@datagrok-libraries/bio 5.29.0 → 5.29.2

package/src/utils/macromolecule/consts.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,0BAAkB,QAAQ;IACxB,KAAK,UAAU;IACf,SAAS,cAAc;IACvB,IAAI,SAAS;CACd;AAED,0BAAkB,SAAS;IACzB,OAAO,YAAY;IACnB,GAAG,QAAQ;CACZ;AAED,0BAAkB,QAAQ;IACxB,GAAG,QAAQ;IACX,GAAG,QAAQ;IACX,EAAE,OAAO;IACT,cAAc;IACd,EAAE,OAAO;CACV;AAED,0BAAkB,IAAI;IACpB,OAAO,YAAY;IACnB,QAAQ,aAAa;IACrB,YAAY,kBAAkB;IAC9B,mBAAmB,yBAAyB;IAC5C,SAAS,cAAc;CACxB;AAED,eAAO,MAAM,SAAS,EAAE,MAA8B,CAAC;AAEvD,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC"}

package/src/utils/macromolecule/consts.js

@@ -0,0 +1,20 @@
+import { CandidateType } from './types';
+export const monomerRe = /\[(\w+)\]|(\w)|(-)/g;
+export const Alphabets = new class {
+    constructor() {
+        this.fasta = {
+            peptide: new Set([
+                'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',
+                'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',
+            ]),
+            dna: new Set(['A', 'C', 'G', 'T']),
+            rna: new Set(['A', 'C', 'G', 'U']),
+        };
+    }
+}();
+export const candidateAlphabets = [
+    new CandidateType("PT" /* ALPHABET.PT */, Alphabets.fasta.peptide, 0.50),
+    new CandidateType("DNA" /* ALPHABET.DNA */, Alphabets.fasta.dna, 0.55),
+    new CandidateType("RNA" /* ALPHABET.RNA */, Alphabets.fasta.rna, 0.55),
+];
+//# sourceMappingURL=consts.js.map

package/src/utils/macromolecule/consts.js.map

@@ -0,0 +1 @@
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package/src/utils/macromolecule/index.d.ts

@@ -0,0 +1,4 @@
+export { SplitterFunc, } from './types';
+export { TAGS, NOTATION, ALPHABET, ALIGNMENT, } from './consts';
+export { getSplitter, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getStats, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, } from './utils';
+//# sourceMappingURL=index.d.ts.map

package/src/utils/macromolecule/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAIA,OAAO,EACL,YAAY,GAEb,MAAM,SAAS,CAAC;AAEjB,OAAO,EACL,IAAI,EACJ,QAAQ,EACR,QAAQ,EACR,SAAS,GACV,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,WAAW,EACX,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,QAAQ,EACR,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,GACjB,MAAM,SAAS,CAAC"}

package/src/utils/macromolecule/index.js

@@ -0,0 +1,2 @@
+export { getSplitter, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getStats, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, } from './utils';
+//# sourceMappingURL=index.js.map

package/src/utils/macromolecule/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAgBA,OAAO,EACL,WAAW,EACX,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,QAAQ,EACR,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,GACjB,MAAM,SAAS,CAAC"}

package/src/utils/macromolecule/types.d.ts

@@ -0,0 +1,23 @@
+export type SeqColStats = {
+    freq: MonomerFreqs;
+    sameLength: boolean;
+};
+export type SplitterFunc = (seq: string) => string[];
+export type MonomerFreqs = {
+    [m: string]: number;
+};
+/** Alphabet candidate type */
+export declare class CandidateType {
+    name: string;
+    alphabet: Set<string>;
+    cutoff: number;
+    constructor(name: string, alphabet: Set<string>, cutoff: number);
+}
+/** Alphabet candidate similarity type */
+export declare class CandidateSimType extends CandidateType {
+    freq: MonomerFreqs;
+    /** Cos, max = 1, min = 0 */
+    similarity: number;
+    constructor(candidate: CandidateType, freq: MonomerFreqs, similarity: number);
+}
+//# sourceMappingURL=types.d.ts.map

