@datagrok-libraries/bio 5.29.2 → 5.29.3

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 (29) hide show
  1. package/package.json +2 -1
  2. package/src/utils/units-handler.d.ts +3 -3
  3. package/src/utils/units-handler.d.ts.map +1 -1
  4. package/src/utils/units-handler.js +5 -5
  5. package/src/utils/units-handler.js.map +1 -1
  6. package/src/distance-functions/hamming.d.ts +0 -3
  7. package/src/distance-functions/hamming.d.ts.map +0 -1
  8. package/src/distance-functions/hamming.js +0 -16
  9. package/src/distance-functions/hamming.js.map +0 -1
  10. package/src/distance-functions/index.d.ts +0 -2
  11. package/src/distance-functions/index.d.ts.map +0 -1
  12. package/src/distance-functions/index.js +0 -2
  13. package/src/distance-functions/index.js.map +0 -1
  14. package/src/distance-functions/levenstein.d.ts +0 -3
  15. package/src/distance-functions/levenstein.d.ts.map +0 -1
  16. package/src/distance-functions/levenstein.js +0 -7
  17. package/src/distance-functions/levenstein.js.map +0 -1
  18. package/src/distance-functions/macromolecule-distance-functions.d.ts +0 -13
  19. package/src/distance-functions/macromolecule-distance-functions.d.ts.map +0 -1
  20. package/src/distance-functions/macromolecule-distance-functions.js +0 -21
  21. package/src/distance-functions/macromolecule-distance-functions.js.map +0 -1
  22. package/src/distance-functions/needleman-wunsch.d.ts +0 -13
  23. package/src/distance-functions/needleman-wunsch.d.ts.map +0 -1
  24. package/src/distance-functions/needleman-wunsch.js +0 -90
  25. package/src/distance-functions/needleman-wunsch.js.map +0 -1
  26. package/src/distance-functions/types.d.ts +0 -2
  27. package/src/distance-functions/types.d.ts.map +0 -1
  28. package/src/distance-functions/types.js +0 -2
  29. package/src/distance-functions/types.js.map +0 -1
package/package.json CHANGED
@@ -8,11 +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": "5.29.2",
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+ "version": "5.29.3",
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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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  "@deck.gl/core": "8.8.12",
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  "cash-dom": "latest",
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  "datagrok-api": "^1.10.2",
package/src/utils/units-handler.d.ts CHANGED
@@ -1,8 +1,8 @@
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  import * as DG from 'datagrok-api/dg';
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  import { NOTATION } from './macromolecule/consts';
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  import { SplitterFunc } from './macromolecule/types';
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- import { mmDistanceFunctionsNames } from '../distance-functions';
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- import { mmDistanceFunctionType } from '../distance-functions/types';
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+ import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
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+ import { mmDistanceFunctionType } from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
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  /** Class for handling notation units in Macromolecule columns */
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  export declare class UnitsHandler {
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  protected readonly _column: DG.Column;
@@ -74,7 +74,7 @@ export declare class UnitsHandler {
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  * @return {DG.Column}
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  */
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  static getNewColumnFromParams(len: number, name: string, units: string): DG.Column;
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- getDistanceFunctionName(): mmDistanceFunctionsNames;
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+ getDistanceFunctionName(): MmDistanceFunctionsNames;
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  getDistanceFunction(): mmDistanceFunctionType;
