npm - @datagrok-libraries/bio - Versions diffs - 5.53.3 → 5.54.0 - Mend

@datagrok-libraries/bio 5.53.3 → 5.54.0

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 (21) hide show

package/package.json +5 -5
package/src/utils/cell-renderer-consts.d.ts +5 -0
package/src/utils/cell-renderer-consts.d.ts.map +1 -1
package/src/utils/cell-renderer-consts.js +5 -0
package/src/utils/cell-renderer-consts.js.map +1 -1
package/src/utils/cell-renderer-monomer-placer.d.ts +8 -1
package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.js +218 -108
package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/src/utils/cell-renderer.d.ts +2 -0
package/src/utils/cell-renderer.d.ts.map +1 -1
package/src/utils/cell-renderer.js +43 -6
package/src/utils/cell-renderer.js.map +1 -1
package/src/utils/composition-table.d.ts +6 -0
package/src/utils/composition-table.d.ts.map +1 -0
package/src/utils/composition-table.js +46 -0
package/src/utils/composition-table.js.map +1 -0
package/src/utils/sequence-position-scroller.d.ts +12 -8
package/src/utils/sequence-position-scroller.d.ts.map +1 -1
package/src/utils/sequence-position-scroller.js +45 -57
package/src/utils/sequence-position-scroller.js.map +1 -1

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

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

@@ -28,6 +28,8 @@ export declare const PrintOptionsDefaults: {
     };
     /** */ logger?: ILogger;
     selectedPosition?: number;
+    isMultiLineContext: boolean;
+    lineNumber: number;
 };
 export type PrintOptions = typeof PrintOptionsDefaults;
 /** A function that prints a string aligned to left or centered.

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

	@@ -1 +1 @@
1	- {"version":3,"file":"cell-renderer.d.ts","sourceRoot":"","sources":["cell-renderer.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAOjC,oBAAY,IAAI;IACd,gBAAgB,sCAAsC;CACvD;AAED,oBAAY,qBAAqB;IAC/B,iBAAiB,sCAAsC;CACxD;AAED,oBAAY,SAAS;IACnB,GAAG,QAAQ;IACX,OAAO,YAAY;CACpB;AAED,eAAO,MAAM,oBAAoB;IAC/B,6BAA6B,QAAQ,MAAM;IAC3C,MAAM,QAAQ,MAAM;IACpB,sBAAsB,OAAO,OAAO;IACpC,uDAAuD,mBAAmB,MAAM;IAChF,wCAAwC,YAAY,MAAM;IAC1D,wCAAwC,OAAO,OAAO;IACtD,iDAAiD,YAAY,SAAS;IACtE,oDAAoD,UAAU,MAAM,EAAE;IACtE,mCAAmC,UAAU,MAAM;IACnD,OAAO,WAAW,EAAE,CAAC,QAAQ,GAAG,IAAI;IACpC,uCAAuC,oBAAoB,MAAM,EAAE,GAAG,IAAI;IAC1E,8BAA8B,qBAAqB,MAAM,GAAG,IAAI;IAChE,kCAAkC,qBAAqB;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;KAAE;IACrF,MAAM,UAAU,OAAO;uBACJ,MAAM;~~CACxB~~,CAAC;AAEJ,MAAM,MAAM,YAAY,GAAG,OAAO,oBAAoB,CAAC;AAEvD;;;;;;;;wDAQwD;~~AACxD~~,wBAAgB,mBAAmB,CAAC,CAAC,EAAE,wBAAwB,EAC7D,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,YAAY,CAAC,GACpF,MAAM,~~CAuER~~"}
1	+ {"version":3,"file":"cell-renderer.d.ts","sourceRoot":"","sources":["cell-renderer.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAGtC,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAOjC,oBAAY,IAAI;IACd,gBAAgB,sCAAsC;CACvD;AAED,oBAAY,qBAAqB;IAC/B,iBAAiB,sCAAsC;CACxD;AAED,oBAAY,SAAS;IACnB,GAAG,QAAQ;IACX,OAAO,YAAY;CACpB;AAED,eAAO,MAAM,oBAAoB;IAC/B,6BAA6B,QAAQ,MAAM;IAC3C,MAAM,QAAQ,MAAM;IACpB,sBAAsB,OAAO,OAAO;IACpC,uDAAuD,mBAAmB,MAAM;IAChF,wCAAwC,YAAY,MAAM;IAC1D,wCAAwC,OAAO,OAAO;IACtD,iDAAiD,YAAY,SAAS;IACtE,oDAAoD,UAAU,MAAM,EAAE;IACtE,mCAAmC,UAAU,MAAM;IACnD,OAAO,WAAW,EAAE,CAAC,QAAQ,GAAG,IAAI;IACpC,uCAAuC,oBAAoB,MAAM,EAAE,GAAG,IAAI;IAC1E,8BAA8B,qBAAqB,MAAM,GAAG,IAAI;IAChE,kCAAkC,qBAAqB;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;KAAE;IACrF,MAAM,UAAU,OAAO;uBACJ,MAAM;wBAEL,OAAO;gBACf,MAAM;CACjB,CAAC;AAEJ,MAAM,MAAM,YAAY,GAAG,OAAO,oBAAoB,CAAC;AAEvD;;;;;;;;wDAQwD;AAIxD,wBAAgB,mBAAmB,CAAC,CAAC,EAAE,wBAAwB,EAC7D,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,YAAY,CAAC,GACpF,MAAM,CAmHR"}