package/src/utils/macromolecule/types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAOA,MAAM,MAAM,WAAW,GAAG;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CAAA;AACrE,MAAM,MAAM,YAAY,GAAG,CAAC,GAAG,EAAE,MAAM,KAAK,MAAM,EAAE,CAAC;AACrD,MAAM,MAAM,YAAY,GAAG;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,CAAC;AAEnD,8BAA8B;AAC9B,qBAAa,aAAa;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;gBAEH,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,MAAM;CAKhE;AAED,yCAAyC;AACzC,qBAAa,gBAAiB,SAAQ,aAAa;IACjD,IAAI,EAAE,YAAY,CAAC;IACnB,4BAA4B;IAC5B,UAAU,EAAE,MAAM,CAAC;gBAEP,SAAS,EAAE,aAAa,EAAE,IAAI,EAAE,YAAY,EAAE,UAAU,EAAE,MAAM;CAK7E"}

package/src/utils/macromolecule/types.js

@@ -0,0 +1,17 @@
+/** Alphabet candidate type */
+export class CandidateType {
+    constructor(name, alphabet, cutoff) {
+        this.name = name;
+        this.alphabet = alphabet;
+        this.cutoff = cutoff;
+    }
+}
+/** Alphabet candidate similarity type */
+export class CandidateSimType extends CandidateType {
+    constructor(candidate, freq, similarity) {
+        super(candidate.name, candidate.alphabet, candidate.cutoff);
+        this.freq = freq;
+        this.similarity = similarity;
+    }
+}
+//# sourceMappingURL=types.js.map

package/src/utils/macromolecule/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAWA,8BAA8B;AAC9B,MAAM,OAAO,aAAa;IAKxB,YAAY,IAAY,EAAE,QAAqB,EAAE,MAAc;QAC7D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;QACzB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;IACvB,CAAC;CACF;AAED,yCAAyC;AACzC,MAAM,OAAO,gBAAiB,SAAQ,aAAa;IAKjD,YAAY,SAAwB,EAAE,IAAkB,EAAE,UAAkB;QAC1E,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,SAAS,CAAC,QAAQ,EAAE,SAAS,CAAC,MAAM,CAAC,CAAC;QAC5D,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC;QACjB,IAAI,CAAC,UAAU,GAAG,UAAU,CAAC;IAC/B,CAAC;CACF"}

package/src/utils/{macromolecule.d.ts → macromolecule/utils.d.ts}

@@ -1,37 +1,7 @@
 import * as DG from 'datagrok-api/dg';
-import { SeqPalette } from '../seq-palettes';
-/** enum type to simplify setting "user-friendly" notation if necessary */
-export declare const enum NOTATION {
-    FASTA = "fasta",
-    SEPARATOR = "separator",
-    HELM = "helm"
-}
-export declare const enum ALIGNMENT {
-    SEQ_MSA = "SEQ.MSA",
-    SEQ = "SEQ"
-}
-export declare const enum ALPHABET {
-    DNA = "DNA",
-    RNA = "RNA",
-    PT = "PT",
-    /** Unknown */
-    UN = "UN"
-}
-export declare const enum TAGS {
-    aligned = "aligned",
-    alphabet = "alphabet",
-    alphabetSize = ".alphabetSize",
-    alphabetIsMultichar = ".alphabetIsMultichar",
-    separator = "separator"
-}
-export type SeqColStats = {
-    freq: MonomerFreqs;
-    sameLength: boolean;
-};
-export type SplitterFunc = (seq: string) => string[];
-export type MonomerFreqs = {
-    [m: string]: number;
-};
+import { CandidateType, MonomerFreqs, SeqColStats, SplitterFunc } from './types';
+import { ALPHABET } from './consts';
+import { SeqPalette } from '../../seq-palettes';
 /** Stats of sequences with specified splitter func, returns { freq, sameLength }.
  * @param {DG.Column} seqCol
  * @param {number} minLength
@@ -39,7 +9,6 @@ export type MonomerFreqs = {
  * @return { SeqColStats }, sameLength: boolean } stats of column sequences
  */
 export declare function getStats(seqCol: DG.Column, minLength: number, splitter: SplitterFunc): SeqColStats;
-export declare const monomerRe: RegExp;
 /** Split sequence for single character monomers, square brackets multichar monomer names or gap symbol.
  * @param {any} seq object with sequence
  * @return {string[]} array of monomers
@@ -80,9 +49,6 @@ export declare function getAlphabet(alphabet: ALPHABET): Set<string>;
  * @return {number} Cosine similarity
  */
 export declare function getAlphabetSimilarity(freq: MonomerFreqs, alphabet: Set<string>, gapSymbol?: string): number;
-export declare const candidateAlphabets: [string, Set<string>, number][];
-/** Alphabet candidate type */
-type CandidateType = [string, Set<string>, number];
 /** From detectMacromolecule */
 export declare function detectAlphabet(freq: MonomerFreqs, candidates: CandidateType[], gapSymbol?: string): string;
 /** Selects a suitable palette based on column data
@@ -93,5 +59,4 @@ export declare function detectAlphabet(freq: MonomerFreqs, candidates: Candidate
 export declare function pickUpPalette(seqCol: DG.Column, minLength?: number): SeqPalette;
 export declare function getPaletteByType(paletteType: string): SeqPalette;
 export declare function pickUpSeqCol(df: DG.DataFrame): DG.Column | null;
-export {};
-//# sourceMappingURL=macromolecule.d.ts.map
+//# sourceMappingURL=utils.d.ts.map