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  constructor(col: DG.Column);
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  }
package/src/utils/units-handler.d.ts.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"units-handler.d.ts","sourceRoot":"","sources":["units-handler.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAA0C,QAAQ,EAAO,MAAM,wBAAwB,CAAC;AAC/F,OAAO,EAAc,YAAY,EAAC,MAAM,uBAAuB,CAAC;AAShE,OAAO,EAAsB,wBAAwB,EAAC,MAC/C,6DAA6D,CAAC;AACrE,OAAO,EAAC,sBAAsB,EAAC,MAAM,mEAAmE,CAAC;AAEzG,iEAAiE;AACjE,qBAAa,YAAY;IACvB,SAAS,CAAC,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC;IACtC,SAAS,CAAC,MAAM,EAAE,MAAM,CAAC;IACzB,SAAS,CAAC,SAAS,EAAE,QAAQ,CAAC;IAC9B,SAAS,CAAC,iBAAiB,EAAE,MAAM,CAAC;IACpC,SAAS,CAAC,MAAM,CAAC,QAAQ,CAAC,sBAAsB;;;;MAI9C;WAEY,qBAAqB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM;WAQpC,yBAAyB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,SAAS,CAAC,EAAE,MAAM;WAW5D,oBAAoB,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM;IAQjD,+BAA+B;WACjB,OAAO,CAAC,GAAG,EAAE,EAAE,CAAC,MAAM,EAAE,QAAQ,EAAE,YAAY,GAAG,IAAI;IAuBnE,SAAS,KAAK,KAAK,IAAI,MAAM,CAAwB;IAErD,SAAS,KAAK,MAAM,IAAI,EAAE,CAAC,MAAM,CAAyB;IAE1D,IAAW,QAAQ,IAAI,QAAQ,CAA2B;IAE1D,IAAW,gBAAgB,IAAI,MAAM,CAAmC;IAExE,IAAW,SAAS,IAAI,MAAM,GAAG,SAAS,CAKzC;IAED,IAAW,OAAO,IAAI,MAAM,CAQ3B;IAED,iCAAiC;IACjC,IAAW,QAAQ,IAAI,MAAM,CAQ5B;IAEM,eAAe,IAAI,MAAM;IA6BzB,sBAAsB,IAAI,OAAO;IASjC,OAAO,IAAI,OAAO;IAElB,WAAW,IAAI,OAAO;IAEtB,MAAM,IAAI,OAAO;IAEjB,KAAK,IAAI,OAAO;IAEhB,KAAK,IAAI,OAAO;IAEhB,SAAS,IAAI,OAAO;IAEpB,KAAK,IAAI,OAAO;IAEvB,4DAA4D;IAC5D;;OAEG;IACH,SAAS,CAAC,WAAW,IAAI,QAAQ;IAWjC;;;;;;OAMG;IACH,SAAS,CAAC,YAAY,CAAC,cAAc,EAAE,QAAQ,EAAE,SAAS,CAAC,EAAE,MAAM,GAAG,EAAE,CAAC,MAAM;IAsC/E;;;;;;OAMG;WACW,YAAY,CAAC,WAAW,EAAE,EAAE,CAAC,MAAM,GAAG,EAAE,CAAC,MAAM;IAM7D;;;;;OAKG;WACW,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO;IASxD;;;;;;;;OAQG;WACW,sBAAsB,CAClC,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,GACZ,EAAE,CAAC,MAAM;IAYL,uBAAuB,IAAI,wBAAwB;IAoBnD,mBAAmB,IAAI,sBAAsB;gBAIjC,GAAG,EAAE,EAAE,CAAC,MAAM;CA+ClC"}
package/src/utils/units-handler.js CHANGED
@@ -1,7 +1,7 @@
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  import * as DG from 'datagrok-api/dg';
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  import { candidateAlphabets } from './macromolecule/consts';
3
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  import { detectAlphabet, getSplitterForColumn, getSplitterWithSeparator, getStats, splitterAsFasta, splitterAsHelm } from './macromolecule/utils';
4
- import { mmDistanceFunctions, mmDistanceFunctionsNames } from '../distance-functions';
4
+ import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
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  /** Class for handling notation units in Macromolecule columns */
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  export class UnitsHandler {
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  static setUnitsToFastaColumn(col) {
@@ -220,18 +220,18 @@ export class UnitsHandler {
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  if (!this.isFasta())
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  throw new Error('Only FASTA notation is supported');
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  if (this.isMsa())
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- return mmDistanceFunctionsNames.HAMMING;
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+ return MmDistanceFunctionsNames.HAMMING;
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  switch (this.alphabet) {
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  // As DNA and RNA scoring matrices are same as identity matrices(mostly),
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  // we can use very fast and optimized Levenshtein distance library
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  case "DNA" /* ALPHABET.DNA */:
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  case "RNA" /* ALPHABET.RNA */:
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- return mmDistanceFunctionsNames.LEVENSHTEIN;
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+ return MmDistanceFunctionsNames.LEVENSHTEIN;
