From 8d763605a34e20aeb87114f8aeadc6024f4cd285 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Wed, 30 Aug 2023 22:30:33 +0200
Subject: [PATCH] Make `StripedSequence::new` return an error when given an
invalid length
---
lightmotif/src/pli/mod.rs | 4 ++--
lightmotif/src/seq.rs | 17 +++++++++++------
2 files changed, 13 insertions(+), 8 deletions(-)
diff --git a/lightmotif/src/pli/mod.rs b/lightmotif/src/pli/mod.rs
index f124ce6..d7b0872 100644
--- a/lightmotif/src/pli/mod.rs
+++ b/lightmotif/src/pli/mod.rs
@@ -142,7 +142,7 @@ pub trait Stripe<A: Alphabet, C: StrictlyPositive> {
let s = seq.as_ref();
let length = s.len();
let rows = (length / C::USIZE) + ((length % C::USIZE > 0) as usize);
- let mut striped = StripedSequence::new(DenseMatrix::new(rows), length);
+ let mut striped = StripedSequence::new(DenseMatrix::new(rows), length).unwrap();
self.stripe_into(s, &mut striped);
striped
}
@@ -159,7 +159,7 @@ pub trait Stripe<A: Alphabet, C: StrictlyPositive> {
for (i, &x) in s.iter().enumerate() {
data[i % rows][i / rows] = x;
}
- for i in s.len()..matrix.rows() * matrix.columns() {
+ for i in s.len()..data.rows() * data.columns() {
data[i % rows][i / rows] = A::default_symbol();
}
}
diff --git a/lightmotif/src/seq.rs b/lightmotif/src/seq.rs
index 3e48a88..12abfc2 100644
--- a/lightmotif/src/seq.rs
+++ b/lightmotif/src/seq.rs
@@ -11,6 +11,7 @@ use typenum::marker_traits::Unsigned;
use super::abc::Alphabet;
use super::abc::Symbol;
use super::dense::DenseMatrix;
+use super::err::InvalidData;
use super::err::InvalidSymbol;
use super::num::StrictlyPositive;
use super::pwm::ScoringMatrix;
@@ -145,12 +146,16 @@ pub struct StripedSequence<A: Alphabet, C: StrictlyPositive> {
impl<A: Alphabet, C: StrictlyPositive> StripedSequence<A, C> {
/// Create a new striped sequence from the given dense matrix.
- pub fn new(data: DenseMatrix<A::Symbol, C>, length: usize) -> Self {
- Self {
- data,
- length,
- wrap: 0,
- alphabet: std::marker::PhantomData,
+ pub fn new(data: DenseMatrix<A::Symbol, C>, length: usize) -> Result<Self, InvalidData> {
+ if data.rows() * data.columns() < length {
+ Err(InvalidData)
+ } else {
+ Ok(Self {
+ data,
+ length,
+ wrap: 0,
+ alphabet: std::marker::PhantomData,
+ })
}
}
--
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