npm - @datagrok-libraries/bio - Versions diffs - 5.37.0 → 5.38.1 - Mend

@datagrok-libraries/bio 5.37.0 → 5.38.1

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Files changed (29) hide show

package/CHANGELOG.md +11 -0
package/package.json +1 -1
package/src/monomer-works/to-atomic-level.d.ts.map +1 -1
package/src/monomer-works/to-atomic-level.js +17 -27
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/utils/macromolecule/consts.d.ts +5 -1
package/src/utils/macromolecule/consts.d.ts.map +1 -1
package/src/utils/macromolecule/consts.js +1 -0
package/src/utils/macromolecule/consts.js.map +1 -1
package/src/utils/macromolecule/index.d.ts +1 -1
package/src/utils/macromolecule/index.d.ts.map +1 -1
package/src/utils/macromolecule/index.js +1 -1
package/src/utils/macromolecule/index.js.map +1 -1
package/src/utils/macromolecule/scoring.d.ts +1 -1
package/src/utils/macromolecule/scoring.d.ts.map +1 -1
package/src/utils/macromolecule/scoring.js +1 -1
package/src/utils/macromolecule/scoring.js.map +1 -1
package/src/utils/units-handler.d.ts +42 -3
package/src/utils/units-handler.d.ts.map +1 -1
package/src/utils/units-handler.js +218 -3
package/src/utils/units-handler.js.map +1 -1
package/src/viewers/web-logo.d.ts +0 -3
package/src/viewers/web-logo.d.ts.map +1 -1
package/src/viewers/web-logo.js +1 -4
package/src/viewers/web-logo.js.map +1 -1
package/src/utils/notation-converter.d.ts +0 -34
package/src/utils/notation-converter.d.ts.map +0 -1
package/src/utils/notation-converter.js +0 -147
package/src/utils/notation-converter.js.map +0 -1

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,16 @@
 # bio changelog
+## 5.38.0 (2023-09-06)
+### Features
+* Add UnitsHandler `maxLength`, `posList`, `splitter` properties.
+* Add UnitsHandler `getJoiner`, `getConverter` methods, granulate joiners and converters methods.
+### Breaking changes
+* Remove NotationConverter class, merge functionality into UnitsHandler.
 ## 5.37.0 (2023-08-30)
 ### Features

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.37.0",
+  "version": "5.38.1",
   "description": "",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.64",

package/src/monomer-works/to-atomic-level.d.ts.map CHANGED Viewed

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package/src/monomer-works/to-atomic-level.js CHANGED Viewed

