@datagrok-libraries/bio 5.26.0 → 5.27.1

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 (26) hide show
  1. package/.eslintrc.json +1 -1
  2. package/package.json +6 -2
  3. package/src/trees/distance-matrix.d.ts +6 -2
  4. package/src/trees/distance-matrix.d.ts.map +1 -1
  5. package/src/trees/distance-matrix.js +27 -2
  6. package/src/trees/distance-matrix.js.map +1 -1
  7. package/src/trees/index.d.ts +13 -0
  8. package/src/trees/index.d.ts.map +1 -1
  9. package/src/trees/index.js +15 -0
  10. package/src/trees/index.js.map +1 -1
  11. package/src/trees/tree-helper.d.ts +2 -1
  12. package/src/trees/tree-helper.d.ts.map +1 -1
  13. package/src/trees/tree-helper.js.map +1 -1
  14. package/src/viewers/vd-regions.d.ts +39 -0
  15. package/src/viewers/vd-regions.d.ts.map +1 -0
  16. package/src/viewers/vd-regions.js +19 -0
  17. package/src/viewers/vd-regions.js.map +1 -0
  18. package/src/viewers/web-logo.d.ts +17 -0
  19. package/src/viewers/web-logo.d.ts.map +1 -1
  20. package/src/viewers/web-logo.js +17 -0
  21. package/src/viewers/web-logo.js.map +1 -1
  22. package/tsconfig.json +1 -1
  23. package/src/vd-regions.d.ts +0 -34
  24. package/src/vd-regions.d.ts.map +0 -1
  25. package/src/vd-regions.js +0 -30
  26. package/src/vd-regions.js.map +0 -1
package/.eslintrc.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
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2
  "env": {
3
3
  "browser": true,
4
- "es2021": true
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+ "es2022": true
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  },
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  "extends": [
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  "google"
package/package.json CHANGED
@@ -1,10 +1,14 @@
1
1
  {
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2
  "name": "@datagrok-libraries/bio",
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+ "author": {
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+ "name": "Aleksandr Tanas",
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+ "email": "atanas@datagrok.ai"
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+ },
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7
  "publishConfig": {
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8
  "access": "public"
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  },
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10
  "friendlyName": "Datagrok bio library",
7
- "version": "5.26.0",
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+ "version": "5.27.1",
8
12
  "description": "",
9
13
  "dependencies": {
10
14
  "@datagrok-libraries/gridext": "^1.3.22",
@@ -30,7 +34,7 @@
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  "link": "npm link",
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  "link-api": "npm link datagrok-api",
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  "link-utils": "npm link @datagrok-libraries/utils",
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- "link-all": "npm link datagrok-api @datagrok-libraries/utils",
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+ "link-all": "npm link datagrok-api @datagrok-libraries/utils @datagrok-libraries/gridext",
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  "build-bio": "tsc",
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  "build": "tsc",
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40
  "lint": "eslint \"./src/**/*.ts\"",
package/src/trees/distance-matrix.d.ts CHANGED
@@ -5,14 +5,18 @@ export declare class DistanceMatrix {
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5
  get data(): Float32Array;
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6
  get size(): number;
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  /**
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- * @param {Float64Array} data Distance data
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- * @param {number} m Number of original observations
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+ * @param {Float32Array} data Distance data
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+ * @param {number} size Number of original observations
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  */
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  constructor(data?: Float32Array, size?: number);
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  private _linearizeIJ;
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  get(i: number, j: number): number;
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  set(i: number, j: number, value: number): void;
