npm - @datagrok-libraries/bio - Versions diffs - 5.44.2 → 5.44.4 - Mend

@datagrok-libraries/bio 5.44.2 → 5.44.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (35) hide show

package/CHANGELOG.md +17 -0
package/eslint.config.mjs +63 -0
package/package.json +5 -4
package/src/molecule-3d/molecule-3d-units-handler.js.map +1 -1
package/src/monomer-works/lib-settings.js +2 -2
package/src/monomer-works/lib-settings.js.map +1 -1
package/src/monomer-works/monomer-hover.js +1 -2
package/src/monomer-works/monomer-hover.js.map +1 -1
package/src/monomer-works/monomer-works.d.ts +2 -2
package/src/monomer-works/monomer-works.d.ts.map +1 -1
package/src/monomer-works/monomer-works.js.map +1 -1
package/src/monomer-works/to-atomic-level.js +1 -2
package/src/monomer-works/to-atomic-level.js.map +1 -1
package/src/types/index.d.ts +2 -2
package/src/types/index.d.ts.map +1 -1
package/src/unknown.js +1 -1
package/src/unknown.js.map +1 -1
package/src/utils/cell-renderer-monomer-placer.d.ts +2 -0
package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.js +71 -14
package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/src/utils/macromolecule/utils.d.ts.map +1 -1
package/src/utils/macromolecule/utils.js +1 -2
package/src/utils/macromolecule/utils.js.map +1 -1
package/src/utils/monomer-ui.d.ts.map +1 -1
package/src/utils/monomer-ui.js.map +1 -1
package/src/utils/seq-handler.d.ts +2 -0
package/src/utils/seq-handler.d.ts.map +1 -1
package/src/utils/seq-handler.js +6 -0
package/src/utils/seq-handler.js.map +1 -1
package/src/utils/splitter.js +2 -2
package/src/utils/splitter.js.map +1 -1
package/src/viewers/vd-regions.d.ts.map +1 -1
package/.eslintignore +0 -1
package/.eslintrc.json +0 -47

package/CHANGELOG.md CHANGED Viewed

@@ -1,5 +1,22 @@
 # bio changelog
+## 5.44.4 (2024-10-02)
+### New features
+* Add use monomer colors from monomer lib for MonomerPlacer
+### Bug fixes
+* Fix splitAlignedSequences for canonical monomer symbol
+* Fix monomer colors for empty monomer lib
+* Fix for grok.userSettings
+* Fixes for eslint
+## 5.44.3 (2024-10-02)
+Correct color for monomer lib configs
 ## 5.44.2 (2024-09-27)
 ### New features

package/eslint.config.mjs ADDED Viewed

@@ -0,0 +1,63 @@
+import typescriptEslint from '@typescript-eslint/eslint-plugin';
+import deprecation from 'eslint-plugin-deprecation';
+import globals from 'globals';
+import tsParser from '@typescript-eslint/parser';
+import path from 'node:path';
+import {fileURLToPath} from 'node:url';
+import js from '@eslint/js';
+import {FlatCompat} from '@eslint/eslintrc';
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = path.dirname(__filename);
+const compat = new FlatCompat({
+  baseDirectory: __dirname,
+  recommendedConfig: js.configs.recommended,
+  allConfig: js.configs.all,
+});
+// console.debug(JSON.stringify(compat.extends('google'), undefined, 2));
+const globalsBrowserFixed = Object.assign({}, globals.browser, {
+  AudioWorkletGlobalScope: globals.browser['AudioWorkletGlobalScope '],
+});
+delete globalsBrowserFixed['AudioWorkletGlobalScope '];
+export default [{
+  ignores: ['src/**/*.d.ts*'],
+}, ...compat.extends('google'), {
+  plugins: {
+    '@typescript-eslint': typescriptEslint,
+    deprecation,
+  },
+  languageOptions: {
+    globals: {...globalsBrowserFixed},
+    parser: tsParser,
+    parserOptions: {project: 'tsconfig.json'},
+    ecmaVersion: 12,
+    sourceType: 'module',
+  },
+  rules: {
+    'deprecation/deprecation': 'error',
+    'indent': ['error', 2, {SwitchCase: 0}],
+    'max-len': ['error', 120],
+    'no-throw-literal': 'error',
+    'no-unused-vars': 'off',
+    '@typescript-eslint/no-unused-vars': ['warn', {varsIgnorePattern: '^(_|ui$|grok$|DG$)', argsIgnorePattern: '^_'}],
+    'require-jsdoc': 'off',
+    'valid-jsdoc': 'warn',
+    'spaced-comment': 'off',
+    'linebreak-style': 'off',
+    'curly': ['error', 'multi-or-nest'],
+    'brace-style': ['error', '1tbs', {allowSingleLine: true}],
+    'block-spacing': [2, 'always'],
+    'comma-dangle': 'off',
+    'comma-spacing': 'error',
+    'comma-style': 'error',
+    'guard-for-in': 'off',
+    'space-infix-ops': 'error',
+  },
+  files: ['**/*.ts'],
+}];

