@datagrok/bio 2.15.2 → 2.15.5

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Files changed (54) hide show
  1. package/CHANGELOG.md +32 -0
  2. package/detectors.js +3 -1
  3. package/dist/284.js +1 -1
  4. package/dist/284.js.map +1 -1
  5. package/dist/455.js +2 -0
  6. package/dist/455.js.map +1 -0
  7. package/dist/980.js +1 -1
  8. package/dist/980.js.map +1 -1
  9. package/dist/package-test.js +3 -3
  10. package/dist/package-test.js.map +1 -1
  11. package/dist/package.js +2 -2
  12. package/dist/package.js.map +1 -1
  13. package/files/tests/to-atomic-level-msa-fasta-output.csv +683 -683
  14. package/files/tests/to-atomic-level-msa-separator-output.csv +104 -104
  15. package/package.json +9 -9
  16. package/src/analysis/sequence-activity-cliffs.ts +3 -1
  17. package/src/calculations/monomerLevelMols.ts +2 -1
  18. package/src/demo/bio03-atomic-level.ts +1 -1
  19. package/src/package-test.ts +6 -1
  20. package/src/package.ts +151 -38
  21. package/src/tests/WebLogo-positions-test.ts +1 -1
  22. package/src/tests/bio-tests.ts +1 -1
  23. package/src/tests/detectors-tests.ts +10 -10
  24. package/src/tests/monomer-libraries-tests.ts +1 -1
  25. package/src/tests/seq-handler-splitted-tests.ts +6 -2
  26. package/src/tests/splitters-test.ts +6 -6
  27. package/src/tests/to-atomic-level-tests.ts +21 -14
  28. package/src/tests/to-atomic-level-ui-tests.ts +75 -35
  29. package/src/tests/utils.ts +2 -2
  30. package/src/utils/cell-renderer-custom.ts +62 -0
  31. package/src/utils/cell-renderer.ts +58 -126
  32. package/src/utils/cyclized.ts +28 -14
  33. package/src/utils/dimerized.ts +0 -2
  34. package/src/utils/helm-to-molfile/converter/converter.ts +75 -54
  35. package/src/utils/helm-to-molfile/converter/monomer-wrapper.ts +2 -2
  36. package/src/utils/helm-to-molfile/converter/polymer.ts +23 -16
  37. package/src/utils/helm-to-molfile/converter/types.ts +0 -10
  38. package/src/utils/helm-to-molfile/utils.ts +10 -7
  39. package/src/utils/monomer-cell-renderer.ts +8 -4
  40. package/src/utils/monomer-lib/lib-manager.ts +2 -2
  41. package/src/utils/monomer-lib/monomer-colors.ts +68 -0
  42. package/src/utils/monomer-lib/monomer-lib-base.ts +165 -0
  43. package/src/utils/monomer-lib/monomer-lib.ts +19 -68
  44. package/src/utils/monomer-lib/web-editor-monomer-dummy.ts +121 -0
  45. package/src/utils/monomer-lib/web-editor-monomer-of-library.ts +102 -0
  46. package/src/utils/save-as-fasta.ts +1 -1
  47. package/src/utils/seq-helper/seq-helper.ts +20 -49
  48. package/src/utils/sequence-to-mol.ts +24 -28
  49. package/src/viewers/web-logo-viewer.ts +2 -1
  50. package/src/widgets/composition-analysis-widget.ts +4 -3
  51. package/src/widgets/representations.ts +8 -10
  52. package/dist/248.js +0 -2
  53. package/dist/248.js.map +0 -1
  54. package/src/utils/cell-renderer-consts.ts +0 -31
package/CHANGELOG.md CHANGED
@@ -1,5 +1,37 @@
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  # Bio changelog
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+ ## 2.15.5 (2024-09-25)
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+
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+ ### New features
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+
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+ * Add custom notation, fix tests
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+ * Add overriding monomer library for toAtomicLevel
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+
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+ ### Bug fixes
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+
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+ * Fix skipping tests depending on new Helm
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+
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+ ## 2.15.4 (2024-09-24)
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+
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+ ### New features
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+
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+ * Add monomer hover handling for substruct
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+ * Add highlight param for toAtomicLevel
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+ * Add HelmHelper parse and removeGaps methods
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+ * Add naturalMonomerColors for monomers of MonomerLib
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+ * Add MonomerLib.getWebEditorMonomer (for color)
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+ * Add function Identity for Add new Column
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+
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+ ### Bug fixes
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+
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+ * Fix toAtomicLevel for sequences with gaps
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+ * Fix ISeqSplitted remove .canonicals and .originals
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+ * Fix toAtomicLevel tests for linear with gaps
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+
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+ ## 2.15.3 (2024-09-22)
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+
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+ Add monomer background coloring
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+
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  ## 2.15.2 (2024-09-18)
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  Add monomer coloring for fasta/separator from monomer library
package/detectors.js CHANGED
@@ -183,6 +183,7 @@ class BioPackageDetectors extends DG.Package {
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  // col.setTag(SeqHandler.TAGS.alphabetSize, alphabetSize.toString());
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  col.setTag(SeqHandler.TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
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+ col.setTag(DG.TAGS.CELL_RENDERER, 'helm');
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  return DG.SEMTYPE.MACROMOLECULE;
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  }
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@@ -262,6 +263,7 @@ class BioPackageDetectors extends DG.Package {
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  const alphabetIsMultichar = Object.keys(stats.freq).some((m) => m.length > 1);
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  col.setTag(SeqHandler.TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
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  }
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+ col.setTag(DG.TAGS.CELL_RENDERER, 'sequence');
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  return DG.SEMTYPE.MACROMOLECULE;
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  } else {
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  const stats = this.getStats(categoriesSample, seqMinLength, splitter);
@@ -300,7 +302,7 @@ class BioPackageDetectors extends DG.Package {
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  }
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  refineSeqSplitter(col, stats, separator).then(() => { });
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-
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+ col.setTag(DG.TAGS.CELL_RENDERER, 'sequence');
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  return DG.SEMTYPE.MACROMOLECULE;
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  }
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  } catch (err) {