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  static calc<TObj>(list: Indexable<TObj>, method: (a: TObj, b: TObj) => number): DistanceMatrix;
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+ square(): void;
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+ add(other: DistanceMatrix): void;
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+ sqrt(): void;
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+ normalize(): void;
16
20
  }
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  export interface Indexable<TObj> {
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  [index: number]: TObj;
package/src/trees/distance-matrix.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"distance-matrix.d.ts","sourceRoot":"","sources":["distance-matrix.ts"],"names":[],"mappings":"AAIA,2FAA2F;AAC3F,qBAAa,cAAc;IACzB,KAAK,EAAE,YAAY,CAAC;IACpB,KAAK,EAAE,MAAM,CAAC;IAEd,IAAI,IAAI,IAAI,YAAY,CAAuB;IAE/C,IAAI,IAAI,IAAI,MAAM,CAAuB;IAEzC;;;OAGG;gBACS,IAAI,CAAC,EAAE,YAAY,EAAE,IAAI,CAAC,EAAE,MAAM;IAqB9C,OAAO,CAAC,YAAY;IAKpB,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM;IASxB,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM;IAIvC,MAAM,CAAC,IAAI,CAAC,IAAI,EAAE,IAAI,EAAE,SAAS,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,IAAI,KAAK,MAAM,GAAG,cAAc;IAWvF,MAAM;IAMN,GAAG,CAAC,KAAK,EAAE,cAAc;IAQzB,IAAI;IAMJ,SAAS;CAOjB;AAED,MAAM,WAAW,SAAS,CAAC,IAAI;IAC7B,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,IAAI,MAAM,IAAI,MAAM,CAAC;CACtB"}
package/src/trees/distance-matrix.js CHANGED
@@ -3,8 +3,8 @@ export class DistanceMatrix {
3
3
  get data() { return this._data; }
4
4
  get size() { return this._size; }
5
5
  /**
6
- * @param {Float64Array} data Distance data
7
- * @param {number} m Number of original observations
6
+ * @param {Float32Array} data Distance data
7
+ * @param {number} size Number of original observations
8
8
  */
9
9
  constructor(data, size) {
10
10
  if (size == undefined) {
@@ -53,5 +53,30 @@ export class DistanceMatrix {
53
53
  }
54
54
  return res;
55
55
  }
56
+ // squares each value in matrix in place
57
+ square() {
58
+ for (let i = 0; i < this._data.length; i++)
59
+ this._data[i] = Math.pow(this._data[i], 2);
60
+ }
61
+ // adds another matrix to this one in place
62
+ add(other) {
63
+ if (this._size !== other._size)
64
+ throw new Error(`Matrices must have the same size. This size: ${this._size}, other size: ${other._size}`);
65
+ for (let i = 0; i < this._data.length; i++)
66
+ this._data[i] += other._data[i];
67
+ }
68
+ // square root each value in matrix in place
69
+ sqrt() {
70
+ for (let i = 0; i < this._data.length; i++)
71
+ this._data[i] = Math.sqrt(this._data[i]);
72
+ }
73
+ //normilze distance matrix in place
74
+ normalize() {
75
+ const max = Math.max(...this._data);
76
+ const min = Math.min(...this._data);
77
+ const range = max - min;
78
+ for (let i = 0; i < this._data.length; i++)
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+ this._data[i] = range === 0 ? this._data[i] - min : (this._data[i] - min) / (max - min);
80
+ }
56
81
  }
57
82
  //# sourceMappingURL=distance-matrix.js.map
package/src/trees/distance-matrix.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"distance-matrix.js","sourceRoot":"","sources":["distance-matrix.ts"],"names":[],"mappings":"AAIA,2FAA2F;AAC3F,MAAM,OAAO,cAAc;IAIzB,IAAI,IAAI,KAAmB,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;IAE/C,IAAI,IAAI,KAAa,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;IAEzC;;;OAGG;IACH,YAAY,IAAmB,EAAE,IAAa;QAC5C,IAAI,IAAI,IAAI,SAAS,EAAE;YACrB,IAAI,IAAI,IAAI,SAAS;gBAAE,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAC;YAErF,IAAI,CAAC,KAAK,GAAG,IAAK,CAAC;YACnB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC;YAChE,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC;gBACtC,MAAM,IAAI,KAAK,CAAC,uBAAuB,IAAI,CAAC,KAAK,CAAC,MAAM,8BAA8B,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC;SACvG;aAAM;YACL,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC;YAClB,MAAM,UAAU,GAAW,IAAI,GAAG,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;YACjD,IAAI,IAAI,EAAE;gBACR,IAAI,IAAI,CAAC,MAAM,IAAI,UAAU;oBAC3B,MAAM,IAAI,KAAK,CAAC,0CAA0C,IAAI,yBAAyB,UAAU,GAAG,CAAC,CAAC;gBACxG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC;aACnB;iBAAM;gBACL,IAAI,CAAC,KAAK,GAAG,IAAI,YAAY,CAAC,UAAU,CAAC,CAAC;aAC3C;SACF;IACH,CAAC;IAEO,YAAY,CAAC,CAAS,EAAE,CAAS;QACvC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YAAE,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAC;QACvD,OAAO,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;IAClE,CAAC;IAED,GAAG,CAAC,CAAS,EAAE,CAAS;QACtB,IAAI,CAAC,IAAI,CAAC;YACR,OAAO,CAAC,CAAC;aACN,IAAI,CAAC,GAAG,CAAC;YACZ,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;;YAE3C,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IAC/C,CAAC;IAED,GAAG,CAAC,CAAS,EAAE,CAAS,EAAE,KAAa;QACrC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC;IAC9C,CAAC;IAED,MAAM,CAAC,IAAI,CAAO,IAAqB,EAAE,MAAoC;QAC3E,MAAM,IAAI,GAAW,IAAI,CAAC,MAAM,CAAC;QACjC,MAAM,GAAG,GAAG,IAAI,cAAc,CAAC,SAAS,EAAE,IAAI,CAAC,CAAC;QAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;YAC7B,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE;gBAC/B,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;SAC3C;QACD,OAAO,GAAG,CAAC;IACb,CAAC;CACF"}
