@datagrok-libraries/bio 5.42.0 → 5.42.2

package/CHANGELOG.md

@@ -1,5 +1,13 @@
 # bio changelog
 
+## 5.42.2 (2024-06-25)
+
+Bump dependencies versions JSDraw.Lite and HELMWebEditor
+
+## 5.42.1 (2024-06-24)
+
+Fix for JSDraw types
+
 ## 5.42.0 (2024-06-21)
 
 Use types of forked JSDraw.Lite and HELMWebEditor

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.42.0",
+  "version": "5.42.2",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/gridext": "^1.3.71",
@@ -26,8 +26,8 @@
     "wu": "latest"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.4",
-    "@datagrok-libraries/js-draw-lite": "^0.0.2",
+    "@datagrok-libraries/helm-web-editor": "^1.1.5",
+    "@datagrok-libraries/js-draw-lite": "^0.0.3",
     "@types/signals": "1.0.1",
     "@types/three": "^0.159.0",
     "@types/uuid": "^9.0.1",

package/src/helm/helm-helper.d.ts

@@ -1,8 +1,7 @@
 import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
-import { Atom, HelmType, IHelmWebEditor, IWebEditorMonomer } from './types';
+import { IHelmWebEditor } from './types';
 import { IMonomerLib } from '../types/index';
-export type GetMonomerResType = IWebEditorMonomer | null;
-export type GetMonomerFunc = (a: Atom<HelmType> | HelmType, name?: string) => GetMonomerResType;
+import { GetMonomerFunc } from '../helm/types';
 export interface IHelmHelper {
     createHelmWebEditor(): IHelmWebEditor;
     createWebEditorApp(host: HTMLDivElement, helm?: string): App;

package/src/helm/helm-helper.d.ts.map

@@ -1 +1 @@
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package/src/helm/helm-helper.js.map

@@ -1 +1 @@
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package/src/helm/types.d.ts

@@ -1,11 +1,11 @@
-import type { HelmType, PolymerType, MonomerType, IWebEditorMonomer, WebEditorRGroups } from '@datagrok-libraries/js-draw-lite/src/types/org';
+import type { HelmType, PolymerType, MonomerType, IWebEditorMonomer, WebEditorRGroups, IMonomerColors } from '@datagrok-libraries/js-draw-lite/src/types/org';
 import type { Atom } from '@datagrok-libraries/js-draw-lite/src/Atom';
 import type { IJsAtom } from '@datagrok-libraries/js-draw-lite/src/types/jsdraw2';
 import type { Bond } from '@datagrok-libraries/js-draw-lite/src/Bond';
 import type { Mol } from '@datagrok-libraries/js-draw-lite/src/Mol';
 import type { Editor } from '@datagrok-libraries/js-draw-lite/src/JSDraw.Editor';
 import type { App } from '@datagrok-libraries/helm-web-editor/helm/App';
-import type { IOrgHelmWebEditor, IOrgHelmMonomers } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
+import type { IOrgHelmWebEditor, IOrgHelmMonomers, GetMonomerFunc, GetMonomerResType } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
 import type { HweWindow } from '@datagrok-libraries/helm-web-editor/src/types';
 import type { JSDraw2ModuleType, ScilModuleType } from '@datagrok-libraries/js-draw-lite/src/types';
 import type { OrgType } from '@datagrok-libraries/helm-web-editor/src/types/org-helm';
@@ -13,7 +13,7 @@ import type { Monomers } from '@datagrok-libraries/helm-web-editor/helm/Monomers
 import type { DojoType, DojoxType } from '@datagrok-libraries/js-draw-lite/src/types/dojo';
 export { HelmType, PolymerType, MonomerType, WebEditorRGroups };
 export { Atom, IJsAtom, Bond, Mol, Editor };
-export { IWebEditorMonomer, IOrgHelmWebEditor, IOrgHelmMonomers, App, Monomers };
+export { IWebEditorMonomer, IMonomerColors, IOrgHelmWebEditor, IOrgHelmMonomers, App, Monomers, GetMonomerFunc, GetMonomerResType };
 export { DojoType, DojoxType };
 export { HweWindow, ScilModuleType, JSDraw2ModuleType, OrgType };
 export interface IHelmWebEditor {

package/src/helm/types.d.ts.map

@@ -1 +1 @@
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package/src/utils/cell-renderer.d.ts

