pymafft 0.1.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (211) hide show
  1. pymafft-0.1.0/Cargo.lock +1047 -0
  2. pymafft-0.1.0/Cargo.toml +31 -0
  3. pymafft-0.1.0/PKG-INFO +143 -0
  4. pymafft-0.1.0/README.md +113 -0
  5. pymafft-0.1.0/crates/mafft-align/Cargo.toml +19 -0
  6. pymafft-0.1.0/crates/mafft-align/README.md +39 -0
  7. pymafft-0.1.0/crates/mafft-align/src/constrained_align.rs +207 -0
  8. pymafft-0.1.0/crates/mafft-align/src/constraints.rs +1168 -0
  9. pymafft-0.1.0/crates/mafft-align/src/dp.rs +116 -0
  10. pymafft-0.1.0/crates/mafft-align/src/fft_align.rs +380 -0
  11. pymafft-0.1.0/crates/mafft-align/src/genaffine.rs +386 -0
  12. pymafft-0.1.0/crates/mafft-align/src/global.rs +578 -0
  13. pymafft-0.1.0/crates/mafft-align/src/lib.rs +41 -0
  14. pymafft-0.1.0/crates/mafft-align/src/local.rs +355 -0
  15. pymafft-0.1.0/crates/mafft-align/src/msalign.rs +1143 -0
  16. pymafft-0.1.0/crates/mafft-align/src/multimtx.rs +315 -0
  17. pymafft-0.1.0/crates/mafft-align/src/profile.rs +2240 -0
  18. pymafft-0.1.0/crates/mafft-align/tests/imp_matrix_correctness.rs +155 -0
  19. pymafft-0.1.0/crates/mafft-align/tests/imp_zero_equiv.rs +44 -0
  20. pymafft-0.1.0/crates/mafft-c-bindings/Cargo.toml +17 -0
  21. pymafft-0.1.0/crates/mafft-c-bindings/build.rs +81 -0
  22. pymafft-0.1.0/crates/mafft-c-bindings/src/lib.rs +793 -0
  23. pymafft-0.1.0/crates/mafft-c-bindings/wrappers/blend_helpers.c +210 -0
  24. pymafft-0.1.0/crates/mafft-c-bindings/wrappers/msalignmm_instr.c +1246 -0
  25. pymafft-0.1.0/crates/mafft-c-bindings/wrappers/parttree_helpers.c +397 -0
  26. pymafft-0.1.0/crates/mafft-core/Cargo.toml +28 -0
  27. pymafft-0.1.0/crates/mafft-core/README.md +59 -0
  28. pymafft-0.1.0/crates/mafft-core/infile.tree +73 -0
  29. pymafft-0.1.0/crates/mafft-core/src/add.rs +396 -0
  30. pymafft-0.1.0/crates/mafft-core/src/adjust_direction.rs +448 -0
  31. pymafft-0.1.0/crates/mafft-core/src/engine.rs +1629 -0
  32. pymafft-0.1.0/crates/mafft-core/src/external.rs +335 -0
  33. pymafft-0.1.0/crates/mafft-core/src/lib.rs +23 -0
  34. pymafft-0.1.0/crates/mafft-core/src/progressive.rs +2152 -0
  35. pymafft-0.1.0/crates/mafft-core/src/refinement.rs +2308 -0
  36. pymafft-0.1.0/crates/mafft-core/src/varidist.rs +155 -0
  37. pymafft-0.1.0/crates/mafft-core/tests/cross_validate_bb20027_dp.rs +479 -0
  38. pymafft-0.1.0/crates/mafft-core/tests/cross_validate_bl50_fft.rs +307 -0
  39. pymafft-0.1.0/crates/mafft-core/tests/cross_validate_constrained_align.rs +1840 -0
  40. pymafft-0.1.0/crates/mafft-core/tests/cross_validate_counteff.rs +126 -0
  41. pymafft-0.1.0/crates/mafft-core/tests/cross_validate_cpmx.rs +624 -0
  42. pymafft-0.1.0/crates/mafft-core/tests/cross_validate_fft.rs +103 -0
  43. pymafft-0.1.0/crates/mafft-core/tests/cross_validate_insertnewgaps.rs +488 -0
  44. pymafft-0.1.0/crates/mafft-core/tests/cross_validate_msalign.rs +661 -0
  45. pymafft-0.1.0/crates/mafft-core/tests/cross_validate_profile.rs +409 -0
  46. pymafft-0.1.0/crates/mafft-core/tests/cross_validate_profile_align.rs +617 -0
  47. pymafft-0.1.0/crates/mafft-core/tests/end_to_end.rs +3467 -0
  48. pymafft-0.1.0/crates/mafft-core/tests/exp_residual_dump_compare.rs +271 -0
  49. pymafft-0.1.0/crates/mafft-core/tests/exp_residual_step10.rs +188 -0
  50. pymafft-0.1.0/crates/mafft-core/tests/fixtures/README.md +83 -0
  51. pymafft-0.1.0/crates/mafft-core/tests/fixtures/bali3.BB12019.fa +53 -0
  52. pymafft-0.1.0/crates/mafft-core/tests/fixtures/bali3.BB12019.fftnsi.iter5 +80 -0
  53. pymafft-0.1.0/crates/mafft-core/tests/fixtures/bali3.BB20027.fa +224 -0
  54. pymafft-0.1.0/crates/mafft-core/tests/fixtures/combined_17_r6.fa +178 -0
  55. pymafft-0.1.0/crates/mafft-core/tests/fixtures/dna_adjustdirection_input.fa +46 -0
