@datagrok-libraries/bio 5.29.1 → 5.29.2
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.
- package/.eslintrc.json +2 -1
- package/package.json +4 -3
- package/src/distance-functions/hamming.d.ts +3 -0
- package/src/distance-functions/hamming.d.ts.map +1 -0
- package/src/distance-functions/hamming.js +16 -0
- package/src/distance-functions/hamming.js.map +1 -0
- package/src/distance-functions/index.d.ts +2 -0
- package/src/distance-functions/index.d.ts.map +1 -0
- package/src/distance-functions/index.js +2 -0
- package/src/distance-functions/index.js.map +1 -0
- package/src/distance-functions/levenstein.d.ts +3 -0
- package/src/distance-functions/levenstein.d.ts.map +1 -0
- package/src/distance-functions/levenstein.js +7 -0
- package/src/distance-functions/levenstein.js.map +1 -0
- package/src/distance-functions/macromolecule-distance-functions.d.ts +13 -0
- package/src/distance-functions/macromolecule-distance-functions.d.ts.map +1 -0
- package/src/distance-functions/macromolecule-distance-functions.js +21 -0
- package/src/distance-functions/macromolecule-distance-functions.js.map +1 -0
- package/src/distance-functions/needleman-wunsch.d.ts +13 -0
- package/src/distance-functions/needleman-wunsch.d.ts.map +1 -0
- package/src/distance-functions/needleman-wunsch.js +90 -0
- package/src/distance-functions/needleman-wunsch.js.map +1 -0
- package/src/distance-functions/types.d.ts +2 -0
- package/src/distance-functions/types.d.ts.map +1 -0
- package/src/distance-functions/types.js +2 -0
- package/src/distance-functions/types.js.map +1 -0
- package/src/utils/units-handler.d.ts +4 -0
- package/src/utils/units-handler.d.ts.map +1 -1
- package/src/utils/units-handler.js +23 -0
- package/src/utils/units-handler.js.map +1 -1
package/.eslintrc.json
CHANGED
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@@ -17,7 +17,8 @@
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"rules": {
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"indent": ["error", 2, {"SwitchCase": 1}],
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"max-len": ["error", 120],
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"no-unused-vars": "
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"no-unused-vars": "off",
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"@typescript-eslint/no-unused-vars": "warn",
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"require-jsdoc": "off",
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"valid-jsdoc": "off",
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"spaced-comment": "off",
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package/package.json
CHANGED
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@@ -8,7 +8,7 @@
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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.
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"version": "5.29.2",
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"description": "",
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"dependencies": {
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"@datagrok-libraries/gridext": "^1.3.22",
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@@ -17,6 +17,7 @@
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"cash-dom": "latest",
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"datagrok-api": "^1.10.2",
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"dayjs": "latest",
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"fastest-levenshtein": "^1.0.16",
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"mjolnir.js": "^2.7.0",
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"rxjs": "^6.5.5",
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"wu": "latest"
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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 @datagrok-libraries/gridext",
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"build-bio": "git clean -f -
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"build": "git clean -f -
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"build-bio": "git clean -f -X -d ./src && tsc",
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"build": "git clean -f -X -d ./src && tsc",
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"lint": "eslint \"./src/**/*.ts\"",
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"lint-fix": "eslint \"./src/**/*.ts\" --fix"
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}
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@@ -0,0 +1 @@
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{"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"}
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export function hamming() {
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return (seq1, seq2) => {
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// hamming distance should only be used with same size strings,
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// but still, lets add a check and if they are not same length add the difference to the result
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let diff = 0;
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if (seq1.length !== seq2.length)
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diff = Math.abs(seq1.length - seq2.length);