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.44.2",
+  "version": "5.44.4",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",
@@ -21,7 +21,7 @@
     "dayjs": "latest",
     "fastest-levenshtein": "^1.0.16",
     "js-base64": "^3.7.5",
-    "lru-cache": "^11.0.1",
+    "lru-cache": "^10.4.3",
     "mjolnir.js": "^2.7.0",
     "rxjs": "^6.5.5",
     "uuid": "^9.0.1",
@@ -39,8 +39,9 @@
     "datagrok-tools": "latest",
     "eslint": "latest",
     "eslint-config-google": "latest",
-    "ts-loader": "^9.5.1",
-    "typescript": "^5.5.3"
+    "eslint-plugin-deprecation": "latest",
+    "ts-loader": "latest",
+    "typescript": "latest"
   },
   "scripts": {
     "link": "npm link",

package/src/molecule-3d/molecule-3d-units-handler.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/monomer-works/lib-settings.js CHANGED Viewed

@@ -6,7 +6,7 @@ let userLibSettingsPromise = Promise.resolve();
 export async function getUserLibSettings() {
     let res;
     userLibSettingsPromise = userLibSettingsPromise.then(async () => {
-        const resStr = await grok.dapi.userDataStorage.getValue(LIB_STORAGE_NAME, 'Settings', true);
+        const resStr = grok.userSettings.getValue(LIB_STORAGE_NAME, 'Settings', true);
         res = resStr ? JSON.parse(resStr) : { exclude: [], explicit: [], duplicateMonomerPreferences: {} };
         // Fix empty object returned in case there is no settings stored for user
         res.exclude = res.exclude instanceof Array ? res.exclude : [];
@@ -21,7 +21,7 @@ export async function getUserLibSettings() {
 export async function setUserLibSettings(value) {
     userLibSettingsPromise = userLibSettingsPromise.then(async () => {
         console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(value, undefined, 2)}`);
-        await grok.dapi.userDataStorage.postValue(LIB_STORAGE_NAME, 'Settings', JSON.stringify(value), true);
+        grok.userSettings.add(LIB_STORAGE_NAME, 'Settings', JSON.stringify(value), true);
     });
     await userLibSettingsPromise;
 }

package/src/monomer-works/lib-settings.js.map CHANGED Viewed

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package/src/monomer-works/monomer-hover.js CHANGED Viewed