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  case "PT" /* ALPHABET.PT */:
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- return mmDistanceFunctionsNames.NEEDLEMANN_WUNSCH;
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+ return MmDistanceFunctionsNames.NEEDLEMANN_WUNSCH;
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  // For default case, let's use Levenshtein distance
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  default:
234
- return mmDistanceFunctionsNames.LEVENSHTEIN;
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+ return MmDistanceFunctionsNames.LEVENSHTEIN;
235
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  }
236
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  }
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  getDistanceFunction() {
package/src/utils/units-handler.js.map CHANGED
@@ -1 +1 @@
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package/src/distance-functions/hamming.d.ts DELETED
@@ -1,3 +0,0 @@
1
- import { mmDistanceFunctionType } from './types';
2
- export declare function hamming(): mmDistanceFunctionType;
3
- //# sourceMappingURL=hamming.d.ts.map
package/src/distance-functions/hamming.d.ts.map DELETED
@@ -1 +0,0 @@
1
- {"version":3,"file":"hamming.d.ts","sourceRoot":"","sources":["hamming.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,sBAAsB,EAAC,MAAM,SAAS,CAAC;AAE/C,wBAAgB,OAAO,IAAI,sBAAsB,CAehD"}
package/src/distance-functions/hamming.js DELETED
@@ -1,16 +0,0 @@
1
- export function hamming() {
2
- return (seq1, seq2) => {
3
- // hamming distance should only be used with same size strings,
4
- // but still, lets add a check and if they are not same length add the difference to the result
5
- let diff = 0;
6
- if (seq1.length !== seq2.length)
7
- diff = Math.abs(seq1.length - seq2.length);
8
- let result = 0;
9
- for (let i = 0; i < Math.min(seq1.length, seq2.length); i++) {
10
- if (seq1[i] !== seq2[i])
11
- result++;
12
- }
13
- return result + diff;
14
- };
15
- }
16
- //# sourceMappingURL=hamming.js.map
package/src/distance-functions/hamming.js.map DELETED
@@ -1 +0,0 @@
1
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package/src/distance-functions/index.d.ts DELETED
@@ -1,2 +0,0 @@
1
- export { mmDistanceFunctionsNames, mmDistanceFunctions } from './macromolecule-distance-functions';
2
- //# sourceMappingURL=index.d.ts.map
package/src/distance-functions/index.d.ts.map DELETED
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package/src/distance-functions/index.js DELETED
@@ -1,2 +0,0 @@
1
- export { mmDistanceFunctionsNames, mmDistanceFunctions } from './macromolecule-distance-functions';
2
- //# sourceMappingURL=index.js.map
package/src/distance-functions/index.js.map DELETED
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package/src/distance-functions/levenstein.d.ts DELETED
@@ -1,3 +0,0 @@
1
- import { mmDistanceFunctionType } from './types';
2
- export declare function levenstein(): mmDistanceFunctionType;
3
- //# sourceMappingURL=levenstein.d.ts.map
package/src/distance-functions/levenstein.d.ts.map DELETED
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package/src/distance-functions/levenstein.js DELETED
@@ -1,7 +0,0 @@
1
- import { distance } from 'fastest-levenshtein';
2
- export function levenstein() {
3
- return (seq1, seq2) => {
4
- return distance(seq1, seq2);
5
- };
6
- }
7
- //# sourceMappingURL=levenstein.js.map
package/src/distance-functions/levenstein.js.map DELETED
@@ -1 +0,0 @@
1
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package/src/distance-functions/macromolecule-distance-functions.d.ts DELETED
@@ -1,13 +0,0 @@
1
- import { mmDistanceFunctionType } from './types';
2
- /** Enum containing currently supported macromolecule distance functions
3
- * Hamming distance will be used if the sequences are already aligned
4
- * Needleman distance will be used for protein sequences with known BLOSUM62 matrix
5
- * Levenshtein distance will be used for nucleotide sequences as for them substitution matrix is same as identity matrix
6
- */
7
- export declare enum mmDistanceFunctionsNames {
8