package/src/utils/macromolecule/utils.d.ts.map

@@ -0,0 +1 @@
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package/src/utils/{macromolecule.js → macromolecule/utils.js}

@@ -1,12 +1,13 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
+import { CandidateSimType } from './types';
+import { Alphabets, candidateAlphabets, monomerRe } from './consts';
+import { UnitsHandler } from '../units-handler';
 import { Vector } from '@datagrok-libraries/utils/src/type-declarations';
-import { vectorLength, vectorDotProduct } from '@datagrok-libraries/utils/src/vector-operations';
-import { AminoacidsPalettes } from '../aminoacids';
-import { NucleotidesPalettes } from '../nucleotides';
-import { UnknownSeqPalettes } from '../unknown';
-import { UnitsHandler } from '../utils/units-handler';
-;
+import { vectorDotProduct, vectorLength } from '@datagrok-libraries/utils/src/vector-operations';
+import { AminoacidsPalettes } from '../../aminoacids';
+import { NucleotidesPalettes } from '../../nucleotides';
+import { UnknownSeqPalettes } from '../../unknown';
 /** Stats of sequences with specified splitter func, returns { freq, sameLength }.
  * @param {DG.Column} seqCol
  * @param {number} minLength
@@ -33,7 +34,6 @@ export function getStats(seqCol, minLength, splitter) {
     }
     return { freq: freq, sameLength: sameLength };
 }
-export const monomerRe = /\[(\w+)\]|(\w)|(-)/g;
 /** Split sequence for single character monomers, square brackets multichar monomer names or gap symbol.
  * @param {any} seq object with sequence
  * @return {string[]} array of monomers
@@ -119,11 +119,11 @@ export function monomerToShort(amino, maxLengthOfMonomer) {
 export function getAlphabet(alphabet) {
     switch (alphabet) {
         case "DNA" /* ALPHABET.DNA */:
-            return UnitsHandler.DnaFastaAlphabet;
+            return Alphabets.fasta.dna;
         case "RNA" /* ALPHABET.RNA */:
-            return UnitsHandler.RnaFastaAlphabet;
+            return Alphabets.fasta.rna;
         case "PT" /* ALPHABET.PT */:
-            return UnitsHandler.PeptideFastaAlphabet;
+            return Alphabets.fasta.peptide;
         default:
             throw new Error(`Unsupported alphabet '${alphabet}'.`);
     }
@@ -148,22 +148,17 @@ export function getAlphabetSimilarity(freq, alphabet, gapSymbol = '-') {
     const alphabetV = new Vector(alphabetA);
     return vectorDotProduct(freqV, alphabetV) / (vectorLength(freqV) * vectorLength(alphabetV));
 }
-export const candidateAlphabets = [
-    ["PT" /* ALPHABET.PT */, UnitsHandler.PeptideFastaAlphabet, 0.50],
-    ["DNA" /* ALPHABET.DNA */, UnitsHandler.DnaFastaAlphabet, 0.55],
-    ["RNA" /* ALPHABET.RNA */, UnitsHandler.RnaFastaAlphabet, 0.55],
-];
 /** From detectMacromolecule */
 export function detectAlphabet(freq, candidates, gapSymbol = '-') {
     const candidatesSims = candidates.map((c) => {
-        const sim = getAlphabetSimilarity(freq, c[1], gapSymbol);
-        return [c[0], c[1], c[2], freq, sim];
+        const sim = getAlphabetSimilarity(freq, c.alphabet, gapSymbol);
+        return new CandidateSimType(c, freq, sim);
     });
     let alphabetName;
-    const maxSim = Math.max(...candidatesSims.map((cs) => cs[4] > cs[2] ? cs[4] : -1));
+    const maxSim = Math.max(...candidatesSims.map((cs) => cs.similarity > cs.cutoff ? cs.similarity : -1));
     if (maxSim > 0) {
-        const sim = candidatesSims.find((cs) => cs[4] === maxSim);
-        alphabetName = sim[0];
+        const sim = candidatesSims.find((cs) => cs.similarity === maxSim);
+        alphabetName = sim.name;
     }
     else {
         alphabetName = "UN" /* ALPHABET.UN */;
@@ -190,11 +185,10 @@ export function pickUpPalette(seqCol, minLength = 5) {
 }
 export function getPaletteByType(paletteType) {
     switch (paletteType) {
-        case 'PT':
+        case "PT" /* ALPHABET.PT */:
             return AminoacidsPalettes.GrokGroups;
-        case 'NT':
-        case 'DNA':
-        case 'RNA':
+        case "DNA" /* ALPHABET.DNA */:
+        case "RNA" /* ALPHABET.RNA */:
             return NucleotidesPalettes.Chromatogram;
         // other
         default:
@@ -212,4 +206,4 @@ export function pickUpSeqCol(df) {
         resCol = semTypeColList[0];
     return resCol;
 }
-//# sourceMappingURL=macromolecule.js.map
+//# sourceMappingURL=utils.js.map

