@datagrok/peptides 1.17.0 → 1.17.1

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 (58) hide show
  1. package/.eslintrc.json +17 -6
  2. package/dist/196.js +2 -0
  3. package/dist/23.js +2 -0
  4. package/dist/282.js +2 -0
  5. package/dist/361.js +2 -2
  6. package/dist/40.js +2 -0
  7. package/dist/436.js +2 -2
  8. package/dist/65.js +2 -0
  9. package/dist/704.js +2 -0
  10. package/dist/package-test.js +2 -3
  11. package/dist/package.js +2 -3
  12. package/package.json +14 -14
  13. package/src/demo/fasta.ts +8 -2
  14. package/src/model.ts +780 -531
  15. package/src/package-test.ts +1 -3
  16. package/src/package.ts +15 -28
  17. package/src/tests/benchmarks.ts +31 -11
  18. package/src/tests/core.ts +11 -6
  19. package/src/tests/misc.ts +6 -6
  20. package/src/tests/model.ts +79 -44
  21. package/src/tests/table-view.ts +48 -38
  22. package/src/tests/utils.ts +0 -76
  23. package/src/tests/viewers.ts +30 -12
  24. package/src/tests/widgets.ts +30 -11
  25. package/src/utils/algorithms.ts +115 -38
  26. package/src/utils/cell-renderer.ts +181 -72
  27. package/src/utils/constants.ts +33 -7
  28. package/src/utils/misc.ts +244 -10
  29. package/src/utils/parallel-mutation-cliffs.ts +18 -15
  30. package/src/utils/statistics.ts +70 -15
  31. package/src/utils/tooltips.ts +42 -17
  32. package/src/utils/types.ts +29 -26
  33. package/src/utils/worker-creator.ts +5 -0
  34. package/src/viewers/logo-summary.ts +591 -130
  35. package/src/viewers/sar-viewer.ts +893 -239
  36. package/src/widgets/distribution.ts +305 -64
  37. package/src/widgets/manual-alignment.ts +18 -11
  38. package/src/widgets/mutation-cliffs.ts +44 -18
  39. package/src/widgets/peptides.ts +86 -91
  40. package/src/widgets/selection.ts +56 -22
  41. package/src/widgets/settings.ts +94 -44
  42. package/src/workers/dimensionality-reducer.ts +5 -6
  43. package/src/workers/mutation-cliffs-worker.ts +3 -16
  44. package/dist/209.js +0 -2
  45. package/dist/381.js +0 -2
  46. package/dist/770.js +0 -2
  47. package/dist/831.js +0 -2
  48. package/dist/868.js +0 -2
  49. package/dist/931.js +0 -3
  50. package/dist/931.js.LICENSE.txt +0 -51
  51. package/dist/932.js +0 -2
  52. package/dist/package-test.js.LICENSE.txt +0 -51
  53. package/dist/package.js.LICENSE.txt +0 -51
  54. package/src/tests/peptide-space-test.ts +0 -48
  55. package/src/tests/test-data.ts +0 -649
  56. package/src/utils/molecular-measure.ts +0 -174
  57. package/src/utils/peptide-similarity-space.ts +0 -216
  58. package/src/viewers/peptide-space-viewer.ts +0 -150
package/package.json CHANGED
@@ -1,10 +1,10 @@
1
1
  {
2
2
  "name": "@datagrok/peptides",
3
3
  "friendlyName": "Peptides",
4
- "version": "1.17.0",
4
+ "version": "1.17.1",
5
5
  "author": {
6
- "name": "Volodymyr Dyma",
7
- "email": "vdyma@datagrok.ai"
6
+ "name": "Davit Rizhinashvili",
7
+ "email": "drizhinashvili@datagrok.ai"
8
8
  },
9
9
  "description": "Advanced tools for analyzing collections of peptides.",
10
10
  "repository": {
@@ -13,14 +13,14 @@
13
13
  "directory": "packages/Peptides"
14
14
  },
15
15
  "dependencies": {
16
- "@datagrok-libraries/bio": "^5.39.7",
17
