@datagrok/peptides 1.17.0 → 1.17.2

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 (55) hide show
  1. package/.eslintrc.json +17 -6
  2. package/CHANGELOG.md +4 -0
  3. package/dist/214.js +2 -0
  4. package/dist/436.js +2 -2
  5. package/dist/802.js +2 -0
  6. package/dist/package-test.js +2 -3
  7. package/dist/package.js +2 -3
  8. package/package.json +14 -14
  9. package/src/demo/fasta.ts +8 -2
  10. package/src/model.ts +783 -532
  11. package/src/package-test.ts +1 -3
  12. package/src/package.ts +15 -28
  13. package/src/tests/benchmarks.ts +31 -11
  14. package/src/tests/core.ts +11 -6
  15. package/src/tests/misc.ts +6 -6
  16. package/src/tests/model.ts +79 -44
  17. package/src/tests/table-view.ts +48 -38
  18. package/src/tests/utils.ts +0 -76
  19. package/src/tests/viewers.ts +30 -12
  20. package/src/tests/widgets.ts +30 -11
  21. package/src/utils/algorithms.ts +115 -38
  22. package/src/utils/cell-renderer.ts +181 -72
  23. package/src/utils/constants.ts +33 -7
  24. package/src/utils/misc.ts +244 -10
  25. package/src/utils/parallel-mutation-cliffs.ts +18 -15
  26. package/src/utils/statistics.ts +70 -15
  27. package/src/utils/tooltips.ts +42 -17
  28. package/src/utils/types.ts +29 -26
  29. package/src/utils/worker-creator.ts +5 -0
  30. package/src/viewers/logo-summary.ts +591 -130
  31. package/src/viewers/sar-viewer.ts +893 -239
  32. package/src/widgets/distribution.ts +305 -64
  33. package/src/widgets/manual-alignment.ts +18 -11
  34. package/src/widgets/mutation-cliffs.ts +44 -18
  35. package/src/widgets/peptides.ts +86 -91
  36. package/src/widgets/selection.ts +56 -22
  37. package/src/widgets/settings.ts +94 -44
  38. package/src/workers/mutation-cliffs-worker.ts +3 -16
  39. package/dist/209.js +0 -2
  40. package/dist/361.js +0 -2
  41. package/dist/381.js +0 -2
  42. package/dist/770.js +0 -2
  43. package/dist/831.js +0 -2
  44. package/dist/868.js +0 -2
  45. package/dist/931.js +0 -3
  46. package/dist/931.js.LICENSE.txt +0 -51
  47. package/dist/932.js +0 -2
  48. package/dist/package-test.js.LICENSE.txt +0 -51
  49. package/dist/package.js.LICENSE.txt +0 -51
  50. package/src/tests/peptide-space-test.ts +0 -48
  51. package/src/tests/test-data.ts +0 -649
  52. package/src/utils/molecular-measure.ts +0 -174
  53. package/src/utils/peptide-similarity-space.ts +0 -216
  54. package/src/viewers/peptide-space-viewer.ts +0 -150
  55. package/src/workers/dimensionality-reducer.ts +0 -25
package/package.json CHANGED
@@ -1,10 +1,10 @@
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  {
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  "name": "@datagrok/peptides",
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  "friendlyName": "Peptides",
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- "version": "1.17.0",
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+ "version": "1.17.2",
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  "author": {
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- "name": "Volodymyr Dyma",
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- "email": "vdyma@datagrok.ai"
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+ "name": "Davit Rizhinashvili",
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+ "email": "drizhinashvili@datagrok.ai"
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  },
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  "description": "Advanced tools for analyzing collections of peptides.",
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  "repository": {
@@ -13,14 +13,14 @@
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  "directory": "packages/Peptides"
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  },
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  "dependencies": {
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- "@datagrok-libraries/bio": "^5.39.7",
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- "@datagrok-libraries/ml": "^6.3.55",
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- "@datagrok-libraries/statistics": "^1.2.10",
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- "@datagrok-libraries/utils": "^4.1.25",
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- "@datagrok-libraries/tutorials": "^1.3.10",
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- "cash-dom": "^8.1.5",
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- "datagrok-api": "^1.16.4",
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- "file-loader": "^6.2.0",
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+ "@datagrok-libraries/bio": "^5.39.14",
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+ "@datagrok-libraries/ml": "^6.4.0",
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+ "@datagrok-libraries/statistics": "^1.2.11",
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+ "@datagrok-libraries/utils": "^4.1.36",
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+ "@datagrok-libraries/tutorials": "^1.3.11",
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+ "cash-dom": "latest",
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+ "datagrok-api": "^1.17.9",
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+ "file-loader": "latest",
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  "rxjs": "^6.5.5",
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  "wu": "latest",
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  "uuid": "latest"
@@ -30,10 +30,10 @@
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  "@types/uuid": "latest",
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  "@typescript-eslint/eslint-plugin": "latest",
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  "@typescript-eslint/parser": "latest",
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- "css-loader": "^5.2.4",
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+ "css-loader": "latest",
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  "eslint": "latest",
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  "eslint-config-google": "latest",
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- "style-loader": "^2.0.0",
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+ "style-loader": "latest",
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  "ts-loader": "latest",
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  "typescript": "latest",
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  "webpack": "latest",
@@ -75,4 +75,4 @@
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  "All users"
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  ],
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  "category": "Bioinformatics"
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- }
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+ }
package/src/demo/fasta.ts CHANGED
@@ -7,12 +7,15 @@ import * as C from '../utils/constants';
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  import {scaleActivity} from '../utils/misc';
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  import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
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  import {PeptidesModel} from '../model';
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+ import {delay} from '@datagrok-libraries/utils/src/test';
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  export async function macromoleculeSarFastaDemoUI(): Promise<void> {
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  grok.shell.windows.showContextPanel = true;
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  const alignedSequenceCol = 'AlignedSequence';
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  const simpleActivityColName = 'IC50';
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  const simpleTable = DG.DataFrame.fromCsv(await _package.files.readAsText('aligned.csv'));
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+ grok.shell.addTableView(simpleTable);
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+ await delay(0);
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  const simpleActivityCol = simpleTable.getCol(simpleActivityColName);
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  const simpleAlignedSeqCol = simpleTable.getCol(alignedSequenceCol);
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  simpleAlignedSeqCol.semType = DG.SEMTYPE.MACROMOLECULE;
@@ -21,8 +24,11 @@ export async function macromoleculeSarFastaDemoUI(): Promise<void> {
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  simpleAlignedSeqCol.setTag(bioTAGS.aligned, ALIGNMENT.SEQ_MSA);
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  const simpleScaledCol = scaleActivity(simpleActivityCol, C.SCALING_METHODS.MINUS_LG);
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  const clustersCol = DG.Column.string('Cluster', simpleTable.rowCount).init('0');
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- const alignedCol: DG.Column<string> = await grok.functions.call('Bio:alignSequences', {sequenceCol: simpleAlignedSeqCol, clustersCol});
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+ const alignedCol: DG.Column<string> = await grok.functions.call('Bio:alignSequences', {
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+ sequenceCol: simpleAlignedSeqCol,
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+ clustersCol,
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+ });
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  const model: PeptidesModel = await startAnalysis(simpleActivityCol, alignedCol, null, simpleTable, simpleScaledCol,
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  C.SCALING_METHODS.MINUS_LG) as PeptidesModel;
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- model.modifyMutationCliffsSelection({monomerOrCluster: 'D', positionOrClusterType: '13'});
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+ model.modifyWebLogoSelection({monomerOrCluster: 'D', positionOrClusterType: '13'});
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  }