1
+ {"version":3,"file":"distance-matrix.js","sourceRoot":"","sources":["distance-matrix.ts"],"names":[],"mappings":"AAIA,2FAA2F;AAC3F,MAAM,OAAO,cAAc;IAIzB,IAAI,IAAI,KAAmB,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;IAE/C,IAAI,IAAI,KAAa,OAAO,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;IAEzC;;;OAGG;IACH,YAAY,IAAmB,EAAE,IAAa;QAC5C,IAAI,IAAI,IAAI,SAAS,EAAE;YACrB,IAAI,IAAI,IAAI,SAAS;gBAAE,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAC;YAErF,IAAI,CAAC,KAAK,GAAG,IAAK,CAAC;YACnB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC;YAChE,IAAI,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC;gBACtC,MAAM,IAAI,KAAK,CAAC,uBAAuB,IAAI,CAAC,KAAK,CAAC,MAAM,8BAA8B,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC;SACvG;aAAM;YACL,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC;YAClB,MAAM,UAAU,GAAW,IAAI,GAAG,CAAC,IAAI,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;YACjD,IAAI,IAAI,EAAE;gBACR,IAAI,IAAI,CAAC,MAAM,IAAI,UAAU;oBAC3B,MAAM,IAAI,KAAK,CAAC,0CAA0C,IAAI,yBAAyB,UAAU,GAAG,CAAC,CAAC;gBACxG,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC;aACnB;iBAAM;gBACL,IAAI,CAAC,KAAK,GAAG,IAAI,YAAY,CAAC,UAAU,CAAC,CAAC;aAC3C;SACF;IACH,CAAC;IAEO,YAAY,CAAC,CAAS,EAAE,CAAS;QACvC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YAAE,MAAM,IAAI,KAAK,CAAC,uBAAuB,CAAC,CAAC;QACvD,OAAO,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;IAClE,CAAC;IAED,GAAG,CAAC,CAAS,EAAE,CAAS;QACtB,IAAI,CAAC,IAAI,CAAC;YACR,OAAO,CAAC,CAAC;aACN,IAAI,CAAC,GAAG,CAAC;YACZ,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;;YAE3C,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IAC/C,CAAC;IAED,GAAG,CAAC,CAAS,EAAE,CAAS,EAAE,KAAa;QACrC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC;IAC9C,CAAC;IAED,MAAM,CAAC,IAAI,CAAO,IAAqB,EAAE,MAAoC;QAC3E,MAAM,IAAI,GAAW,IAAI,CAAC,MAAM,CAAC;QACjC,MAAM,GAAG,GAAG,IAAI,cAAc,CAAC,SAAS,EAAE,IAAI,CAAC,CAAC;QAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;YAC7B,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE;gBAC/B,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;SAC3C;QACD,OAAO,GAAG,CAAC;IACb,CAAC;IAED,wCAAwC;IACjC,MAAM;QACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE;YACxC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,SAAA,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAI,CAAC,CAAA,CAAC;IACvC,CAAC;IAED,2CAA2C;IACpC,GAAG,CAAC,KAAqB;QAC9B,IAAI,IAAI,CAAC,KAAK,KAAK,KAAK,CAAC,KAAK;YAC5B,MAAM,IAAI,KAAK,CAAC,gDAAgD,IAAI,CAAC,KAAK,iBAAiB,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAC5G,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE;YACxC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;IACpC,CAAC;IAED,4CAA4C;IACrC,IAAI;QACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE;YACxC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;IAC7C,CAAC;IAED,mCAAmC;IAC5B,SAAS;QACd,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC;QACpC,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC;QACpC,MAAM,KAAK,GAAG,GAAG,GAAG,GAAG,CAAC;QACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE;YACxC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,GAAG,GAAG,GAAG,CAAC,CAAC;IAC5F,CAAC;CACF"}
package/src/trees/index.d.ts CHANGED
@@ -29,6 +29,19 @@ export declare enum TreeColorNames {
29
29
  MouseOver = "MouseOver",
30
30
  Selection = "Selection"
31
31
  }
32
+ export declare enum DistanceMetric {
33
+ Euclidean = "euclidean",
34
+ Manhattan = "manhattan"
35
+ }
36
+ export declare enum LinkageMethod {
37
+ Single = "single",
38
+ Complete = "complete",
39
+ Average = "average",
40
+ Weighted = "weighted",
41
+ Centroid = "centroid",
42
+ Median = "median",
43
+ Ward = "ward"
44
+ }
32
45
  export declare const TreeDefaultPalette: {
33
46
  [name: string]: number;
34
47
  };