  56. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.add6.aln +504 -0
  57. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.add6.mapout.compact.map +40 -0
  58. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.add6.mapout.full.map +2724 -0
  59. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.anysymbol.expected +6 -0
  60. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.anysymbol.input.fa +6 -0
  61. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.auto +504 -0
  62. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.bl30.fftns2 +504 -0
  63. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.bl45.fftns2 +504 -0
  64. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.bl50.fftns2 +468 -0
  65. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.bl80.fftns2 +468 -0
  66. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.bl80.nwns2 +468 -0
  67. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.einsi.maxit0 +504 -0
  68. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.fftnsi.exp0_1 +468 -0
  69. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.fftnsi.hat2 +108 -0
  70. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first12.fa +85 -0
  71. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first12.linsi.iter5 +96 -0
  72. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first13.fa +92 -0
  73. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first13.linsi.iter2 +104 -0
  74. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first14.einsi.iter2 +126 -0
  75. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first14.fa +100 -0
  76. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first14.fa.tree +29 -0
  77. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first14.ginsi.iter2 +112 -0
  78. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first14.linsi.iter1 +112 -0
  79. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first14.linsi.iter2 +112 -0
  80. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first14.linsi.maxit0 +112 -0
  81. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first15.fa +108 -0
  82. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first15.fa.tree +31 -0
  83. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first15.linsi.iter2 +120 -0
  84. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first15.linsi.maxit0 +135 -0
  85. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first30.fa +230 -0
  86. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first30.fa.tree +61 -0
  87. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first30.fftns2.aln +330 -0
  88. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first36.einsi.iter2 +504 -0
  89. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first36.fa +285 -0
  90. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first36.ginsi.iter2 +504 -0
  91. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first36.linsi.iter2 +504 -0
  92. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first36.linsi.maxit0 +468 -0
  93. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first9.fa +61 -0
  94. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.first9.linsi.iter2 +72 -0
  95. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.ginsi.maxit0 +504 -0
  96. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.hat2 +108 -0
  97. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.jtt200.fftns2 +504 -0
  98. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.last6_for_add.fa +55 -0
  99. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.leavegappyregion +468 -0
  100. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.linsi.maxit0 +468 -0
  101. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.memsave.fftns2 +468 -0