@@ -2,9 +2,7 @@
 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import { errorToConsole } from '@datagrok-libraries/utils';
 import { NOTATION } from '../utils/macromolecule/consts';
-import { NotationConverter } from '../utils/notation-converter';
 import { UnitsHandler } from '../utils/units-handler';
 import { getFormattedMonomerLib, keepPrecision } from './to-atomic-level-utils';
 import { seqToMolFileWorker } from './seq-to-molfile';
@@ -30,8 +28,7 @@ export async function _toAtomicLevel(df, seqCol, monomerLib) {
     const seqUh = UnitsHandler.getOrCreate(seqCol);
     // convert 'helm' to 'separator' units
     if (seqUh.isHelm()) {
-        const converter = new NotationConverter(seqCol);
-        srcCol = converter.convert(NOTATION.SEPARATOR, '.');
+        srcCol = seqUh.convert(NOTATION.SEPARATOR, '.');
         srcCol.name = seqCol.name; // Replace converted col name 'separator(<original>)' to '<original>';
     }
     const srcUh = UnitsHandler.getOrCreate(srcCol);
@@ -39,12 +36,10 @@ export async function _toAtomicLevel(df, seqCol, monomerLib) {
     // determine the polymer type according to HELM specifications
     let polymerType;
     // todo: an exception from dart comes before this check if the alphabet is UN
-    if (alphabet === "PT" /* ALPHABET.PT */ || alphabet === "UN" /* ALPHABET.UN */) {
+    if (alphabet === "PT" /* ALPHABET.PT */ || alphabet === "UN" /* ALPHABET.UN */)
         polymerType = "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */;
-    }
-    else if (alphabet === "RNA" /* ALPHABET.RNA */ || alphabet === "DNA" /* ALPHABET.DNA */) {
+    else if (alphabet === "RNA" /* ALPHABET.RNA */ || alphabet === "DNA" /* ALPHABET.DNA */)
         polymerType = "RNA" /* HELM_POLYMER_TYPE.RNA */;
-    }
     else {
         const msg = `Unexpected column's '${srcCol.name}' alphabet '${alphabet}'.`;
         return { col: null, warnings: [msg] };
@@ -112,9 +107,10 @@ export async function getMonomersDictFromLib(monomerSequencesArray, monomerLib,
                 addMonomerToDict(monomersDict, sym, formattedMonomerLib, moduleRdkit, polymerType, pointerToBranchAngle);
             }
             catch (err) {
-                const errTxt = errorToConsole(err);
-                console.error(`bio lib: getMonomersDictFromLib() sym='${sym}', error:\n` + errTxt);
-                const errMsg = `Сan't get monomer '${sym}' from library: ${errTxt}`; // Text for Datagrok error baloon
+                const errTxt = err instanceof Error ? err.message : err.toString();
+                const errStack = err instanceof Error ? err.stack : undefined;
+                console.error(`bio lib: getMonomersDictFromLib() sym='${sym}', error:\n${errTxt}\n${errStack}`);
+                const errMsg = `Can't get monomer '${sym}' from library: ${errTxt}`; // Text for Datagrok error baloon
                 throw new Error(errMsg);
             }
         }
@@ -133,9 +129,10 @@ function addMonomerToDict(monomersDict, sym, formattedMonomerLib, moduleRdkit, p
         const monomerData = getMolGraph(sym, formattedMonomerLib, moduleRdkit, polymerType, pointerToBranchAngle);
         if (monomerData)
             monomersDict.set(sym, monomerData);
-        else
+        else {
+            // todo: handle exception
             throw new Error(`Monomer with symbol '${sym}' is absent the monomer library`);
-        // todo: handle exception
+        }
     }
 }
 /** Construct the MolGraph object for specified monomerSymbol: the associated
@@ -147,9 +144,8 @@ function addMonomerToDict(monomersDict, sym, formattedMonomerLib, moduleRdkit, p
  * @param {NumberWrapper} pointerToBranchAngle - Pointer to branch angle
  * @return {MolGraph | null} - MolGraph object or null if monomerSymbol is absent in the library*/
 function getMolGraph(monomerSymbol, formattedMonomerLib, moduleRdkit, polymerType, pointerToBranchAngle) {
-    if (!formattedMonomerLib.has(monomerSymbol)) {
+    if (!formattedMonomerLib.has(monomerSymbol))
         return null;
-    }
     else {
         const libObject = formattedMonomerLib.get(monomerSymbol);
         const capGroups = parseCapGroups(libObject["rgroups" /* HELM_FIELDS.RGROUPS */]);
@@ -160,9 +156,8 @@ function getMolGraph(monomerSymbol, formattedMonomerLib, moduleRdkit, polymerTyp
         const bonds = parseBondBlock(molfileV3K, counts.bondCount);
         const meta = getMonomerMetadata(atoms, bonds, capGroups, capGroupIdxMap);
         const monomerGraph = { atoms: atoms, bonds: bonds, meta: meta };
-        if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */) {
+        if (polymerType === "PEPTIDE" /* HELM_POLYMER_TYPE.PEPTIDE */)
             adjustPeptideMonomerGraph(monomerGraph);
-        }
         else { // nucleotides
             if (monomerSymbol === C.RIBOSE || monomerSymbol === C.DEOXYRIBOSE)
                 adjustSugarMonomerGraph(monomerGraph, pointerToBranchAngle);
@@ -309,10 +304,8 @@ function setShifts(molGraph, polymerType) {
  * @return {number[]} - Shift between nodes*/
 function getShiftBetweenNodes(molGraph, rightNodeIdx, leftNodeIdx) {
     return [
-        keepPrecision(molGraph.atoms.x[rightNodeIdx] -
-            molGraph.atoms.x[leftNodeIdx]),
-        keepPrecision(molGraph.atoms.y[rightNodeIdx] -
-            molGraph.atoms.y[leftNodeIdx]),
+        keepPrecision(molGraph.atoms.x[rightNodeIdx] - molGraph.atoms.x[leftNodeIdx]),
+        keepPrecision(molGraph.atoms.y[rightNodeIdx] - molGraph.atoms.y[leftNodeIdx]),
     ];
 }
 /** Helper function necessary to build a correct V3000 molfile out of V2000 with
@@ -637,9 +630,8 @@ function adjustBaseMonomerGraph(monomer, pointerToBranchAngle) {
     if (sugarBranchToOYAngle) {
         rotateCenteredGraph(monomer.atoms, Math.PI - baseBranchToOYAngle + sugarBranchToOYAngle);
     }
-    else {
+    else
         throw new Error('The value of sugarBranchToOYAngle is null');
-    }
     // scale graph in case its size does not fit the scale of phosphate and sugar
     // todo: consider extending to other monomer types
     const p1 = {
@@ -679,12 +671,10 @@ function flipCarboxylAndRadical(monomer, doubleBondedOxygen) {
  * @return {number} angle in radians*/
 function findAngleWithOY(x, y) {
     let angle;
-    if (x === 0) {
+    if (x === 0)
         angle = y > 0 ? 0 : Math.PI;
-    }
-    else if (y === 0) {
+    else if (y === 0)
         angle = x > 0 ? -Math.PI / 2 : Math.PI / 2;
-    }
     else {
         const tan = y / x;
         const atan = Math.atan(tan);

package/src/monomer-works/to-atomic-level.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/src/utils/macromolecule/consts.d.ts CHANGED Viewed

@@ -22,8 +22,12 @@ export declare const enum TAGS {
     alphabetSize = ".alphabetSize",
     alphabetIsMultichar = ".alphabetIsMultichar",
     separator = "separator",
-    isHelmCompatible = ".isHelmCompatible"
+    isHelmCompatible = ".isHelmCompatible",
+    positionNames = ".positionNames",
+    positionLabels = ".positionLabels",
+    regions = ".regions"
 }
+export declare const positionSeparator: string;
 export declare const monomerRe: RegExp;
 export declare const Alphabets: {
     fasta: {