package/src/trees/index.d.ts.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,kHAAkH;AAClH,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,MAAM,CAAC;IACb,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,QAAQ,EAAE,CAAC;CACvB;AAED,MAAM,WAAW,cAAe,SAAQ,QAAQ;IAC9C,kBAAkB,EAAE,MAAM,EAAE,CAAC;IAC7B,cAAc,CAAC,EAAE,QAAQ,EAAE,CAAC;CAC7B;AAED,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,QAAQ,CAAA;CAAE,CAAC;AAC5D,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAC1D,MAAM,MAAM,gBAAgB,GAAG,CAAC,QAAQ,EAAE,MAAM,KAAK,IAAI,CAAC;AAE1D,oBAAY,IAAI;IACd,MAAM,YAAY;IAClB,WAAW,iBAAiB;IAC5B,OAAO,oBAAoB;IAC3B,oBAAoB,sBAAsB;CAC3C;AAED,wBAAgB,MAAM,CAAC,IAAI,EAAE,QAAQ,WAEpC;AAED,oBAAY,cAAc;IACxB,IAAI,SAAS;IACb,KAAK,UAAU;IACf,OAAO,YAAY;IACnB,SAAS,cAAc;IACvB,SAAS,cAAc;CACxB;AAED,oBAAY,cAAc;IACxB,SAAS,cAAc;IACvB,SAAS,cAAc;CACxB;AAED,oBAAY,aAAa;IACvB,MAAM,WAAW;IACjB,QAAQ,aAAa;IACrB,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,QAAQ,aAAa;IACrB,MAAM,WAAW;IACjB,IAAI,SAAS;CACd;AAGD,eAAO,MAAM,kBAAkB,EAAE;IAAE,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAAA;CAMxD,CAAC"}
package/src/trees/index.js CHANGED
@@ -17,6 +17,21 @@ export var TreeColorNames;
17
17
  TreeColorNames["MouseOver"] = "MouseOver";
18
18
  TreeColorNames["Selection"] = "Selection";
19
19
  })(TreeColorNames || (TreeColorNames = {}));
20
+ export var DistanceMetric;
21
+ (function (DistanceMetric) {
22
+ DistanceMetric["Euclidean"] = "euclidean";
23
+ DistanceMetric["Manhattan"] = "manhattan";
24
+ })(DistanceMetric || (DistanceMetric = {}));
25
+ export var LinkageMethod;
26
+ (function (LinkageMethod) {
27
+ LinkageMethod["Single"] = "single";
28
+ LinkageMethod["Complete"] = "complete";
29
+ LinkageMethod["Average"] = "average";
30
+ LinkageMethod["Weighted"] = "weighted";
31
+ LinkageMethod["Centroid"] = "centroid";
32
+ LinkageMethod["Median"] = "median";
33
+ LinkageMethod["Ward"] = "ward";
34
+ })(LinkageMethod || (LinkageMethod = {}));
20
35
  export const TreeDefaultPalette = {
21
36
  [TreeColorNames.Main]: DG.Color.categoricalPalette[12],
22
37
  [TreeColorNames.Light]: DG.Color.categoricalPalette[13],
package/src/trees/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAkBtC,MAAM,CAAN,IAAY,IAKX;AALD,WAAY,IAAI;IACd,0BAAkB,CAAA;IAClB,oCAA4B,CAAA;IAC5B,mCAA2B,CAAA;IAC3B,kDAA0C,CAAA;AAC5C,CAAC,EALW,IAAI,KAAJ,IAAI,QAKf;AAED,MAAM,UAAU,MAAM,CAAC,IAAc;IACnC,OAAO,CAAC,IAAI,CAAC,QAAQ,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,IAAI,CAAC,CAAC;AACrD,CAAC;AAED,MAAM,CAAN,IAAY,cAMX;AAND,WAAY,cAAc;IACxB,+BAAa,CAAA;IACb,iCAAe,CAAA;IACf,qCAAmB,CAAA;IACnB,yCAAuB,CAAA;IACvB,yCAAuB,CAAA;AACzB,CAAC,EANW,cAAc,KAAd,cAAc,QAMzB;AAED,MAAM,CAAC,MAAM,kBAAkB,GAA+B;IAC5D,CAAC,cAAc,CAAC,IAAI,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,EAAE,CAAC;IACtD,CAAC,cAAc,CAAC,KAAK,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,EAAE,CAAC;IACvD,CAAC,cAAc,CAAC,OAAO,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,UAAU;IAC7C,CAAC,cAAc,CAAC,SAAS,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,aAAa;IAClD,CAAC,cAAc,CAAC,SAAS,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,YAAY;CAClD,CAAC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAkBtC,MAAM,CAAN,IAAY,IAKX;AALD,WAAY,IAAI;IACd,0BAAkB,CAAA;IAClB,oCAA4B,CAAA;IAC5B,mCAA2B,CAAA;IAC3B,kDAA0C,CAAA;AAC5C,CAAC,EALW,IAAI,KAAJ,IAAI,QAKf;AAED,MAAM,UAAU,MAAM,CAAC,IAAc;IACnC,OAAO,CAAC,IAAI,CAAC,QAAQ,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,IAAI,CAAC,CAAC;AACrD,CAAC;AAED,MAAM,CAAN,IAAY,cAMX;AAND,WAAY,cAAc;IACxB,+BAAa,CAAA;IACb,iCAAe,CAAA;IACf,qCAAmB,CAAA;IACnB,yCAAuB,CAAA;IACvB,yCAAuB,CAAA;AACzB,CAAC,EANW,cAAc,KAAd,cAAc,QAMzB;AAED,MAAM,CAAN,IAAY,cAGX;AAHD,WAAY,cAAc;IACxB,yCAAuB,CAAA;IACvB,yCAAuB,CAAA;AACzB,CAAC,EAHW,cAAc,KAAd,cAAc,QAGzB;AAED,MAAM,CAAN,IAAY,aAQX;AARD,WAAY,aAAa;IACvB,kCAAiB,CAAA;IACjB,sCAAqB,CAAA;IACrB,oCAAmB,CAAA;IACnB,sCAAqB,CAAA;IACrB,sCAAqB,CAAA;IACrB,kCAAiB,CAAA;IACjB,8BAAa,CAAA;AACf,CAAC,EARW,aAAa,KAAb,aAAa,QAQxB;AAGD,MAAM,CAAC,MAAM,kBAAkB,GAA+B;IAC5D,CAAC,cAAc,CAAC,IAAI,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,EAAE,CAAC;IACtD,CAAC,cAAc,CAAC,KAAK,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,EAAE,CAAC;IACvD,CAAC,cAAc,CAAC,OAAO,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,UAAU;IAC7C,CAAC,cAAc,CAAC,SAAS,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,aAAa;IAClD,CAAC,cAAc,CAAC,SAAS,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,YAAY;CAClD,CAAC"}
package/src/trees/tree-helper.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  import * as DG from 'datagrok-api/dg';
2
- import { NodeCuttedType, NodeType } from './index';
2
+ import { DistanceMetric, NodeCuttedType, NodeType } from './index';
3
3
  import { DistanceMatrix } from './distance-matrix';
4
4
  export interface ITreeHelper {
5
5
  /** Generates data frame with row per node, parent relation, distance, annotation
@@ -43,6 +43,7 @@ export interface ITreeHelper {
43
43
  generateTree(size: number): NodeType;
44
44
