: &Self) -> bool {
if self.rows() != other.rows() {
return false;
diff --git a/lightmotif/src/pli/mod.rs b/lightmotif/src/pli/mod.rs
index f10c829..dcc8e2c 100644
--- a/lightmotif/src/pli/mod.rs
+++ b/lightmotif/src/pli/mod.rs
@@ -36,6 +36,7 @@ pub mod platform;
/// Used for encoding a sequence into rank-based encoding.
pub trait Encode<A: Alphabet> {
/// Encode the given sequence into a vector of symbols.
+ #[allow(clippy::uninit_vec)]
fn encode_raw<S: AsRef<[u8]>>(&self, seq: S) -> Result<Vec<A::Symbol>, InvalidSymbol> {
let s = seq.as_ref();
let mut buffer = Vec::with_capacity(s.len());
@@ -84,7 +85,7 @@ pub trait Score<T: MatrixElement + AddAssign, A: Alphabet, C: StrictlyPositive +
let seq = seq.as_ref();
let pssm = pssm.as_ref();
- if seq.len() < pssm.rows() || rows.len() == 0 {
+ if seq.len() < pssm.rows() || rows.is_empty() {
scores.resize(0, 0);
return;
}
@@ -115,7 +116,7 @@ pub trait Score<T: MatrixElement + AddAssign, A: Alphabet, C: StrictlyPositive +
{
let s = seq.as_ref();
let rows = s.matrix().rows() - s.wrap();
- Self::score_rows_into(&self, pssm, s, 0..rows, scores)
+ self.score_rows_into(pssm, s, 0..rows, scores)
}
/// Compute the PSSM scores for every sequence positions.
@@ -272,14 +273,14 @@ impl<A: Alphabet> Pipeline<A, Dispatch> {
alphabet: std::marker::PhantomData,
};
}
- #[cfg(any(target_arch = "x86"))]
+ #[cfg(target_arch = "x86")]
if std::is_x86_feature_detected!("sse2") {
return Self {
backend: Dispatch::Sse2,
alphabet: std::marker::PhantomData,
};
}
- #[cfg(any(target_arch = "x86_64"))]
+ #[cfg(target_arch = "x86_64")]
return Self {
backend: Dispatch::Sse2,
alphabet: std::marker::PhantomData,
diff --git a/lightmotif/src/pli/platform/avx2.rs b/lightmotif/src/pli/platform/avx2.rs
index 36c31f8..a0990ca 100644
--- a/lightmotif/src/pli/platform/avx2.rs
+++ b/lightmotif/src/pli/platform/avx2.rs
@@ -84,8 +84,8 @@ where
// If an invalid symbol was encountered, recover which one.
// FIXME: run a vectorize the error search?
if _mm256_testz_si256(error, error) != 1 {
- for i in 0..l {
- A::Symbol::from_ascii(seq[i])?;
+ for s in seq.iter() {
+ A::Symbol::from_ascii(*s)?;
}
}
@@ -540,6 +540,7 @@ unsafe fn max_u8_avx2(scores: &StripedScores<u8, <Avx2 as Backend>::LANES>) -> O
#[cfg(any(target_arch = "x86", target_arch = "x86_64"))]
#[target_feature(enable = "avx2")]
+#[allow(clippy::erasing_op, clippy::identity_op)]
unsafe fn stripe_avx2<A>(
seq: &[A::Symbol],
striped: &mut StripedSequence<A, <Avx2 as Backend>::LANES>,
@@ -598,38 +599,38 @@ unsafe fn stripe_avx2<A>(
// Process sequence block by block
let mut i = 0;
while i + <Avx2 as Backend>::LANES::USIZE <= src_stride {
- let mut r00 = _mm256_loadu_si256(src.add(00 * src_stride) as _);
- let mut r01 = _mm256_loadu_si256(src.add(src_stride) as _);
- let mut r02 = _mm256_loadu_si256(src.add(02 * src_stride) as _);
- let mut r03 = _mm256_loadu_si256(src.add(03 * src_stride) as _);
- let mut r04 = _mm256_loadu_si256(src.add(04 * src_stride) as _);
- let mut r05 = _mm256_loadu_si256(src.add(05 * src_stride) as _);
- let mut r06 = _mm256_loadu_si256(src.add(06 * src_stride) as _);
- let mut r07 = _mm256_loadu_si256(src.add(07 * src_stride) as _);
