Add ability to find canonical substitution of DNA

Cargo.toml

@@ -16,6 +16,7 @@ serde = {version = "1.0", features = ["derive"], optional = true}
 
 [dev-dependencies]
 criterion = "0.5.1"
+quickcheck = "1.0.3"
 rand = "0.8.5"
 serde_json = "1"
 
@@ -32,6 +33,9 @@ default = ["python-support"]
 name = "all_windows"
 harness = false
 
+[[bench]]
+name = "canonical"
+harness = false
 
 [[bench]]
 name = "expansions"

benches/canonical.rs

@@ -0,0 +1,62 @@
+// Copyright 2021-2023 SecureDNA Stiftung (SecureDNA Foundation) <[email protected]>
+// SPDX-License-Identifier: MIT OR Apache-2.0
+
+use std::hint::black_box;
+
+use criterion::{criterion_group, criterion_main, BenchmarkId, Criterion, Throughput};
+use rand::{rngs::OsRng, seq::SliceRandom};
+
+use quickdna::canonical::{Canonical, ForwardCanonical};
+use quickdna::Nucleotide;
+
+pub fn criterion_benchmark(c: &mut Criterion) {
+    const NUM_WINDOWS: u64 = 10000;
+    const WINDOW_LEN: usize = 42;
+    let dna_len = (NUM_WINDOWS as usize) + WINDOW_LEN - 1;
+    let dna: Vec<_> = (0..dna_len)
+        .map(|_| Nucleotide::ALL.choose(&mut OsRng).unwrap())
+        .collect();
+
+    let num_windows_desc = format!("{NUM_WINDOWS} windows");
+
+    let mut group = c.benchmark_group("canonicalization");
+    group.throughput(Throughput::Elements(NUM_WINDOWS));
+    group.bench_with_input(
+        BenchmarkId::new("bidirectional", &num_windows_desc),
+        &(&dna, WINDOW_LEN),
+        |b, &(dna, window_len)| {
+            b.iter(|| {
+                let canonicalized_windows = dna.windows(window_len).map(|window| {
+                    let mut canonical = Canonical::new(window.iter().copied().copied());
+                    let window: [_; WINDOW_LEN] =
+                        std::array::from_fn(|_| canonical.next().unwrap());
+                    window
+                });
+                for window in canonicalized_windows {
+                    black_box(&window);
+                }
+            })
+        },
+    );
+    group.bench_with_input(
+        BenchmarkId::new("forward-only", &num_windows_desc),
+        &(&dna, WINDOW_LEN),
+        |b, &(dna, window_len)| {
+            b.iter(|| {
+                let canonicalized_windows = dna.windows(window_len).map(|window| {
+                    let mut canonical = ForwardCanonical::new(window.iter().copied().copied());
+                    let window: [_; WINDOW_LEN] =
+                        std::array::from_fn(|_| canonical.next().unwrap());
+                    window
+                });
+                for window in canonicalized_windows {
+                    black_box(&window);
+                }
+            })
+        },
+    );
+    group.finish();
+}
+
+criterion_group!(benches, criterion_benchmark);
+criterion_main!(benches);