  hierarchicalClustering(df: DG.DataFrame, distance: string, linkage: string): Promise<NodeType>;
45
45
  hierarchicalClusteringByDistance(distance: DistanceMatrix, linkage: string): Promise<NodeType>;
46
+ calcDistanceMatrix(df: DG.DataFrame, colNames: string[], distanceMetric?: DistanceMetric): Promise<DistanceMatrix | null>;
46
47
  }
47
48
  export declare function getTreeHelper(): Promise<ITreeHelper>;
48
49
  //# sourceMappingURL=tree-helper.d.ts.map
package/src/trees/tree-helper.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"tree-helper.d.ts","sourceRoot":"","sources":["tree-helper.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,cAAc,EAAE,cAAc,EAAE,QAAQ,EAAC,MAAM,SAAS,CAAC;AACjE,OAAO,EAAC,cAAc,EAAC,MAAM,mBAAmB,CAAC;AAEjD,MAAM,WAAW,WAAW;IAC1B;;;;;OAKG;IACH,UAAU,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,MAAM,GAAG,EAAE,CAAC,SAAS,CAAC;IAE5E,QAAQ,CAAC,IAAI,EAAE,QAAQ,GAAG,IAAI,GAAG,MAAM,CAAC;IAExC,WAAW,CAAC,KAAK,SAAS,QAAQ,EAAE,IAAI,EAAE,KAAK,GAAG,IAAI,GAAG,KAAK,EAAE,CAAC;IAEjE,WAAW,CAAC,KAAK,SAAS,QAAQ,EAAE,IAAI,EAAE,KAAK,GAAG,IAAI,GAAG,KAAK,EAAE,CAAC;IAEjE;;OAEG;IACH,kBAAkB,CAAC,IAAI,EAAE,QAAQ,GAAG,IAAI,EAAE,MAAM,EAAE;QAAE,CAAC,IAAI,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,GAAG,QAAQ,GAAG,IAAI,CAAC;IAE5F;;OAEG;IACH,gBAAgB,CAAC,KAAK,SAAS,QAAQ,EAAE,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,MAAM,EAAE;QAAE,CAAC,IAAI,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,GAAG,KAAK,EAAE,CAAC;IAEvG,eAAe,CAAC,IAAI,EAAE,QAAQ,GAAG,IAAI,EAAE,SAAS,EAAE,MAAM,EAAE,aAAa,CAAC,EAAE,MAAM,GAAG,QAAQ,EAAE,CAAC;IAE9F,aAAa,CACX,IAAI,EAAE,QAAQ,GAAG,IAAI,EAAE,SAAS,EAAE,MAAM,EAAE,UAAU,CAAC,EAAE,OAAO,EAAE,aAAa,CAAC,EAAE,MAAM,GAAG,QAAQ,GAAG,IAAI,CAAC;IAE3G;;OAEG;IACH,YAAY,CAAC,IAAI,EAAE,QAAQ,GAAG,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,WAAW,CAAC,EAAE,MAAM,GAAG,CAAC,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC;IAE/F,YAAY,CAAC,IAAI,EAAE,cAAc,EAC/B,MAAM,EAAE,EAAE,CAAC,SAAS,EAAE,WAAW,EAAE,MAAM,GAAG,IAAI,EAAE,cAAc,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,GAAG,GAAG,IAAI,CAAC;IAE5F;;OAEG;IACH,aAAa,CAAC,IAAI,EAAE,cAAc,EAAE,SAAS,EAAE,EAAE,CAAC,SAAS,EAAE,cAAc,EAAE,MAAM,EAAE,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAEjH;;OAEG;IACH,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,SAAS,EACnE,WAAW,EAAE,MAAM,EAAE,cAAc,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,GAAG,GAAG,IAAI,CAAC;IAE/D,kFAAkF;IAClF,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,QAAQ,CAAC;IAErC,sBAAsB,CAAC,EAAE,EAAE,EAAE,CAAC,SAAS,EAAE,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;IAE/F,gCAAgC,CAAC,QAAQ,EAAE,cAAc,EAAE,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAC;IAE/F,kBAAkB,CAAC,EAAE,EAAE,EAAE,CAAC,SAAS,EAAE,QAAQ,EAAE,MAAM,EAAE,EACrD,cAAc,CAAC,EAAE,cAAc,GAAG,OAAO,CAAC,cAAc,GAAG,IAAI,CAAC,CAAC;CACpE;AAED,wBAAsB,aAAa,IAAI,OAAO,CAAC,WAAW,CAAC,CAO1D"}
package/src/trees/tree-helper.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"tree-helper.js","sourceRoot":"","sources":["tree-helper.ts"],"names":[],"mappings":";;;;;;;;;AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AA8DtC,MAAM,UAAgB,aAAa;;QACjC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,YAAY,EAAE,IAAI,EAAE,eAAe,EAAC,CAAC,CAAC;QAC9E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;YACvB,MAAM,IAAI,KAAK,CAAC,8DAA8D,CAAC,CAAC;QAElF,MAAM,GAAG,GAAgB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAiB,CAAC;QACnG,OAAO,GAAG,CAAC;IACb,CAAC;CAAA"}
1
+ {"version":3,"file":"tree-helper.js","sourceRoot":"","sources":["tree-helper.ts"],"names":[],"mappings":";;;;;;;;;AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAiEtC,MAAM,UAAgB,aAAa;;QACjC,MAAM,QAAQ,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAC,OAAO,EAAE,YAAY,EAAE,IAAI,EAAE,eAAe,EAAC,CAAC,CAAC;QAC9E,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC;YACvB,MAAM,IAAI,KAAK,CAAC,8DAA8D,CAAC,CAAC;QAElF,MAAM,GAAG,GAAgB,CAAC,MAAM,QAAQ,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,EAAE,CAAC,CAAC,mBAAmB,EAAiB,CAAC;QACnG,OAAO,GAAG,CAAC;IACb,CAAC;CAAA"}
package/src/viewers/vd-regions.d.ts ADDED
@@ -0,0 +1,39 @@
1
+ import * as DG from 'datagrok-api/dg';
2
+ import { IViewer } from './viewer';
3
+ import { PositionHeight } from './web-logo';
4
+ export declare enum VdRegionType {
5
+ Unknown = "unknown",
6
+ FR = "framework",
7
+ CDR = "cdr"
8
+ }
9
+ /** Describes V-DOMAIN (IG and TR) region (of multiple alignment)
10
+ * https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html
11
+ * Attributes {@link positionStartName} and {@link positionEndName} are strings because
12
+ * they correspond to position names as column names in ANARCI output (with a character index possible).