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"consts.d.ts","sourceRoot":"","sources":["consts.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,aAAa,EAAC,MAAM,SAAS,CAAC;AAEtC,0EAA0E;AAC1E,oBAAY,QAAQ;IAClB,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;IACvB,gBAAgB,sBAAsB;IACtC,aAAa,mBAAmB;IAChC,cAAc,oBAAoB;IAClC,OAAO,aAAa;CACrB;AAED,eAAO,MAAM,iBAAiB,EAAE,MAAa,CAAC;AAE9C,eAAO,MAAM,SAAS,EAAE,MAAqD,CAAC;AAE9E,eAAO,MAAM,SAAS;;;;;;CASnB,CAAC;AAEJ,eAAO,MAAM,kBAAkB,EAAE,aAAa,EAI7C,CAAC"}

package/src/utils/macromolecule/consts.js CHANGED Viewed

@@ -6,6 +6,7 @@ export var NOTATION;
     NOTATION["SEPARATOR"] = "separator";
     NOTATION["HELM"] = "helm";
 })(NOTATION || (NOTATION = {}));
+export const positionSeparator = ', ';
 export const monomerRe = /(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g;
 export const Alphabets = new class {
     constructor() {

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

	@@ -1 +1 @@
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package/src/utils/macromolecule/index.d.ts CHANGED Viewed

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

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

	@@ -1 +1 @@
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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,EACT,kBAAkB,EAClB,iBAAiB,EAClB,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAChB,kBAAkB,EAClB,oBAAoB,EACrB,MAAM,SAAS,CAAC"}

package/src/utils/macromolecule/index.js CHANGED Viewed

@@ -1,3 +1,3 @@
-export { NOTATION, } from './consts';
+export { NOTATION, candidateAlphabets, positionSeparator } from './consts';
 export { splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, getAlphabet, getAlphabetSimilarity, monomerToShort, pickUpPalette, pickUpSeqCol, getPaletteByType, getSplitterForColumn } from './utils';
 //# sourceMappingURL=index.js.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AASA,OAAO,EAEL,QAAQ,EAGR,kBAAkB,EAClB,iBAAiB,EAClB,MAAM,UAAU,CAAC;AAElB,OAAO,EACL,eAAe,EACf,wBAAwB,EACxB,cAAc,EACd,WAAW,EACX,qBAAqB,EACrB,cAAc,EACd,aAAa,EACb,YAAY,EACZ,gBAAgB,EAEhB,oBAAoB,EACrB,MAAM,SAAS,CAAC"}

package/src/utils/macromolecule/scoring.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
-import { ISeqSplitted } from '../../utils/macromolecule/types';
 import * as DG from 'datagrok-api/dg';
+import { ISeqSplitted } from '../../utils/macromolecule/types';
 export declare enum SCORE {
     IDENTITY = "identity",
     SIMILARITY = "similarity"

package/src/utils/macromolecule/scoring.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/macromolecule/scoring.js CHANGED Viewed

@@ -1,5 +1,5 @@
-import { sequenceChemSimilarity } from '../../monomer-works/monomer-utils';
 import * as DG from 'datagrok-api/dg';
+import { sequenceChemSimilarity } from '../../monomer-works/monomer-utils';
 import { splitAlignedSequences } from '../splitter';
 import { getSplitter } from './utils';
 export var SCORE;