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

@@ -22,7 +22,7 @@ export const PrintOptionsDefaults = new class {
         /** 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;
+        /** Transparency rate where 1.0 is fully transparent */ this.transparencyRate = 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;
@@ -34,6 +34,9 @@ export const PrintOptionsDefaults = new class {
         /** Map of monomers' text sizes */ this.monomerTextSizeMap = {};
         /** */ this.logger = undefined;
         this.selectedPosition = undefined;
+        // Multiline stuff
+        this.isMultiLineContext = false;
+        this.lineNumber = 0;
     }
 }();
 /** A function that prints a string aligned to left or centered.
@@ -45,10 +48,44 @@ export const PrintOptionsDefaults = new class {
  * @param {number} h Height
  * @param {PrintOptions} options
  * @return {number} x coordinate to start printing at.*/
+// Updated printLeftOrCentered function to use font-based spacing
+// Replace the multiline section in your printLeftOrCentered function
 export function printLeftOrCentered(g, s, x, y, w, h, options) {
     var _a, _b, _c;
-    const opts = Object.assign(Object.assign({}, PrintOptionsDefaults), options);
+    const opts = { ...PrintOptionsDefaults, ...options };
     const logPrefix = `Bio: printLeftOrCentered()`;
+    if (opts.isMultiLineContext) {
+        g.textBaseline = 'middle';
+        g.textAlign = 'center'; // Center text horizontally
+        let colorPart = s;
+        if (opts.maxLengthOfMonomer != null)
+            colorPart = monomerToShortFunction(colorPart, opts.maxLengthOfMonomer);
+        // Apply transparency
+        const alpha = Math.max(0.1, 1.0 - (opts.transparencyRate ?? 0.0));
+        g.globalAlpha = alpha;
+        const metrics = g.measureText(colorPart);
+        const textHeight = metrics.fontBoundingBoxAscent + metrics.fontBoundingBoxDescent;
+        const centerY = y + (h - textHeight) / 2 + metrics.fontBoundingBoxAscent;
+        let fillColor = opts.color ?? undefinedColor;
+        if (!fillColor || fillColor === undefinedColor)
+            fillColor = blackColor;
+        g.fillStyle = fillColor;
+        if (opts.selectedPosition === opts.wordIdx + 1) {
+            g.save();
+            g.fillStyle = 'rgba(60, 177, 115, 0.2)';
+            g.fillRect(x, y, w, h); // Fill the entire column bounds
+            g.restore();
+            g.fillStyle = fillColor;
+        }
+        // To center, provide the midpoint of the bounds
+        g.fillText(colorPart, x + w / 2, centerY);
+        // Reset alpha and other properties
+        g.globalAlpha = 1.0;
+        g.textBaseline = 'top';
+        g.textAlign = 'start'; // Reset to default
+        return x + w;
+    }
+    // ... rest of the existing single-line logic remains unchanged
     options.logger?.debug(`${logPrefix}, start`);
     g.textAlign = 'start';
     let colorPart = s.substring(0);
@@ -66,9 +103,9 @@ export function printLeftOrCentered(g, s, x, y, w, h, options) {
     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;
+            opts.transparencyRate = (colorPart == currentMonomerCanonical) ? 0.7 : opts.transparencyRate;
         if (compareWithCurrent && (opts.referenceSequence.length > 0) && (highlightDifference === 'equal'))
-            opts.transparencyRate = (colorPart != currentMonomerCanonical) ? 0.3 : opts.transparencyRate;
+            opts.transparencyRate = (colorPart != currentMonomerCanonical) ? 0.7 : opts.transparencyRate;
     }
     if (opts.maxLengthOfMonomer != null)
         colorPart = monomerToShortFunction(colorPart, opts.maxLengthOfMonomer);
@@ -85,7 +122,6 @@ export function printLeftOrCentered(g, s, x, y, w, h, options) {
         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) {
         let drawColor = colorCode ? opts.color : blackColor;
         if (opts.selectedPosition === opts.wordIdx + 1) {
@@ -94,7 +130,7 @@ export function printLeftOrCentered(g, s, x, y, w, h, options) {
             drawColor = DG.Color.toHtml(DG.Color.setAlpha(DG.Color.fromHtml(drawColor), 255));
         }
         g.fillStyle = drawColor;
-        g.globalAlpha = opts.transparencyRate;
+        g.globalAlpha = 1.0 - opts.transparencyRate; // FIX: Use consistent transparency logic
         if (opts.drawStyle === DrawStyle.classic) {
             g.fillText(colorPart, x + dx1, y + dy);
             g.fillStyle = grayColor;
@@ -102,6 +138,7 @@ export function printLeftOrCentered(g, s, x, y, w, h, options) {
         }
         if (opts.drawStyle === DrawStyle.MSA)
             g.fillText(colorPart, x + dx1, y + dy);
+        g.globalAlpha = 1.0; // Reset alpha
     }
     const placeX = (opts.maxWord[opts.wordIdx] ?? 0) - (opts.maxWord[0] ?? 0);
     if (opts.left || textSize > w) {

