@datagrok-libraries/bio 5.41.0 → 5.41.2

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 (61) hide show
  1. package/CHANGELOG.md +19 -0
  2. package/package.json +1 -1
  3. package/src/helm/helm-helper.d.ts +1 -0
  4. package/src/helm/helm-helper.d.ts.map +1 -1
  5. package/src/helm/helm-helper.js +1 -0
  6. package/src/helm/helm-helper.js.map +1 -1
  7. package/src/monomer-works/monomer-utils.d.ts +19 -0
  8. package/src/monomer-works/monomer-utils.d.ts.map +1 -1
  9. package/src/monomer-works/monomer-utils.js +2 -2
  10. package/src/monomer-works/monomer-utils.js.map +1 -1
  11. package/src/monomer-works/monomer-works.d.ts +3 -2
  12. package/src/monomer-works/monomer-works.d.ts.map +1 -1
  13. package/src/monomer-works/monomer-works.js +27 -0
  14. package/src/monomer-works/monomer-works.js.map +1 -1
  15. package/src/monomer-works/to-atomic-level.js +1 -1
  16. package/src/tests/monomer-lib-tests.d.ts +7 -0
  17. package/src/tests/monomer-lib-tests.d.ts.map +1 -0
  18. package/src/tests/monomer-lib-tests.js +27 -0
  19. package/src/tests/monomer-lib-tests.js.map +1 -0
  20. package/src/types/helm-web-editor.d.ts +26 -0
  21. package/src/types/helm-web-editor.d.ts.map +1 -0
  22. package/src/types/helm-web-editor.js +2 -0
  23. package/src/types/helm-web-editor.js.map +1 -0
  24. package/src/types/helm.d.ts +53 -14
  25. package/src/types/helm.d.ts.map +1 -1
  26. package/src/types/index.d.ts +28 -9
  27. package/src/types/index.d.ts.map +1 -1
  28. package/src/types/index.js +1 -0
  29. package/src/types/index.js.map +1 -1
  30. package/src/types/jsdraw2.d.ts +36 -0
  31. package/src/types/jsdraw2.d.ts.map +1 -1
  32. package/src/types/renderer.d.ts +2 -2
  33. package/src/types/renderer.d.ts.map +1 -1
  34. package/src/types/renderer.js +5 -4
  35. package/src/types/renderer.js.map +1 -1
  36. package/src/utils/cell-renderer-async-base.d.ts +2 -5
  37. package/src/utils/cell-renderer-async-base.d.ts.map +1 -1
  38. package/src/utils/cell-renderer-async-base.js +12 -17
  39. package/src/utils/cell-renderer-async-base.js.map +1 -1
  40. package/src/utils/cell-renderer-back-base.d.ts +10 -3
  41. package/src/utils/cell-renderer-back-base.d.ts.map +1 -1
  42. package/src/utils/cell-renderer-back-base.js +24 -0
  43. package/src/utils/cell-renderer-back-base.js.map +1 -1
  44. package/src/utils/cell-renderer-monomer-placer.d.ts +4 -5
  45. package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
  46. package/src/utils/cell-renderer-monomer-placer.js +51 -20
  47. package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
  48. package/src/utils/const.d.ts +10 -10
  49. package/src/utils/const.d.ts.map +1 -1
  50. package/src/utils/const.js +1 -0
  51. package/src/utils/const.js.map +1 -1
  52. package/src/utils/macromolecule/utils.d.ts.map +1 -1
  53. package/src/utils/macromolecule/utils.js +14 -1
  54. package/src/utils/macromolecule/utils.js.map +1 -1
  55. package/src/utils/seq-handler.d.ts +1 -1
  56. package/src/utils/seq-handler.d.ts.map +1 -1
  57. package/src/utils/seq-handler.js +4 -4
  58. package/src/utils/seq-handler.js.map +1 -1
  59. package/src/viewers/viewer.d.ts.map +1 -1
  60. package/src/viewers/viewer.js +2 -2
  61. package/src/viewers/viewer.js.map +1 -1
package/src/utils/const.js.map CHANGED
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package/src/utils/macromolecule/utils.d.ts.map CHANGED
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package/src/utils/macromolecule/utils.js CHANGED
@@ -114,7 +114,20 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
114
114
  if (!seq)
115
115
  return new StringListSeqSplitted([], GapOriginals[NOTATION.SEPARATOR]);
116
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  else {
117
- const mmList = seq.replaceAll('\"-\"', '').replaceAll('\'-\'', '').split(separator, limit);
117
+ let mmList;
118
+ const mRe = new RegExp(String.raw `"-"|'-'|[^${separator}]+`, 'g'); // depends on separator args
119
+ if (limit !== undefined) {
120
+ mRe.lastIndex = 0;
121
+ mmList = new Array(limit);
122
+ let mEa = null;
123
+ let mI = 0;
124
+ while ((mEa = mRe.exec(seq)) !== null && mI < limit) {
125
+ mmList[mI++] = mEa[0].replace(`"-"`, '').replace(`'-'`, '');
