Implement & integrate all dynamic character pairwise alignment techniques

amnh / PCG

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

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Implement & integrate all dynamic character pairwise alignment techniques #21

Open recursion-ninja opened 7 years ago

recursion-ninja commented 7 years ago

The various implementations of alignments for dynamic characters.

Completion indicates that the implementation has been tested and integrated into a PCG binary.

[x] C DO 2D
[x] C DO 2D Affine
[x] Haskell DO constant-value
[x] Haskell DO recalculate medians
[x] Haskell DO Memoized TCM
[x] Haskell DO Ukkonen
[ ] Haskell DO Affine

recursion-ninja commented 5 years ago

I removed the C FFI binding to the 3D DO alignment task item from this issue. Because it is not one of the pairwise alignment, it's integration with the codebase falls into a very different place in the product timeline than integrating the pairwise alignment implementations.

All that is left for this issue is the Haskell affine pairwise alignment implementation.

The old task item is preserved below for reference:

[ ] C DO 3D