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let result = 0;
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for (let i = 0; i < Math.min(seq1.length, seq2.length); i++) {
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if (seq1[i] !== seq2[i])
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result++;
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}
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return result + diff;
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};
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}
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//# sourceMappingURL=hamming.js.map
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{"version":3,"file":"hamming.js","sourceRoot":"","sources":["hamming.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,OAAO;IACrB,OAAO,CAAC,IAAY,EAAE,IAAY,EAAE,EAAE;QACpC,+DAA+D;QAC/D,+FAA+F;QAC/F,IAAI,IAAI,GAAG,CAAC,CAAC;QACb,IAAI,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM;YAC7B,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC;QAE7C,IAAI,MAAM,GAAG,CAAC,CAAC;QACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,EAAE;YAC3D,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC;gBACrB,MAAM,EAAE,CAAC;SACZ;QACD,OAAO,MAAM,GAAG,IAAI,CAAC;IACvB,CAAC,CAAC;AACJ,CAAC"}
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{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,wBAAwB,EAAE,mBAAmB,EAAC,MAAM,oCAAoC,CAAC"}
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{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,wBAAwB,EAAE,mBAAmB,EAAC,MAAM,oCAAoC,CAAC"}
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{"version":3,"file":"levenstein.d.ts","sourceRoot":"","sources":["levenstein.ts"],"names":[],"mappings":"AACA,OAAO,EAAC,sBAAsB,EAAC,MAAM,SAAS,CAAC;AAE/C,wBAAgB,UAAU,IAAI,sBAAsB,CAInD"}
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{"version":3,"file":"levenstein.js","sourceRoot":"","sources":["levenstein.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,QAAQ,EAAC,MAAM,qBAAqB,CAAC;AAG7C,MAAM,UAAU,UAAU;IACxB,OAAO,CAAC,IAAY,EAAE,IAAY,EAAE,EAAE;QACpC,OAAO,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAC;IAC9B,CAAC,CAAC;AACJ,CAAC"}
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import { mmDistanceFunctionType } from './types';
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/** Enum containing currently supported macromolecule distance functions
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* Hamming distance will be used if the sequences are already aligned
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* Needleman distance will be used for protein sequences with known BLOSUM62 matrix
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* Levenshtein distance will be used for nucleotide sequences as for them substitution matrix is same as identity matrix
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*/
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export declare enum mmDistanceFunctionsNames {
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HAMMING = "Hamming",
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LEVENSHTEIN = "Levenshtein",
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NEEDLEMANN_WUNSCH = "Needlemann-Wunsch"
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}
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export declare const mmDistanceFunctions: Record<mmDistanceFunctionsNames, (value?: any) => mmDistanceFunctionType>;
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//# sourceMappingURL=macromolecule-distance-functions.d.ts.map
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{"version":3,"file":"macromolecule-distance-functions.d.ts","sourceRoot":"","sources":["macromolecule-distance-functions.ts"],"names":[],"mappings":"AAGA,OAAO,EAAC,sBAAsB,EAAC,MAAM,SAAS,CAAC;AAE/C;;;;GAIG;AACH,oBAAY,wBAAwB;IAChC,OAAO,YAAY;IACnB,WAAW,gBAAgB;IAC3B,iBAAiB,sBAAsB;CAC1C;AAED,eAAO,MAAM,mBAAmB,EAAE,MAAM,CAAC,wBAAwB,EAAE,CAAC,KAAK,CAAC,EAAE,GAAG,KAAK,sBAAsB,CAIzG,CAAC"}
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import { hamming } from './hamming';
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import { levenstein } from './levenstein';
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import { needlemanWunch } from './needleman-wunsch';
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/** Enum containing currently supported macromolecule distance functions
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* Hamming distance will be used if the sequences are already aligned
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* Needleman distance will be used for protein sequences with known BLOSUM62 matrix
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* Levenshtein distance will be used for nucleotide sequences as for them substitution matrix is same as identity matrix
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*/
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export var mmDistanceFunctionsNames;
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(function (mmDistanceFunctionsNames) {
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mmDistanceFunctionsNames["HAMMING"] = "Hamming";
