diff --git a/lightmotif/src/pli.rs b/lightmotif/src/pli.rs
index 88bc619fc8e345c91cb2eb2f44f6f4b503cd5cd0..5549b9c53156d030e04d988b2ac561173e3aa464 100644
--- a/lightmotif/src/pli.rs
+++ b/lightmotif/src/pli.rs
@@ -20,14 +20,14 @@ mod seal {
}
pub struct Pipeline<A: Alphabet, V: Vector> {
- alphabet: A,
+ alphabet: std::marker::PhantomData<A>,
vector: std::marker::PhantomData<V>,
}
impl<A: Alphabet, V: Vector> Pipeline<A, V> {
pub fn new() -> Self {
Self {
- alphabet: A::default(),
+ alphabet: std::marker::PhantomData,
vector: std::marker::PhantomData,
}
}
@@ -41,7 +41,7 @@ impl Pipeline<DnaAlphabet, f32> {
scores: &mut StripedScores<f32, C>,
) {
let seq_rows = seq.data.rows() - seq.wrap;
- let mut result = &mut scores.data;
+ let result = &mut scores.data;
if result.rows() < seq_rows {
panic!("not enough rows for scores: {}", pwm.len());
}
@@ -79,7 +79,7 @@ impl Pipeline<DnaAlphabet, __m256> {
pwm: &WeightMatrix<DnaAlphabet, { DnaAlphabet::K }>,
scores: &mut StripedScores<__m256, { std::mem::size_of::<__m256i>() }>,
) {
- let mut result = &mut scores.data;
+ let result = &mut scores.data;
scores.length = seq.length - pwm.len() + 1;
if seq.wrap < pwm.len() - 1 {
@@ -262,7 +262,7 @@ impl<const C: usize> StripedScores<__m256, C> {
let mut col = 0;
let mut row = 0;
let mut vec = Vec::with_capacity(self.length);
- for i in 0..self.length {
+ while vec.len() < self.length {
vec.push(self.data[row][COLS[col]]);
row += 1;
if row == self.data.rows() {
diff --git a/lightmotif/src/pwm.rs b/lightmotif/src/pwm.rs
index e6ed40de6475b356fd1c450019c4e64071230d76..8b40ad1b9c9040057d29f40db98e03533254ea06 100644
--- a/lightmotif/src/pwm.rs
+++ b/lightmotif/src/pwm.rs
@@ -2,18 +2,18 @@ use super::abc::Alphabet;
use super::abc::Symbol;
use super::dense::DenseMatrix;
use super::seq::EncodedSequence;
-use super::seq::StripedSequence;
+
#[derive(Clone, Debug)]
pub struct Pseudocount<A: Alphabet, const K: usize> {
- pub alphabet: A,
+ alphabet: std::marker::PhantomData<A>,
pub counts: [f32; K],
}
impl<A: Alphabet, const K: usize> From<[f32; K]> for Pseudocount<A, K> {
fn from(counts: [f32; K]) -> Self {
Self {
- alphabet: A::default(),
+ alphabet: std::marker::PhantomData,
counts,
}
}
@@ -22,7 +22,7 @@ impl<A: Alphabet, const K: usize> From<[f32; K]> for Pseudocount<A, K> {
impl<A: Alphabet, const K: usize> From<f32> for Pseudocount<A, K> {
fn from(count: f32) -> Self {
Self {
- alphabet: A::default(),
+ alphabet: std::marker::PhantomData,
counts: [count; K],
}
}
@@ -30,7 +30,7 @@ impl<A: Alphabet, const K: usize> From<f32> for Pseudocount<A, K> {
#[derive(Clone, Debug)]
pub struct CountMatrix<A: Alphabet, const K: usize> {
- pub alphabet: A,
+ alphabet: std::marker::PhantomData<A>,
pub data: DenseMatrix<u32, K>,
pub name: String, // FIXME: Use `Rc` instead to avoid copies.