package/src/utils/macromolecule/scoring.js.map CHANGED Viewed

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

@@ -1,5 +1,5 @@
 import * as DG from 'datagrok-api/dg';
-import { NOTATION } from './macromolecule/consts';
+import { NOTATION } from './macromolecule';
 import { ISeqSplitted, SeqColStats, SplitterFunc } from './macromolecule/types';
 import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { mmDistanceFunctionType } from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
@@ -10,12 +10,17 @@ export declare const Tags: {
 export declare const GapSymbols: {
     [units: string]: string;
 };
-/** Class for handling notation units in Macromolecule columns */
+export type ConvertFunc = (src: string) => string;
+export type JoinerFunc = (src: ISeqSplitted) => string;
+/** Class for handling notation units in Macromolecule columns and
+ * conversion of notation systems in Macromolecule columns
+ */
 export declare class UnitsHandler {
     protected readonly _column: DG.Column;
     protected _units: string;
     protected _notation: NOTATION;
     protected _defaultGapSymbol: string;
+    private _splitter;
     static setUnitsToFastaColumn(uh: UnitsHandler): void;
     static setUnitsToSeparatorColumn(uh: UnitsHandler, separator?: string): void;
     static setUnitsToHelmColumn(uh: UnitsHandler): void;
@@ -37,6 +42,10 @@ export declare class UnitsHandler {
     get splitted(): ISeqSplitted[];
     private _stats;
     get stats(): SeqColStats;
+    private _maxLength;
+    get maxLength(): number;
+    private _posList;
+    get posList(): string[];
     isFasta(): boolean;
     isSeparator(): boolean;
     isHelm(): boolean;
@@ -65,7 +74,7 @@ export declare class UnitsHandler {
      * @param {NOTATION} tgtNotation
      * @return {DG.Column}
      */
-    protected getNewColumn(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column;
+    protected getNewColumn(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column<string>;
     /**
      * Create a new empty column using templateCol as a template
      *
@@ -96,6 +105,36 @@ export declare class UnitsHandler {
     getDistanceFunctionName(): MmDistanceFunctionsNames;
     getDistanceFunction(): mmDistanceFunctionType;
     checkHelmCompatibility(): Promise<boolean>;
+    protected get splitter(): SplitterFunc;
+    toFasta(targetNotation: NOTATION): boolean;
+    toSeparator(targetNotation: NOTATION): boolean;
+    toHelm(targetNotation: NOTATION): boolean;
+    /**
+     *  Convert HELM string to FASTA/SEPARATOR
+     *
+     * @param {string} helmPolymer    A string to be converted
+     * @param {string} tgtNotation    Target notation: FASTA or SEPARATOR
+     * @param {string} tgtSeparator   Optional target separator (for HELM ->
+     * @param {string | null} tgtGapSymbol   Optional target gap symbol
+     * SEPARATOR)
+     * @return {string} Converted string
+     */
+    convertHelmToFastaSeparator(helmPolymer: string, tgtNotation: string, tgtSeparator?: string, tgtGapSymbol?: string): string;
+    /** Dispatcher method for notation conversion
+     *
+     * @param {NOTATION} tgtNotation   Notation we want to convert to
+     * @param {string | null} tgtSeparator   Possible separator
+     * @return {DG.Column}                Converted column
+     */
+    convert(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column;
+    /**
+     * @param name
+     * @param startIdx Start position index of the region (0-based)
+     * @param endIdx   End position index of the region (0-based, inclusive)
+     */
+    getRegion(startIdx: number | null, endIdx: number | null, name: string): DG.Column<string>;
+    getJoiner(): JoinerFunc;
+    getConverter(tgtUnits: NOTATION, tgtSeparator?: string | undefined): ConvertFunc;
     protected constructor(col: DG.Column<string>);
     /** Gets a column's UnitsHandler object from temp slot or creates a new and stores it to the temp slot. */
     static getOrCreate(col: DG.Column<string>): UnitsHandler;

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package/src/utils/units-handler.js CHANGED Viewed