package/src/utils/macromolecule/utils.js.map

@@ -0,0 +1 @@
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package/src/utils/notation-converter.d.ts

@@ -1,6 +1,7 @@
 import * as DG from 'datagrok-api/dg';
 import { UnitsHandler } from './units-handler';
-import { NOTATION, SplitterFunc } from './macromolecule';
+import { SplitterFunc } from './macromolecule/types';
+import { NOTATION } from './macromolecule/consts';
 /** Class for handling conversion of notation systems in Macromolecule columns */
 export declare class NotationConverter extends UnitsHandler {
     private _splitter;

package/src/utils/notation-converter.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"notation-converter.d.ts","sourceRoot":"","sources":["notation-converter.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,YAAY,EAAC,MAAM,iBAAiB,CAAC;AAC7C,OAAO,EAAc,YAAY,EAAC,MAAM,uBAAuB,CAAC;AAChE,OAAO,EAAC,QAAQ,EAAO,MAAM,wBAAwB,CAAC;AAGtD,iFAAiF;AACjF,qBAAa,iBAAkB,SAAQ,YAAY;IACjD,OAAO,CAAC,SAAS,CAA6B;IAE9C,SAAS,KAAK,QAAQ,IAAI,YAAY,CAIrC;IAEM,OAAO,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE1C,WAAW,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAE9C,MAAM,CAAC,cAAc,EAAE,QAAQ,GAAG,OAAO;IAEhD;;;;;;OAMG;IACH,OAAO,CAAC,uBAAuB;IAmB/B;;;;;OAKG;IACH,OAAO,CAAC,eAAe;IAiBvB,OAAO,CAAC,mBAAmB;IAkB3B;;;;;;;OAOG;IACI,mBAAmB,CACxB,aAAa,EAAE,MAAM,EACrB,eAAe,GAAE,MAAM,GAAG,IAAW,GACpC,MAAM;IAOT;;;;;OAKG;IACH,OAAO,CAAC,aAAa;IAgBrB;;;;;OAKG;IACH,OAAO,CAAC,uBAAuB;IA6B/B;;;;;;;;;OASG;IACI,2BAA2B,CAChC,WAAW,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,GACrF,MAAM;IAgCT;;;;;;;;OAQG;IACH,OAAO,CAAC,WAAW;IAsBnB,OAAO,CAAC,sBAAsB;IAK9B;;;;;OAKG;IACI,OAAO,CAAC,WAAW,EAAE,QAAQ,EAAE,YAAY,GAAE,MAAM,GAAG,IAAW,GAAG,EAAE,CAAC,MAAM;gBAsBjE,GAAG,EAAE,EAAE,CAAC,MAAM;CAGlC"}

package/src/utils/notation-converter.js

@@ -1,6 +1,6 @@
 import * as DG from 'datagrok-api/dg';
 import { UnitsHandler } from './units-handler';
-import { getSplitterForColumn, getStats } from './macromolecule';
+import { getSplitterForColumn, getStats } from './macromolecule/utils';
 /** Class for handling conversion of notation systems in Macromolecule columns */
 export class NotationConverter extends UnitsHandler {
     get splitter() {

package/src/utils/notation-converter.js.map

@@ -1 +1 @@
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package/src/utils/splitter.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"splitter.d.ts","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAItC,wBAAgB,qBAAqB,CAAC,cAAc,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,SAAS,CA0BrF"}
+{"version":3,"file":"splitter.d.ts","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,wBAAgB,qBAAqB,CAAC,cAAc,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,SAAS,CA0BrF"}

