feat: add WatermanSmithBeyer algorithm#20
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MavenRain wants to merge 1 commit intolignum-vitae:mainfrom
Open
feat: add WatermanSmithBeyer algorithm#20MavenRain wants to merge 1 commit intolignum-vitae:mainfrom
MavenRain wants to merge 1 commit intolignum-vitae:mainfrom
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Summary
Closes #7.
Adds the WatermanSmithBeyer algorithm, a global alignment algorithm that uses
affine gap penalties and considers all possible gap lengths (O(n^3)).
Design
ExtendedGapScoring(gap open + gap extend) with cost functionw(k) = gap_open + (k-1) * gap_extendAlignmentData::new_gotoh(), avoiding any changes toAlignmentDataorMatrix2DWsbAlignertraceback iterator handles variable-length gaps (pushesmultiple characters per gap step)
GlobalAlignmentMatrixtrait pattern as NeedlemanWunschFiles
src/alignment/edit/waterman_smith_beyer.rs(new) -- scoring matrixcomputation
src/alignment/global_base.rs-- addedWatermanSmithBeyervariant andWsbAlignertracebacksrc/alignment/edit/mod.rs,src/lib.rs-- module registration andre-export
tests/wsb_test.rs(new) -- 9 testsTest plan
cargo clippycleancargo fmtclean