- let mut r08 = _mm256_loadu_si256(src.add(08 * src_stride) as _);
- let mut r09 = _mm256_loadu_si256(src.add(09 * src_stride) as _);
- let mut r10 = _mm256_loadu_si256(src.add(10 * src_stride) as _);
- let mut r11 = _mm256_loadu_si256(src.add(11 * src_stride) as _);
- let mut r12 = _mm256_loadu_si256(src.add(12 * src_stride) as _);
- let mut r13 = _mm256_loadu_si256(src.add(13 * src_stride) as _);
- let mut r14 = _mm256_loadu_si256(src.add(14 * src_stride) as _);
- let mut r15 = _mm256_loadu_si256(src.add(15 * src_stride) as _);
- let mut r16 = _mm256_loadu_si256(src.add(16 * src_stride) as _);
- let mut r17 = _mm256_loadu_si256(src.add(17 * src_stride) as _);
- let mut r18 = _mm256_loadu_si256(src.add(18 * src_stride) as _);
- let mut r19 = _mm256_loadu_si256(src.add(19 * src_stride) as _);
- let mut r20 = _mm256_loadu_si256(src.add(20 * src_stride) as _);
- let mut r21 = _mm256_loadu_si256(src.add(21 * src_stride) as _);
- let mut r22 = _mm256_loadu_si256(src.add(22 * src_stride) as _);
- let mut r23 = _mm256_loadu_si256(src.add(23 * src_stride) as _);
- let mut r24 = _mm256_loadu_si256(src.add(24 * src_stride) as _);
- let mut r25 = _mm256_loadu_si256(src.add(25 * src_stride) as _);
- let mut r26 = _mm256_loadu_si256(src.add(26 * src_stride) as _);
- let mut r27 = _mm256_loadu_si256(src.add(27 * src_stride) as _);
- let mut r28 = _mm256_loadu_si256(src.add(28 * src_stride) as _);
- let mut r29 = _mm256_loadu_si256(src.add(29 * src_stride) as _);
- let mut r30 = _mm256_loadu_si256(src.add(30 * src_stride) as _);
- let mut r31 = _mm256_loadu_si256(src.add(31 * src_stride) as _);
+ let mut r00 = _mm256_loadu_si256(src.add(0x00 * src_stride) as _);
+ let mut r01 = _mm256_loadu_si256(src.add(0x01 * src_stride) as _);
+ let mut r02 = _mm256_loadu_si256(src.add(0x02 * src_stride) as _);
+ let mut r03 = _mm256_loadu_si256(src.add(0x03 * src_stride) as _);
+ let mut r04 = _mm256_loadu_si256(src.add(0x04 * src_stride) as _);
+ let mut r05 = _mm256_loadu_si256(src.add(0x05 * src_stride) as _);
+ let mut r06 = _mm256_loadu_si256(src.add(0x06 * src_stride) as _);
+ let mut r07 = _mm256_loadu_si256(src.add(0x07 * src_stride) as _);
+ let mut r08 = _mm256_loadu_si256(src.add(0x08 * src_stride) as _);
+ let mut r09 = _mm256_loadu_si256(src.add(0x09 * src_stride) as _);
+ let mut r10 = _mm256_loadu_si256(src.add(0x0a * src_stride) as _);
+ let mut r11 = _mm256_loadu_si256(src.add(0x0b * src_stride) as _);
+ let mut r12 = _mm256_loadu_si256(src.add(0x0c * src_stride) as _);
+ let mut r13 = _mm256_loadu_si256(src.add(0x0d * src_stride) as _);
+ let mut r14 = _mm256_loadu_si256(src.add(0x0e * src_stride) as _);
+ let mut r15 = _mm256_loadu_si256(src.add(0x0f * src_stride) as _);
+ let mut r16 = _mm256_loadu_si256(src.add(0x10 * src_stride) as _);
+ let mut r17 = _mm256_loadu_si256(src.add(0x11 * src_stride) as _);
+ let mut r18 = _mm256_loadu_si256(src.add(0x12 * src_stride) as _);
+ let mut r19 = _mm256_loadu_si256(src.add(0x13 * src_stride) as _);
+ let mut r20 = _mm256_loadu_si256(src.add(0x14 * src_stride) as _);
+ let mut r21 = _mm256_loadu_si256(src.add(0x15 * src_stride) as _);
+ let mut r22 = _mm256_loadu_si256(src.add(0x16 * src_stride) as _);
