From ed79dd5cc64b5030b42fb95e4e3905c34dd2f342 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Sat, 15 Jun 2024 09:37:41 +0200
Subject: [PATCH] Rename JASPAR (2016) benchmark in `lightmotif-io`
---
lightmotif-io/benches/{jaspar.rs => jaspar16.rs} | 0
lightmotif-io/src/jaspar/mod.rs | 7 +++++++
lightmotif-io/src/jaspar16/mod.rs | 1 +
3 files changed, 8 insertions(+)
rename lightmotif-io/benches/{jaspar.rs => jaspar16.rs} (100%)
diff --git a/lightmotif-io/benches/jaspar.rs b/lightmotif-io/benches/jaspar16.rs
similarity index 100%
rename from lightmotif-io/benches/jaspar.rs
rename to lightmotif-io/benches/jaspar16.rs
diff --git a/lightmotif-io/src/jaspar/mod.rs b/lightmotif-io/src/jaspar/mod.rs
index 0f5ca17..58a1cac 100644
--- a/lightmotif-io/src/jaspar/mod.rs
+++ b/lightmotif-io/src/jaspar/mod.rs
@@ -26,6 +26,10 @@ mod parse;
// ---
+/// A JASPAR (raw) record.
+///
+/// The JASPAR (raw) format only supports count matrices in the DNA
+/// alphabet.
#[derive(Debug, Clone)]
pub struct Record {
id: String,
@@ -34,14 +38,17 @@ pub struct Record {
}
impl Record {
+ /// Get the identifier of the record.
pub fn id(&self) -> &str {
&self.id
}
+ /// Get the description of the record, if any.
pub fn description(&self) -> Option<&str> {
self.description.as_deref()
}
+ /// Get the count matrix of the record.
pub fn matrix(&self) -> &CountMatrix<Dna> {
&self.matrix
}
diff --git a/lightmotif-io/src/jaspar16/mod.rs b/lightmotif-io/src/jaspar16/mod.rs
index 16c9fe9..1eae03b 100644
--- a/lightmotif-io/src/jaspar16/mod.rs
+++ b/lightmotif-io/src/jaspar16/mod.rs
@@ -26,6 +26,7 @@ mod parse;
// ---
+/// A JASPAR (2016) record.
#[derive(Debug, Clone)]
pub struct Record<A: Alphabet> {
id: String,
--
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