- HAMMING = "Hamming",
9
- LEVENSHTEIN = "Levenshtein",
10
- NEEDLEMANN_WUNSCH = "Needlemann-Wunsch"
11
- }
12
- export declare const mmDistanceFunctions: Record<mmDistanceFunctionsNames, (value?: any) => mmDistanceFunctionType>;
13
- //# sourceMappingURL=macromolecule-distance-functions.d.ts.map
package/src/distance-functions/macromolecule-distance-functions.d.ts.map DELETED
@@ -1 +0,0 @@
1
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package/src/distance-functions/macromolecule-distance-functions.js DELETED
@@ -1,21 +0,0 @@
1
- import { hamming } from './hamming';
2
- import { levenstein } from './levenstein';
3
- import { needlemanWunch } from './needleman-wunsch';
4
- /** Enum containing currently supported macromolecule distance functions
5
- * Hamming distance will be used if the sequences are already aligned
6
- * Needleman distance will be used for protein sequences with known BLOSUM62 matrix
7
- * Levenshtein distance will be used for nucleotide sequences as for them substitution matrix is same as identity matrix
8
- */
9
- export var mmDistanceFunctionsNames;
10
- (function (mmDistanceFunctionsNames) {
11
- mmDistanceFunctionsNames["HAMMING"] = "Hamming";
12
- mmDistanceFunctionsNames["LEVENSHTEIN"] = "Levenshtein";
13
- mmDistanceFunctionsNames["NEEDLEMANN_WUNSCH"] = "Needlemann-Wunsch";
14
- })(mmDistanceFunctionsNames || (mmDistanceFunctionsNames = {}));
15
- ;
16
- export const mmDistanceFunctions = {
17
- [mmDistanceFunctionsNames.HAMMING]: hamming,
18
- [mmDistanceFunctionsNames.LEVENSHTEIN]: levenstein,
19
- [mmDistanceFunctionsNames.NEEDLEMANN_WUNSCH]: needlemanWunch
20
- };
21
- //# sourceMappingURL=macromolecule-distance-functions.js.map
package/src/distance-functions/macromolecule-distance-functions.js.map DELETED
@@ -1 +0,0 @@
1
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package/src/distance-functions/needleman-wunsch.d.ts DELETED
@@ -1,13 +0,0 @@
1
- import { mmDistanceFunctionType } from './types';
2
- interface needlemanWunchArgs {
3
- gapOpen: number;
4
- gapExtend: number;
5
- scoringMatrix: number[][];
6
- alphabetIndexes: {
7
- [id: string]: number;
8
- };
9
- }
10
- /** Returns a function that calculates the distance between two sequences based on gap penalty and matrix */
11
- export declare function needlemanWunch(args: Partial<needlemanWunchArgs>): mmDistanceFunctionType;
12
- export {};
13
- //# sourceMappingURL=needleman-wunsch.d.ts.map
package/src/distance-functions/needleman-wunsch.d.ts.map DELETED
@@ -1 +0,0 @@
1
- {"version":3,"file":"needleman-wunsch.d.ts","sourceRoot":"","sources":["needleman-wunsch.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,sBAAsB,EAAC,MAAM,SAAS,CAAC;AAoC/C,UAAU,kBAAkB;IAC1B,OAAO,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,aAAa,EAAE,MAAM,EAAE,EAAE,CAAC;IAC1B,eAAe,EAAE;QAAC,CAAC,EAAE,EAAC,MAAM,GAAE,MAAM,CAAA;KAAC,CAAC;CACvC;AASD,4GAA4G;AAC5G,wBAAgB,cAAc,CAAC,IAAI,EAAE,OAAO,CAAC,kBAAkB,CAAC,GAAG,sBAAsB,CAqDxF"}
package/src/distance-functions/needleman-wunsch.js DELETED
@@ -1,90 +0,0 @@
1
- // Blosum 62 matrix for protein sequences
2
- const BLOSUM62 = [[4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4],
3
- [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4],
4
- [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4],
5
- [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4],
6
- [0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4],
7
- [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4],
8
- [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4],
9
- [0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4],
10
- [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4],
11
- [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4],
12
- [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4],
13
- [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4],
14
- [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4],
15
- [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4],
16
- [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4],
17
- [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4],
18
- [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4],