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

	@@ -1 +1 @@
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package/src/utils/composition-table.d.ts ADDED Viewed

@@ -0,0 +1,6 @@
+import { IMonomerLibBase } from './../types';
+import { HelmType } from './../helm/types';
+export declare function buildCompositionTable(counts: {
+    [m: string]: number;
+}, biotype: HelmType, monomerLib: IMonomerLibBase): HTMLTableElement;
+//# sourceMappingURL=composition-table.d.ts.map

package/src/utils/composition-table.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"composition-table.d.ts","sourceRoot":"","sources":["composition-table.ts"],"names":[],"mappings":"AAKA,OAAO,EAAC,eAAe,EAAC,MAAM,YAAY,CAAC;AAC3C,OAAO,EAAC,QAAQ,EAAC,MAAM,iBAAiB,CAAC;AAEzC,wBAAgB,qBAAqB,CACnC,MAAM,EAAE;IAAE,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAAA;CAAE,EAAE,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,eAAe,GAC9E,gBAAgB,CA0ClB"}

package/src/utils/composition-table.js ADDED Viewed

@@ -0,0 +1,46 @@
+import * as ui from 'datagrok-api/ui';
+import * as DG from 'datagrok-api/dg';
+import { GAP_SYMBOL } from './macromolecule/consts';
+export function buildCompositionTable(counts, biotype, monomerLib) {
+    let sumValue = 0;
+    let maxValue = null;
+    for (const value of Object.values(counts)) {
+        sumValue = sumValue + value;
+        maxValue = maxValue === null ? value : Math.max(maxValue, value);
+    }
+    const maxRatio = maxValue / sumValue;
+    const elMap = Object.assign({}, ...Array.from(Object.entries(counts))
+        .sort((a, b) => b[1] - a[1])
+        .map(([cm, value]) => {
+        const ratio = value / sumValue;
+        let color;
+        try {
+            const colors = monomerLib.getMonomerColors(biotype, cm);
+            color = colors?.backgroundcolor || '#CCCCCC';
+        }
+        catch (error) {
+            console.warn(`Failed to get colors for monomer ${cm}:`, error);
+            color = '#CCCCCC';
+        }
+        const barDiv = ui.div('', { classes: 'macromolecule-cell-comp-analysis-bar' });
+        barDiv.style.width = `${50 * ratio / maxRatio}px`;
+        barDiv.style.backgroundColor = color;
+        if (GAP_SYMBOL === cm) {
+            barDiv.style.borderWidth = '1px';
+            barDiv.style.borderStyle = 'solid';
+            barDiv.style.borderColor = DG.Color.toHtml(DG.Color.lightGray);
+        }
+        const displayMonomer = GAP_SYMBOL === cm ? '-' : cm;
+        const valueDiv = ui.div(`${(100 * ratio).toFixed(2)}%`);
+        const el = ui.div([barDiv, valueDiv], { classes: 'macromolecule-cell-comp-analysis-value' });
+        return ({ [displayMonomer]: el });
+    }));
+    const table = ui.tableFromMap(elMap);
+    Array.from(table.rows).forEach((row) => {