@@ -1,6 +1,7 @@
 import * as DG from 'datagrok-api/dg';
-import { candidateAlphabets, NOTATION } from './macromolecule/consts';
-import { detectAlphabet, splitterAsFasta, getSplitterWithSeparator, splitterAsHelm, splitterAsFastaSimple } from './macromolecule/utils';
+import wu from 'wu';
+import { NOTATION, candidateAlphabets, positionSeparator } from './macromolecule';
+import { detectAlphabet, getSplitterForColumn, getSplitterWithSeparator, splitterAsFasta, splitterAsFastaSimple, splitterAsHelm } from './macromolecule/utils';
 import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
 export const Tags = new class {
@@ -14,7 +15,9 @@ export const GapSymbols = {
     [NOTATION.SEPARATOR]: '',
     [NOTATION.HELM]: '*',
 };
-/** Class for handling notation units in Macromolecule columns */
+/** Class for handling notation units in Macromolecule columns and
+ * conversion of notation systems in Macromolecule columns
+ */
 export class UnitsHandler {
     static setUnitsToFastaColumn(uh) {
         if (uh.column.semType !== DG.SEMTYPE.MACROMOLECULE || uh.column.getTag(DG.TAGS.UNITS) !== NOTATION.FASTA)
@@ -157,6 +160,19 @@ export class UnitsHandler {
         }
         return this._stats;
     }
+    get maxLength() {
+        if (this._maxLength === null)
+            this._maxLength = Math.max(...this.splitted.map((seqS) => seqS.length));
+        return this._maxLength;
+    }
+    get posList() {
+        if (this._posList === null) {
+            const posListTxt = this.column.getTag(".positionNames" /* TAGS.positionNames */);
+            this._posList = posListTxt ? posListTxt.split(positionSeparator).map((p) => p.trim()) :
+                wu.count(1).take(this.maxLength).map((pos) => pos.toString()).toArray();
+        }
+        return this._posList;
+    }
     isFasta() { return this.notation === NOTATION.FASTA; }
     isSeparator() { return this.notation === NOTATION.SEPARATOR; }
     isHelm() { return this.notation === NOTATION.HELM; }
@@ -350,9 +366,140 @@ export class UnitsHandler {
         this.column.setTag(".isHelmCompatible" /* TAGS.isHelmCompatible */, 'true');
         return true;
     }
+    // -- Notation Converter --
+    get splitter() {
+        if (this._splitter === null)
+            this._splitter = getSplitterForColumn(this.column);
+        return this._splitter;
+    }
+    toFasta(targetNotation) { return targetNotation === NOTATION.FASTA; }
+    toSeparator(targetNotation) { return targetNotation === NOTATION.SEPARATOR; }
+    toHelm(targetNotation) { return targetNotation === NOTATION.HELM; }
+    /**
+     *  Convert HELM string to FASTA/SEPARATOR
+     *
+     * @param {string} helmPolymer    A string to be converted
+     * @param {string} tgtNotation    Target notation: FASTA or SEPARATOR
+     * @param {string} tgtSeparator   Optional target separator (for HELM ->
+     * @param {string | null} tgtGapSymbol   Optional target gap symbol
+     * SEPARATOR)
+     * @return {string} Converted string
+     */
+    convertHelmToFastaSeparator(helmPolymer, tgtNotation, tgtSeparator, tgtGapSymbol) {
+        if (!tgtGapSymbol) {
+            tgtGapSymbol = (this.toFasta(tgtNotation)) ?
+                GapSymbols[NOTATION.FASTA] :
+                GapSymbols[NOTATION.SEPARATOR];
+        }
+        if (!tgtSeparator)
+            tgtSeparator = (this.toFasta(tgtNotation)) ? '' : this.separator;
+        const helmWrappersRe = /(R\(|D\(|\)|P)/g;
+        const isNucleotide = helmPolymer.startsWith('DNA') || helmPolymer.startsWith('RNA');
+        // items can be monomers or helms
+        const helmItemsArray = this.splitter(helmPolymer);
+        const tgtMonomersArray = [];
+        for (let i = 0; i < helmItemsArray.length; i++) {
+            let item = helmItemsArray[i];
+            if (isNucleotide)
+                item = item.replace(helmWrappersRe, '');
+            if (item === GapSymbols[NOTATION.HELM])
+                tgtMonomersArray.push(tgtGapSymbol);
+            else if (this.toFasta(tgtNotation) && item.length > 1) {
+                // the case of a multi-character monomer converted to FASTA
+                const monomer = '[' + item + ']';
+                tgtMonomersArray.push(monomer);
+            }
+            else
+                tgtMonomersArray.push(item);
+        }
+        return tgtMonomersArray.join(tgtSeparator);
+    }
+    /** Dispatcher method for notation conversion
+     *
+     * @param {NOTATION} tgtNotation   Notation we want to convert to
+     * @param {string | null} tgtSeparator   Possible separator
+     * @return {DG.Column}                Converted column
+     */
+    convert(tgtNotation, tgtSeparator) {
+        const convert = this.getConverter(tgtNotation, tgtSeparator);
+        const newColumn = this.getNewColumn(tgtNotation, tgtSeparator);
+        // assign the values to the newly created empty column
+        newColumn.init((rowI) => { return convert(this.column.get(rowI)); });
+        // newColumn.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
+        return newColumn;
+    }
+    /**
+     * @param name
+     * @param startIdx Start position index of the region (0-based)
+     * @param endIdx   End position index of the region (0-based, inclusive)
+     */
+    getRegion(startIdx, endIdx, name) {
+        const regCol = this.getNewColumn(this.notation, this.separator);
+        regCol.name = name;
+        const maxLength = Math.max(...this.splitted.map((seqS) => seqS.length));
+        const startIdxVal = startIdx ?? 0;
+        const endIdxVal = endIdx ?? this.maxLength - 1;
+        const join = this.getJoiner();
+        const regLength = endIdxVal - startIdxVal + 1;
+        regCol.init((rowI) => {
+            const seqS = this.splitted[rowI];
+            // Custom slicing instead of array method to maintain gaps
