refactor(packed_seq): unify kmer iterators with generic storage

Merge PackedSeqKmerIter and OwnedPackedSeqKmerIter into a single generic PackedSeqKmerIter<S> parameterized over the storage type. Add an AsRef<PackedSeq> implementation to PackedSeq to enable this abstraction, allowing the zero-allocation sliding-window kmer iterator to seamlessly accept both borrowed and owned sequences without code duplication.

src/obikseq/src/packed_seq.rs

@@ -222,7 +222,7 @@ impl PackedSeq {
 
     /// Iterate over all kmers of length `params::k()` in order. Zero allocation.
     #[inline]
-    pub fn iter_kmers(&self) -> PackedSeqKmerIter<'_> {
+    pub fn iter_kmers(&self) -> PackedSeqKmerIter<&PackedSeq> {
         PackedSeqKmerIter::new(self)
     }
 
@@ -282,11 +282,18 @@ impl PackedSeq {
     }
 }
 
+impl AsRef<PackedSeq> for PackedSeq {
+    fn as_ref(&self) -> &PackedSeq { self }
+}
+
 // ── PackedSeqKmerIter ─────────────────────────────────────────────────────────
 
 /// Sliding-window kmer iterator over a [`PackedSeq`]. Zero allocation.
-pub struct PackedSeqKmerIter<'a> {
-    seq: &'a PackedSeq,
+///
+/// `S` is the storage: `&PackedSeq` (borrowing) or `PackedSeq` (owning).
+/// Both implement `AsRef<PackedSeq>` via std blanket impls.
+pub struct PackedSeqKmerIter<S> {
+    seq: S,
     mask: u64,
     lshift: usize,
     current: u64,
@@ -294,61 +301,18 @@ pub struct PackedSeqKmerIter<'a> {
     max_pos: usize,
 }
 
-impl<'a> PackedSeqKmerIter<'a> {
-    fn new(seq: &'a PackedSeq) -> Self {
-        let seql = seq.seql();
-        let klen = k();
-        let lshift = 64 - klen * 2;
-        let mask = ((!0u128) << (lshift + 2)) as u64;
-        Self {
-            seq,
-            mask,
-            lshift,
-            current: if seql >= klen { seq.extract::<KLen>(0).map(|km| km.raw()).unwrap_or(0) } else { 0 },
-            pos: klen,
-            max_pos: seql,
-        }
-    }
-}
+/// Owning alias: the iterator moves the [`PackedSeq`] into itself.
+pub type OwnedPackedSeqKmerIter = PackedSeqKmerIter<PackedSeq>;
 
-impl Iterator for PackedSeqKmerIter<'_> {
-    type Item = Kmer;
-
-    fn next(&mut self) -> Option<Kmer> {
-        if self.pos > self.max_pos {
-            return None;
-        }
-        let result = Kmer::from_raw(self.current);
-        if self.pos < self.max_pos {
-            let inner_shift = 6 - 2 * (self.pos & 3);
-            let nuc = ((self.seq.seq[self.pos / 4] >> inner_shift) & 3) as u64;
-            self.current = ((self.current << 2) & self.mask) | (nuc << self.lshift);
-        }
-        self.pos += 1;
-        Some(result)
-    }
-}
-
-// ── OwnedPackedSeqKmerIter ────────────────────────────────────────────────────
-
-/// Sliding-window kmer iterator that owns its [`PackedSeq`]. Zero allocation.
-pub struct OwnedPackedSeqKmerIter {
-    seq: PackedSeq,
-    mask: u64,
-    lshift: usize,
-    current: u64,
-    pos: usize,
-    max_pos: usize,
-}
-
-impl OwnedPackedSeqKmerIter {
-    fn new(seq: PackedSeq) -> Self {
-        let seql = seq.seql();
+impl<S: AsRef<PackedSeq>> PackedSeqKmerIter<S> {
+    fn new(seq: S) -> Self {
+        let ps = seq.as_ref();
+        let seql = ps.seql();
         let klen = k();
         let lshift = 64 - klen * 2;
         let mask = ((!0u128) << (lshift + 2)) as u64;
         let current = if seql >= klen {
-            seq.extract::<KLen>(0).map(|km| km.raw()).unwrap_or(0)
+            ps.extract::<KLen>(0).map(|km| km.raw()).unwrap_or(0)
         } else {
             0
         };
@@ -356,7 +320,7 @@ impl OwnedPackedSeqKmerIter {
     }
 }
 
-impl Iterator for OwnedPackedSeqKmerIter {
+impl<S: AsRef<PackedSeq>> Iterator for PackedSeqKmerIter<S> {
     type Item = Kmer;
 
     fn next(&mut self) -> Option<Kmer> {
@@ -366,7 +330,7 @@ impl Iterator for OwnedPackedSeqKmerIter {
         let result = Kmer::from_raw(self.current);
         if self.pos < self.max_pos {
             let inner_shift = 6 - 2 * (self.pos & 3);
-            let nuc = ((self.seq.seq[self.pos / 4] >> inner_shift) & 3) as u64;
+            let nuc = ((self.seq.as_ref().seq[self.pos / 4] >> inner_shift) & 3) as u64;
             self.current = ((self.current << 2) & self.mask) | (nuc << self.lshift);
         }
         self.pos += 1;