@@ -1,7 +1,6 @@
 import wu from 'wu';
 import { LRUCache } from 'lru-cache';
 import { addSubstructProvider, getMonomerHover, setMonomerHover } from '@datagrok-libraries/chem-meta/src/types';
-import { HelmTypes } from '../helm/consts';
 import { SeqHandler } from '../utils/seq-handler';
 import { ALPHABET } from '../utils/macromolecule';
 import { getMonomersDictFromLib } from './to-atomic-level';
@@ -19,7 +18,7 @@ export function buildMonomerHoverLink(seqCol, molCol, monomerLib, rdKitModule) {
     function buildMonomerMap(seqCol, tableRowIdx) {
         const seqSH = SeqHandler.forColumn(seqCol);
         const seqSS = seqSH.getSplitted(tableRowIdx);
-        const biotype = seqSH.alphabet == ALPHABET.RNA || seqSH.alphabet == ALPHABET.DNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
+        const biotype = seqSH.defaultBiotype;
         const seqMList = wu.count(0).take(seqSS.length)
             .map((posIdx) => { return { position: posIdx, symbol: seqSS.getCanonical(posIdx), biotype: biotype }; })
             .toArray();

package/src/monomer-works/monomer-hover.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/src/monomer-works/monomer-works.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import { IMonomerLib } from '../types';
+import { IMonomerLibBase } from '../types';
 import { HelmType, PolymerType } from '../helm/types';
 /** Hypothetical interface to convert mol block notation.
  * It should be placed in the chem-meta package, and have an implementation in the Chem package.
@@ -10,7 +10,7 @@ export interface IMolfileConverter {
 }
 export declare class MonomerWorks {
     private monomerLib;
-    constructor(monomerLib: IMonomerLib);
+    constructor(monomerLib: IMonomerLibBase);
     getCappedRotatedMonomer(monomerType: PolymerType, monomerName: string): string | null;
 }
 export declare function helmTypeToPolymerType(helmType: HelmType): PolymerType;

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

	@@ -1 +1 @@
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package/src/monomer-works/monomer-works.js.map CHANGED Viewed

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

@@ -10,7 +10,6 @@ import { hasMolGraph, setMolGraph } from './types';
 import { errInfo } from '../utils/err-info';
 import { alphabetToPolymerType } from './utils';
 import { monomerWorksConsts as C } from './consts';
-import { HelmTypes } from '../helm/consts';
 // todo: verify that all functions have return types
 /** Convert Macromolecule column into Molecule column storing molfile V3000 with the help of a monomer library
  * @param {DG.DataFrame} df - DataFrame containing the column to be converted
@@ -58,7 +57,7 @@ export function getMonomerSequencesArray(macroMolCol) {
     // split the string into monomers
     const sh = SeqHandler.forColumn(macroMolCol);
     let containsEmptyValues = false;
-    const biotype = sh.alphabet === ALPHABET.RNA || sh.alphabet === ALPHABET.DNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
+    const biotype = sh.defaultBiotype;
     for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
         const seqSS = sh.getSplitted(rowIdx);
         containsEmptyValues || (containsEmptyValues = seqSS.length === 0);

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package/src/types/index.d.ts CHANGED Viewed

@@ -59,6 +59,7 @@ export type MonomerLibData = {
     };
 };
 export interface IMonomerLibBase {
+    get isEmpty(): boolean;
     get onChanged(): Observable<any>;
     addMissingMonomer(polymerType: PolymerType, monomerSymbol: string): Monomer;
     getMonomer(polymerType: PolymerType | null, monomerSymbol: string): Monomer | null;
@@ -67,6 +68,7 @@ export interface IMonomerLibBase {
     getRS(smiles: string): {
         [r: string]: string;
     };
+    getTooltip(biotype: HelmType, monomerSymbol: string): HTMLElement;
 }
 export interface IMonomerLib extends IMonomerLibBase {
     get source(): string | undefined;
@@ -77,7 +79,6 @@ export interface IMonomerLib extends IMonomerLibBase {
     getMonomerSymbolsByRGroup(rGroupNumber: number, polymerType: PolymerType, element?: string): string[];
     getMonomerSymbolsByType(polymerType: PolymerType): string[];
     getPolymerTypes(): PolymerType[];
-    update(lib: IMonomerLib): void;
     toJSON(): Monomer[];
     /** Summary string with lib monomer count by type
      * @deprecated Keep for backward compatibility */
@@ -86,7 +87,6 @@ export interface IMonomerLib extends IMonomerLibBase {
     getSummaryObj(): MonomerLibSummaryType;
     /** Gets dataframe with columns 'polymerType', 'count'. */
     getSummaryDf(): DG.DataFrame;
-    getTooltip(biotype: HelmType, monomerSymbol: string): HTMLElement;
     getMonomerSet(biotype: HelmType): MonomerSetType | null;
     override(overrideData: MonomerLibData): IMonomerLibBase;
 }

package/src/types/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/src/unknown.js CHANGED Viewed