+            const regMList = new Array(regLength);
+            for (let regJPos = 0; regJPos < regLength; ++regJPos) {
+                const seqJPos = startIdxVal + regJPos;
+                regMList[regJPos] = seqJPos < seqS.length ? seqS[seqJPos] : GapSymbols[this.notation];
+            }
+            return join(regMList);
+        });
+        const getRegionOfPositionNames = (str) => {
+            const srcPosList = str.split(',').map((p) => p.trim());
+            const regPosList = new Array(regLength);
+            for (let regJPos = 0; regJPos < regLength; ++regJPos) {
+                const srcJPos = startIdxVal + regJPos;
+                regPosList[regJPos] = srcJPos < srcPosList.length ? srcPosList[srcJPos] : '?';
+            }
+            return regPosList.join(positionSeparator);
+        };
+        const srcPositionNamesStr = this.column.getTag(".positionNames" /* TAGS.positionNames */);
+        if (srcPositionNamesStr)
+            regCol.setTag(".positionNames" /* TAGS.positionNames */, getRegionOfPositionNames(srcPositionNamesStr));
+        const srcPositionLabelsStr = this.column.getTag(".positionLabels" /* TAGS.positionLabels */);
+        if (srcPositionLabelsStr)
+            regCol.setTag(".positionLabels" /* TAGS.positionLabels */, getRegionOfPositionNames(srcPositionLabelsStr));
+        return regCol;
+    }
+    getJoiner() {
+        const srcUh = this;
+        if (this.notation === NOTATION.FASTA)
+            return function (srcS) { return joinToFasta(srcUh, srcS); };
+        else if (this.notation === NOTATION.SEPARATOR)
+            return function (srcS) { return joinToSeparator(srcUh, srcS, srcUh.separator); };
+        else if (this.notation === NOTATION.HELM) {
+            const isDnaOrRna = srcUh.alphabet === "DNA" /* ALPHABET.DNA */ || srcUh.alphabet === "RNA" /* ALPHABET.RNA */;
+            return function (srcS) { return joinToHelm(srcUh, srcS, isDnaOrRna); };
+        }
+        else
+            throw new Error();
+    }
+    getConverter(tgtUnits, tgtSeparator = undefined) {
+        if (tgtUnits === NOTATION.SEPARATOR && !tgtSeparator)
+            throw new Error(`Target separator is not specified for target units '${NOTATION.SEPARATOR}'.`);
+        const srcUh = this;
+        if (tgtUnits === NOTATION.FASTA)
+            return function (src) { return convertToFasta(srcUh, src); };
+        if (tgtUnits === NOTATION.HELM)
+            return function (src) { return convertToHelm(srcUh, src); };
+        else if (tgtUnits === NOTATION.SEPARATOR)
+            return function (src) { return convertToSeparator(srcUh, src, tgtSeparator); };
+        else
+            throw new Error();
+    }
     constructor(col) {
+        this._splitter = null;
         this._splitted = null;
         this._stats = null;
+        this._maxLength = null;
+        this._posList = null;
         if (col.type != DG.TYPE.STRING)
             throw new Error(`Unexpected column type '${col.type}', must be '${DG.TYPE.STRING}'.`);
         this._column = col;
@@ -404,4 +551,72 @@ export class UnitsHandler {
         return col.temp[Tags.uhTemp];
     }
 }
+const helmWrappersRe = /[RD]\((\w)\)P?/g;
+function joinToFasta(srcUh, seqS) {
+    const resMList = new Array(seqS.length);
+    for (const [srcM, mI] of wu.enumerate(seqS)) {
+        let m = srcM;
+        if (srcUh.isHelm())
+            m = srcM.replace(helmWrappersRe, '$1');
+        if (srcUh.isGap(m))
+            m = GapSymbols[NOTATION.FASTA];
+        else if (m.length > 1)
+            m = '[' + seqS[mI] + ']';
+        resMList[mI] = m;
+    }
+    return resMList.join('');
+}
+function convertToFasta(srcUh, src) {
+    const srcMList = srcUh.isHelm() ? splitterAsHelmNucl(srcUh, src) : srcUh.getSplitter()(src);
+    return joinToFasta(srcUh, srcMList);
+}
+function joinToSeparator(srcUh, seqS, tgtSeparator) {
+    const resMList = new Array(seqS.length);
+    for (const [srcM, mI] of wu.enumerate(seqS)) {
+        let m = srcM;
+        if (srcUh.isGap(m))
+            m = GapSymbols[NOTATION.SEPARATOR];
+        resMList[mI] = m;
+    }
+    return resMList.map((m) => m ?? '').join(tgtSeparator);
+}
+function convertToSeparator(srcUh, src, tgtSeparator) {
+    const srcMList = srcUh.isHelm() ? splitterAsHelmNucl(srcUh, src) : srcUh.getSplitter()(src);
+    return joinToSeparator(srcUh, srcMList, tgtSeparator);
+}
+function joinToHelm(srcUh, seqS, isDnaOrRna) {
+    const [prefix, leftWrapper, rightWrapper, postfix] = srcUh.getHelmWrappers();
+    const resMList = wu(seqS).map((srcM) => {
+        let m = srcM;
+        if (srcUh.isGap(m))
+            m = GapSymbols[NOTATION.HELM];
+        else if (isDnaOrRna)
+            m = m.replace(helmWrappersRe, '$1');
+        else
+            m = srcM.length == 1 ? `${leftWrapper}${srcM}${rightWrapper}` : `${leftWrapper}[${srcM}]${rightWrapper}`;
+        return m;
+    }).toArray();
+    return `${prefix}${resMList.join('.')}${postfix}`;
+}
+function convertToHelm(srcUh, src) {
+    const isDnaOrRna = src.startsWith('DNA') || src.startsWith('RNA');
+    const srcS = srcUh.getSplitter()(src);
+    return joinToHelm(srcUh, srcS, isDnaOrRna);
+}
+/** Splits Helm sequence adjusting nucleotides to single char symbols. (!) Removes lone phosphorus. */
+function splitterAsHelmNucl(srcUh, src) {
+    const srcMList = srcUh.getSplitter()(src);
+    const tgtMList = new Array(srcMList.length);
+    const isDna = src.startsWith('DNA');
+    const isRna = src.startsWith('RNA');
+    for (const [srcM, mI] of wu.enumerate(srcMList)) {
+        let m = srcM;
+        if (isDna || isRna) {
+            m = m.replace(helmWrappersRe, '$1');
+            m = m === 'P' ? null : m;
+        }
+        tgtMList[mI] = m;
+    }
+    return tgtMList.filter((m) => m !== null);
+}
 //# sourceMappingURL=units-handler.js.map

