From b0e1043247010e0da34e5b21ae4b2ec8b8e93325 Mon Sep 17 00:00:00 2001
From: jeff-k <jeff_k@fastmail.com>
Date: Wed, 23 Oct 2024 19:56:17 +0100
Subject: [PATCH] more useful 1-bit degenerate DNA encoding

---
 bio-seq/src/codec/degenerate/dna.rs | 54 +++++++++++++++++++++++++++--
 1 file changed, 51 insertions(+), 3 deletions(-)

diff --git a/bio-seq/src/codec/degenerate/dna.rs b/bio-seq/src/codec/degenerate/dna.rs
index 58055bc..37fa2c3 100644
--- a/bio-seq/src/codec/degenerate/dna.rs
+++ b/bio-seq/src/codec/degenerate/dna.rs
@@ -2,15 +2,63 @@ use crate::codec::Codec;
 use crate::codec::Complement;
 use crate::seq::{ReverseComplement, Seq};
 
-/// 1-bit encoding for `S`trong (`G`/`C`) and `W`eak (`A`/`T`) nucleotides
-#[derive(Clone, Copy, Debug, PartialEq, Eq, PartialOrd, Ord, Hash, Codec)]
-#[bits(1)]
+/// 1-bit encoding for `S`trong (`G`/`C`) and `W`eak (`A`/`T`) binding nucleotides
+#[derive(Clone, Copy, Debug, PartialEq, Eq, PartialOrd, Ord, Hash)]
 #[repr(u8)]
 pub enum Dna {
     W = 0b0,
     S = 0b1,
 }
 
+impl Codec for Dna {
+    const BITS: u8 = 1;
+
+    /// Transmute a `u8` into a degenerate 1-bit nucleotide
+    ///
+    /// SAFETY: This only looks at the lower 2 bits of the `u8`
+    fn unsafe_from_bits(b: u8) -> Self {
+        debug_assert!(b < 2);
+        unsafe { std::mem::transmute(b & 0b1) }
+    }
+
+    /// Valid values are `0` and `1`
+    fn try_from_bits(b: u8) -> Option<Self> {
+        if b < 2 {
+            Some(unsafe { std::mem::transmute::<u8, Dna>(b) })
+        } else {
+            None
+        }
+    }
+
+    /// TODO: fast translation of A, T, W to 0 and C, G, S to 1
+    fn unsafe_from_ascii(_b: u8) -> Self {
+        todo!()
+    }
+
+    fn try_from_ascii(c: u8) -> Option<Self> {
+        match c {
+            b'S' | b'C' | b'G' => Some(Dna::S),
+            b'W' | b'A' | b'T' => Some(Dna::W),
+            _ => None,
+        }
+    }
+
+    fn to_char(self) -> char {
+        match self {
+            Dna::S => 'S',
+            Dna::W => 'W',
+        }
+    }
+
+    fn to_bits(self) -> u8 {
+        self as u8
+    }
+
+    fn items() -> impl Iterator<Item = Self> {
+        vec![Dna::S, Dna::W].into_iter()
+    }
+}
+
 impl Complement for Dna {
     /// This representation collapses complements; `comp(x) == x`
     fn comp(&self) -> Self {