@datagrok-libraries/bio 5.30.2 → 5.31.0

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.
package/package.json CHANGED
@@ -8,12 +8,12 @@
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  "access": "public"
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  },
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  "friendlyName": "Datagrok bio library",
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- "version": "5.30.2",
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+ "version": "5.31.0",
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  "description": "",
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  "dependencies": {
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  "@datagrok-libraries/gridext": "^1.3.22",
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  "@datagrok-libraries/utils": "^2.5.0",
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- "@datagrok-libraries/ml": "^6.3.22",
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+ "@datagrok-libraries/ml": "^6.3.28",
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  "@deck.gl/core": "8.8.12",
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  "cash-dom": "latest",
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  "datagrok-api": "^1.10.2",
@@ -1,5 +1,5 @@
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  import * as DG from 'datagrok-api/dg';
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- import { DistanceMatrix } from './distance-matrix';
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+ import { DistanceMatrix } from '@datagrok-libraries/ml/src/distance-matrix';
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  import { ClusterMatrix, NodeCuttedType, NodeType } from './types';
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  import { DistanceMetric } from './consts';
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  export interface ITreeHelper {
@@ -1 +1 @@
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,EAAC,MAAM,mBAAmB,CAAC;AACjD,OAAO,EAAC,aAAa,EAAE,cAAc,EAAE,QAAQ,EAAC,MAAM,SAAS,CAAC;AAChE,OAAO,EAAC,cAAc,EAAC,MAAM,UAAU,CAAC;AAExC,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;IAEnE,kBAAkB,CAAC,aAAa,EAAE,aAAa,GAAG,QAAQ,CAAC;CAC5D;AAED,wBAAsB,aAAa,IAAI,OAAO,CAAC,WAAW,CAAC,CAQ1D"}
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,EAAC,MAAM,4CAA4C,CAAC;AAC1E,OAAO,EAAC,aAAa,EAAE,cAAc,EAAE,QAAQ,EAAC,MAAM,SAAS,CAAC;AAChE,OAAO,EAAC,cAAc,EAAC,MAAM,UAAU,CAAC;AAExC,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;IAEnE,kBAAkB,CAAC,aAAa,EAAE,aAAa,GAAG,QAAQ,CAAC;CAC5D;AAED,wBAAsB,aAAa,IAAI,OAAO,CAAC,WAAW,CAAC,CAQ1D"}
@@ -23,6 +23,7 @@ export type Monomer = {
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  };
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  };
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  export interface IMonomerLib {
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+ get error(): string | undefined;
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  getMonomer(polymerType: string, monomerSymbol: string): Monomer | null;
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  getMonomerMolsByPolymerType(polymerType: string): {
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  [monomerSymbol: string]: string;
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,EAAC,UAAU,EAAC,MAAM,MAAM,CAAC;AAChC,OAAO,EACL,oBAAoB,IAAI,GAAG,EAC3B,kBAAkB,IAAI,GAAG,EAAE,oBAAoB,IAAI,GAAG,EACvD,MAAM,gBAAgB,CAAC;AAExB,KAAK,MAAM,GAAG;IACZ,CAAC,GAAG,CAAC,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC/B,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,cAAc,CAAC,EAAE,MAAM,CAAC;IAC7B,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC;CACrB,CAAA;AACD,MAAM,MAAM,OAAO,GAAG;IACpB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,MAAM,CAAC;IACnB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,CAAC;IACtB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,MAAM,CAAC;IACjB,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,CAAC;IACrB,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC3B,CAAC,GAAG,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACjC,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC,EAAE,MAAM,CAAC;IAC9B,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,EAAE;QAAE,CAAC,QAAQ,EAAE,MAAM,GAAG,GAAG,CAAA;KAAE,CAAA;CACzC,CAAC;AAEF,MAAM,WAAW,WAAW;IAC1B,IAAI,KAAK,IAAI,MAAM,GAAG,SAAS,CAAC;IAChC,UAAU,CAAC,WAAW,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI,CAAC;IACvE,2BAA2B,CAAC,WAAW,EAAE,MAAM,GAAG;QAAE,CAAC,aAAa,EAAE,MAAM,GAAG,MAAM,CAAA;KAAE,GAAG,IAAI,CAAC;IAC7F,uBAAuB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;IACvD,eAAe,IAAI,MAAM,EAAE,CAAC;IAC5B,MAAM,CAAC,GAAG,EAAE,WAAW,GAAG,IAAI,CAAC;IAC/B,IAAI,SAAS,IAAI,UAAU,CAAC,GAAG,CAAC,CAAC;CAClC"}
@@ -1,25 +0,0 @@
1
- /** Distance matrix class compatible with data structure of scipy.spatial.distance.pdist */
2
- export declare class DistanceMatrix {
3
- _data: Float32Array;