+        const barCol = row.getElementsByClassName('macromolecule-cell-comp-analysis-bar')[0]
+            .style.backgroundColor;
+        row.cells[0].style.color = barCol;
+    });
+    return table;
+}
+//# sourceMappingURL=composition-table.js.map

package/src/utils/composition-table.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"composition-table.js","sourceRoot":"","sources":["composition-table.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AACtC,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAEtC,OAAO,EAAC,UAAU,EAAC,MAAM,wBAAwB,CAAC;AAIlD,MAAM,UAAU,qBAAqB,CACnC,MAA+B,EAAE,OAAiB,EAAE,UAA2B;IAE/E,IAAI,QAAQ,GAAW,CAAC,CAAC;IACzB,IAAI,QAAQ,GAAkB,IAAI,CAAC;IACnC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC;QAC1C,QAAQ,GAAG,QAAQ,GAAG,KAAK,CAAC;QAC5B,QAAQ,GAAG,QAAQ,KAAK,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;IACnE,CAAC;IACD,MAAM,QAAQ,GAAG,QAAS,GAAG,QAAQ,CAAC;IACtC,MAAM,KAAK,GAAiC,MAAM,CAAC,MAAM,CAAC,EAAE,EAAE,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;SAChG,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;SAC3B,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE;QACnB,MAAM,KAAK,GAAG,KAAK,GAAG,QAAQ,CAAC;QAC/B,IAAI,KAAa,CAAC;QAClB,IAAI,CAAC;YACH,MAAM,MAAM,GAAG,UAAU,CAAC,gBAAgB,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;YACxD,KAAK,GAAG,MAAM,EAAE,eAAe,IAAI,SAAS,CAAC;QAC/C,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,OAAO,CAAC,IAAI,CAAC,oCAAoC,EAAE,GAAG,EAAE,KAAK,CAAC,CAAC;YAC/D,KAAK,GAAG,SAAS,CAAC;QACpB,CAAC;QAED,MAAM,MAAM,GAAG,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,EAAC,OAAO,EAAE,sCAAsC,EAAC,CAAC,CAAC;QAC7E,MAAM,CAAC,KAAK,CAAC,KAAK,GAAG,GAAG,EAAE,GAAG,KAAK,GAAG,QAAQ,IAAI,CAAC;QAClD,MAAM,CAAC,KAAK,CAAC,eAAe,GAAG,KAAK,CAAC;QACrC,IAAI,UAAU,KAAK,EAAE,EAAE,CAAC;YACtB,MAAM,CAAC,KAAK,CAAC,WAAW,GAAG,KAAK,CAAC;YACjC,MAAM,CAAC,KAAK,CAAC,WAAW,GAAG,OAAO,CAAC;YACnC,MAAM,CAAC,KAAK,CAAC,WAAW,GAAG,EAAE,CAAC,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC;QACjE,CAAC;QACD,MAAM,cAAc,GAAW,UAAU,KAAK,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;QAC5D,MAAM,QAAQ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,GAAG,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;QACxD,MAAM,EAAE,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,QAAQ,CAAC,EAAE,EAAC,OAAO,EAAE,wCAAwC,EAAC,CAAC,CAAC;QAC3F,OAAO,CAAC,EAAC,CAAC,cAAc,CAAC,EAAE,EAAE,EAAC,CAAC,CAAC;IAClC,CAAC,CAAC,CAAC,CAAC;IAEN,MAAM,KAAK,GAAG,EAAE,CAAC,YAAY,CAAC,KAAK,CAAC,CAAC;IACrC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,EAAE;QACrC,MAAM,MAAM,GAAI,GAAG,CAAC,sBAAsB,CAAC,sCAAsC,CAAC,CAAC,CAAC,CAAoB;aACrG,KAAK,CAAC,eAAe,CAAC;QACzB,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,GAAG,MAAM,CAAC;IACpC,CAAC,CAAC,CAAC;IACH,OAAO,KAAK,CAAC;AACf,CAAC"}