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mmDistanceFunctionsNames["LEVENSHTEIN"] = "Levenshtein";
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mmDistanceFunctionsNames["NEEDLEMANN_WUNSCH"] = "Needlemann-Wunsch";
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})(mmDistanceFunctionsNames || (mmDistanceFunctionsNames = {}));
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;
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export const mmDistanceFunctions = {
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[mmDistanceFunctionsNames.HAMMING]: hamming,
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[mmDistanceFunctionsNames.LEVENSHTEIN]: levenstein,
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[mmDistanceFunctionsNames.NEEDLEMANN_WUNSCH]: needlemanWunch
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};
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//# sourceMappingURL=macromolecule-distance-functions.js.map
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{"version":3,"file":"macromolecule-distance-functions.js","sourceRoot":"","sources":["macromolecule-distance-functions.ts"],"names":[],"mappings":"AAAA,OAAO,EAAC,OAAO,EAAC,MAAM,WAAW,CAAC;AAClC,OAAO,EAAC,UAAU,EAAC,MAAM,cAAc,CAAC;AACxC,OAAO,EAAC,cAAc,EAAC,MAAM,oBAAoB,CAAC;AAGlD;;;;GAIG;AACH,MAAM,CAAN,IAAY,wBAIX;AAJD,WAAY,wBAAwB;IAChC,+CAAmB,CAAA;IACnB,uDAA2B,CAAA;IAC3B,mEAAuC,CAAA;AAC3C,CAAC,EAJW,wBAAwB,KAAxB,wBAAwB,QAInC;AAAA,CAAC;AAEF,MAAM,CAAC,MAAM,mBAAmB,GAA8E;IAC5G,CAAC,wBAAwB,CAAC,OAAO,CAAC,EAAE,OAAO;IAC3C,CAAC,wBAAwB,CAAC,WAAW,CAAC,EAAE,UAAU;IAClD,CAAC,wBAAwB,CAAC,iBAAiB,CAAC,EAAE,cAAc;CAC7D,CAAC"}
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import { mmDistanceFunctionType } from './types';
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interface needlemanWunchArgs {
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gapOpen: number;
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gapExtend: number;
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scoringMatrix: number[][];
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alphabetIndexes: {
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[id: string]: number;
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};
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}
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/** Returns a function that calculates the distance between two sequences based on gap penalty and matrix */
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export declare function needlemanWunch(args: Partial<needlemanWunchArgs>): mmDistanceFunctionType;
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export {};
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//# sourceMappingURL=needleman-wunsch.d.ts.map
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{"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"}
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// Blosum 62 matrix for protein sequences
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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],
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[-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4],
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[-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4],
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[-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4],
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[0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4],
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[-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4],
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[-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4],
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[0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4],
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[-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4],
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[-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4],
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[-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4],
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[-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4],
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[-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4],
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[-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4],
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[-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4],
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[1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4],
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[0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4],
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[-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4],
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[-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4],
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[0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4],
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[-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4],
