add first iteration of A*PA2 figures

justfile

@@ -8,3 +8,12 @@ codecoverage:
 
 vis:
    cargo run -r --example aligners_vis --features sdl
+
+fig name:
+  cargo run -r --example fig-{{name}}-2 --features sdl
+  mogrify -format png imgs/astarpa2-paper/{{name}}/*bmp
+  rm imgs/astarpa2-paper/{{name}}/*bmp
+
+fig-intro: (fig "intro")
+fig-limitations: (fig "limitations")
+fig-layers: (fig "layers")

pa-bin/Cargo.toml

@@ -11,6 +11,7 @@ pa-types.workspace = true
 pa-generate.workspace = true
 pa-heuristic.workspace = true
 astarpa.workspace = true
+astarpa2.workspace = true
 itertools.workspace = true
 clap.workspace = true
 pa-vis = {workspace = true, optional=true}
@@ -47,3 +48,14 @@ path = "examples/astarpa-figures/comparison.rs"
 [[example]]
 name = "fig-limitations"
 path = "examples/astarpa-figures/limitations.rs"
+
+# A*PA2 figures
+[[example]]
+name = "fig-intro-2"
+path = "examples/astarpa2-figures/intro.rs"
+[[example]]
+name = "fig-limitations-2"
+path = "examples/astarpa2-figures/limitations.rs"
+[[example]]
+name = "fig-layers-2"
+path = "examples/astarpa2-figures/layers.rs"

pa-bin/examples/astarpa2-figures/intro.rs

@@ -0,0 +1,110 @@
+#![feature(trait_upcasting)]
+//! This generates the visualizations used in figure 1 in the paper and in the slides.
+
+use astarpa::{astar, AstarPa};
+use pa_affine_types::AffineCost;
+use pa_base_algos::{
+    dt::{DiagonalTransition, GapCostHeuristic},
+    nw::{AffineFront, NW},
+};
+use pa_generate::uniform_fixed;
+use pa_heuristic::{MatchConfig, NoCost, Pruning, GCSH};
+use pa_types::Aligner;
+use pa_vis::visualizer::{self, Gradient, When};
+use pa_vis_types::NoVis;
+use std::{path::PathBuf, time::Duration};
+
+fn main() {
+    let n = 8000;
+    let e = 0.20;
+    let (ref a, ref b) = uniform_fixed(n, e);
+    eprintln!("Length {}", a.len());
+    let cost = astar(&a, &b, &NoCost, &NoVis).0 .0;
+    eprintln!("Distance {cost}");
+    eprintln!("Divergence {}", cost as f32 / a.len() as f32);
+
+    let cm = AffineCost::unit();
+    let mut config = visualizer::Config::default();
+    config.draw = When::None;
+    config.save = When::None;
+    config.save_last = true;
+    config.delay = Duration::from_secs_f32(0.0001);
+    config.downscaler = 4;
+    config.cell_size = 1;
+    config.style.bg_color = (255, 255, 255, 128);
+    config.style.expanded = Gradient::TurboGradient(0.25..0.90);
+    config.style.path = Some((0, 0, 0, 0));
+    config.style.path_width = Some(4);
+    config.layer_drawing = false;
+    config.style.draw_dt = false;
+    config.style.draw_f = false;
+    config.style.draw_labels = false;
+    config.transparent_bmp = true;
+    config.draw_old_on_top = true;
+    config.filepath = PathBuf::from("imgs/astarpa2-paper/intro");
+    config.clear_after_meeting_point = false;
+
+    let aligners: &mut [Box<dyn Aligner>] = &mut [
+        Box::new(NW {
+            cm,
+            strategy: pa_base_algos::Strategy::band_doubling(),
+            domain: pa_base_algos::Domain::gap_gap(),
+            block_width: 1,
+            v: config.with_filename("0_ukkonen"),
+            front: AffineFront,
+            trace: true,
+            sparse_h: false,
+            prune: false,
+        }),
+        Box::new(NW {
+            cm,
+            strategy: pa_base_algos::Strategy::band_doubling(),
+            domain: pa_base_algos::Domain::dist_gap(),
+            block_width: 1,
+            v: config.with_filename("1_edlib"),
+            front: AffineFront,
+            trace: true,
+            sparse_h: false,
+            prune: false,
+        }),
+        Box::new(AstarPa {
+            dt: false,
+            h: NoCost,
+            v: config.with_filename("2_dijkstra"),
+        }),
+        Box::new(DiagonalTransition::new(
+            cm,
+            GapCostHeuristic::Disable,
+            NoCost,
+            false,
+            config.with_filename("3_diagonal-transition"),
+        )),
+        Box::new(DiagonalTransition::new(
+            cm,
+            GapCostHeuristic::Disable,
+            NoCost,
+            true,
+            {
+                let mut c = config.with_filename("4_dt-divide-and-conquer");
+                c.draw_old_on_top = false;
+                c
+            },
+        )),
+        Box::new(AstarPa {
+            h: GCSH::new(MatchConfig::exact(5), Pruning::both()),
+            dt: true,
+            v: config.with_filename("5_astarpa"),
+        }),
+        astarpa2::AstarPa2Params::simple()
+            .make_aligner_with_visualizer(true, config.with_filename("6_astarpa2_simple")),
+        {
+            let mut params = astarpa2::AstarPa2Params::full();
+            params.heuristic.k = 5;
+            params
+        }
+        .make_aligner_with_visualizer(true, config.with_filename("7_astarpa2_full")),
+    ];
+    for aligner in aligners {
+        aligner.align(a, b);
+    }
+}