4
- _size: number;
5
- get data(): Float32Array;
6
- get size(): number;
7
- /**
8
- * @param {Float32Array} data Distance data
9
- * @param {number} size Number of original observations
10
- */
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- constructor(data?: Float32Array, size?: number);
12
- private _linearizeIJ;
13
- get(i: number, j: number): number;
14
- 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;
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- }
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- export interface Indexable<TObj> {
22
- [index: number]: TObj;
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- get length(): number;
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- }
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- //# sourceMappingURL=distance-matrix.d.ts.map
@@ -1 +0,0 @@
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;CAajB;AAED,MAAM,WAAW,SAAS,CAAC,IAAI;IAC7B,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,IAAI,MAAM,IAAI,MAAM,CAAC;CACtB"}
@@ -1,88 +0,0 @@
1
- /** Distance matrix class compatible with data structure of scipy.spatial.distance.pdist */
2
- export class DistanceMatrix {
3
- get data() { return this._data; }
4
- get size() { return this._size; }
5
- /**
6
- * @param {Float32Array} data Distance data
7
- * @param {number} size Number of original observations
8
- */
9
- constructor(data, size) {
10
- if (size == undefined) {
11
- if (data == undefined)
12
- throw new Error('Arguments error: data or size is required.');
13
- this._data = data;
14
- this._size = (1 + Math.sqrt(1 + 4 * 2 * this._data.length)) / 2;
15
- if (this._size != Math.floor(this._size))
16
- throw new Error(`Invalid data length ${this._data.length} leads to non integer size ${this._size}`);
17
- }
18
- else {
19
- this._size = size;
20
- const dataLength = size * (size - 1) / 2;
21
- if (data) {
22
- if (data.length != dataLength)
23
- throw new Error(`Invalid data length. Observations size ${size} requires data length ${dataLength}.`);
24
- this._data = data;
25
- }
26
- else {
27
- this._data = new Float32Array(dataLength);
28
- }
29
- }
30
- }
31
- _linearizeIJ(i, j) {
32
- if (!(i < j))
33
- throw new Error('i must be less than j');
34
- return this._size * i + j - Math.floor(((i + 2) * (i + 1)) / 2);
35
- }
36
- get(i, j) {
37
- if (i == j)
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- return 0;
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- else if (i < j)
40
- return this._data[this._linearizeIJ(i, j)];
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- else
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- return this._data[this._linearizeIJ(j, i)];
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- }
44
- set(i, j, value) {
45
- this._data[this._linearizeIJ(i, j)] = value;
46
- }
47
- static calc(list, method) {
48
- const size = list.length;
49
- const res = new DistanceMatrix(undefined, size);
50
- for (let i = 0; i < size; i++) {
51
- for (let j = i + 1; j < size; j++)
52
- res.set(i, j, method(list[i], list[j]));
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- }
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- return res;
55
- }
56
- // squares each value in matrix in place
57
- square() {
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- 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++)
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- this._data[i] += other._data[i];
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- }
68
- // square root each value in matrix in place
69
- sqrt() {
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- for (let i = 0; i < this._data.length; i++)
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- this._data[i] = Math.sqrt(this._data[i]);
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- }
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- //normilze distance matrix in place
74
- normalize() {
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- let min = this._data[0];
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- let max = this._data[0];
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- for (let i = 0; i < this._data.length; i++) {
78
- if (this._data[i] < min)
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- min = this._data[i];
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- if (this._data[i] > max)
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- max = this._data[i];
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- }
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- const range = max - min;
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- 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);
86
- }
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- }
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- //# sourceMappingURL=distance-matrix.js.map
@@ -1 +0,0 @@
1
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