  102. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.memsave.fftns2.retree1 +504 -0
  103. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.memsave.fftnsi.iter2 +468 -0
  104. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.memsavetree +468 -0
  105. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.nwns2 +468 -0
  106. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.nwns2.ep05 +468 -0
  107. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.nwns2.op25 +504 -0
  108. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.nwns2.steps +70 -0
  109. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.retree3.einsi +504 -0
  110. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.retree3.fftns2 +504 -0
  111. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.retree3.fftnsi.iter2 +504 -0
  112. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.retree3.ginsi +504 -0
  113. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.retree3.linsi +468 -0
  114. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.retree5.fftns2 +504 -0
  115. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.retree5.linsi +468 -0
  116. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.seed.combined.fa +39 -0
  117. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.seed.einsi.iter2 +64 -0
  118. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.seed.fftnsi.iter2 +64 -0
  119. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.seed.ginsi.iter2 +64 -0
  120. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.seed.hat3 +6 -0
  121. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.seed.linsi.iter2 +64 -0
  122. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.seed3.aln +21 -0
  123. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.seed_input5.fa +32 -0
  124. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.tm100.nwns2 +504 -0
  125. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.tm200.nwns2 +504 -0
  126. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.treein.einsi +468 -0
  127. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.treein.fftns2 +504 -0
  128. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.treein.ginsi +504 -0
  129. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.treein.linsi +468 -0
  130. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.treein.nwns2 +504 -0
  131. pymafft-0.1.0/crates/mafft-core/tests/fixtures/sample.treein.tree +35 -0
  132. pymafft-0.1.0/crates/mafft-core/tests/fixtures/samplerna.nwns2 +35 -0
  133. pymafft-0.1.0/crates/mafft-core/tests/trace_refinement.rs +2745 -0
  134. pymafft-0.1.0/crates/mafft-fft/Cargo.toml +18 -0
  135. pymafft-0.1.0/crates/mafft-fft/README.md +42 -0
  136. pymafft-0.1.0/crates/mafft-fft/src/block_align.rs +316 -0
  137. pymafft-0.1.0/crates/mafft-fft/src/candidates.rs +87 -0
  138. pymafft-0.1.0/crates/mafft-fft/src/correlation.rs +121 -0
  139. pymafft-0.1.0/crates/mafft-fft/src/fft_c_compat.rs +202 -0
  140. pymafft-0.1.0/crates/mafft-fft/src/lib.rs +20 -0
  141. pymafft-0.1.0/crates/mafft-fft/src/segments.rs +174 -0
  142. pymafft-0.1.0/crates/mafft-fft/src/vectorize.rs +174 -0
  143. pymafft-0.1.0/crates/mafft-io/Cargo.toml +20 -0
  144. pymafft-0.1.0/crates/mafft-io/README.md +50 -0
  145. pymafft-0.1.0/crates/mafft-io/src/clustal.rs +366 -0
  146. pymafft-0.1.0/crates/mafft-io/src/detect.rs +67 -0
  147. pymafft-0.1.0/crates/mafft-io/src/error.rs +22 -0
  148. pymafft-0.1.0/crates/mafft-io/src/fasta.rs +251 -0
  149. pymafft-0.1.0/crates/mafft-io/src/hat2.rs +210 -0
  150. pymafft-0.1.0/crates/mafft-io/src/lib.rs +20 -0
  151. pymafft-0.1.0/crates/mafft-io/src/localhom.rs +165 -0
  152. pymafft-0.1.0/crates/mafft-io/src/phylip.rs +119 -0