13
+ */
14
+ export interface VdRegion {
15
+ readonly type: VdRegionType;
16
+ readonly name: string;
17
+ readonly chain: string;
18
+ readonly order: number;
19
+ /** Name of the column containing sequence */
20
+ readonly sequenceColumnName: string;
21
+ /** Region start position (inclusive) */
22
+ readonly positionStartName: string;
23
+ /** Region end position (inclusive) */
24
+ readonly positionEndName: string;
25
+ }
26
+ export declare class VdRegionsPropsDefault {
27
+ regionTypes: VdRegionType[];
28
+ chains: string[];
29
+ skipEmptyPositions: boolean;
30
+ positionWidth: number;
31
+ positionHeight: PositionHeight;
32
+ }
33
+ export type VdRegionsProps = Required<VdRegionsPropsDefault>;
34
+ /** Interface for VdRegionsViewer from @datagrok/bio to unbind dependency to Bio package */
35
+ export interface IVdRegionsViewer extends VdRegionsProps, IViewer {
36
+ init(): Promise<void>;
37
+ setData(mlbDf: DG.DataFrame, regions: VdRegion[]): void;
38
+ }
39
+ //# sourceMappingURL=vd-regions.d.ts.map
package/src/viewers/vd-regions.d.ts.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"vd-regions.d.ts","sourceRoot":"","sources":["vd-regions.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AACjC,OAAO,EAAC,cAAc,EAAC,MAAM,YAAY,CAAC;AAI1C,oBAAY,YAAY;IACtB,OAAO,YAAY;IACnB,EAAE,cAAc;IAChB,GAAG,QAAQ;CACZ;AAED;;;;GAIG;AACH,MAAM,WAAW,QAAQ;IACvB,QAAQ,CAAC,IAAI,EAAE,YAAY,CAAC;IAC5B,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IAEvB,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IAEvB,6CAA6C;IAC7C,QAAQ,CAAC,kBAAkB,EAAE,MAAM,CAAC;IAEpC,wCAAwC;IACxC,QAAQ,CAAC,iBAAiB,EAAE,MAAM,CAAC;IAEnC,sCAAsC;IACtC,QAAQ,CAAC,eAAe,EAAE,MAAM,CAAC;CAClC;AAED,qBAAa,qBAAqB;IAChC,WAAW,EAAE,YAAY,EAAE,CAAsB;IACjD,MAAM,EAAE,MAAM,EAAE,CAAsB;IAGtC,kBAAkB,EAAE,OAAO,CAAS;IACpC,aAAa,EAAE,MAAM,CAAM;IAC3B,cAAc,EAAE,cAAc,CAA0B;CACzD;AAED,MAAM,MAAM,cAAc,GAAG,QAAQ,CAAC,qBAAqB,CAAC,CAAC;AAE7D,2FAA2F;AAC3F,MAAM,WAAW,gBAAiB,SAAQ,cAAc,EAAE,OAAO;IAC/D,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC;IAEtB,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC;CACzD"}
package/src/viewers/vd-regions.js ADDED
@@ -0,0 +1,19 @@
1
+ import { PositionHeight } from './web-logo';
2
+ // Data structures for V-Domain regions of antibodies
3
+ export var VdRegionType;
4
+ (function (VdRegionType) {
5
+ VdRegionType["Unknown"] = "unknown";
6
+ VdRegionType["FR"] = "framework";
7
+ VdRegionType["CDR"] = "cdr";
8
+ })(VdRegionType || (VdRegionType = {}));
9
+ export class VdRegionsPropsDefault {
10
+ constructor() {
11
+ this.regionTypes = [VdRegionType.CDR];
12
+ this.chains = ['Heavy', 'Light'];
13
+ //sequenceColumnNamePostfix: string = 'chain sequence';
14
+ this.skipEmptyPositions = false;
15
+ this.positionWidth = 16;
16
+ this.positionHeight = PositionHeight.Entropy;
17
+ }
18
+ }
19
+ //# sourceMappingURL=vd-regions.js.map
package/src/viewers/vd-regions.js.map ADDED
@@ -0,0 +1 @@
1
+ {"version":3,"file":"vd-regions.js","sourceRoot":"","sources":["vd-regions.ts"],"names":[],"mappings":"AAGA,OAAO,EAAC,cAAc,EAAC,MAAM,YAAY,CAAC;AAE1C,qDAAqD;AAErD,MAAM,CAAN,IAAY,YAIX;AAJD,WAAY,YAAY;IACtB,mCAAmB,CAAA;IACnB,gCAAgB,CAAA;IAChB,2BAAW,CAAA;AACb,CAAC,EAJW,YAAY,KAAZ,YAAY,QAIvB;AAwBD,MAAM,OAAO,qBAAqB;IAAlC;QACE,gBAAW,GAAmB,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC;QACjD,WAAM,GAAa,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;QACtC,uDAAuD;QAEvD,uBAAkB,GAAY,KAAK,CAAC;QACpC,kBAAa,GAAW,EAAE,CAAC;QAC3B,mBAAc,GAAmB,cAAc,CAAC,OAAO,CAAC;IAC1D,CAAC;CAAA"}
package/src/viewers/web-logo.d.ts CHANGED
@@ -1,5 +1,22 @@
1
+ import { IViewer } from './viewer';
1
2
  export declare enum PositionHeight {
2
3
  Entropy = "Entropy",
3
4
  full = "100%"
4
5
  }
6
+ export declare class WebLogoPropsDefault {
7
+ sequenceColumnName: string | null;
8
+ startPositionName: string | null;
9
+ endPositionName: string | null;
10
+ skipEmptySequences: boolean;
11