+ let mut r23 = _mm256_loadu_si256(src.add(0x17 * src_stride) as _);
+ let mut r24 = _mm256_loadu_si256(src.add(0x18 * src_stride) as _);
+ let mut r25 = _mm256_loadu_si256(src.add(0x19 * src_stride) as _);
+ let mut r26 = _mm256_loadu_si256(src.add(0x1a * src_stride) as _);
+ let mut r27 = _mm256_loadu_si256(src.add(0x1b * src_stride) as _);
+ let mut r28 = _mm256_loadu_si256(src.add(0x1c * src_stride) as _);
+ let mut r29 = _mm256_loadu_si256(src.add(0x1d * src_stride) as _);
+ let mut r30 = _mm256_loadu_si256(src.add(0x1e * src_stride) as _);
+ let mut r31 = _mm256_loadu_si256(src.add(0x1f * src_stride) as _);
unpack!(epi8, r00, r01);
unpack!(epi8, r02, r03);
@@ -717,7 +718,7 @@ unsafe fn stripe_avx2<A>(
unpack!(epi128, r15, r31);
_mm256_stream_si256(out.add(0x00 * out_stride) as _, r00);
- _mm256_stream_si256(out.add(out_stride) as _, r08);
+ _mm256_stream_si256(out.add(0x01 * out_stride) as _, r08);
_mm256_stream_si256(out.add(0x02 * out_stride) as _, r04);
_mm256_stream_si256(out.add(0x03 * out_stride) as _, r12);
_mm256_stream_si256(out.add(0x04 * out_stride) as _, r02);
@@ -816,7 +817,7 @@ impl Avx2 {
);
}
- if seq.len() < pssm.rows() || rows.len() == 0 {
+ if seq.len() < pssm.rows() || rows.is_empty() {
scores.resize(0, 0);
return;
}
@@ -851,7 +852,7 @@ impl Avx2 {
);
}
- if seq.len() < pssm.rows() || rows.len() == 0 {
+ if seq.len() < pssm.rows() || rows.is_empty() {
scores.resize(0, 0);
return;
}
@@ -888,7 +889,7 @@ impl Avx2 {
);
}
- if seq.len() < pssm.rows() || rows.len() == 0 {
+ if seq.len() < pssm.rows() || rows.is_empty() {
scores.resize(0, 0);
return;
}
diff --git a/lightmotif/src/pli/platform/neon.rs b/lightmotif/src/pli/platform/neon.rs
index 2bddb8a..0fb7f9c 100644
--- a/lightmotif/src/pli/platform/neon.rs
+++ b/lightmotif/src/pli/platform/neon.rs
@@ -264,7 +264,7 @@ impl Neon {
);
}
- if seq.len() < pssm.rows() || rows.len() == 0 {
+ if seq.len() < pssm.rows() || rows.is_empty() {
scores.resize(0, 0);
return;
}
@@ -302,7 +302,7 @@ impl Neon {
);
}
- if seq.len() < pssm.rows() || rows.len() == 0 {
+ if seq.len() < pssm.rows() || rows.is_empty() {
scores.resize(0, 0);
return;
}
diff --git a/lightmotif/src/pli/platform/sse2.rs b/lightmotif/src/pli/platform/sse2.rs
index fad275f..274201a 100644
--- a/lightmotif/src/pli/platform/sse2.rs
+++ b/lightmotif/src/pli/platform/sse2.rs
@@ -87,8 +87,8 @@ where
let mut x: [u8; 16] = [0; 16];
_mm_storeu_si128(x.as_mut_ptr() as *mut __m128i, error);
if x.iter().any(|&x| x != 0) {
- for i in 0..l {
- let _ = A::Symbol::from_ascii(seq[i])?;
+ for x in seq.iter() {
+ let _ = A::Symbol::from_ascii(*x)?;
}
}
@@ -292,7 +292,7 @@ impl Sse2 {
);
}
- if seq.len() < pssm.rows() || rows.len() == 0 {
+ if seq.len() < pssm.rows() || rows.is_empty() {
scores.resize(0, 0);
return;
}
diff --git a/lightmotif/src/pwm.rs b/lightmotif/src/pwm.rs
index 432225b..adfcf28 100644
--- a/lightmotif/src/pwm.rs
+++ b/lightmotif/src/pwm.rs
@@ -28,11 +28,17 @@ macro_rules! matrix_traits {
&self.data
}
- /// The length of the motif encoded in this matrix.
+ /// Get the length of the motif encoded in this matrix.
#[inline]
pub const fn len(&self) -> usize {
self.data.rows()
}
+
+ /// Check whether the matrix is empty.
