npm - @datagrok-libraries/bio - Versions diffs - 5.63.5 → 5.63.7 - Mend

@datagrok-libraries/bio 5.63.5 → 5.63.7

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 (22) hide show

package/CLAUDE.md +0 -13
package/package.json +1 -1
package/src/molecule/molecule-units-handler.js +1 -1
package/src/molecule/molecule-units-handler.js.map +1 -1
package/src/molecule-3d/molecule-3d-units-handler.js +1 -1
package/src/molecule-3d/molecule-3d-units-handler.js.map +1 -1
package/src/utils/cell-renderer-async-base.js +2 -2
package/src/utils/cell-renderer-async-base.js.map +1 -1
package/src/utils/cell-renderer-monomer-placer.d.ts +3 -0
package/src/utils/cell-renderer-monomer-placer.d.ts.map +1 -1
package/src/utils/cell-renderer-monomer-placer.js +74 -13
package/src/utils/cell-renderer-monomer-placer.js.map +1 -1
package/src/utils/composition-table.js +1 -1
package/src/utils/composition-table.js.map +1 -1
package/src/utils/macromolecule/scoring.js +1 -1
package/src/utils/macromolecule/scoring.js.map +1 -1
package/src/utils/macromolecule-highlight.d.ts +87 -0
package/src/utils/macromolecule-highlight.d.ts.map +1 -0
package/src/utils/macromolecule-highlight.js +87 -0
package/src/utils/macromolecule-highlight.js.map +1 -0
package/src/utils/monomer-selection-dialog.js +1 -1
package/src/utils/monomer-selection-dialog.js.map +1 -1

package/CLAUDE.md CHANGED Viewed

@@ -1,24 +1,11 @@
 # CLAUDE.md
-This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
 ## Overview
 **@datagrok-libraries/bio** is the core shared library for all bioinformatics functionality in the Datagrok platform. It provides types, utilities, renderers, and service interfaces for working with macromolecules (peptides, DNA, RNA, HELM), 3D molecular structures (PDB/PDBQT/mmCIF), phylogenetic trees, and monomer libraries.
 This is a **library** (not a package) — it has no `package.ts`, no webpack, no platform registration. It is compiled with `tsc` to `.js`/`.d.ts` and consumed by multiple packages (`Bio`, `Helm`, `Peptides`, `BiostructureViewer`, `Dendrogram`, `HitTriage`, etc.).
-## Build Commands
-```bash
-npm install
-npm run build              # grok check --soft && tsc
-npm run build-all          # Builds chem-meta → js-api → gridext → utils → ml → this library
-npm run lint               # eslint "./src/**/*.ts"
-npm run lint-fix
-npm run link-all           # Links chem-meta, datagrok-api, gridext, utils, ml
-```
 ## Key Dependencies
 - `datagrok-api` — platform API (`DG`, `grok`, `ui`)

package/package.json CHANGED Viewed

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.63.5",
+  "version": "5.63.7",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

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

@@ -38,7 +38,7 @@ export class MoleculeUnitsHandler extends UnitsHandlerBase {
         const resCol = DG.Column.fromType(DG.TYPE.STRING, this.column.name, colLength);
         for (let rowI = 0; rowI < colLength; ++rowI) {
             const molVal = this.column.get(rowI);
-            const pdbVal = molVal === null ? null : await ph.molToPdb(molVal);
+            const pdbVal = !molVal ? null : await ph.molToPdb(molVal);
             resCol.set(rowI, pdbVal);
         }
         return resCol;

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

	@@ -1 +1 @@
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package/src/molecule-3d/molecule-3d-units-handler.js CHANGED Viewed