@@ -1,4 +1,5 @@
 import * as DG from 'datagrok-api/dg';
+import { ILogger } from './logger';
 export declare enum TAGS {
     maxMonomerLength = ".mm.cellRenderer.maxMonomerLength"
 }
@@ -6,28 +7,33 @@ export declare enum DrawStyle {
     MSA = "MSA",
     classic = "classic"
 }
+export declare const PrintOptionsDefaults: {
+    /** Color of text to print */ color: string;
+    /** */ pivot: number;
+    /** Is left aligned */ left: boolean;
+    /** Transparency rate where 1.0 is fully transparent */ transparencyRate: number;
+    /** Monomer's separator, if specified */ separator: string;
+    /** Is checker if element last or not */ last: boolean;
+    /** MSA - for aligned, classic - for other seq */ drawStyle: DrawStyle;
+    /** Max word lengths per position (index of list) */ maxWord: number[];
+    /** Word index we currently draw */ wordIdx: number;
+    /**  */ gridCell: DG.GridCell | null;
+    /** Reference sequence for diff mode */ referenceSequence: string[] | null;
+    /** Max length of a monomer */ maxLengthOfMonomer: number | null;
+    /** Map of monomers' text sizes */ monomerTextSizeMap: {
+        [key: string]: TextMetrics;
+    };
+    /** */ logger?: ILogger | undefined;
+};
+export type PrintOptions = typeof PrintOptionsDefaults;
 /** A function that prints a string aligned to left or centered.
- * @param {number}x x coordinate.
- * @param {number}y y coordinate.
- * @param {number}w Width.
- * @param {number}h Height.
- * @param {CanvasRenderingContext2D}g Canvas rendering context.
- * @param {string}s String to print.
- * @param {string}color String color.
- * @param {number}pivot Pirvot.
- * @param {boolean}left Is left aligned.
- * @param {number}transparencyRate Transparency rate where 1.0 is fully transparent
- * @param {string}separator Is separator for sequence.
- * @param {boolean}last Is checker if element last or not.
- * @param {DrawStyle}drawStyle Is draw style. MSA - for multicharSeq, classic - for other seq.
- * @param {number[]}maxWord {{[pos: number]: number}}  Max word lengths per position.
- * @param {number}wordIdx Is index of word we currently draw.
- * @param {DG.GridCell}gridCell Is grid cell.
- * @param {string[]}referenceSequence Is reference sequence for diff mode.
- * @param {number}maxLengthOfMonomer Is max length of monomer.
- * @param {{[key: string]: TextMetrics}}monomerTextSizeMap Is map of monomer text sizes.
+ * @param {CanvasRenderingContext2D} g Canvas rendering context
+ * @param {string} s Text to print
+ * @param {number} x x coordinate
+ * @param {number} y y coordinate
+ * @param {number} w Width
+ * @param {number} h Height
+ * @param {PrintOptions} options
  * @return {number} x coordinate to start printing at.*/
-export declare function printLeftOrCentered(x: number, y: number, w: number, h: number, g: CanvasRenderingContext2D, s: string, color?: string, pivot?: number, left?: boolean, transparencyRate?: number, separator?: string, last?: boolean, drawStyle?: DrawStyle, maxWord?: number[], wordIdx?: number, gridCell?: DG.GridCell | null, referenceSequence?: string[] | null, maxLengthOfMonomer?: number | null, monomerTextSizeMap?: {
-    [key: string]: TextMetrics;
-}): number;
+export declare function printLeftOrCentered(g: CanvasRenderingContext2D, s: string, x: number, y: number, w: number, h: number, options: Partial<PrintOptions>): number;
 //# sourceMappingURL=cell-renderer.d.ts.map

package/src/utils/cell-renderer.d.ts.map

@@ -1 +1 @@
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package/src/utils/cell-renderer.js