pa-bin/examples/astarpa2-figures/layers.rs

@@ -0,0 +1,77 @@
+use astarpa::AstarPa;
+use pa_heuristic::{MatchConfig, Prune, Pruning, CSH, GCSH, SH};
+use pa_vis::visualizer::{self, Gradient, When};
+use pa_vis_types::canvas::*;
+use std::path::PathBuf;
+use std::time::Duration;
+
+fn main() {
+    let a = b"ACTCAGCTGTTGCCCGCTGTCGATCCGTAATTTAAAGTAGGTCGAAAC";
+    let b = b"ACTCAACGTTGCGCCTGTCTATCGTAATTAAAGTGGAGAAAC";
+
+    let mut config = visualizer::Config::default();
+    config.draw = When::None;
+    config.save = When::None;
+    config.save_last = true;
+    config.paused = false;
+    config.delay = Duration::from_secs_f32(0.0001);
+    config.cell_size = 12;
+    config.draw_old_on_top = false;
+    config.style.bg_color = WHITE;
+    config.style.expanded = Gradient::Fixed((130, 179, 102, 0));
+    config.style.explored = Some((0, 102, 204, 0));
+    config.style.heuristic = Gradient::Gradient((250, 250, 250, 0)..(180, 180, 180, 0));
+    config.style.max_heuristic = Some(10);
+    config.style.max_layer = Some(20);
+    config.style.pruned_match = RED;
+    config.style.path = None;
+    config.style.match_width = 3;
+    config.style.draw_heuristic = false;
+    config.style.draw_layers = true;
+    config.style.draw_contours = true;
+    config.style.draw_matches = true;
+    config.style.contour = BLACK;
+    config.layer_drawing = false;
+    config.style.draw_dt = false;
+    config.style.draw_f = false;
+    config.style.draw_labels = false;
+
+    config.filepath = PathBuf::from("imgs/astarpa2-paper/layers/");
+
+    if !cfg!(feature = "example") {
+        eprintln!("WARNING: Without the example feature, pruned matches aren't shown red for SH");
+    }
+
+    let mut astarpa2 = astarpa2::AstarPa2Params::full();
+    astarpa2.heuristic.k = 3;
+
+    let k = 2;
+    let mut match_config = MatchConfig {
+        length: pa_heuristic::LengthConfig::Fixed(k),
+        r: 1,
+        local_pruning: 0,
+    };
+    let pruning = Prune::None;
+    for p in [0, 5] {
+        match_config.local_pruning = p;
+        let suf = if p > 0 { "-lp" } else { "" };
+        AstarPa {
+            dt: false,
+            h: SH::new(match_config, Pruning::new(pruning)),
+            v: config.with_filename(&("sh".to_string() + suf)),
+        }
+        .align(a, b);
+        AstarPa {
+            dt: false,
+            h: CSH::new(match_config, Pruning::new(pruning)),
+            v: config.with_filename(&("csh".to_string() + suf)),
+        }
+        .align(a, b);
+        AstarPa {
+            dt: false,
+            h: GCSH::new(match_config, Pruning::new(pruning)),
+            v: config.with_filename(&("gcsh".to_string() + suf)),
+        }
+        .align(a, b);
+    }
+}