@@ -61,7 +61,7 @@ export class UnknownColorPalette extends UnknownSeqPalette {
                                 if (!this.customMonomerColors[monomerSymbol])
                                     this.customMonomerColors[monomerSymbol] = {};
                                 this.customMonomerColors[monomerSymbol][polymerType] =
-                                    correctColor(monomer.meta.colors.default.background, false);
+                                    correctColor(monomer.meta.colors.default.background);
                             }
                         }
                     }

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package/src/utils/cell-renderer-monomer-placer.d.ts CHANGED Viewed

@@ -26,6 +26,7 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
     _monomerStructureMap: {
         [key: string]: HTMLElement;
     };
+    private monomerLib;
     /** View is required to subscribe and handle for data frame changes */
     constructor(gridCol: DG.GridColumn | null, tableCol: DG.Column<string>, logger: ILogger, monomerLengthLimit: number, propsProvider: () => MonomerPlacerProps);
     protected reset(): void;
@@ -40,6 +41,7 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
     isMsa(): boolean;
     private padding;
     render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell, _cellStyle: DG.GridCellStyle): void;
+    onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void;
 }
 export declare function getUpdatedWidth(grid: DG.Grid | null | undefined, g: CanvasRenderingContext2D, x: number, w: number, dpr: number): number;
 export {};

package/src/utils/cell-renderer-monomer-placer.d.ts.map CHANGED Viewed

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package/src/utils/cell-renderer-monomer-placer.js CHANGED Viewed