@@ -12,78 +12,88 @@ export var DrawStyle;
     DrawStyle["MSA"] = "MSA";
     DrawStyle["classic"] = "classic";
 })(DrawStyle || (DrawStyle = {}));
+export const PrintOptionsDefaults = new class {
+    constructor() {
+        /** Color of text to print */ this.color = undefinedColor;
+        /** */ this.pivot = 0;
+        /** Is left aligned */ this.left = false;
+        /** Transparency rate where 1.0 is fully transparent */ this.transparencyRate = 1.0;
+        /** Monomer's separator, if specified */ this.separator = '';
+        /** Is checker if element last or not */ this.last = false;
+        /** MSA - for aligned, classic - for other seq */ this.drawStyle = DrawStyle.classic;
+        /** Max word lengths per position (index of list) */ this.maxWord = [];
+        /** Word index we currently draw */ this.wordIdx = 0;
+        /**  */ this.gridCell = null;
+        /** Reference sequence for diff mode */ this.referenceSequence = null;
+        /** Max length of a monomer */ this.maxLengthOfMonomer = null;
+        /** Map of monomers' text sizes */ this.monomerTextSizeMap = {};
+        /** */ this.logger = undefined;
+    }
+}();
 /** A function that prints a string aligned to left or centered.
- * @param {number}x x coordinate.
- * @param {number}y y coordinate.
- * @param {number}w Width.
- * @param {number}h Height.
- * @param {CanvasRenderingContext2D}g Canvas rendering context.
- * @param {string}s String to print.
- * @param {string}color String color.
- * @param {number}pivot Pirvot.
- * @param {boolean}left Is left aligned.
- * @param {number}transparencyRate Transparency rate where 1.0 is fully transparent
- * @param {string}separator Is separator for sequence.
- * @param {boolean}last Is checker if element last or not.
- * @param {DrawStyle}drawStyle Is draw style. MSA - for multicharSeq, classic - for other seq.
- * @param {number[]}maxWord {{[pos: number]: number}}  Max word lengths per position.
- * @param {number}wordIdx Is index of word we currently draw.
- * @param {DG.GridCell}gridCell Is grid cell.
- * @param {string[]}referenceSequence Is reference sequence for diff mode.
- * @param {number}maxLengthOfMonomer Is max length of monomer.
- * @param {{[key: string]: TextMetrics}}monomerTextSizeMap Is map of monomer text sizes.
+ * @param {CanvasRenderingContext2D} g Canvas rendering context
+ * @param {string} s Text to print
+ * @param {number} x x coordinate
+ * @param {number} y y coordinate
+ * @param {number} w Width
+ * @param {number} h Height
+ * @param {PrintOptions} options
  * @return {number} x coordinate to start printing at.*/
-export function printLeftOrCentered(x, y, w, h, g, s, color = undefinedColor, pivot = 0, left = false, transparencyRate = 1.0, separator = '', last = false, drawStyle = DrawStyle.classic, maxWord = [], wordIdx = 0, gridCell = null, referenceSequence = null, maxLengthOfMonomer = null, monomerTextSizeMap = {}) {
+export function printLeftOrCentered(g, s, x, y, w, h, options) {
+    var _a, _b, _c;
+    const opts = Object.assign(Object.assign({}, PrintOptionsDefaults), options);
+    const logPrefix = `Bio: printLeftOrCentered()`;
+    options.logger?.debug(`${logPrefix}, start`);
     g.textAlign = 'start';
     let colorPart = s.substring(0);
-    let grayPart = last ? '' : separator;
-    if (drawStyle === DrawStyle.MSA)
+    let grayPart = opts.last ? '' : opts.separator;
+    if (opts.drawStyle === DrawStyle.MSA)
         grayPart = '';
     let colorCode = true;
     let compareWithCurrent = true;
     let highlightDifference = 'difference';
-    if ((gridCell != null) && (gridCell.cell.column != null)) {
-        colorCode = gridCell.cell.column.temp['color-code'] ?? true;
-        compareWithCurrent = gridCell.cell.column.temp['compare-with-current'] ?? true;
-        highlightDifference = gridCell.cell.column.temp['highlight-difference'] ?? 'difference';
+    if ((opts.gridCell != null) && (opts.gridCell.cell.column != null)) {
+        colorCode = opts.gridCell.cell.column.temp['color-code'] ?? true;
+        compareWithCurrent = opts.gridCell.cell.column.temp['compare-with-current'] ?? true;
+        highlightDifference = opts.gridCell.cell.column.temp['highlight-difference'] ?? 'difference';