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

	@@ -1 +1 @@
1	- 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package/src/viewers/web-logo.d.ts CHANGED Viewed

@@ -2,8 +2,6 @@ import * as DG from 'datagrok-api/dg';
 import { Observable } from 'rxjs';
 import { IViewer } from './viewer';
 export declare enum TAGS {
-    positionNames = ".wl.positionNames",
-    positionLabels = ".wl.positionLabels",
     /** Controls displaying WebLogo in a Macromolecule column's header tooltip */
     tooltipWebLogo = ".tooltipWebLogo"
 }
@@ -61,7 +59,6 @@ export interface IWebLogoViewer extends WebLogoProps, IViewer {
     get onSizeChanged(): Observable<void>;
     setOptions(options: Partial<WebLogoProps>): void;
 }
-export declare const positionSeparator: string;
 export declare const positionRe: RegExp;
 declare module 'datagrok-api/dg' {
     interface DataFramePlotHelper {

package/src/viewers/web-logo.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/viewers/web-logo.js CHANGED Viewed

@@ -1,7 +1,5 @@
 export var TAGS;
 (function (TAGS) {
-    TAGS["positionNames"] = ".wl.positionNames";
-    TAGS["positionLabels"] = ".wl.positionLabels";
     /** Controls displaying WebLogo in a Macromolecule column's header tooltip */
     TAGS["tooltipWebLogo"] = ".tooltipWebLogo";
 })(TAGS || (TAGS = {}));
@@ -49,7 +47,7 @@ export const WebLogoPropsDefault = new class {
         this.shrinkEmptyTail = true;
         // -- Style --
         this.backgroundColor = 0xFFFFFFFF;
-        this.positionHeight = PositionHeight.full;
+        this.positionHeight = PositionHeight.Entropy; // that is the way in the bioinformatics domain
         this.positionWidth = 16;
         // -- Layout --
         this.verticalAlignment = VerticalAlignments.MIDDLE;
@@ -65,6 +63,5 @@ export const WebLogoPropsDefault = new class {
         this.filterSource = FilterSources.Filtered;
     }
 }();
-export const positionSeparator = ', ';
 export const positionRe = /(\d+)([A-Z]?)/;
 //# sourceMappingURL=web-logo.js.map

package/src/viewers/web-logo.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/utils/notation-converter.d.ts DELETED Viewed

@@ -1,34 +0,0 @@
-import * as DG from 'datagrok-api/dg';
-import { UnitsHandler } from './units-handler';
-import { SplitterFunc } from './macromolecule/types';
-import { NOTATION } from './macromolecule/consts';
-export type ConvertFunc = (src: string) => string;
-/** Class for handling conversion of notation systems in Macromolecule columns */
-export declare class NotationConverter extends UnitsHandler {
-    private _splitter;
-    protected get splitter(): SplitterFunc;
-    toFasta(targetNotation: NOTATION): boolean;
-    toSeparator(targetNotation: NOTATION): boolean;
-    toHelm(targetNotation: NOTATION): boolean;
-    /**
-     *  Convert HELM string to FASTA/SEPARATOR
-     *
-     * @param {string} helmPolymer    A string to be converted
-     * @param {string} tgtNotation    Target notation: FASTA or SEPARATOR
-     * @param {string} tgtSeparator   Optional target separator (for HELM ->
-     * @param {string | null} tgtGapSymbol   Optional target gap symbol
-     * SEPARATOR)
-     * @return {string} Converted string
-     */
-    convertHelmToFastaSeparator(helmPolymer: string, tgtNotation: string, tgtSeparator?: string, tgtGapSymbol?: string): string;
-    /** Dispatcher method for notation conversion
-     *
-     * @param {NOTATION} tgtNotation   Notation we want to convert to
-     * @param {string | null} tgtSeparator   Possible separator
-     * @return {DG.Column}                Converted column
-     */
-    convert(tgtNotation: NOTATION, tgtSeparator?: string): DG.Column;
-    constructor(col: DG.Column);
-    getConverter(tgtUnits: NOTATION, tgtSeparator?: string | null): ConvertFunc;
-}
-//# sourceMappingURL=notation-converter.d.ts.map

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

@@ -1 +0,0 @@

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package/src/utils/notation-converter.js DELETED Viewed