@@ -1,11 +1,14 @@
+import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
 import { SeqHandler } from './seq-handler';
-import { getPaletteByType, NOTATION, TAGS as bioTAGS } from './macromolecule';
-import { CellRendererBackBase } from './cell-renderer-back-base';
+import { ALPHABET, NOTATION, TAGS as bioTAGS } from './macromolecule';
+import { CellRendererBackBase, getGridCellColTemp } from './cell-renderer-back-base';
 import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
 import { errInfo } from './err-info';
 import { DrawStyle, printLeftOrCentered, TAGS as mmcrTAGS } from './cell-renderer';
+import { HelmTypes } from '../helm/consts';
+import { execMonomerHoverLinks } from '../monomer-works/monomer-hover';
 export const undefinedColor = 'rgb(100,100,100)';
 export function hitBounds(bounds, x) {
     let iterationCount = 100;
@@ -40,6 +43,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         this._processedMaxVisibleSeqLength = 0;
         this._monomerLengthMap = {}; // caches the lengths to save time on g.measureText
         this._monomerStructureMap = {}; // caches the atomic structures of monomers
+        this.monomerLib = null;
         this.padding = 5;
         this.props = this.propsProvider();
         this._processedRows = DG.BitSet.create(this.tableCol.length);
@@ -62,8 +66,10 @@ export class MonomerPlacer extends CellRendererBackBase {
         getMonomerLibHelper().then((libHelper) => {
             if (this.destroyed)
                 return;
-            const monomerLib = libHelper.getMonomerLib();
-            this.subs.push(monomerLib.onChanged.subscribe(() => {
+            this.monomerLib = libHelper.getMonomerLib();
+            this.dirty = true;
+            this.gridCol?.grid?.invalidate();
+            this.subs.push(this.monomerLib.onChanged.subscribe(() => {
                 this.dirty = true;
                 this.gridCol?.grid?.invalidate();
             }));
@@ -104,9 +110,8 @@ export class MonomerPlacer extends CellRendererBackBase {
     getCellMonomerLengthsForSeq(rowIdx) {
         const logPrefix = `${this.toLog()}.getCellMonomerLengthsForSeqMsa()`;
         // this.logger.debug(`${logPrefix}, start`);
-        if (this._monomerLengthList === null) {
+        if (this._monomerLengthList === null)
             this._monomerLengthList = new Array(this.tableCol.length).fill(null);
-        }
         const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
         const maxVisibleSeqLength = Math.ceil(this.colWidth / minMonWidth);
         const seqSS = SeqHandler.forColumn(this.tableCol).getSplitted(rowIdx);
@@ -132,9 +137,8 @@ export class MonomerPlacer extends CellRendererBackBase {
         var _a;
         const logPrefix = `${this.toLog()}.getCellMonomerLengthsForSeqMsa()`;
         // this.logger.debug(`${logPrefix}, start`);
-        if (this._monomerLengthList === null) {
+        if (this._monomerLengthList === null)
             this._monomerLengthList = new Array(1).fill(null);
-        }
         (_a = this._monomerLengthList)[0] ?? (_a[0] = new Array(0));
         const res = this._monomerLengthList[0];
         // const startIdx = Math.max(Math.floor((this.grid?.vertScroll.min ?? 0) - 10), 0);
@@ -207,7 +211,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         const gridCol = this.gridCol;
         const tableCol = this.tableCol;
         const dpr = window.devicePixelRatio;
-        let separatorWidth = this.props.separatorWidth;
+        const separatorWidth = this.props.separatorWidth;
         // Cell renderer settings
         let maxLengthOfMonomer = this.monomerLengthLimit;
         if (mmcrTAGS.maxMonomerLength in tableCol.tags) {
@@ -246,7 +250,6 @@ export class MonomerPlacer extends CellRendererBackBase {
             //TODO: can this be replaced/merged with splitSequence?
             const units = tableCol.meta.units;
             const aligned = tableCol.getTag(bioTAGS.aligned);
-            const palette = getPaletteByType(paletteType);
             const separator = tableCol.getTag(bioTAGS.separator) ?? '';
             const minMonWidth = this.props.separatorWidth + 1 * this.props.monomerCharWidth;
             const splitLimit = Math.ceil(w / minMonWidth);
@@ -264,14 +267,21 @@ export class MonomerPlacer extends CellRendererBackBase {
             })();
             const subParts = sh.getSplitted(rowIdx);
             /* let x1 = x; */
-            let color = undefinedColor;