- "@datagrok-libraries/ml": "^6.3.55",
18
- "@datagrok-libraries/statistics": "^1.2.10",
19
- "@datagrok-libraries/utils": "^4.1.25",
20
- "@datagrok-libraries/tutorials": "^1.3.10",
21
- "cash-dom": "^8.1.5",
22
- "datagrok-api": "^1.16.4",
23
- "file-loader": "^6.2.0",
16
+ "@datagrok-libraries/bio": "^5.39.14",
17
+ "@datagrok-libraries/ml": "^6.3.67",
18
+ "@datagrok-libraries/statistics": "^1.2.11",
19
+ "@datagrok-libraries/utils": "^4.1.36",
20
+ "@datagrok-libraries/tutorials": "^1.3.11",
21
+ "cash-dom": "latest",
22
+ "datagrok-api": "^1.17.9",
23
+ "file-loader": "latest",
24
24
  "rxjs": "^6.5.5",
25
25
  "wu": "latest",
26
26
  "uuid": "latest"
@@ -30,10 +30,10 @@
30
30
  "@types/uuid": "latest",
31
31
  "@typescript-eslint/eslint-plugin": "latest",
32
32
  "@typescript-eslint/parser": "latest",
33
- "css-loader": "^5.2.4",
33
+ "css-loader": "latest",
34
34
  "eslint": "latest",
35
35
  "eslint-config-google": "latest",
36
- "style-loader": "^2.0.0",
36
+ "style-loader": "latest",
37
37
  "ts-loader": "latest",
38
38
  "typescript": "latest",
39
39
  "webpack": "latest",
@@ -75,4 +75,4 @@
75
75
  "All users"
76
76
  ],
77
77
  "category": "Bioinformatics"
78
- }
78
+ }
package/src/demo/fasta.ts CHANGED
@@ -7,12 +7,15 @@ import * as C from '../utils/constants';
7
7
  import {scaleActivity} from '../utils/misc';
8
8
  import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
9
9
  import {PeptidesModel} from '../model';
10
+ import {delay} from '@datagrok-libraries/utils/src/test';
10
11
 
11
12
  export async function macromoleculeSarFastaDemoUI(): Promise<void> {
12
13
  grok.shell.windows.showContextPanel = true;
13
14
  const alignedSequenceCol = 'AlignedSequence';
14
15
  const simpleActivityColName = 'IC50';
15
16
  const simpleTable = DG.DataFrame.fromCsv(await _package.files.readAsText('aligned.csv'));
17
+ grok.shell.addTableView(simpleTable);
18
+ await delay(0);
16
19
  const simpleActivityCol = simpleTable.getCol(simpleActivityColName);
17
20
  const simpleAlignedSeqCol = simpleTable.getCol(alignedSequenceCol);
18
21
  simpleAlignedSeqCol.semType = DG.SEMTYPE.MACROMOLECULE;
@@ -21,8 +24,11 @@ export async function macromoleculeSarFastaDemoUI(): Promise<void> {
21
24
  simpleAlignedSeqCol.setTag(bioTAGS.aligned, ALIGNMENT.SEQ_MSA);
22
25
  const simpleScaledCol = scaleActivity(simpleActivityCol, C.SCALING_METHODS.MINUS_LG);
23
26
  const clustersCol = DG.Column.string('Cluster', simpleTable.rowCount).init('0');
24
- const alignedCol: DG.Column<string> = await grok.functions.call('Bio:alignSequences', {sequenceCol: simpleAlignedSeqCol, clustersCol});
27
+ const alignedCol: DG.Column<string> = await grok.functions.call('Bio:alignSequences', {
28
+ sequenceCol: simpleAlignedSeqCol,
29
+ clustersCol,
30
+ });
25
31
  const model: PeptidesModel = await startAnalysis(simpleActivityCol, alignedCol, null, simpleTable, simpleScaledCol,
26
32
  C.SCALING_METHODS.MINUS_LG) as PeptidesModel;
27
- model.modifyMutationCliffsSelection({monomerOrCluster: 'D', positionOrClusterType: '13'});
33
+ model.modifyWebLogoSelection({monomerOrCluster: 'D', positionOrClusterType: '13'});
28
34
  }