package/src/utils/splitter.js

@@ -1,5 +1,5 @@
 import * as DG from 'datagrok-api/dg';
-import { getSplitterForColumn } from './macromolecule';
+import { getSplitterForColumn } from './macromolecule/utils';
 export function splitAlignedSequences(sequenceColumn) {
     const splitter = getSplitterForColumn(sequenceColumn);
     const getCol = (index) => { var _a; return (_a = columnList[index]) !== null && _a !== void 0 ? _a : null; };

package/src/utils/splitter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"splitter.js","sourceRoot":"","sources":["splitter.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,oBAAoB,EAAC,MAAM,uBAAuB,CAAC;AAG3D,MAAM,UAAU,qBAAqB,CAAC,cAAiC;IACrE,MAAM,QAAQ,GAAG,oBAAoB,CAAC,cAAc,CAAC,CAAC;IACtD,MAAM,MAAM,GAAG,CAAC,KAAa,EAA4B,EAAE,WAAC,OAAA,MAAA,UAAU,CAAC,KAAK,CAAC,mCAAI,IAAI,CAAA,EAAA,CAAC;IACtF,MAAM,SAAS,GAAG,CAAC,KAAa,EAAqB,EAAE;QACrD,MAAM,WAAW,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;QAC1E,UAAU,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;QAC7B,OAAO,WAAW,CAAC;IACrB,CAAC,CAAC;IAEF,MAAM,UAAU,GAAwB,EAAE,CAAC;IAC3C,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,CAAC;IACvC,MAAM,QAAQ,GAAG,EAAE,CAAC,SAAS,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;IAE/C,KAAK,IAAI,QAAQ,GAAG,CAAC,EAAE,QAAQ,GAAG,QAAQ,EAAE,EAAE,QAAQ,EAAE;QACtD,MAAM,QAAQ,GAAG,cAAc,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC9C,IAAI,QAAQ,IAAI,IAAI;YAClB,SAAS;QAEX,MAAM,kBAAkB,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC;QAC9C,kBAAkB,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,aAAa,EAAE,EAAE;YACpD,MAAM,GAAG,GAAG,MAAM,CAAC,aAAa,CAAC,IAAI,SAAS,CAAC,aAAa,CAAC,CAAC;YAC9D,GAAG,CAAC,GAAG,CAAC,QAAQ,EAAE,OAAO,IAAI,GAAG,EAAE,KAAK,CAAC,CAAC;QAC3C,CAAC,CAAC,CAAC;KACJ;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC"}

package/src/utils/units-handler.d.ts

@@ -1,5 +1,8 @@
 import * as DG from 'datagrok-api/dg';
-import { NOTATION, SplitterFunc } from './macromolecule';
+import { NOTATION } from './macromolecule/consts';
+import { SplitterFunc } from './macromolecule/types';
+import { mmDistanceFunctionsNames } from '../distance-functions';
+import { mmDistanceFunctionType } from '../distance-functions/types';
 /** Class for handling notation units in Macromolecule columns */
 export declare class UnitsHandler {
     protected readonly _column: DG.Column;
@@ -11,9 +14,6 @@ export declare class UnitsHandler {
         SEPARATOR: string;
         FASTA: string;
     };
-    static readonly PeptideFastaAlphabet: Set<string>;
-    static readonly DnaFastaAlphabet: Set<string>;
-    static readonly RnaFastaAlphabet: Set<string>;
     static setUnitsToFastaColumn(col: DG.Column): void;
     static setUnitsToSeparatorColumn(col: DG.Column, separator?: string): void;
     static setUnitsToHelmColumn(col: DG.Column): void;
@@ -74,6 +74,8 @@ export declare class UnitsHandler {
      * @return {DG.Column}
      */
     static getNewColumnFromParams(len: number, name: string, units: string): DG.Column;
+    getDistanceFunctionName(): mmDistanceFunctionsNames;
+    getDistanceFunction(): mmDistanceFunctionType;
     constructor(col: DG.Column);
 }
 //# sourceMappingURL=units-handler.d.ts.map

package/src/utils/units-handler.d.ts.map

@@ -1 +1 @@
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+{"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"}