@@ -52,7 +52,7 @@ export class Molecule3DUnitsHandler extends UnitsHandlerBase {
         const resCol = DG.Column.fromType(DG.TYPE.STRING, this.column.name, colLength);
         for (let rowI = 0; rowI < colLength; ++rowI) {
             const srcVal = this.column.get(rowI);
-            const pdbVal = srcVal === null ? null : await convertToPdb(srcVal);
+            const pdbVal = !srcVal ? null : await convertToPdb(srcVal);
             resCol.set(rowI, pdbVal);
         }
         return resCol;

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

	@@ -1 +1 @@
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package/src/utils/cell-renderer-async-base.js CHANGED Viewed

@@ -62,7 +62,7 @@ export class RenderServiceBase {
             this._queueDict[key] = task;
         }
         this.logger.debug(`${logPrefix}, _queue.push(), ` + `key: ${key?.toString()}`);
-        if (consumerId === null)
+        if (consumerId == null)
             consumerId = ++this.consumerCounter;
         this._queue.push({ consumerId, key, task, tryCount, dt: window.performance.now() });
         // Purge off-screen tasks when queue grows too large (e.g. during fast scrolling)
@@ -226,7 +226,7 @@ export class RenderServiceBase {
             window.clearInterval(this._sweeperHandle);
             this._sweeperHandle = null;
         }
-        if (busy && this._sweeperHandle === null) {
+        if (busy && this._sweeperHandle == null) {
             this.logger.debug(`${logPrefix}, enable queue sweeper (busy)`);
             this._sweeperHandle = window.setInterval(() => { this._sweepQueue(); }, 500);
         }

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

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

@@ -44,6 +44,9 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
     private shouldUseMultilineRendering;
     private calculateMultiLineLayoutDynamic;
     init(): Promise<void>;
+    private handleHighlightEvent;
+    private getHighlightForRow;
+    private drawHighlightBackground;
     static getFontSettings(tableCol?: DG.Column): {
         font: string;
         fontWidth: number;

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

	@@ -1 +1 @@
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package/src/utils/cell-renderer-monomer-placer.js CHANGED Viewed