package/src/utils/sequence-position-scroller.d.ts CHANGED Viewed

@@ -4,6 +4,9 @@
  * with position markers, slider navigation, and position selection.
  */
 import * as DG from 'datagrok-api/dg';
+import { ISeqHandler } from './macromolecule/seq-handler';
+import { HelmType } from '../helm/types';
+import { IMonomerLib } from '../types';
 interface WindowRange {
     start: number;
     end: number;
@@ -39,20 +42,20 @@ export declare abstract class MSAHeaderTrack {
     protected defaultHeight: number;
     protected title: string;
     protected tooltipEnabled: boolean;
-    protected tooltipContent: ((position: number, data: any) => HTMLElement) | null;
+    protected tooltipContent: ((position: number, monomer: string | null, data: Map<string, number>) => HTMLElement) | null;
     constructor(height?: number, minHeight?: number, title?: string);
     /**
      * Initialize the track with a canvas context
      */
     init(ctx: CanvasRenderingContext2D): void;
-    getMonomerAt(x: number, y: number, position: number): string | null;
+    getMonomerAt(_x: number, _y: number, _position: number): string | null;
     enableTooltip(enabled: boolean): void;
-    setTooltipContentGenerator(contentGenerator: (position: number, data: any) => HTMLElement): void;
-    getTooltipContent(position: number): HTMLElement | null;
+    setTooltipContentGenerator(contentGenerator: (position: number, monomer: string | null, data: Map<string, number>) => HTMLElement): void;
+    getTooltipContent(position: number, monomer: string | null): HTMLElement | null;
     /**
      * Get data for a specific position (to be implemented by subclasses)
      */
-    protected getPositionData(position: number): any;
+    protected getPositionData(position: number): Map<string, number> | null;
     setVisible(visible: boolean): void;
     getHeight(): number;
     getDefaultHeight(): number;
@@ -79,8 +82,8 @@ export declare class WebLogoTrack extends MSAHeaderTrack {
     setupDefaultTooltip(): void;
     private createFrequencyTable;
     private createTooltipContent;
-    setMonomerLib(monomerLib: any): void;
-    setBiotype(biotype: string): void;
+    setMonomerLib(monomerLib: IMonomerLib): void;
+    setBiotype(biotype: HelmType): void;
     /**
      * Calculate which monomer is at the specified coordinates within a WebLogo column
      */
@@ -122,6 +125,7 @@ export declare class MSAScrollingHeader {
     private tracks;
     private currentHoverPosition;
     private currentHoverTrack;
+    private currentHoverMonomer;
     private previousHoverPosition;
     private previousHoverTrack;
     private previousHoverMonomer;
@@ -144,7 +148,7 @@ export declare class MSAScrollingHeader {
     private drawColumnTitle;
     private clearHoverStates;
     private redraw;
-    setSelectionData(dataFrame: DG.DataFrame, seqColumn: DG.Column<string>, seqHandler: any, callback?: (position: number, monomer: string) => void): void;
+    setSelectionData(dataFrame: DG.DataFrame, seqColumn: DG.Column<string>, seqHandler: ISeqHandler, callback?: (position: number, monomer: string) => void): void;
     setupTooltipHandling(): void;
     private handleTooltipMouseMove;
     private handleTooltipMouseLeave;

package/src/utils/sequence-position-scroller.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/src/utils/sequence-position-scroller.js CHANGED Viewed