+ skipEmptyPositions: boolean;
12
+ shrinkEmptyTail: boolean;
13
+ }
14
+ export type WebLogoProps = Required<WebLogoPropsDefault>;
15
+ export interface IWebLogoViewer extends WebLogoProps, IViewer {
16
+ }
17
+ export declare const positionSeparator: string;
18
+ export declare const positionRe: RegExp;
19
+ export declare enum TAGS {
20
+ positionNames = ".positionNames"
21
+ }
5
22
  //# sourceMappingURL=web-logo.d.ts.map
package/src/viewers/web-logo.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"web-logo.d.ts","sourceRoot":"","sources":["web-logo.ts"],"names":[],"mappings":"AAIA,oBAAY,cAAc;IACxB,OAAO,YAAY;IACnB,IAAI,SAAS;CACd"}
1
+ {"version":3,"file":"web-logo.d.ts","sourceRoot":"","sources":["web-logo.ts"],"names":[],"mappings":"AAGA,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAEjC,oBAAY,cAAc;IACxB,OAAO,YAAY;IACnB,IAAI,SAAS;CACd;AAED,qBAAa,mBAAmB;IAE9B,kBAAkB,EAAE,MAAM,GAAG,IAAI,CAAQ;IACzC,iBAAiB,EAAE,MAAM,GAAG,IAAI,CAAQ;IACxC,eAAe,EAAE,MAAM,GAAG,IAAI,CAAQ;IACtC,kBAAkB,EAAE,OAAO,CAAQ;IACnC,kBAAkB,EAAE,OAAO,CAAS;IACpC,eAAe,EAAE,OAAO,CAAQ;CACjC;AAED,MAAM,MAAM,YAAY,GAAG,QAAQ,CAAC,mBAAmB,CAAC,CAAC;AAEzD,MAAM,WAAW,cAAe,SAAQ,YAAY,EAAE,OAAO;CAE5D;AAED,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAC9C,eAAO,MAAM,UAAU,EAAE,MAAwB,CAAC;AAElD,oBAAY,IAAI;IACd,aAAa,mBAAmB;CACjC"}
package/src/viewers/web-logo.js CHANGED
@@ -3,4 +3,21 @@ export var PositionHeight;
3
3
  PositionHeight["Entropy"] = "Entropy";
4
4
  PositionHeight["full"] = "100%";
5
5
  })(PositionHeight || (PositionHeight = {}));
6
+ export class WebLogoPropsDefault {
7
+ constructor() {
8
+ // -- Data --
9
+ this.sequenceColumnName = null;
10
+ this.startPositionName = null;
11
+ this.endPositionName = null;
12
+ this.skipEmptySequences = true;
13
+ this.skipEmptyPositions = false;
14
+ this.shrinkEmptyTail = true;
15
+ }
16
+ }
17
+ export const positionSeparator = ', ';
18
+ export const positionRe = /(\d+)([A-Z]?)/;
19
+ export var TAGS;
20
+ (function (TAGS) {
21
+ TAGS["positionNames"] = ".positionNames";
22
+ })(TAGS || (TAGS = {}));
6
23
  //# sourceMappingURL=web-logo.js.map
package/src/viewers/web-logo.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"web-logo.js","sourceRoot":"","sources":["web-logo.ts"],"names":[],"mappings":"AAIA,MAAM,CAAN,IAAY,cAGX;AAHD,WAAY,cAAc;IACxB,qCAAmB,CAAA;IACnB,+BAAa,CAAA;AACf,CAAC,EAHW,cAAc,KAAd,cAAc,QAGzB"}
1
+ {"version":3,"file":"web-logo.js","sourceRoot":"","sources":["web-logo.ts"],"names":[],"mappings":"AAKA,MAAM,CAAN,IAAY,cAGX;AAHD,WAAY,cAAc;IACxB,qCAAmB,CAAA;IACnB,+BAAa,CAAA;AACf,CAAC,EAHW,cAAc,KAAd,cAAc,QAGzB;AAED,MAAM,OAAO,mBAAmB;IAAhC;QACE,aAAa;QACb,uBAAkB,GAAkB,IAAI,CAAC;QACzC,sBAAiB,GAAkB,IAAI,CAAC;QACxC,oBAAe,GAAkB,IAAI,CAAC;QACtC,uBAAkB,GAAY,IAAI,CAAC;QACnC,uBAAkB,GAAY,KAAK,CAAC;QACpC,oBAAe,GAAY,IAAI,CAAC;IAClC,CAAC;CAAA;AAQD,MAAM,CAAC,MAAM,iBAAiB,GAAW,IAAI,CAAC;AAC9C,MAAM,CAAC,MAAM,UAAU,GAAW,eAAe,CAAC;AAElD,MAAM,CAAN,IAAY,IAEX;AAFD,WAAY,IAAI;IACd,wCAAgC,CAAA;AAClC,CAAC,EAFW,IAAI,KAAJ,IAAI,QAEf"}
package/tsconfig.json CHANGED
@@ -6,7 +6,7 @@
6
6
  // "incremental": true, /* Enable incremental compilation */
7
7
  "target": "es6", /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
8
8
  "module": "es2020", /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
9
- "lib": ["ES2021", "dom"], /* Specify library files to be included in the compilation. */
9
+ "lib": ["ES2022", "dom"], /* Specify library files to be included in the compilation. */
10
10
  // "allowJs": true, /* Allow javascript files to be compiled. */
11
11
  // "checkJs": true, /* Report errors in .js files. */
12
12
  // "jsx": "preserve", /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */
package/src/vd-regions.d.ts DELETED
@@ -1,34 +0,0 @@
1
- import * as DG from 'datagrok-api/dg';
2
- import { IViewer } from './viewers/viewer';
3
- export declare enum VdRegionType {
4
- Unknown = "unknown",
5
- FR = "framework",
6
- CDR = "cdr"