+ #[inline]
+ pub const fn is_empty(&self) -> bool {
+ self.data.rows() == 0
+ }
}
impl<A: Alphabet> AsRef<$mx<A>> for $mx<A> {
@@ -115,7 +121,7 @@ impl<A: Alphabet> CountMatrix<A> {
/// ]);
/// assert!(result.is_err());
/// ```
- pub fn from_sequences<'seq, I>(sequences: I) -> Result<Self, InvalidData>
+ pub fn from_sequences<I>(sequences: I) -> Result<Self, InvalidData>
where
I: IntoIterator,
<I as IntoIterator>::Item: AsRef<EncodedSequence<A>>,
diff --git a/lightmotif/src/scan.rs b/lightmotif/src/scan.rs
index 4123526..c67e524 100644
--- a/lightmotif/src/scan.rs
+++ b/lightmotif/src/scan.rs
@@ -40,7 +40,7 @@ impl<T> std::ops::Deref for CowMut<'_, T> {
fn deref(&self) -> &T {
match self {
CowMut::Owned(it) => it,
- CowMut::Borrowed(it) => *it,
+ CowMut::Borrowed(it) => it,
}
}
}
@@ -49,7 +49,7 @@ impl<T> std::ops::DerefMut for CowMut<'_, T> {
fn deref_mut(&mut self) -> &mut T {
match self {
CowMut::Owned(it) => it,
- CowMut::Borrowed(it) => *it,
+ CowMut::Borrowed(it) => it,
}
}
}
diff --git a/lightmotif/src/seq.rs b/lightmotif/src/seq.rs
index b91bb6f..7e7043d 100644
--- a/lightmotif/src/seq.rs
+++ b/lightmotif/src/seq.rs
@@ -3,6 +3,7 @@
use std::fmt::Display;
use std::fmt::Formatter;
use std::fmt::Result as FmtResult;
+use std::fmt::Write;
use std::ops::Index;
use std::str::FromStr;
@@ -80,6 +81,12 @@ impl<A: Alphabet> EncodedSequence<A> {
self.data.len()
}
+ /// Check whether the sequence is empty.
+ #[inline]
+ pub fn is_empty(&self) -> bool {
+ self.data.is_empty()
+ }
+
/// Iterate over the symbols in the sequence.
#[inline]
pub fn iter(&self) -> <&[A::Symbol] as IntoIterator>::IntoIter {
@@ -98,15 +105,6 @@ impl<A: Alphabet> EncodedSequence<A> {
let pli = Pipeline::<A, _>::dispatch();
pli.stripe(&self.data)
}
-
- /// Convert the encoded sequence back to its textual representation.
- pub fn to_string(&self) -> String {
- let mut s = String::with_capacity(self.len());
- for c in self.data.iter() {
- s.push(c.as_char());
- }
- s
- }
}
impl<A: Alphabet> AsRef<EncodedSequence<A>> for EncodedSequence<A> {
@@ -130,7 +128,7 @@ impl<A: Alphabet> Default for EncodedSequence<A> {
impl<A: Alphabet> Display for EncodedSequence<A> {
fn fmt(&self, f: &mut Formatter) -> FmtResult {
for c in self.data.iter() {
- write!(f, "{}", c.as_char())?;
+ f.write_char(c.as_char())?;
}
Ok(())
}
@@ -184,12 +182,6 @@ where
let r = other.as_ref();
l == r
}
-
- fn ne(&self, other: &S) -> bool {
- let l = self.data.as_slice();
- let r = other.as_ref();
- l != r
- }
}
// --- StripedSequence ---------------------------------------------------------
@@ -243,6 +235,12 @@ impl<A: Alphabet, C: StrictlyPositive + ArrayLength> StripedSequence<A, C> {
self.length
}
+ /// Check whether the sequence is empty.
+ #[inline]
+ pub const fn is_empty(&self) -> bool {
+ self.length == 0
+ }
+
/// Get the number of wrapping rows in the striped matrix.
#[inline]
pub const fn wrap(&self) -> usize {
@@ -263,7 +261,7 @@ impl<A: Alphabet, C: StrictlyPositive + ArrayLength> StripedSequence<A, C> {
/// Reconfigure the striped sequence for searching with a motif.
pub fn configure(&mut self, motif: &ScoringMatrix<A>) {
- if motif.len() > 0 {
+ if !motif.is_empty() {
self.configure_wrap(motif.len() - 1);
}
}
--
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