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[-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4],
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[0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4],
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[-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1]];
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// Protein indexes for BLOSUM matrix
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const ProtIndexes = {
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'A': 0, 'R': 1, 'N': 2, 'D': 3, 'C': 4, 'Q': 5, 'E': 6, 'G': 7, 'H': 8,
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'I': 9, 'L': 10, 'K': 11, 'M': 12, 'F': 13, 'P': 14, 'S': 15, 'T': 16,
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'W': 17, 'Y': 18, 'V': 19, 'B': 20, 'Z': 21, 'X': 22, '*': 23
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};
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const defaultArgs = {
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gapOpen: 8,
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gapExtend: 2,
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scoringMatrix: BLOSUM62,
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alphabetIndexes: ProtIndexes
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};
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/** Returns a function that calculates the distance between two sequences based on gap penalty and matrix */
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export function needlemanWunch(args) {
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+
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
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
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@@ -0,0 +1 @@
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|
|
1
|
+
{"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"}
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":""}
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|
@@ -1,6 +1,8 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import { NOTATION } from './macromolecule/consts';
|
|
3
3
|
import { SplitterFunc } from './macromolecule/types';
|
|
4
|
+
import { mmDistanceFunctionsNames } from '../distance-functions';
|
|
5
|
+
import { mmDistanceFunctionType } from '../distance-functions/types';
|
|
4
6
|
/** Class for handling notation units in Macromolecule columns */
|
|
5
7
|
export declare class UnitsHandler {
|
|
6
8
|
protected readonly _column: DG.Column;
|
|
@@ -72,6 +74,8 @@ export declare class UnitsHandler {
|
|
|
72
74
|
* @return {DG.Column}
|
|
73
75
|
*/
|
|
74
76
|
static getNewColumnFromParams(len: number, name: string, units: string): DG.Column;
|
|
77
|
+
getDistanceFunctionName(): mmDistanceFunctionsNames;
|
|
78
|
+
getDistanceFunction(): mmDistanceFunctionType;
|
|
75
79
|
constructor(col: DG.Column);
|
|
76
80
|
}
|
|
77
81
|
//# sourceMappingURL=units-handler.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
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;
|
|
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,MAAM,uBAAuB,CAAC;AACpF,OAAO,EAAC,sBAAsB,EAAC,MAAM,6BAA6B,CAAC;AAEnE,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"}
|
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import * as DG from 'datagrok-api/dg';
|
|
2
2
|
import { candidateAlphabets } from './macromolecule/consts';
|
|
3
3
|
import { detectAlphabet, getSplitterForColumn, getSplitterWithSeparator, getStats, splitterAsFasta, splitterAsHelm } from './macromolecule/utils';
|
|
4
|
+
import { mmDistanceFunctions, mmDistanceFunctionsNames } from '../distance-functions';
|
|
4
5
|
/** Class for handling notation units in Macromolecule columns */
|
|
5
6
|
export class UnitsHandler {
|
|
6
7
|
static setUnitsToFastaColumn(col) {
|
|
@@ -214,6 +215,28 @@ export class UnitsHandler {
|
|
|
214
215
|
newColumn.setTag(DG.TAGS.UNITS, units);
|
|
215
216
|
return newColumn;
|
|
216
217
|
}
|
|
218
|
+
getDistanceFunctionName() {
|
|
219
|
+
// TODO add support for helm and separator notation
|
|
220
|
+
if (!this.isFasta())
|
|
221
|
+
throw new Error('Only FASTA notation is supported');
|
|
222
|
+
if (this.isMsa())
|
|
223
|
+
return mmDistanceFunctionsNames.HAMMING;
|
|
224
|
+
switch (this.alphabet) {
|
|
225
|
+
// As DNA and RNA scoring matrices are same as identity matrices(mostly),
|
|
226
|
+
// we can use very fast and optimized Levenshtein distance library
|
|
227
|
+
case "DNA" /* ALPHABET.DNA */:
|
|
228
|
+
case "RNA" /* ALPHABET.RNA */:
|
|
229
|
+
return mmDistanceFunctionsNames.LEVENSHTEIN;
|
|
230
|
+
case "PT" /* ALPHABET.PT */:
|
|
231
|
+
return mmDistanceFunctionsNames.NEEDLEMANN_WUNSCH;
|
|
232
|
+
// For default case, let's use Levenshtein distance
|
|
233
|
+
default:
|
|
234
|
+
return mmDistanceFunctionsNames.LEVENSHTEIN;
|
|
235
|
+
}
|
|
236
|
+
}
|
|
237
|
+
getDistanceFunction() {
|
|
238
|
+
return mmDistanceFunctions[this.getDistanceFunctionName()]();
|
|
239
|
+
}
|
|
217
240
|
constructor(col) {
|
|
218
241
|
this._column = col;
|
|
219
242
|
const units = this._column.getTag(DG.TAGS.UNITS);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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