126
+ }
127
+ mmList.splice(mI);
128
+ }
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+ else
130
+ mmList = seq.replaceAll('\"-\"', '').replaceAll('\'-\'', '').split(separator, limit);
118
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  return new StringListSeqSplitted(mmList, GapOriginals[NOTATION.SEPARATOR]);
119
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  }
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  };
package/src/utils/macromolecule/utils.js.map CHANGED
@@ -1 +1 @@
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package/src/utils/seq-handler.d.ts CHANGED
@@ -44,7 +44,7 @@ export declare class SeqHandler {
44
44
  private cached;
45
45
  private _splitted;
46
46
  private columnVersion;
47
- getSplitted(rowIdx: number): ISeqSplitted;
47
+ getSplitted(rowIdx: number, limit?: number): ISeqSplitted;
48
48
  private _stats;
49
49
  get stats(): SeqColStats;
50
50
  private _maxLength;
package/src/utils/seq-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
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package/src/utils/seq-handler.js CHANGED
@@ -206,10 +206,10 @@ export class SeqHandler {
206
206
  // }
207
207
  // return this._splitted;
208
208
  // }
209
- getSplitted(rowIdx) {
210
- if (!this.cached) {
209
+ getSplitted(rowIdx, limit) {
210
+ if (!this.cached || limit !== undefined) {
211
211
  const seq = this.column.get(rowIdx);
212
- return this.splitter(seq);
212
+ return this.getSplitter(limit)(seq);
213
213
  }
214
214
  else {
215
215
  if (this.column.version !== this.columnVersion || this._splitted === null) {
@@ -450,7 +450,7 @@ export class SeqHandler {
450
450
  const monomerLibHelper = await getMonomerLibHelper();
451
451
  const bioLib = monomerLibHelper.getBioLib();
452
452
  // retrieve peptides
453
- const peptides = bioLib.getMonomerSymbolsByType("PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */.toString());
453
+ const peptides = bioLib.getMonomerSymbolsByType("PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */);
454
454
  // convert the peptides list to a set for faster lookup
455
455
  const peptidesSet = new Set(peptides);
456
456
  // get splitter for given separator and check if all monomers are in the lib
package/src/utils/seq-handler.js.map CHANGED
@@ -1 +1 @@
1
- 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package/src/viewers/viewer.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"viewer.d.ts","sourceRoot":"","sources":["viewer.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,SAAS,EAAc,MAAM,mBAAmB,CAAC;AAEzD,MAAM,WAAW,OAAQ,SAAQ,SAAS;IACxC,mCAAmC;IACnC,IAAI,IAAI,IAAI,WAAW,CAAC;IAExB,2BAA2B;IAC3B,KAAK,IAAI,IAAI,CAAC;IAEd,mCAAmC;IACnC,cAAc,IAAI,GAAG,CAAC;CACvB;AAED,wBAAgB,SAAS,CAAC,KAAK,EAAE,OAAO,GAAG,KAAK,IAAI,OAAO,CAG1D;AAED,wBAAgB,SAAS,CAAC,CAAC,EAAE,GAAG,GAAG,OAAO,GAAG,IAAI,CAEhD"}
1
+ {"version":3,"file":"viewer.d.ts","sourceRoot":"","sources":["viewer.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,SAAS,EAAa,MAAM,mBAAmB,CAAC;AAExD,MAAM,WAAW,OAAQ,SAAQ,SAAS;IACxC,mCAAmC;IACnC,IAAI,IAAI,IAAI,WAAW,CAAC;IAExB,2BAA2B;IAC3B,KAAK,IAAI,IAAI,CAAC;IAEd,mCAAmC;IACnC,cAAc,IAAI,GAAG,CAAC;CACvB;AAED,wBAAgB,SAAS,CAAC,KAAK,EAAE,OAAO,GAAG,KAAK,IAAI,OAAO,CAG1D;AAED,wBAAgB,SAAS,CAAC,CAAC,EAAE,GAAG,GAAG,OAAO,GAAG,IAAI,CAEhD"}
package/src/viewers/viewer.js CHANGED
@@ -1,6 +1,6 @@
1
- import { isIRenderer } from '../types/renderer';
1
+ import { isRenderer } from '../types/renderer';
2
2
  export function isIViewer(value) {
3
- return isIRenderer(value) &&
3
+ return isRenderer(value) &&
4
4
  value.root !== undefined && value.close !== undefined && value.removeFromView !== undefined;
5
5
  }
6
6
  export function asIViewer(o) {
package/src/viewers/viewer.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"viewer.js","sourceRoot":"","sources":["viewer.ts"],"names":[],"mappings":"AAIA,OAAO,EAAY,UAAU,EAAC,MAAM,mBAAmB,CAAC;AAaxD,MAAM,UAAU,SAAS,CAAC,KAAc;IACtC,OAAO,UAAU,CAAC,KAAK,CAAC;QACtB,KAAK,CAAC,IAAI,KAAK,SAAS,IAAI,KAAK,CAAC,KAAK,KAAK,SAAS,IAAI,KAAK,CAAC,cAAc,KAAK,SAAS,CAAC;AAChG,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,CAAM;IAC9B,OAAO,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;AACjC,CAAC"}