@@ -1,147 +0,0 @@
-import wu from 'wu';
-import { GapSymbols, UnitsHandler } from './units-handler';
-import { NOTATION } from './macromolecule/consts';
-import { getSplitterForColumn } from './macromolecule/utils';
-/** Class for handling conversion of notation systems in Macromolecule columns */
-export class NotationConverter extends UnitsHandler {
-    get splitter() {
-        if (this._splitter === null)
-            this._splitter = getSplitterForColumn(this.column);
-        return this._splitter;
-    }
-    toFasta(targetNotation) { return targetNotation === NOTATION.FASTA; }
-    toSeparator(targetNotation) { return targetNotation === NOTATION.SEPARATOR; }
-    toHelm(targetNotation) { return targetNotation === NOTATION.HELM; }
-    /**
-     *  Convert HELM string to FASTA/SEPARATOR
-     *
-     * @param {string} helmPolymer    A string to be converted
-     * @param {string} tgtNotation    Target notation: FASTA or SEPARATOR
-     * @param {string} tgtSeparator   Optional target separator (for HELM ->
-     * @param {string | null} tgtGapSymbol   Optional target gap symbol
-     * SEPARATOR)
-     * @return {string} Converted string
-     */
-    convertHelmToFastaSeparator(helmPolymer, tgtNotation, tgtSeparator, tgtGapSymbol) {
-        if (!tgtGapSymbol) {
-            tgtGapSymbol = (this.toFasta(tgtNotation)) ?
-                GapSymbols[NOTATION.FASTA] :
-                GapSymbols[NOTATION.SEPARATOR];
-        }
-        if (!tgtSeparator)
-            tgtSeparator = (this.toFasta(tgtNotation)) ? '' : this.separator;
-        const helmWrappersRe = /(R\(|D\(|\)|P)/g;
-        const isNucleotide = helmPolymer.startsWith('DNA') || helmPolymer.startsWith('RNA');
-        // items can be monomers or helms
-        const helmItemsArray = this.splitter(helmPolymer);
-        const tgtMonomersArray = [];
-        for (let i = 0; i < helmItemsArray.length; i++) {
-            let item = helmItemsArray[i];
-            if (isNucleotide)
-                item = item.replace(helmWrappersRe, '');
-            if (item === GapSymbols[NOTATION.HELM])
-                tgtMonomersArray.push(tgtGapSymbol);
-            else if (this.toFasta(tgtNotation) && item.length > 1) {
-                // the case of a multi-character monomer converted to FASTA
-                const monomer = '[' + item + ']';
-                tgtMonomersArray.push(monomer);
-            }
-            else
-                tgtMonomersArray.push(item);
-        }
-        return tgtMonomersArray.join(tgtSeparator);
-    }
-    /** Dispatcher method for notation conversion
-     *
-     * @param {NOTATION} tgtNotation   Notation we want to convert to
-     * @param {string | null} tgtSeparator   Possible separator
-     * @return {DG.Column}                Converted column
-     */
-    convert(tgtNotation, tgtSeparator) {
-        const convert = this.getConverter(tgtNotation, tgtSeparator);
-        const newColumn = this.getNewColumn(tgtNotation, tgtSeparator);
-        // assign the values to the newly created empty column
-        newColumn.init((rowI) => { return convert(this.column.get(rowI)); });
-        // newColumn.setTag(DG.TAGS.UNITS, NOTATION.SEPARATOR);
-        return newColumn;
-    }
-    constructor(col) {
-        super(col);
-        this._splitter = null;
-    }
-    getConverter(tgtUnits, tgtSeparator = null) {
-        if (tgtUnits === NOTATION.SEPARATOR && !tgtSeparator)
-            throw new Error(`Target separator is not specified for target units '${NOTATION.SEPARATOR}'.`);
-        const srcUh = this;
-        if (tgtUnits === NOTATION.FASTA)
-            return function (src) { return convertToFasta(srcUh, src); };
-        if (tgtUnits === NOTATION.HELM)
-            return function (src) { return convertToHelm(srcUh, src); };
-        else if (tgtUnits === NOTATION.SEPARATOR)
-            return function (src) { return convertToSeparator(srcUh, src, tgtSeparator); };
-        else
-            throw new Error();
-    }
-}
-const helmWrappersRe = /[RD]\((\w)\)P?/g;
-function convertToFasta(srcUh, src) {
-    const srcMList = srcUh.isHelm() ? splitterAsHelmNucl(srcUh, src) : srcUh.getSplitter()(src);
-    const tgtMList = new Array(srcMList.length);
-    for (const [srcM, mI] of wu.enumerate(srcMList)) {
-        let m = srcM;
-        if (srcUh.isHelm())
-            m = srcM.replace(helmWrappersRe, '$1');
-        if (srcUh.isGap(m))
-            m = GapSymbols[NOTATION.FASTA];
-        else if (m.length > 1)
-            m = '[' + srcMList[mI] + ']';
-        tgtMList[mI] = m;
-    }
-    return tgtMList.join('');
-}
-function convertToSeparator(srcUh, src, tgtSeparator) {
-    const srcMList = srcUh.isHelm() ? splitterAsHelmNucl(srcUh, src) : srcUh.getSplitter()(src);
-    const tgtMList = new Array(srcMList.length);
-    const isPT = src.startsWith('PEPTIDE');
-    for (const [srcM, mI] of wu.enumerate(srcMList)) {
-        let m = srcM;
-        if (srcUh.isGap(m))
-            m = GapSymbols[NOTATION.SEPARATOR];
-        tgtMList[mI] = m;
-    }
-    return tgtMList.filter((m) => m !== null).join(tgtSeparator);
-}
-function convertToHelm(srcUh, src) {
-    const isDna = src.startsWith('DNA');
-    const isRna = src.startsWith('RNA');
-    const [prefix, leftWrapper, rightWrapper, postfix] = srcUh.getHelmWrappers();
-    const srcS = srcUh.getSplitter()(src);
-    const tgtMList = wu(srcS).map((srcM) => {
-        let m = srcM;
-        if (srcUh.isGap(m))
-            m = GapSymbols[NOTATION.HELM];
-        else if (isDna || isRna)
-            m = m.replace(helmWrappersRe, '$1');
-        else
-            m = srcM.length == 1 ? `${leftWrapper}${srcM}${rightWrapper}` : `${leftWrapper}[${srcM}]${rightWrapper}`;
-        return m;
-    }).toArray();
-    return `${prefix}${tgtMList.join('.')}${postfix}`;
-}
-/** Splits Helm sequence adjusting nucleotides to single char symbols. (!) Removes lone phosphorus. */
-function splitterAsHelmNucl(srcUh, src) {
-    const srcMList = srcUh.getSplitter()(src);
-    const tgtMList = new Array(srcMList.length);
-    const isDna = src.startsWith('DNA');
-    const isRna = src.startsWith('RNA');
-    for (const [srcM, mI] of wu.enumerate(srcMList)) {
-        let m = srcM;
-        if (isDna || isRna) {
-            m = m.replace(helmWrappersRe, '$1');
-            m = m === 'P' ? null : m;
-        }
-        tgtMList[mI] = m;
-    }
-    return tgtMList.filter((m) => m !== null);
-}
-//# sourceMappingURL=notation-converter.js.map

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

@@ -1 +0,0 @@

- 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