@datagrok/bio 2.4.31 → 2.4.39

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Files changed (99) hide show
  1. package/.eslintrc.json +6 -8
  2. package/README.md +22 -7
  3. package/detectors.js +21 -12
  4. package/dist/1.js +2 -0
  5. package/dist/1.js.map +1 -0
  6. package/dist/18.js +2 -0
  7. package/dist/18.js.map +1 -0
  8. package/dist/190.js +2 -0
  9. package/dist/190.js.map +1 -0
  10. package/dist/452.js +2 -0
  11. package/dist/452.js.map +1 -0
  12. package/dist/729.js +2 -0
  13. package/dist/729.js.map +1 -0
  14. package/dist/package-test.js +1 -1
  15. package/dist/package-test.js.map +1 -1
  16. package/dist/package.js +1 -1
  17. package/dist/package.js.map +1 -1
  18. package/files/libraries/broken-lib.sdf +136 -0
  19. package/files/libraries/group1/mock-lib-3.json +74 -0
  20. package/files/libraries/mock-lib-2.json +48 -0
  21. package/files/tests/100_3_clustests.csv +100 -0
  22. package/files/tests/100_3_clustests_empty_vals.csv +100 -0
  23. package/files/tests/peptides_motif-with-random_10000.csv +9998 -0
  24. package/package.json +4 -4
  25. package/scripts/sequence_generator.py +164 -48
  26. package/src/analysis/sequence-activity-cliffs.ts +7 -9
  27. package/src/analysis/sequence-diversity-viewer.ts +8 -3
  28. package/src/analysis/sequence-search-base-viewer.ts +4 -3
  29. package/src/analysis/sequence-similarity-viewer.ts +13 -7
  30. package/src/analysis/sequence-space.ts +15 -12
  31. package/src/analysis/workers/mm-distance-array-service.ts +48 -0
  32. package/src/analysis/workers/mm-distance-array-worker.ts +29 -0
  33. package/src/analysis/workers/mm-distance-worker-creator.ts +6 -9
  34. package/src/apps/web-logo-app.ts +34 -0
  35. package/src/calculations/monomerLevelMols.ts +10 -12
  36. package/src/demo/bio01-similarity-diversity.ts +4 -5
  37. package/src/demo/bio01a-hierarchical-clustering-and-sequence-space.ts +6 -7
  38. package/src/demo/bio01b-hierarchical-clustering-and-activity-cliffs.ts +7 -8
  39. package/src/demo/bio03-atomic-level.ts +1 -4
  40. package/src/demo/bio05-helm-msa-sequence-space.ts +6 -4
  41. package/src/demo/utils.ts +3 -4
  42. package/src/package-test.ts +1 -2
  43. package/src/package.ts +135 -82
  44. package/src/seq_align.ts +482 -483
  45. package/src/substructure-search/substructure-search.ts +3 -3
  46. package/src/tests/Palettes-test.ts +1 -1
  47. package/src/tests/WebLogo-positions-test.ts +12 -35
  48. package/src/tests/_first-tests.ts +1 -1
  49. package/src/tests/activity-cliffs-tests.ts +10 -7
  50. package/src/tests/activity-cliffs-utils.ts +6 -5
  51. package/src/tests/bio-tests.ts +20 -25
  52. package/src/tests/checkInputColumn-tests.ts +5 -11
  53. package/src/tests/converters-test.ts +19 -37
  54. package/src/tests/detectors-benchmark-tests.ts +35 -37
  55. package/src/tests/detectors-tests.ts +29 -34
  56. package/src/tests/detectors-weak-and-likely-tests.ts +11 -21
  57. package/src/tests/fasta-export-tests.ts +3 -3
  58. package/src/tests/fasta-handler-test.ts +2 -3
  59. package/src/tests/lib-tests.ts +2 -4
  60. package/src/tests/mm-distance-tests.ts +25 -17
  61. package/src/tests/monomer-libraries-tests.ts +1 -1
  62. package/src/tests/msa-tests.ts +12 -9
  63. package/src/tests/pepsea-tests.ts +6 -3
  64. package/src/tests/renderers-test.ts +13 -11
  65. package/src/tests/sequence-space-test.ts +10 -8
  66. package/src/tests/sequence-space-utils.ts +6 -4
  67. package/src/tests/similarity-diversity-tests.ts +47 -61
  68. package/src/tests/splitters-test.ts +14 -20
  69. package/src/tests/to-atomic-level-tests.ts +9 -17
  70. package/src/tests/units-handler-splitted-tests.ts +106 -0
  71. package/src/tests/units-handler-tests.ts +22 -26
  72. package/src/tests/utils/sequences-generators.ts +6 -2
  73. package/src/tests/utils.ts +10 -4
  74. package/src/tests/viewers.ts +1 -1
  75. package/src/utils/atomic-works.ts +49 -57
  76. package/src/utils/cell-renderer.ts +25 -8
  77. package/src/utils/check-input-column.ts +19 -4
  78. package/src/utils/constants.ts +3 -3
  79. package/src/utils/convert.ts +56 -23
  80. package/src/utils/monomer-lib.ts +83 -64
  81. package/src/utils/multiple-sequence-alignment-ui.ts +24 -21
  82. package/src/utils/multiple-sequence-alignment.ts +2 -2
  83. package/src/utils/pepsea.ts +17 -7
  84. package/src/utils/save-as-fasta.ts +11 -4
  85. package/src/utils/ui-utils.ts +1 -1
  86. package/src/viewers/vd-regions-viewer.ts +21 -22
  87. package/src/viewers/web-logo-viewer.ts +189 -154
  88. package/src/widgets/bio-substructure-filter.ts +9 -6
  89. package/src/widgets/representations.ts +11 -12
  90. package/tsconfig.json +1 -1
  91. package/dist/258.js +0 -2
  92. package/dist/258.js.map +0 -1
  93. package/dist/457.js +0 -2
  94. package/dist/457.js.map +0 -1
  95. package/dist/562.js +0 -2
  96. package/dist/562.js.map +0 -1
  97. package/dist/925.js +0 -2
  98. package/dist/925.js.map +0 -1
  99. package/src/analysis/workers/mm-distance-worker.ts +0 -16

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