@@ -1,3 +1,5 @@
+/* eslint-disable max-len */
+import * as grok from 'datagrok-api/grok';
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
@@ -11,6 +13,7 @@ import { rendererSettingsChangedState } from './cell-renderer-consts';
 import { AnnotationRenderer } from './cell-renderer-annotations';
 import { HelmTypes } from '../helm/consts';
 import { execMonomerHoverLinks } from '../monomer-works/monomer-hover';
+import { DEFAULT_MACROMOLECULE_HIGHLIGHT_FILL, MACROMOLECULE_HIGHLIGHT_EVENT_ID, MACROMOLECULE_HIGHLIGHT_TEMP, macromoleculeHighlightColorToCss, } from './macromolecule-highlight';
 import * as operators from 'rxjs/operators';
 export const undefinedColor = 'rgb(100,100,100)';
 export const shiftedLeftPaddingText = '...';
@@ -181,8 +184,58 @@ export class MonomerPlacer extends CellRendererBackBase {
         this.subs.push(this.sysMonomerLib.onChanged.subscribe(() => {
             this.reset();
         }));
+        this.subs.push(grok.events.onCustomEvent(MACROMOLECULE_HIGHLIGHT_EVENT_ID)
+            .subscribe((args) => this.handleHighlightEvent(args)));
         this.reset();
     }
+    handleHighlightEvent(args) {
+        var _a;
+        if (!args || !this.tableCol || !this.tableCol.dataFrame)
+            return;
+        if (args.columnName !== this.tableCol.name)
+            return;
+        const df = this.tableCol.dataFrame;
+        if (args.tableId && df.id !== args.tableId)
+            return;
+        if (args.tableName && df.name !== args.tableName)
+            return;
+        const map = ((_a = this.tableCol.temp)[MACROMOLECULE_HIGHLIGHT_TEMP] ?? (_a[MACROMOLECULE_HIGHLIGHT_TEMP] = new Map()));
+        if (args.monomers == null || args.monomers.length === 0)
+            map.delete(args.rowIdx);
+        else {
+            map.set(args.rowIdx, {
+                monomers: args.monomers.slice(),
+                fillColor: args.fillColor,
+                strokeColor: args.strokeColor,
+            });
+        }
+        this.invalidateGrid();
+    }
+    getHighlightForRow(rowIdx) {
+        if (rowIdx == null)
+            return null;
+        const map = this.tableCol.temp[MACROMOLECULE_HIGHLIGHT_TEMP];
+        return map?.get(rowIdx) ?? null;
+    }
+    // Paints a translucent background behind the monomer at `posIdx` if this row has a highlight
+    // entry that includes that position. Uses the entry's `fillColor` (alpha forced) or the
+    // default fill color. Called from both single-line and multi-line render paths.
+    drawHighlightBackground(g, rowIdx, posIdx, rectX, rectY, rectW, rectH) {
+        const entry = this.getHighlightForRow(rowIdx);
+        if (!entry || !entry.monomers || entry.monomers.length === 0)
+            return;
+        if (!entry.monomers.includes(posIdx))
+            return;
+        const fillCss = macromoleculeHighlightColorToCss(entry.fillColor ?? DEFAULT_MACROMOLECULE_HIGHLIGHT_FILL);
+        g.save();
+        try {
+            g.fillStyle = fillCss;
+            g.fillRect(rectX, rectY, rectW, rectH);
+        }
+        finally {
+            g.restore();
+        }
+    }
     static getFontSettings(tableCol) {
         const fontFamily = 'monospace';
         let fontSize = 12;
@@ -273,7 +326,7 @@ export class MonomerPlacer extends CellRendererBackBase {
     getCellMonomerLengthsForSeq(rowIdx) {
         const logPrefix = `${this.toLog()}.getCellMonomerLengthsForSeq()`;
         // this.logger.debug(`${logPrefix}, start`);
-        if (this._monomerLengthList === null)
+        if (this._monomerLengthList == null)
             this._monomerLengthList = new Array(this.tableCol.length).fill(null);
         const visibleSeqStart = this.positionShift;
         const sh = this.seqHelper.getSeqHandler(this.tableCol);
@@ -282,7 +335,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         const seqSS = sh.getSplitted(rowIdx);
         const visibleSeqEnd = Math.min(maxVisibleSeqLength, seqSS.length);
         let res = this._monomerLengthList[rowIdx];
-        if (res === null || res.length != visibleSeqEnd - visibleSeqStart) {
+        if (res == null || res.length != visibleSeqEnd - visibleSeqStart) {
             res = this._monomerLengthList[rowIdx] = new Array(seqSS.length);
             let seqWidth = 0;
             for (let seqMonI = visibleSeqStart; seqMonI < visibleSeqEnd; ++seqMonI) {
@@ -302,7 +355,7 @@ 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];
@@ -475,6 +528,7 @@ export class MonomerPlacer extends CellRendererBackBase {
                         });
                         if (annotRenderer)
                             annotRenderer.drawPositionBackground(g, elementX, lineY, element.width + 2, layout.lineHeight, monomerIndex, gridCell.tableRowIndex);