+            const color = undefinedColor;
             let drawStyle = DrawStyle.classic;
             if (aligned && aligned.includes('MSA') && units == NOTATION.SEPARATOR)
                 drawStyle = DrawStyle.MSA;
             const visibleSeqLength = Math.min(subParts.length, splitLimit);
             for (let posIdx = 0; posIdx < visibleSeqLength; ++posIdx) {
-                const amino = subParts.getOriginal(posIdx);
-                color = palette.get(amino);
+                const cm = subParts.getCanonical(posIdx);
+                let color = undefinedColor;
+                if (this.monomerLib) {
+                    const sh = SeqHandler.forColumn(this.tableCol);
+                    const biotype = sh.defaultBiotype;
+                    //this.logger.debug(`${logPrefix}, biotype: ${biotype}, amino: ${amino}`);
+                    const wem = this.monomerLib.getWebEditorMonomer(biotype, cm);
+                    color = wem.backgroundcolor;
+                }
                 g.fillStyle = undefinedColor;
                 const last = posIdx === subParts.length - 1;
                 /*x1 = */
@@ -281,7 +291,7 @@ export class MonomerPlacer extends CellRendererBackBase {
                     referenceSequence: referenceSequence, maxLengthOfMonomer: maxLengthOfMonomer,
                     monomerTextSizeMap: this._monomerLengthMap, logger: this.logger
                 };
-                printLeftOrCentered(g, amino, x + this.padding, y, w, h, opts);
+                printLeftOrCentered(g, cm, x + this.padding, y, w, h, opts);
                 if (minDistanceRenderer > w)
                     break;
             }
@@ -296,6 +306,53 @@ export class MonomerPlacer extends CellRendererBackBase {
             g.restore();
         }
     }
+    onMouseMove(gridCell, e) {
+        if (gridCell.tableRowIndex == null)
+            return;
+        // if (gridCell.cell.column.getTag(bioTAGS.aligned) !== ALIGNMENT.SEQ_MSA)
+        //   return;
+        const [_gridCol, tableCol, temp] = getGridCellColTemp(gridCell);
+        const seqColTemp = temp.rendererBack;
+        if (!seqColTemp)
+            return; // Can do nothing without precalculated data
+        const gridCellBounds = gridCell.bounds;
+        // const value: any = gridCell.cell.value;
+        //
+        // const maxLengthWords: number[] = seqColTemp.getCellMonomerLengths(gridCell.tableRowIndex!);
+        // const maxLengthWordsSum: number[] = new Array<number>(maxLengthWords.length).fill(0);
+        // for (let posI: number = 1; posI < maxLengthWords.length; posI++)
+        //   maxLengthWordsSum[posI] = maxLengthWordsSum[posI - 1] + maxLengthWords[posI];
+        // const maxIndex = maxLengthWords.length;
+        const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCellBounds.x);
+        const left = seqColTemp.getPosition(gridCell.tableRowIndex, argsX, gridCellBounds.width);
+        const seqSS = SeqHandler.forColumn(tableCol)
+            .getSplitted(gridCell.tableRowIndex);
+        if (left !== null && left < seqSS.length) {
+            const sh = SeqHandler.forColumn(tableCol);
+            const alphabet = sh.alphabet ?? ALPHABET.UN;
+            const seqMonomer = {
+                position: left,
+                biotype: alphabet === ALPHABET.RNA || alphabet === ALPHABET.DNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA,
+                symbol: seqSS.getCanonical(left),
+            };
+            const tooltipElements = [];
+            let monomerDiv = seqColTemp._monomerStructureMap[seqMonomer.symbol];
+            if (!monomerDiv || true) {
+                monomerDiv = seqColTemp._monomerStructureMap[seqMonomer.symbol] = (() => {
+                    return this.monomerLib ? this.monomerLib.getTooltip(seqMonomer.biotype, seqMonomer.symbol) :
+                        ui.divText('Monomer library is not available');
+                })();
+            }
+            tooltipElements.push(monomerDiv);
+            ui.tooltip.show(ui.divV(tooltipElements), e.x + 16, e.y + 16);
+            execMonomerHoverLinks(gridCell, seqMonomer);
+        }
+        else {
+            //
+            ui.tooltip.hide();
+            execMonomerHoverLinks(gridCell, null);
+        }
+    }
 }
 export function getUpdatedWidth(grid, g, x, w, dpr) {
     return !!grid ? Math.max(Math.min(grid.canvas.width / dpr - x, w)) : Math.max(g.canvas.width / dpr - x, 0);