@@ -8,18 +8,8 @@
  */
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
-// Layout Constants
-// const LAYOUT_CONSTANTS = {
-//   TITLE_HEIGHT: 16,
-//   TRACK_GAP: 4,
-//   DOTTED_CELL_HEIGHT: 30,
-//   SLIDER_HEIGHT: 8,
-//   TOP_PADDING: 5,
-//   DEFAULT_TRACK_HEIGHT: 45,
-//   MIN_TRACK_HEIGHT: 35,
-//   TRACK_SELECTOR_SIZE: 20,
-//   TRACK_SELECTOR_MARGIN: 5
-// } as const;
+import { HelmTypes } from '../helm/consts';
+import { buildCompositionTable } from './composition-table';
 // WebLogo Constants
 const WEBLOGO_CONSTANTS = {
     PADDING: 2,
@@ -83,7 +73,7 @@ export class MSAHeaderTrack {
     init(ctx) {
         this.ctx = ctx;
     }
-    getMonomerAt(x, y, position) {
+    getMonomerAt(_x, _y, _position) {
         return null;
     }
     enableTooltip(enabled) {
@@ -92,11 +82,11 @@ export class MSAHeaderTrack {
     setTooltipContentGenerator(contentGenerator) {
         this.tooltipContent = contentGenerator;
     }
-    getTooltipContent(position) {
+    getTooltipContent(position, monomer) {
         if (!this.tooltipEnabled || !this.tooltipContent)
             return null;
-        const positionData = this.getPositionData(position);
-        return this.tooltipContent(position, positionData);
+        const positionData = this.getPositionData(position) ?? new Map();
+        return this.tooltipContent(position, monomer, positionData);
     }
     /**
      * Get data for a specific position (to be implemented by subclasses)
@@ -137,7 +127,7 @@ export class WebLogoTrack extends MSAHeaderTrack {
         super(height, LAYOUT_CONSTANTS.DEFAULT_TRACK_HEIGHT, title);
         this.data = new Map();
         this.monomerLib = null;
-        this.biotype = 'PEPTIDE';
+        this.biotype = 'HELM_AA';
         this.hoveredPosition = -1;
         this.hoveredMonomer = null;
         this.data = data;
@@ -152,54 +142,51 @@ export class WebLogoTrack extends MSAHeaderTrack {
     }
     setupDefaultTooltip() {
         this.enableTooltip(true);
-        this.setTooltipContentGenerator((position, data) => {
-            return this.createTooltipContent(position, data);
+        this.setTooltipContentGenerator((position, monomer, data) => {
+            return this.createTooltipContent(position, monomer, data);
         });
     }
     createFrequencyTable(data) {
-        const sortedResidues = Array.from(data.entries()).sort((a, b) => b[1] - a[1]);
-        const table = document.createElement('table');
-        table.style.borderCollapse = 'collapse';
-        table.style.marginTop = '4px';
-        table.style.fontSize = '11px';
-        // Create header
-        const headerRow = table.insertRow();
-        const headerCell1 = headerRow.insertCell();
-        const headerCell2 = headerRow.insertCell();
-        headerCell1.textContent = 'Residue';
-        headerCell2.textContent = 'Frequency';
-        headerCell1.style.fontWeight = 'bold';
-        headerCell2.style.fontWeight = 'bold';
-        headerCell1.style.padding = '4px 8px';
-        headerCell2.style.padding = '4px 8px';
-        headerCell1.style.borderBottom = '1px solid #ccc';
-        headerCell2.style.borderBottom = '1px solid #ccc';
-        for (const [residue, freq] of sortedResidues) {
-            const row = table.insertRow();
-            const cell1 = row.insertCell();
-            const cell2 = row.insertCell();
-            const backgroundColor = this.getMonomerBackgroundColor(residue);
-            const textColor = this.getMonomerTextColor(residue);
-            cell1.textContent = residue;
-            cell1.style.backgroundColor = backgroundColor;
-            cell1.style.color = textColor;
-            cell1.style.textAlign = 'center';
-            cell1.style.fontWeight = 'bold';
-            cell1.style.padding = '4px 8px';
