Merge pull request #59 from triblespace/codex/add-bytes-field-to-waveletmatrix

Optimize wavelet matrix storage

Author: somethingelseentirely

CHANGELOG.md

@@ -62,3 +62,4 @@
 - Documented `WaveletMatrix` usage in `README.md`.
 - Moved README usage examples to runnable files in `examples/`.
 - Added `compact_vector` example showing construction and retrieval.
+- WaveletMatrix now stores its serialized word buffer for zero-copy access and preallocates building memory.

src/char_sequences/wavelet_matrix.rs

@@ -8,8 +8,7 @@ use anybytes::Bytes;
 use anyhow::{anyhow, Result};
 
 use crate::bit_vector::{
-    Access, BitVector, BitVectorBuilder, BitVectorData, BitVectorIndex, NumBits, Rank, Select,
-    WORD_LEN,
+    Access, BitVector, BitVectorData, BitVectorIndex, NumBits, Rank, Select, WORD_LEN,
 };
 use crate::int_vectors::{CompactVector, CompactVectorBuilder};
 use crate::utils;
@@ -56,10 +55,21 @@ use crate::utils;
 /// # References
 ///
 /// - F. Claude, and G. Navarro, "The Wavelet Matrix," In SPIRE 2012.
-#[derive(Default, Debug, Clone, PartialEq, Eq)]
+#[derive(Debug, Clone, PartialEq, Eq)]
 pub struct WaveletMatrix<I> {
     layers: Vec<BitVector<I>>,
     alph_size: usize,
+    bytes: Bytes,
+}
+
+impl<I> Default for WaveletMatrix<I> {
+    fn default() -> Self {
+        Self {
+            layers: Vec::new(),
+            alph_size: 0,
+            bytes: Bytes::empty(),
+        }
+    }
 }
 
 /// Metadata describing the serialized form of a [`WaveletMatrix`].
@@ -89,55 +99,79 @@ where
             return Err(anyhow!("seq must not be empty."));
         }
 
+        let len = seq.len();
         let alph_size = seq.iter().max().unwrap() + 1;
         let alph_width = utils::needed_bits(alph_size);
+        let num_words = (len + WORD_LEN - 1) / WORD_LEN;
+
+        let mut store = vec![0usize; alph_width * num_words];
 
         let mut zeros = seq;
         let mut ones = CompactVector::new(alph_width)?.freeze();
-        let mut layers = vec![];
 
         for depth in 0..alph_width {
             let mut next_zeros = CompactVectorBuilder::new(alph_width).unwrap();
             let mut next_ones = CompactVectorBuilder::new(alph_width).unwrap();
-            let mut bv = BitVectorBuilder::new();
-            Self::filter(
+            let layer = &mut store[depth * num_words..(depth + 1) * num_words];
+            let mut pos = 0;
+            Self::filter_into(
                 &zeros,
                 alph_width - depth - 1,
                 &mut next_zeros,
                 &mut next_ones,
-                &mut bv,
+                layer,
+                &mut pos,
             );
-            Self::filter(
+            Self::filter_into(
                 &ones,
                 alph_width - depth - 1,
                 &mut next_zeros,
                 &mut next_ones,
-                &mut bv,
+                layer,
+                &mut pos,
             );
             zeros = next_zeros.freeze();
             ones = next_ones.freeze();
-            let bits = bv.freeze::<I>();
-            layers.push(bits);
         }
 
-        Ok(Self { layers, alph_size })
+        let bytes = Bytes::from_source(store);
+        let mut layer_bytes = bytes.clone();
+        let mut layers = Vec::with_capacity(alph_width);
+        for _ in 0..alph_width {
+            let words = layer_bytes
+                .view_prefix_with_elems::<[usize]>(num_words)
+                .map_err(|e| anyhow!(e))?;
+            let data = BitVectorData { words, len };
+            let index = I::build(&data);
+            layers.push(BitVector::new(data, index));
+        }
+
+        Ok(Self {
+            layers,
+            alph_size,
+            bytes,
+        })
     }
 
-    fn filter(
+    fn filter_into(
         seq: &CompactVector,
         shift: usize,
         next_zeros: &mut CompactVectorBuilder,
         next_ones: &mut CompactVectorBuilder,
-        bv: &mut BitVectorBuilder,
+        layer: &mut [usize],
+        pos: &mut usize,
     ) {
         for val in seq.iter() {
             let bit = ((val >> shift) & 1) == 1;
-            bv.push_bit(bit);
             if bit {
+                let idx = *pos / WORD_LEN;
+                let sh = *pos % WORD_LEN;
+                layer[idx] |= 1usize << sh;
                 next_ones.push_int(val).unwrap();
             } else {
                 next_zeros.push_int(val).unwrap();
             }
+            *pos += 1;
         }
     }
 
@@ -577,24 +611,21 @@ where
 
     /// Serializes the sequence into a [`Bytes`] buffer along with its metadata.
     pub fn to_bytes(&self) -> (WaveletMatrixMeta, Bytes) {
-        let mut store: Vec<usize> = Vec::new();
-        for layer in &self.layers {
-            store.extend_from_slice(layer.data.words());
-        }
         let meta = WaveletMatrixMeta {
             alph_size: self.alph_size,
             alph_width: self.alph_width(),
             len: self.len(),
         };
-        (meta, Bytes::from_source(store))
+        (meta, self.bytes.clone())
     }
 
     /// Reconstructs the sequence from metadata and a zero-copy [`Bytes`] buffer.
-    pub fn from_bytes(meta: WaveletMatrixMeta, mut bytes: Bytes) -> Result<Self> {
+    pub fn from_bytes(meta: WaveletMatrixMeta, bytes: Bytes) -> Result<Self> {
         let mut layers = Vec::with_capacity(meta.alph_width);
         let num_words = (meta.len + WORD_LEN - 1) / WORD_LEN;
+        let mut slice = bytes.clone();
         for _ in 0..meta.alph_width {
-            let words = bytes
+            let words = slice
                 .view_prefix_with_elems::<[usize]>(num_words)
                 .map_err(|e| anyhow!(e))?;
             let data = BitVectorData {
@@ -607,6 +638,7 @@ where
         Ok(Self {
             layers,
             alph_size: meta.alph_size,
+            bytes,
         })
     }
 }