package/src/utils/cell-renderer-monomer-placer.js.map CHANGED Viewed

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

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

@@ -119,9 +119,8 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
                 mmList = new Array(Math.ceil(limit));
                 let mEa = null;
                 let mI = 0;
-                while ((mEa = mRe.exec(seq)) !== null && mI < limit) {
+                while ((mEa = mRe.exec(seq)) !== null && mI < limit)
                     mmList[mI++] = mEa[0].replace(`"-"`, '').replace(`'-'`, '');
-                }
                 mmList.splice(mI);
             }
             else

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

	@@ -1 +1 @@
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package/src/utils/monomer-ui.js.map CHANGED Viewed

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

@@ -4,6 +4,7 @@ import { INotationProvider, ISeqSplitted, SeqColStats, SplitterFunc } from './ma
 import { MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { mmDistanceFunctionType } from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
 import { CellRendererBackBase } from './cell-renderer-back-base';
+import { HelmType } from '../helm/types';
 export declare const SeqTemps: {
     /** Column's temp slot name for a SeqHandler object */
     seqHandler: string;
@@ -36,6 +37,7 @@ export declare class SeqHandler {
     get aligned(): string;
     /** Alphabet name (upper case) */
     get alphabet(): string;
+    get defaultBiotype(): HelmType;
     protected get helmCompatible(): string | undefined;
     getAlphabetSize(): number;
     getAlphabetIsMultichar(): boolean;

package/src/utils/seq-handler.d.ts.map CHANGED Viewed

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

@@ -1,11 +1,14 @@
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
+/* eslint-disable max-len */
 import { ALPHABET, candidateAlphabets, getSplitterWithSeparator, NOTATION, positionSeparator, splitterAsFasta, splitterAsHelm, TAGS } from './macromolecule';
 import { detectAlphabet, splitterAsFastaSimple, StringListSeqSplitted } from './macromolecule/utils';
 import { mmDistanceFunctions, MmDistanceFunctionsNames } from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 import { getMonomerLibHelper } from '../monomer-works/monomer-utils';
 import { HELM_WRAPPERS_REGEXP, PHOSPHATE_SYMBOL } from './const';
 import { GAP_SYMBOL, GapOriginals } from './macromolecule/consts';
+import { HelmTypes } from '../helm/consts';
+/* eslint-enable max-len */
 export const SeqTemps = new class {
     constructor() {
         /** Column's temp slot name for a SeqHandler object */
@@ -148,6 +151,9 @@ export class SeqHandler {
             throw new Error('Tag alphabet not set');
         return alphabet;
     }
+    get defaultBiotype() {
+        return this.alphabet === ALPHABET.RNA || this.alphabet === ALPHABET.DNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA;
+    }
     get helmCompatible() {
         return this.column.getTag(TAGS.isHelmCompatible);
     }

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

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

@@ -14,9 +14,9 @@ export function splitAlignedSequences(sequenceColumn) {
     for (let rowIdx = 0; rowIdx < rowCount; ++rowIdx) {
         const currentMonomerList = uh.getSplitted(rowIdx);
         for (let posIdx = 0; posIdx < currentMonomerList.length; ++posIdx) {
-            const om = currentMonomerList.getOriginal(posIdx);
+            const cm = currentMonomerList.getCanonical(posIdx);
             const col = getCol(posIdx) || createCol(posIdx);
-            col.set(rowIdx, om, false);
+            col.set(rowIdx, cm, false);
         }
     }
     return resultDf;

package/src/utils/splitter.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/.eslintignore DELETED Viewed

	@@ -1 +0,0 @@
1	- src/*/.d.ts*

package/.eslintrc.json DELETED Viewed

@@ -1,47 +0,0 @@
-{
-  "env": {
-    "browser": true,
-    "es2020": true
-  },
-  "extends": [
-    "google"
-  ],
-  "parser": "@typescript-eslint/parser",
-  "parserOptions": {
-    "ecmaVersion": 12,
-    "sourceType": "module"
-  },
-  "plugins": [
-    "@typescript-eslint"
-  ],
-  "rules": {
-    "indent": ["error", 2, {"SwitchCase": 0}],
-    "max-len": ["error", 120],
-    "no-throw-literal": "error",
-    "no-unused-vars": "off",
-    "@typescript-eslint/no-unused-vars": [
-      "warn", {"varsIgnorePattern": "^(_|ui$|grok$|DG$)", "argsIgnorePattern": "^_"}
-    ],
-    "require-jsdoc": "off",
-    "valid-jsdoc": "warn",
-    "spaced-comment": "off",
-    "linebreak-style": "off",
-    "curly": [
-      "error",
-      "multi-or-nest"
-    ],
-    "brace-style": [
-      "error",
-      "1tbs",
-      {
-        "allowSingleLine": true
-      }
-    ],
-    "block-spacing": [2, "always"],
-    "comma-dangle": "off",
-    "comma-spacing": "error",
-    "comma-style": "error",
-    "guard-for-in": "off",
-    "space-infix-ops": "error"
-  }
-}