-            cell1.style.border = '1px solid rgba(0,0,0,0.1)';
-            cell2.textContent = `${(freq * 100).toFixed(0)}%`;
-            cell2.style.textAlign = 'right';
-            cell2.style.padding = '4px 8px';
-            cell2.style.border = '1px solid rgba(0,0,0,0.1)';
+        let helmType;
+        switch (this.biotype) {
+            case 'HELM_BASE':
+            case 'HELM_SUGAR':
+            case 'HELM_NUCLETIDE':
+                helmType = HelmTypes.NUCLEOTIDE;
+                break;
+            case 'HELM_AA':
+            case 'HELM_LINKER':
+            default:
+                helmType = HelmTypes.AA;
+                break;
         }
+        const totalFrequency = Array.from(data.values()).reduce((sum, freq) => sum + freq, 0);
+        const displayTotal = 100;
+        const counts = {};
+        for (const [monomer, frequency] of data.entries())
+            counts[monomer] = Math.max(1, Math.round((frequency / totalFrequency) * displayTotal));
+        const table = buildCompositionTable(counts, helmType, this.monomerLib);
+        table.style.fontSize = '11px';
+        table.style.marginTop = '4px';
         return table;
     }
-    createTooltipContent(position, data) {
+    createTooltipContent(position, monomer, data) {
         const tooltipRows = [];
         tooltipRows.push(ui.divText(`Position: ${position + 1}`, {
             style: { fontWeight: 'bold', marginBottom: '6px', fontSize: '13px' }
         }));
+        if (monomer) {
+            tooltipRows.push(ui.divText(`Monomer: ${monomer}`, {
+                style: { marginBottom: '6px', fontSize: '13px' }
+            }));
+            if (data.has(monomer)) {
+                tooltipRows.push(ui.divText(`${(data.get(monomer) * 100).toFixed(2)}%`, {
+                    style: { marginBottom: '6px', fontSize: '13px' }
+                }));
+            }
+        }
         if (data && data.size > 0) {
+            // Use the datagrok buildCompositionTable
             const freqTable = this.createFrequencyTable(data);
             tooltipRows.push(freqTable);
         }
@@ -208,7 +195,6 @@ export class WebLogoTrack extends MSAHeaderTrack {
                 style: { fontStyle: 'italic', color: '#666' }
             }));
         }
-        // Use the standard tooltip container approach
         const tooltipEl = ui.divV(tooltipRows);
         tooltipEl.style.maxHeight = '80vh';
         return tooltipEl;
@@ -489,6 +475,7 @@ export class MSAScrollingHeader {
         // Tooltip and hover state
         this.currentHoverPosition = -1;
         this.currentHoverTrack = null;
+        this.currentHoverMonomer = null;
         this.previousHoverPosition = -1;
         this.previousHoverTrack = null;
         this.previousHoverMonomer = null;
@@ -784,13 +771,14 @@ export class MSAScrollingHeader {
             }
         }
         // Handle tooltips
-        if (hoveredPosition !== this.currentHoverPosition || hoveredTrackId !== this.currentHoverTrack) {
+        if (hoveredPosition !== this.currentHoverPosition || hoveredTrackId !== this.currentHoverTrack || currentHoverMonomer !== this.currentHoverMonomer) {
             this.currentHoverPosition = hoveredPosition;
             this.currentHoverTrack = hoveredTrackId;
+            this.currentHoverMonomer = currentHoverMonomer;
             if (hoveredTrackId) {
                 const track = this.tracks.get(hoveredTrackId);
                 if (track) {
-                    const tooltipContent = track.getTooltipContent(hoveredPosition);
+                    const tooltipContent = track.getTooltipContent(hoveredPosition, currentHoverMonomer);
                     if (tooltipContent) {
                         ui.tooltip.show(tooltipContent, e.clientX + 16, e.clientY + 16);
                         return;