19
- [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4],
20
- [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4],
21
- [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4],
22
- [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4],
23
- [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4],
24
- [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4],
25
- [-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1]];
26
- // Protein indexes for BLOSUM matrix
27
- const ProtIndexes = {
28
- 'A': 0, 'R': 1, 'N': 2, 'D': 3, 'C': 4, 'Q': 5, 'E': 6, 'G': 7, 'H': 8,
29
- 'I': 9, 'L': 10, 'K': 11, 'M': 12, 'F': 13, 'P': 14, 'S': 15, 'T': 16,
30
- 'W': 17, 'Y': 18, 'V': 19, 'B': 20, 'Z': 21, 'X': 22, '*': 23
31
- };
32
- const defaultArgs = {
33
- gapOpen: 8,
34
- gapExtend: 2,
35
- scoringMatrix: BLOSUM62,
36
- alphabetIndexes: ProtIndexes
37
- };
38
- /** Returns a function that calculates the distance between two sequences based on gap penalty and matrix */
39
- export function needlemanWunch(args) {
40
- return (seq1, seq2) => {
41
- const { gapOpen, gapExtend, scoringMatrix, alphabetIndexes } = Object.assign(Object.assign({}, defaultArgs), args);
42
- // As we don't need traceback, no need to store the whole matrix
43
- // Intead, we will store only the last two rows
44
- const matrix = [
45
- new Array(seq1.length + 1).fill(0),
46
- new Array(seq1.length + 1).fill(0)
47
- ];
48
- // similarly, we need to keep track of what operation led to the current cell
49
- // i.e. whether we came from the left, top or diagonal to assign gap open/gap extend penalty
50
- const verticalGaps = new Array(seq1.length + 1).fill(false);
51
- const horizontalGaps = new Array(seq1.length + 1).fill(false);
52
- //variables to keep track which row we are in
53
- // they will swap places on each iteration
54
- let prevRow = 0;
55
- let currRow = 1;
56
- // Initialize first row
57
- for (let i = 0; i < seq1.length + 1; i++)
58
- matrix[0][i] = -gapOpen - i * gapExtend;
59
- // Calculate the rest of the matrix
60
- for (let i = 1; i < seq2.length + 1; i++) {
61
- matrix[currRow][0] = -gapOpen - (i - 1) * gapExtend;
62
- for (let j = 1; j < seq1.length + 1; j++) {
63
- const diagonal = matrix[prevRow][j - 1] + scoringMatrix[alphabetIndexes[seq1[j - 1]]][alphabetIndexes[seq2[i - 1]]];
64
- const top = matrix[prevRow][j] - (verticalGaps[j] ? gapExtend : gapOpen);
65
- const left = matrix[currRow][j - 1] - (horizontalGaps[j - 1] ? gapExtend : gapOpen);
66
- matrix[currRow][j] = Math.max(diagonal, left, top);
67
- // update gap arrays
68
- if (matrix[currRow][j] === diagonal) {
69
- verticalGaps[j] = false;
70
- horizontalGaps[j] = false;
71
- }
72
- else if (matrix[currRow][j] === left) {
73
- verticalGaps[j] = false;
74
- horizontalGaps[j] = true;
75
- }
76
- else {
77
- verticalGaps[j] = true;
78
- horizontalGaps[j] = false;
79
- }
80
- }
81
- // Swap rows
82
- prevRow = currRow;
83
- currRow = (currRow + 1) % 2;
84
- }
85
- // as the matrix is the similarity matrix, but we are interested in distance,
86
- // we need to invert the result
87
- return -matrix[prevRow][seq1.length];
88
- };
89
- }
90
- //# sourceMappingURL=needleman-wunsch.js.map
package/src/distance-functions/needleman-wunsch.js.map DELETED
@@ -1 +0,0 @@
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package/src/distance-functions/types.d.ts DELETED
@@ -1,2 +0,0 @@
1
- export type mmDistanceFunctionType = (seq1: string, seq2: string) => number;
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- //# sourceMappingURL=types.d.ts.map
package/src/distance-functions/types.d.ts.map DELETED
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- {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAAA,MAAM,MAAM,sBAAsB,GAAG,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,KAAK,MAAM,CAAC"}
package/src/distance-functions/types.js DELETED
@@ -1,2 +0,0 @@
1
- export {};
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- //# sourceMappingURL=types.js.map
package/src/distance-functions/types.js.map DELETED
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- {"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":""}