Document methods of `jaspar16::Record` in `lightmotif-io`

lightmotif-io/README.md

@@ -24,7 +24,7 @@ PSSM file formats, including:
 - [x] [TRANSFAC](https://en.wikipedia.org/wiki/TRANSFAC)-formatted records,
   with associated metadata. 
 - [x] [JASPAR](https://jaspar.elixir.no/docs/) count matrices
-  (in JASPAR 2016 bracketed format) with their record header.
+  (in JASPAR 2016 bracketed format or raw format) with their record header.
 - [x] [UniPROBE](http://the_brain.bwh.harvard.edu/uniprobe/index.php) 
   frequency matrices with their record header.
 - [ ] [MEME minimal](https://meme-suite.org/meme/doc/meme-format.html) records

lightmotif-io/src/jaspar/mod.rs

@@ -62,6 +62,7 @@ impl AsRef<CountMatrix<Dna>> for Record {
 
 // ---
 
+/// An iterative reader for the JASPAR format.
 pub struct Reader<B: BufRead> {
     buffer: Vec<u8>,
     bufread: B,
@@ -69,6 +70,7 @@ pub struct Reader<B: BufRead> {
 }
 
 impl<B: BufRead> Reader<B> {
+    /// Create a new `Reader` from a buffered reader.
     pub fn new(mut reader: B) -> Self {
         let mut buffer = Vec::new();
         let start = reader.read_until(b'>', &mut buffer).unwrap_or(1) - 1;
@@ -121,6 +123,7 @@ impl<B: BufRead> Iterator for Reader<B> {
     }
 }
 
+/// Read the records from a file in JASPAR format.
 pub fn read<B: BufRead>(reader: B) -> self::Reader<B> {
     self::Reader::new(reader)
 }

lightmotif-io/src/jaspar16/mod.rs

@@ -35,14 +35,17 @@ pub struct Record<A: Alphabet> {
 }
 
 impl<A: Alphabet> Record<A> {
+    /// 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<A> {
         &self.matrix
     }
@@ -56,6 +59,7 @@ impl<A: Alphabet> AsRef<CountMatrix<A>> for Record<A> {
 
 // ---
 
+/// An iterative reader for the JASPAR (2016) format.
 pub struct Reader<B: BufRead, A: Alphabet> {
     buffer: Vec<u8>,
     bufread: B,
@@ -117,6 +121,7 @@ impl<B: BufRead, A: Alphabet> Iterator for Reader<B, A> {
     }
 }
 
+/// Read the records from a file in JASPAR (2016) format.
 pub fn read<B: BufRead, A: Alphabet>(reader: B) -> self::Reader<B, A> {
     self::Reader::new(reader)
 }

lightmotif-io/src/transfac/mod.rs

@@ -25,26 +25,32 @@ pub struct Record<A: Alphabet> {
 }
 
 impl<A: Alphabet> Record<A> {
+    /// The identifier of the record, if any.
     pub fn id(&self) -> Option<&str> {
         self.id.as_deref()
     }
 
+    /// The accession of the record, if any.
     pub fn accession(&self) -> Option<&str> {
         self.accession.as_deref()
     }
 
+    /// The name of the record, if any.
     pub fn name(&self) -> Option<&str> {
         self.name.as_deref()
     }
 
+    /// The description of the record, if any.
     pub fn description(&self) -> Option<&str> {
         self.description.as_deref()
     }
 
+    /// The raw data found in the matrix.
     pub fn data(&self) -> Option<&DenseMatrix<f32, A::K>> {
         self.data.as_ref()
     }
 
+    /// The raw data found in the matrix.
     pub fn to_counts(&self) -> Option<CountMatrix<A>> {
         if let Some(data) = &self.data {
             let mut counts = DenseMatrix::<u32, A::K>::new(data.rows());