7
- }
8
- /** Describes V-DOMAIN (IG and TR) region (of multiple alignment)
9
- * https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html
10
- */
11
- export declare class VdRegion {
12
- type: VdRegionType;
13
- name: string;
14
- chain: string;
15
- order: number;
16
- positionStartName: string;
17
- positionEndName: string;
18
- /**
19
- * start and position are strings because they correspond to position names as column names in ANARCI output
20
- * @param {VdRegionType} type Type of the region
21
- * @param {string} name Name of the region
22
- * @param {string} chain
23
- * @param {string} order
24
- * @param {string} positionStartName Region start position (inclusive)
25
- * @param {string} positionEndName Region end position (inclusive)
26
- */
27
- constructor(type: VdRegionType, name: string, chain: string, order: number, positionStartName: string, positionEndName: string);
28
- }
29
- /** Interface for VdRegionsViewer from @datagrok/bio to unbind dependency to Bio package */
30
- export interface IVdRegionsViewer extends IViewer {
31
- init(): Promise<void>;
32
- setData(mlbDf: DG.DataFrame, regions: VdRegion[]): void;
33
- }
34
- //# sourceMappingURL=vd-regions.d.ts.map
package/src/vd-regions.d.ts.map DELETED
@@ -1 +0,0 @@
1
- {"version":3,"file":"vd-regions.d.ts","sourceRoot":"","sources":["vd-regions.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,OAAO,EAAC,MAAM,kBAAkB,CAAC;AAIzC,oBAAY,YAAY;IACtB,OAAO,YAAY;IACnB,EAAE,cAAc;IAChB,GAAG,QAAQ;CACZ;AAED;;GAEG;AACH,qBAAa,QAAQ;IACnB,IAAI,EAAE,YAAY,CAAC;IACnB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,iBAAiB,EAAE,MAAM,CAAC;IAC1B,eAAe,EAAE,MAAM,CAAC;IAExB;;;;;;;;OAQG;gBACS,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EACxE,iBAAiB,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM;CAQrD;AAED,2FAA2F;AAC3F,MAAM,WAAW,gBAAiB,SAAQ,OAAO;IAC/C,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC;IAEtB,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC;CACzD"}
package/src/vd-regions.js DELETED
@@ -1,30 +0,0 @@
1
- // Data structures for V-Domain regions of antibodies
2
- export var VdRegionType;
3
- (function (VdRegionType) {
4
- VdRegionType["Unknown"] = "unknown";
5
- VdRegionType["FR"] = "framework";
6
- VdRegionType["CDR"] = "cdr";
7
- })(VdRegionType || (VdRegionType = {}));
8
- /** Describes V-DOMAIN (IG and TR) region (of multiple alignment)
9
- * https://www.imgt.org/IMGTScientificChart/Numbering/IMGTIGVLsuperfamily.html
10
- */
11
- export class VdRegion {
12
- /**
13
- * start and position are strings because they correspond to position names as column names in ANARCI output
14
- * @param {VdRegionType} type Type of the region
15
- * @param {string} name Name of the region
16
- * @param {string} chain
17
- * @param {string} order
18
- * @param {string} positionStartName Region start position (inclusive)
19
- * @param {string} positionEndName Region end position (inclusive)
20
- */
21
- constructor(type, name, chain, order, positionStartName, positionEndName) {
22
- this.type = type;
23
- this.name = name;
24
- this.chain = chain;
25
- this.order = order;
26
- this.positionStartName = positionStartName;
27
- this.positionEndName = positionEndName;
28
- }
29
- }
30
- //# sourceMappingURL=vd-regions.js.map
package/src/vd-regions.js.map DELETED
@@ -1 +0,0 @@
1
- {"version":3,"file":"vd-regions.js","sourceRoot":"","sources":["vd-regions.ts"],"names":[],"mappings":"AAIA,qDAAqD;AAErD,MAAM,CAAN,IAAY,YAIX;AAJD,WAAY,YAAY;IACtB,mCAAmB,CAAA;IACnB,gCAAgB,CAAA;IAChB,2BAAW,CAAA;AACb,CAAC,EAJW,YAAY,KAAZ,YAAY,QAIvB;AAED;;GAEG;AACH,MAAM,OAAO,QAAQ;IAQnB;;;;;;;;OAQG;IACH,YAAY,IAAkB,EAAE,IAAY,EAAE,KAAa,EAAE,KAAa,EACxE,iBAAyB,EAAE,eAAuB;QAClD,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC;QACnB,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC;QACnB,IAAI,CAAC,iBAAiB,GAAG,iBAAiB,CAAC;QAC3C,IAAI,CAAC,eAAe,GAAG,eAAe,CAAC;IACzC,CAAC;CACF"}