}
@@ -43,7 +43,7 @@ impl<A: Alphabet, const K: usize> CountMatrix<A, K> {
Ok(Self {
data,
name: name.into(),
- alphabet: A::default(),
+ alphabet: std::marker::PhantomData,
})
}
@@ -56,7 +56,7 @@ impl<A: Alphabet, const K: usize> CountMatrix<A, K> {
let mut data = None;
for seq in sequences {
let seq = seq.as_ref();
- let mut d = match data.as_mut() {
+ let d = match data.as_mut() {
Some(d) => d,
None => {
data = Some(DenseMatrix::new(seq.len()));
@@ -72,7 +72,7 @@ impl<A: Alphabet, const K: usize> CountMatrix<A, K> {
}
Ok(Self {
- alphabet: A::default(),
+ alphabet: std::marker::PhantomData,
data: data.unwrap_or_else(|| DenseMatrix::new(0)),
name: name.into(),
})
@@ -83,11 +83,11 @@ impl<A: Alphabet, const K: usize> CountMatrix<A, K> {
where
P: Into<Pseudocount<A, K>>,
{
- let mut p = pseudo.into();
+ let p = pseudo.into();
let mut probas = DenseMatrix::new(self.data.rows());
for i in 0..self.data.rows() {
let src = &self.data[i];
- let mut dst = &mut probas[i];
+ let dst = &mut probas[i];
for (j, &x) in src.iter().enumerate() {
dst[j] = x as f32 + p.counts[j] as f32;
}
@@ -97,7 +97,7 @@ impl<A: Alphabet, const K: usize> CountMatrix<A, K> {
}
}
ProbabilityMatrix {
- alphabet: self.alphabet,
+ alphabet: std::marker::PhantomData,
data: probas,
name: self.name.clone(),
}
@@ -106,7 +106,7 @@ impl<A: Alphabet, const K: usize> CountMatrix<A, K> {
#[derive(Clone, Debug)]
pub struct ProbabilityMatrix<A: Alphabet, const K: usize> {
- pub alphabet: A,
+ alphabet: std::marker::PhantomData<A>,
pub data: DenseMatrix<f32, K>,
pub name: String,
}
@@ -120,14 +120,14 @@ impl<A: Alphabet, const K: usize> ProbabilityMatrix<A, K> {
let mut weight = DenseMatrix::new(self.data.rows());
for i in 0..self.data.rows() {
let src = &self.data[i];
- let mut dst = &mut weight[i];
+ let dst = &mut weight[i];
for (j, (&x, &f)) in src.iter().zip(&b.frequencies).enumerate() {
dst[j] = (x / f).log2();
}
}
WeightMatrix {
background: b,
- alphabet: self.alphabet,
+ alphabet: std::marker::PhantomData,
data: weight,
name: self.name.clone(),
}
@@ -137,14 +137,14 @@ impl<A: Alphabet, const K: usize> ProbabilityMatrix<A, K> {
#[derive(Clone, Debug)]
pub struct Background<A: Alphabet, const K: usize> {
pub frequencies: [f32; K],
- _marker: std::marker::PhantomData<A>,
+ alphabet: std::marker::PhantomData<A>,
}
impl<A: Alphabet, const K: usize> Background<A, K> {
pub fn uniform() -> Self {
Self {
frequencies: [1.0 / (K as f32); K],
- _marker: std::marker::PhantomData,
+ alphabet: std::marker::PhantomData,
}
}
}
@@ -153,14 +153,14 @@ impl<A: Alphabet, const K: usize> From<[f32; K]> for Background<A, K> {
fn from(frequencies: [f32; K]) -> Self {
Self {
frequencies,
- _marker: std::marker::PhantomData,
+ alphabet: std::marker::PhantomData,
}
}
}
#[derive(Clone, Debug)]
pub struct WeightMatrix<A: Alphabet, const K: usize> {
- pub alphabet: A,
+ alphabet: std::marker::PhantomData<A>,
pub background: Background<A, K>,
pub data: DenseMatrix<f32, K>,
pub name: String,