  153. pymafft-0.1.0/crates/mafft-io/tests/integration.rs +131 -0
  154. pymafft-0.1.0/crates/mafft-scoring/Cargo.toml +22 -0
  155. pymafft-0.1.0/crates/mafft-scoring/README.md +38 -0
  156. pymafft-0.1.0/crates/mafft-scoring/examples/dump_gap.rs +10 -0
  157. pymafft-0.1.0/crates/mafft-scoring/src/alphabet.rs +110 -0
  158. pymafft-0.1.0/crates/mafft-scoring/src/ambiguity.rs +118 -0
  159. pymafft-0.1.0/crates/mafft-scoring/src/blosum.rs +247 -0
  160. pymafft-0.1.0/crates/mafft-scoring/src/dna.rs +260 -0
  161. pymafft-0.1.0/crates/mafft-scoring/src/jtt.rs +244 -0
  162. pymafft-0.1.0/crates/mafft-scoring/src/lib.rs +299 -0
  163. pymafft-0.1.0/crates/mafft-scoring/src/normalize.rs +136 -0
  164. pymafft-0.1.0/crates/mafft-scoring/src/penalties.rs +98 -0
  165. pymafft-0.1.0/crates/mafft-scoring/src/properties.rs +64 -0
  166. pymafft-0.1.0/crates/mafft-scoring/tests/cross_validate.rs +703 -0
  167. pymafft-0.1.0/crates/mafft-tree/Cargo.toml +22 -0
  168. pymafft-0.1.0/crates/mafft-tree/README.md +40 -0
  169. pymafft-0.1.0/crates/mafft-tree/examples/dump_ktuple_distance.rs +41 -0
  170. pymafft-0.1.0/crates/mafft-tree/src/addonetip.rs +395 -0
  171. pymafft-0.1.0/crates/mafft-tree/src/bsd_qsort.rs +259 -0
  172. pymafft-0.1.0/crates/mafft-tree/src/distance.rs +490 -0
  173. pymafft-0.1.0/crates/mafft-tree/src/lib.rs +29 -0
  174. pymafft-0.1.0/crates/mafft-tree/src/memsavetree.rs +882 -0
  175. pymafft-0.1.0/crates/mafft-tree/src/musclesupg.rs +338 -0
  176. pymafft-0.1.0/crates/mafft-tree/src/newick.rs +134 -0
  177. pymafft-0.1.0/crates/mafft-tree/src/nj.rs +192 -0
  178. pymafft-0.1.0/crates/mafft-tree/src/parttree.rs +291 -0
  179. pymafft-0.1.0/crates/mafft-tree/src/parttree_dist.rs +258 -0
  180. pymafft-0.1.0/crates/mafft-tree/src/parttree_pivot.rs +422 -0
  181. pymafft-0.1.0/crates/mafft-tree/src/parttree_split.rs +895 -0
  182. pymafft-0.1.0/crates/mafft-tree/src/topology.rs +160 -0
  183. pymafft-0.1.0/crates/mafft-tree/src/treein.rs +216 -0
  184. pymafft-0.1.0/crates/mafft-tree/src/upgma.rs +153 -0
  185. pymafft-0.1.0/crates/mafft-tree/src/weighting.rs +625 -0
  186. pymafft-0.1.0/crates/mafft-tree/tests/cross_validate_memsavetree.rs +612 -0
  187. pymafft-0.1.0/crates/mafft-tree/tests/cross_validate_parttree.rs +657 -0
  188. pymafft-0.1.0/crates/mafft-tree/tests/cross_validate_weights.rs +301 -0
  189. pymafft-0.1.0/crates/mafft-tree/tests/fixtures/bali3.BB12041.fa +21 -0
  190. pymafft-0.1.0/crates/mafft-types/Cargo.toml +15 -0
  191. pymafft-0.1.0/crates/mafft-types/README.md +40 -0
  192. pymafft-0.1.0/crates/mafft-types/src/complex.rs +22 -0
  193. pymafft-0.1.0/crates/mafft-types/src/lib.rs +17 -0
  194. pymafft-0.1.0/crates/mafft-types/src/local_hom.rs +85 -0
  195. pymafft-0.1.0/crates/mafft-types/src/scoring.rs +81 -0
  196. pymafft-0.1.0/crates/mafft-types/src/segment.rs +43 -0
  197. pymafft-0.1.0/crates/mafft-types/src/seq.rs +92 -0
  198. pymafft-0.1.0/crates/mafft-types/src/tree.rs +6 -0
  199. pymafft-0.1.0/crates/pymafft/Cargo.toml +21 -0
  200. pymafft-0.1.0/crates/pymafft/README.md +549 -0
  201. pymafft-0.1.0/crates/pymafft/src/lib.rs +354 -0
  202. pymafft-0.1.0/crates/pymafft/tests/test_biopython.py +251 -0
  203. pymafft-0.1.0/crates/pymafft/tests/test_console_script.py +136 -0
  204. pymafft-0.1.0/crates/pymafft/tests/test_parity.py +381 -0
  205. pymafft-0.1.0/crates/pymafft/tests/test_pymafft.py +240 -0
  206. pymafft-0.1.0/crates/pymafft/uv.lock +199 -0
  207. pymafft-0.1.0/pyproject.toml +59 -0
  208. pymafft-0.1.0/python/pymafft/__init__.py +19 -0
  209. pymafft-0.1.0/python/pymafft/__init__.pyi +104 -0
  210. pymafft-0.1.0/python/pymafft/__main__.py +66 -0
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