pa-bin/examples/astarpa2-figures/limitations.rs

@@ -0,0 +1,95 @@
+//! This generates the visualizations used in the limitations section of the paper.
+
+use pa_generate::{uniform_seeded, ErrorModel};
+use pa_vis::visualizer::{self, Gradient, When};
+use pa_vis_types::canvas::RED;
+use rand::SeedableRng;
+use std::time::Duration;
+
+fn main() {
+    let mut config = visualizer::Config::default();
+    config.draw = When::All;
+    config.save = When::None;
+    config.save_last = true;
+    config.delay = Duration::from_secs_f32(1.0);
+    config.paused = true;
+    config.style.bg_color = (255, 255, 255, 128);
+    config.style.expanded = Gradient::TurboGradient(0.25..0.9);
+    config.style.path_width = None;
+    config.draw_old_on_top = false;
+    config.layer_drawing = false;
+    config.transparent_bmp = false;
+    let scale = 16;
+    //config.downscaler = scale as u32;
+    config.downscaler = 16;
+    config.cell_size = 1;
+    config.style.path = None;
+    config.style.draw_matches = true;
+    config.style.match_width = 4;
+    config.style.match_shrink = 0;
+    config.style.pruned_match = RED;
+    config.style.draw_dt = false;
+    config.style.draw_f = false;
+    config.style.draw_labels = false;
+
+    config.filepath = "imgs/astarpa2-paper/limitations".into();
+
+    let mut astarpa2 = astarpa2::AstarPa2Params::full();
+    astarpa2.heuristic.k = 8;
+    astarpa2.block_width = 64;
+
+    {
+        let (mut a, mut b) = uniform_seeded(250 * scale, 0.05, 6);
+        let (mut a2, mut b2) = uniform_seeded(200 * scale, 0.50, 2);
+        let (mut a3, mut b3) = uniform_seeded(50 * scale, 0.08, 3);
+        a.append(&mut a2);
+        b.append(&mut b2);
+        a.append(&mut a3);
+        b.append(&mut b3);
+
+        let cost = astarpa2
+            .make_aligner_with_visualizer(true, config.with_filename("high-error-rate"))
+            .align(&a, &b)
+            .0;
+        println!("cost {cost}");
+    }
+
+    {
+        let (mut a, mut b) = uniform_seeded(350 * scale, 0.08, 5);
+        let (mut a2, _) = uniform_seeded(50 * scale, 0.08, 8);
+        let (mut a3, mut b3) = uniform_seeded(100 * scale, 0.08, 9);
+        a.append(&mut a2);
+        //b.append(&mut b2);
+        a.append(&mut a3);
+        b.append(&mut b3);
+
+        let cost = astarpa2
+            .make_aligner_with_visualizer(true, config.with_filename("deletion"))
+            .align(&a, &b)
+            .0;
+        println!("cost {cost}");
+    }
+
+    {
+        let (mut a, mut b) = uniform_seeded(100 * scale, 0.08, 1);
+        let rng = &mut rand_chacha::ChaCha8Rng::seed_from_u64(2 as u64);
+        let (mut a2, mut b2) = pa_generate::SeqPairGenerator {
+            length: 300 * scale,
+            error_rate: 0.08,
+            error_model: ErrorModel::SymmetricRepeat,
+            pattern_length: Some(10 * scale),
+        }
+        .generate(rng);
+        let (mut a3, mut b3) = uniform_seeded(100 * scale, 0.08, 3);
+        a.append(&mut a2);
+        b.append(&mut b2);
+        a.append(&mut a3);
+        b.append(&mut b3);
+
+        let cost = astarpa2
+            .make_aligner_with_visualizer(true, config.with_filename("repeats"))
+            .align(&a, &b)
+            .0;
+        println!("cost {cost}");
+    }
+}