Add more readme videos

README.org

@@ -11,8 +11,12 @@ An alignment of two sequences of length 500 with 30% error rate using A*PA:
 
 [[file:imgs/readme/layers.gif]]
 
-- Citations ::
-  For A*PA, re recommend reading the bioRxiv version which directly includes the
+An alignment of two sequences of length 10'000 with 15% error rate using A*PA2:
+
+[[file:imgs/readme/astarpa2.gif]]
+
+- Papers ::
+  For A*PA, we recommend reading the bioRxiv version which directly includes the
   supplement and has better formatting. But please cite the Bioinformatics version!
   - A*PA BioRxiv preprint:
 
@@ -152,7 +156,7 @@ comparable due to differences in visualization strategies (cell vs layer updates
 |----------------------------------------------------------------------+----------------------------------------------------------------------------|
 | Dijkstra [[file:imgs/readme/2_dijkstra.gif]]                             | Ukkonen's exponential search (Edlib) [[file:imgs/readme/1_ukkonen.gif]]        |
 | Diagonal transition (WFA) [[file:imgs/readme/3_diagonal_transition.gif]] | DT + Divide & Conquer (BiWFA) [[file:imgs/readme/4_dt-divide-and-conquer.gif]] |
-| A*PA (GCSH+DT) [[file:imgs/readme/5_astarpa.gif]]                        |                                                                            |
+| A*PA (GCSH+DT) [[file:imgs/readme/5_astarpa.gif]]                        | A*PA2-full (8-bit words; block size 32) [[file:imgs/readme/6_astarpa2.gif]] |
 
 * Paper artefacts
 - Figures ::

makefile

@@ -40,22 +40,29 @@ fig-no-matches:
 	rm imgs/paper/no-matches.bmp
 
 # ========== README VIDEOS ==========
-readme: readme-layers readme-intro
+readme: readme-layers readme-astarpa2 readme-intro
 readme-layers:
 	cargo run --features example --release --example readme-layers
 	ffmpeg -y -framerate 20 -i imgs/readme/layers/%d.bmp $(FILTER) imgs/readme/layers.gif
 	gifsicle -O3 --batch imgs/readme/layers.gif
 	rm -rf imgs/readme/layers/
 
+readme-astarpa2:
+	cargo run --features example --release --example readme-astarpa2
+	ffmpeg -y -framerate 10 -i imgs/readme/astarpa2/%d.bmp $(FILTER) imgs/readme/astarpa2.gif
+	gifsicle -O3 --batch imgs/readme/astarpa2.gif
+	rm -rf imgs/readme/astarpa2
+
 # https://superuser.com/questions/1049606/reduce-generated-gif-size-using-ffmpeg
 FILTER = -filter_complex "tpad=stop_mode=clone:stop_duration=3[t];[t]split[s0][s1];[s0]palettegen=max_colors=64[p];[s1][p]paletteuse=dither=bayer"
 readme-videos:
-	cargo run --features example --release --example readme-videos
+	cargo run --features example,small_blocks --release --example readme-videos
 	ffmpeg -y -framerate 1 -i imgs/readme/1_ukkonen/%d.bmp 				$(FILTER) imgs/readme/1_ukkonen.gif
 	ffmpeg -y -framerate 10 -i imgs/readme/2_dijkstra/%d.bmp 				$(FILTER) imgs/readme/2_dijkstra.gif
 	ffmpeg -y -framerate 10 -i imgs/readme/3_diagonal-transition/%d.bmp 	$(FILTER) imgs/readme/3_diagonal_transition.gif
 	ffmpeg -y -framerate 20 -i imgs/readme/4_dt-divide-and-conquer/%d.bmp $(FILTER) imgs/readme/4_dt-divide-and-conquer.gif
 	ffmpeg -y -framerate 2 -i imgs/readme/5_astarpa/%d.bmp 	$(FILTER) imgs/readme/5_astarpa.gif
+	ffmpeg -y -framerate 8 -i imgs/readme/6_astarpa2/%d.bmp 	$(FILTER) imgs/readme/6_astarpa2.gif
 	gifsicle -O3 --batch imgs/readme/*.gif
 	rm -rf imgs/readme/*/
 

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

@@ -8,7 +8,7 @@ fn main() {
         panic!("WARNING: Without the example feature, pruned matches aren't shown red for SH");
     }
     if pa_bitpacking::B::BITS != 8 {
-        panic!("Small blocks feature is required for useful scale");
+        panic!("small_blocks feature is required for useful scale");
     }
 
     let mut config = visualizer::Config::default();

pa-bin/examples/readme-videos.rs

@@ -1,6 +1,8 @@
+#![feature(trait_upcasting)]
 //! This generates the visualizations used in figure 1 in the paper and in the slides.
 
 use astarpa::{astar, AstarPa};
+use astarpa2::AstarPa2Params;
 use pa_affine_types::AffineCost;
 use pa_base_algos::{
     dt::{DiagonalTransition, GapCostHeuristic},
@@ -23,6 +25,13 @@ fn main() {
     eprintln!("Distance {cost}");
     eprintln!("Divergence {}", cost as f32 / a.len() as f32);
 
+    if !cfg!(feature = "example") {
+        panic!("WARNING: Without the example feature, pruned matches aren't shown red for SH");
+    }
+    if pa_bitpacking::B::BITS != 8 {
+        panic!("small_blocks feature is required for useful scale");
+    }
+
     let cm = AffineCost::unit();
     let mut config = visualizer::Config::default();
     config.draw = When::None;
@@ -79,6 +88,14 @@ fn main() {
             dt: true,
             v: config.with_filename("5_astarpa"),
         }),
+        {
+            let mut config = config.with_filename("6_astarpa2");
+            config.save = When::All;
+            config.draw_old_on_top = false;
+            let mut params = AstarPa2Params::full();
+            params.block_width = 32;
+            params.make_aligner_with_visualizer(true, config)
+        },
     ];
     for aligner in aligners {
         aligner.align(a, b);