tsalign 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 (86) hide show
  1. tsalign-0.1.0/Cargo.lock +1448 -0
  2. tsalign-0.1.0/Cargo.toml +16 -0
  3. tsalign-0.1.0/PKG-INFO +25 -0
  4. tsalign-0.1.0/generic_a_star/Cargo.toml +18 -0
  5. tsalign-0.1.0/generic_a_star/src/cost.rs +162 -0
  6. tsalign-0.1.0/generic_a_star/src/lib.rs +581 -0
  7. tsalign-0.1.0/generic_a_star/src/reset.rs +15 -0
  8. tsalign-0.1.0/lib_tsalign/Cargo.toml +33 -0
  9. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/alignment_geometry.rs +74 -0
  10. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/alignment_result/a_star_sequences.rs +41 -0
  11. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/alignment_result/alignment/iter.rs +685 -0
  12. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/alignment_result/alignment.rs +113 -0
  13. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/alignment_result.rs +448 -0
  14. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/configurable_a_star_align.rs +337 -0
  15. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/gap_affine_edit_distance.rs +380 -0
  16. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/alignment_type.rs +188 -0
  17. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/context.rs +764 -0
  18. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/display.rs +162 -0
  19. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/identifier.rs +463 -0
  20. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch.rs +431 -0
  21. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds/template_switch_alignment.rs +308 -0
  22. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/lower_bounds.rs +2 -0
  23. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/chaining.rs +343 -0
  24. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/node_ord.rs +117 -0
  25. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/primary_match.rs +278 -0
  26. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/primary_range.rs +123 -0
  27. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/secondary_deletion.rs +81 -0
  28. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/shortcut.rs +163 -0
  29. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/template_switch_count.rs +119 -0
  30. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/strategies/template_switch_min_length.rs +280 -0
  31. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance/strategies.rs +301 -0
  32. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/template_switch_distance.rs +802 -0
  33. tsalign-0.1.0/lib_tsalign/src/a_star_aligner/tests.rs +29 -0
  34. tsalign-0.1.0/lib_tsalign/src/a_star_aligner.rs +188 -0
  35. tsalign-0.1.0/lib_tsalign/src/alignment_configuration.rs +34 -0
  36. tsalign-0.1.0/lib_tsalign/src/alignment_matrix/index/iterators.rs +139 -0
  37. tsalign-0.1.0/lib_tsalign/src/alignment_matrix/index.rs +77 -0
  38. tsalign-0.1.0/lib_tsalign/src/alignment_matrix.rs +354 -0
  39. tsalign-0.1.0/lib_tsalign/src/config/io.rs +217 -0
  40. tsalign-0.1.0/lib_tsalign/src/config.rs +126 -0
  41. tsalign-0.1.0/lib_tsalign/src/costs/cost_function/io.rs +158 -0
  42. tsalign-0.1.0/lib_tsalign/src/costs/cost_function.rs +313 -0
  43. tsalign-0.1.0/lib_tsalign/src/costs/gap_affine/io/tests.rs +28 -0
  44. tsalign-0.1.0/lib_tsalign/src/costs/gap_affine/io.rs +361 -0
  45. tsalign-0.1.0/lib_tsalign/src/costs/gap_affine.rs +206 -0
  46. tsalign-0.1.0/lib_tsalign/src/costs.rs +4 -0
  47. tsalign-0.1.0/lib_tsalign/src/error.rs +44 -0
  48. tsalign-0.1.0/lib_tsalign/src/io.rs +62 -0
  49. tsalign-0.1.0/lib_tsalign/src/lib.rs +9 -0
  50. tsalign-0.1.0/lib_tsshow/Cargo.toml +20 -0
  51. tsalign-0.1.0/lib_tsshow/src/error.rs +21 -0
  52. tsalign-0.1.0/lib_tsshow/src/lib.rs +24 -0
  53. tsalign-0.1.0/lib_tsshow/src/plain_text/alignment_stream.rs +229 -0
  54. tsalign-0.1.0/lib_tsshow/src/plain_text/mutlipair_alignment_renderer/tests.rs +105 -0
  55. tsalign-0.1.0/lib_tsshow/src/plain_text/mutlipair_alignment_renderer.rs +979 -0
  56. tsalign-0.1.0/lib_tsshow/src/plain_text/parse_template_switches.rs +201 -0
  57. tsalign-0.1.0/lib_tsshow/src/plain_text.rs +494 -0
  58. tsalign-0.1.0/lib_tsshow/src/svg/arrows.rs +273 -0
  59. tsalign-0.1.0/lib_tsshow/src/svg/font/sans_serif_mono.rs +87 -0
  60. tsalign-0.1.0/lib_tsshow/src/svg/font/typewriter.rs +78 -0
  61. tsalign-0.1.0/lib_tsshow/src/svg/font.rs +125 -0
  62. tsalign-0.1.0/lib_tsshow/src/svg/indexed_str.rs +16 -0
  63. tsalign-0.1.0/lib_tsshow/src/svg/labelled_sequence.rs +111 -0
  64. tsalign-0.1.0/lib_tsshow/src/svg/numbers.rs +128 -0
  65. tsalign-0.1.0/lib_tsshow/src/svg.rs +974 -0
  66. tsalign-0.1.0/lib_tsshow/src/ts_arrangement/character.rs +34 -0
  67. tsalign-0.1.0/lib_tsshow/src/ts_arrangement/complement.rs +274 -0
  68. tsalign-0.1.0/lib_tsshow/src/ts_arrangement/index_types.rs +100 -0
  69. tsalign-0.1.0/lib_tsshow/src/ts_arrangement/inner.rs +434 -0
  70. tsalign-0.1.0/lib_tsshow/src/ts_arrangement/row.rs +24 -0
  71. tsalign-0.1.0/lib_tsshow/src/ts_arrangement/source.rs +696 -0
  72. tsalign-0.1.0/lib_tsshow/src/ts_arrangement/template_switch.rs +47 -0
  73. tsalign-0.1.0/lib_tsshow/src/ts_arrangement.rs +198 -0
  74. tsalign-0.1.0/pyproject.toml +16 -0
  75. tsalign-0.1.0/python_bindings/.gitignore +72 -0
  76. tsalign-0.1.0/python_bindings/Cargo.toml +22 -0
  77. tsalign-0.1.0/python_bindings/README.md +10 -0
  78. tsalign-0.1.0/python_bindings/src/lib.rs +100 -0
  79. tsalign-0.1.0/seed_chain/Cargo.toml +16 -0
  80. tsalign-0.1.0/seed_chain/src/chain/context.rs +102 -0
  81. tsalign-0.1.0/seed_chain/src/chain/display.rs +23 -0
  82. tsalign-0.1.0/seed_chain/src/chain/node/display.rs +32 -0
  83. tsalign-0.1.0/seed_chain/src/chain/node.rs +97 -0
  84. tsalign-0.1.0/seed_chain/src/chain.rs +110 -0
  85. tsalign-0.1.0/seed_chain/src/lib.rs +4 -0
  86. tsalign-0.1.0/seed_chain/src/seed.rs +248 -0
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