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Perf: align_multiple speedup from using typed memoryviews #927

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Merged
padix-key merged 1 commit into from
Jul 18, 2026
Merged

Perf: align_multiple speedup from using typed memoryviews #927

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4 changes: 2 additions & 2 deletions src/biotite/sequence/align/multiple.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -373,8 +373,8 @@ def _get_distance_matrix(CodeType[:] _T, sequences, matrix,
for code1 in range(alphabet_size):
for code2 in range(alphabet_size):
score_rand += score_matrix[code1,code2] \
* code_count[i,code1] \
* code_count[j,code2]
* code_count_v[i,code1] \
* code_count_v[j,code2]
score_rand /= alignments[i,j].trace.shape[0]
gap_open_count, gap_ext_count = _count_gaps(
alignments[i,j].trace.astype(np.int64, copy=False),
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