package/src/utils/units-handler.js

@@ -1,5 +1,7 @@
 import * as DG from 'datagrok-api/dg';
-import { candidateAlphabets, detectAlphabet, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getSplitterForColumn, getStats, } from './macromolecule';
+import { candidateAlphabets } from './macromolecule/consts';
+import { detectAlphabet, getSplitterForColumn, getSplitterWithSeparator, getStats, splitterAsFasta, splitterAsHelm } from './macromolecule/utils';
+import { mmDistanceFunctions, mmDistanceFunctionsNames } from '../distance-functions';
 /** Class for handling notation units in Macromolecule columns */
 export class UnitsHandler {
     static setUnitsToFastaColumn(col) {
@@ -213,6 +215,28 @@ export class UnitsHandler {
         newColumn.setTag(DG.TAGS.UNITS, units);
         return newColumn;
     }
+    getDistanceFunctionName() {
+        // TODO add support for helm and separator notation
+        if (!this.isFasta())
+            throw new Error('Only FASTA notation is supported');
+        if (this.isMsa())
+            return mmDistanceFunctionsNames.HAMMING;
+        switch (this.alphabet) {
+            // As DNA and RNA scoring matrices are same as identity matrices(mostly),
+            // we can use very fast and optimized Levenshtein distance library
+            case "DNA" /* ALPHABET.DNA */:
+            case "RNA" /* ALPHABET.RNA */:
+                return mmDistanceFunctionsNames.LEVENSHTEIN;
+            case "PT" /* ALPHABET.PT */:
+                return mmDistanceFunctionsNames.NEEDLEMANN_WUNSCH;
+            // For default case, let's use Levenshtein distance
+            default:
+                return mmDistanceFunctionsNames.LEVENSHTEIN;
+        }
+    }
+    getDistanceFunction() {
+        return mmDistanceFunctions[this.getDistanceFunctionName()]();
+    }
     constructor(col) {
         this._column = col;
         const units = this._column.getTag(DG.TAGS.UNITS);
@@ -266,10 +290,4 @@ UnitsHandler._defaultGapSymbolsDict = {
     SEPARATOR: '',
     FASTA: '-',
 };
-UnitsHandler.PeptideFastaAlphabet = new Set([
-    'G', 'L', 'Y', 'S', 'E', 'Q', 'D', 'N', 'F', 'A',
-    'K', 'R', 'H', 'C', 'V', 'P', 'W', 'I', 'M', 'T',
-]);
-UnitsHandler.DnaFastaAlphabet = new Set(['A', 'C', 'G', 'T']);
-UnitsHandler.RnaFastaAlphabet = new Set(['A', 'C', 'G', 'U']);
 //# sourceMappingURL=units-handler.js.map

package/src/utils/units-handler.js.map

@@ -1 +1 @@
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package/test-dependant-packages.cmd

@@ -0,0 +1,27 @@
+@echo on
+call ./setup-unlink-clean.sh
+
+set base_dir=%cd%
+
+set libDirs=^
+\..\..\js-api\ ^
+\
+
+set packageDirs=^
+\..\..\packages\Bio\ ^
+\..\..\packages\BiostructureViewer\ ^
+\..\..\packages\Dendrogram\ ^
+\..\..\packages\Peptides\ ^
+\..\..\packages\PhyloTreeViewer\
+rem \..\..\packages\SequenceTranslator\
+rem \..\..\packages\Helm
+
+for %%p in (%libDirs%) do cd %base_dir%\%%p & call npm install & if %errorlevel% neq 0 cmd /k
+for %%p in (%libDirs%) do cd %base_dir%\%%p & call npm link datagrok-api & if %errorlevel% neq 0 cmd /k
+for %%p in (%libDirs%) do cd %base_dir%\%%p & call npm run build & if %errorlevel% neq 0 cmd /k
+for %%p in (%libDirs%) do cd %base_dir%\%%p & call npm link & if %errorlevel% neq 0 cmd /k
+
+for %%p in (%packageDirs%) do cd %base_dir%\%%p & call npm install & if %errorlevel% neq 0 cmd /k
+for %%p in (%packageDirs%) do cd %base_dir%\%%p & call npm link datagrok-api @datagrok-libraries/bio & if %errorlevel% neq 0 cmd /k
+for %%p in (%packageDirs%) do cd %base_dir%\%%p & call npm run build & if %errorlevel% neq 0 cmd /k
+for %%p in (%packageDirs%) do cd %base_dir%\%%p & call grok test --skip-build --host local & if %errorlevel% neq 0 cmd /k

package/src/utils/macromolecule.d.ts.map

@@ -1 +0,0 @@
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package/src/utils/macromolecule.js.map

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