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github.com/RagnarGrootKoerkamp/astar-pairwise-aligner @main

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1,127 symbols 3,031 edges 123 files 194 documented · 17%
What it actually does AI analysis from the code graph — generated when you open this
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Extension points exported contracts — how you extend this code

Heuristic (Interface)
An object containing the settings for a heuristic. [17 implementers]
pa-heuristic/src/heuristic.rs
NwFront (Interface)
Front type for the NW algorithm. `Default` is only needed to pass an empty and usused front into `j_range` for the init [2 …
pa-base-algos/src/nw/front.rs
VisualizerT (Interface)
A `Visualizer` can be used to track progress of the A* search using callbacks. The `Visualizer` configuration is `build` [2 …
pa-vis/src/lib.rs
AffineAligner (Interface)
Generic pairwise global alignment interface. [2 implementers]
pa-affine-types/src/lib.rs
Profile (Interface)
Builds a 'profile' of `b` in `64`-bit blocks, and compressed `a` into a `[0,1,2,3]` alphabet. Returns a bitpacked `B` i [2 …
pa-bitpacking/src/profile.rs
AstarPa2StatsAligner (Interface)
Helper trait to erase the type of the heuristic that additionally returns alignment statistics. [1 implementers]
astarpa2/src/lib.rs
AstarStatsAligner (Interface)
Helper trait to erase the type of the heuristic that additionally returns alignment statistics. [1 implementers]
astarpa/src/lib.rs
HeuristicInstance (Interface)
An instantiation of a heuristic for a specific pair of sequences. [16 implementers]
pa-heuristic/src/heuristic.rs

Core symbols most depended-on inside this repo

len
called by 191
pa-base-algos/src/nw/front.rs
iter
called by 161
pa-heuristic/src/prune.rs
map
called by 108
pa-heuristic/src/cli.rs
clone
called by 104
pa-base-algos/src/nw/bitpacking.rs
align
called by 70
pa-base-algos/src/nw.rs
with_filename
called by 70
pa-vis/src/visualizer.rs
append
called by 69
pa-affine-types/src/cigar.rs
push
called by 65
pa-heuristic/src/split_vec.rs

Shape

Method 672
Function 258
Class 142
Enum 31
Interface 24

Languages

Rust99%
TypeScript1%
C++1%
C1%

Modules by API surface

pa-vis/src/visualizer.rs50 symbols
pa-base-algos/src/nw/bitpacking.rs42 symbols
pa-heuristic/src/heuristic/csh.rs35 symbols
pa-base-algos/src/dt.rs35 symbols
pa-heuristic/src/matches.rs31 symbols
pa-affine-types/src/cost_model.rs31 symbols
pa-vis/src/lib.rs28 symbols
pa-base-algos/src/nw.rs27 symbols
pa-heuristic/src/heuristic/distances.rs26 symbols
pa-base-algos/src/front.rs26 symbols
pa-heuristic/src/heuristic.rs25 symbols
pa-heuristic/benches/matches_old.rs25 symbols

For agents

$ claude mcp add astar-pairwise-aligner \
  -- python -m otcore.mcp_server <graph>

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