     }
-    if (referenceSequence) {
-        const currentMonomerCanonical = referenceSequence[wordIdx];
-        if (compareWithCurrent && (referenceSequence.length > 0) && (highlightDifference === 'difference'))
-            transparencyRate = (colorPart == currentMonomerCanonical) ? 0.3 : transparencyRate;
-        if (compareWithCurrent && (referenceSequence.length > 0) && (highlightDifference === 'equal'))
-            transparencyRate = (colorPart != currentMonomerCanonical) ? 0.3 : transparencyRate;
+    if (opts.referenceSequence) {
+        const currentMonomerCanonical = opts.referenceSequence[opts.wordIdx];
+        if (compareWithCurrent && (opts.referenceSequence.length > 0) && (highlightDifference === 'difference'))
+            opts.transparencyRate = (colorPart == currentMonomerCanonical) ? 0.3 : opts.transparencyRate;
+        if (compareWithCurrent && (opts.referenceSequence.length > 0) && (highlightDifference === 'equal'))
+            opts.transparencyRate = (colorPart != currentMonomerCanonical) ? 0.3 : opts.transparencyRate;
     }
-    if (maxLengthOfMonomer != null)
-        colorPart = monomerToShortFunction(colorPart, maxLengthOfMonomer);
+    if (opts.maxLengthOfMonomer != null)
+        colorPart = monomerToShortFunction(colorPart, opts.maxLengthOfMonomer);
     const fullText = colorPart + grayPart;
-    monomerTextSizeMap[fullText] ?? (monomerTextSizeMap[fullText] = g.measureText(fullText));
-    let textSize = monomerTextSizeMap[fullText];
-    monomerTextSizeMap[colorPart] ?? (monomerTextSizeMap[colorPart] = g.measureText(colorPart));
-    let maxColorTextSize = monomerTextSizeMap[colorPart].width;
-    monomerTextSizeMap[grayPart] ?? (monomerTextSizeMap[grayPart] = g.measureText(grayPart));
-    const grayPartSize = monomerTextSizeMap[grayPart].width;
+    (_a = opts.monomerTextSizeMap)[fullText] ?? (_a[fullText] = g.measureText(fullText));
+    let textSize = opts.monomerTextSizeMap[fullText];
+    (_b = opts.monomerTextSizeMap)[colorPart] ?? (_b[colorPart] = g.measureText(colorPart));
+    let maxColorTextSize = opts.monomerTextSizeMap[colorPart].width;
     const dy = h / 2 - (textSize.fontBoundingBoxAscent + textSize.fontBoundingBoxDescent) / 2 + 1;
+    (_c = opts.monomerTextSizeMap)[grayPart] ?? (_c[grayPart] = g.measureText(grayPart));
+    const grayPartSize = opts.monomerTextSizeMap[grayPart].width;
     textSize = textSize.width;
-    if (drawStyle === DrawStyle.MSA) {
-        maxColorTextSize = maxWord[wordIdx];
-        textSize = maxWord[wordIdx];
+    if (opts.drawStyle === DrawStyle.MSA) {
+        maxColorTextSize = opts.maxWord[opts.wordIdx];
+        textSize = opts.maxWord[opts.wordIdx];
     }
     /** Draw color part at {@link dx1}, and gray part at {@link dx2}. */
     function draw(dx1, dx2) {
-        const drawColor = colorCode ? color : blackColor;
+        const drawColor = colorCode ? opts.color : blackColor;
         g.fillStyle = drawColor;
-        g.globalAlpha = transparencyRate;
-        if (drawStyle === DrawStyle.classic) {
+        g.globalAlpha = opts.transparencyRate;
+        if (opts.drawStyle === DrawStyle.classic) {
             g.fillText(colorPart, x + dx1, y + dy);
             g.fillStyle = grayColor;
             g.fillText(grayPart, x + dx2, y + dy);
         }
-        if (drawStyle === DrawStyle.MSA)
+        if (opts.drawStyle === DrawStyle.MSA)
             g.fillText(colorPart, x + dx1, y + dy);
     }
-    const placeX = (maxWord[wordIdx] ?? 0) - (maxWord[0] ?? 0);
-    if (left || textSize > w) {
+    const placeX = (opts.maxWord[opts.wordIdx] ?? 0) - (opts.maxWord[0] ?? 0);
+    if (opts.left || textSize > w) {
         draw(placeX, placeX + maxColorTextSize);
         return x + placeX + maxColorTextSize + grayPartSize;
     }

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package/src/package.d.ts

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package/src/package.d.ts.map

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package/src/package.js

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package/src/package.js.map

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