+                        this.drawHighlightBackground(g, gridCell.tableRowIndex, monomerIndex, elementX, lineY, element.width + 2, layout.lineHeight);
                         printLeftOrCentered(g, monomer.om, elementX, lineY, element.width, layout.lineHeight, {
                             color: color,
                             isMultiLineContext: true,
@@ -497,11 +551,16 @@ export class MonomerPlacer extends CellRendererBackBase {
                 const visibleSeqLength = Math.min(subParts.length, Math.ceil(w / (minMonomerWidth)) + positionShift);
                 // Pre-compute text bottom y for annotation underlines (text is vertically centered)
                 let textBottomY;
+                // Compute a monomer-sized highlight rect (a little taller than the glyph itself) so the
+                // background doesn't span the whole cell height.
+                const monomerMetrics = g.measureText('M');
+                const monomerTextHeight = monomerMetrics.fontBoundingBoxAscent + monomerMetrics.fontBoundingBoxDescent;
+                const hlPadding = 4;
+                const hlRectHeight = Math.min(h, monomerTextHeight + hlPadding);
+                const hlRectY = y + (h - hlRectHeight) / 2;
                 if (annotRenderer) {
-                    const metrics = g.measureText('M');
-                    const textHeight = metrics.fontBoundingBoxAscent + metrics.fontBoundingBoxDescent;
-                    const dy = h / 2 - textHeight / 2 + 1;
-                    textBottomY = y + dy + textHeight;
+                    const dy = h / 2 - monomerTextHeight / 2 + 1;
+                    textBottomY = y + dy + monomerTextHeight;
                 }
                 for (let posIdx = positionShift; posIdx < visibleSeqLength; ++posIdx) {
                     const om = posIdx < subParts.length ? subParts.getOriginal(posIdx) : sh.defaultGapOriginal;
@@ -514,14 +573,16 @@ export class MonomerPlacer extends CellRendererBackBase {
                     // will show where the next disjoint sequence starts, so we check posIdx + 1
                     const drawnSeparator = (subParts?.graphInfo?.disjointSeqStarts?.indexOf(posIdx + 1) ?? 0) > 0 ? '|' : separator;
                     // Draw annotation background before the monomer text
+                    const wordIdx = posIdx - positionShift;
+                    const placeX = (maxLengthWordsSum[wordIdx] ?? 0) - (maxLengthWordsSum[0] ?? 0);
+                    const nextPlaceX = wordIdx + 1 < maxLengthWordsSum.length ?
+                        (maxLengthWordsSum[wordIdx + 1] ?? 0) - (maxLengthWordsSum[0] ?? 0) : placeX + this.props.fontCharWidth;
+                    const monomerW = nextPlaceX - placeX;
+                    const monomerLeftX = x + this.padding + this._leftThreeDotsPadding + placeX;
                     if (annotRenderer && gridCell.tableRowIndex != null) {
-                        const wordIdx = posIdx - positionShift;
-                        const placeX = (maxLengthWordsSum[wordIdx] ?? 0) - (maxLengthWordsSum[0] ?? 0);
-                        const nextPlaceX = wordIdx + 1 < maxLengthWordsSum.length ?
-                            (maxLengthWordsSum[wordIdx + 1] ?? 0) - (maxLengthWordsSum[0] ?? 0) : placeX + this.props.fontCharWidth;
-                        const monomerW = nextPlaceX - placeX;
-                        annotRenderer.drawPositionBackground(g, x + this.padding + this._leftThreeDotsPadding + placeX, y, monomerW, h, posIdx, gridCell.tableRowIndex, textBottomY);
+                        annotRenderer.drawPositionBackground(g, monomerLeftX, y, monomerW, h, posIdx, gridCell.tableRowIndex, textBottomY);
                     }
+                    this.drawHighlightBackground(g, gridCell.tableRowIndex, posIdx, monomerLeftX, hlRectY, monomerW, hlRectHeight);
                     const opts = {
                         color: color, pivot: 0, left: true, transparencyRate: 0.0,
                         separator: drawnSeparator, last: last,

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

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

@@ -7,7 +7,7 @@ export function buildCompositionTable(counts, biotype, monomerLib, monomerBioTyp
     let maxValue = null;
     for (const value of Object.values(counts)) {
         sumValue = sumValue + value;
-        maxValue = maxValue === null ? value : Math.max(maxValue, value);
+        maxValue = maxValue == null ? value : Math.max(maxValue, value);
     }
     const maxRatio = maxValue / sumValue;
     const elMap = Object.assign({}, ...Array.from(Object.entries(counts))

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

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

@@ -22,7 +22,7 @@ export async function calculateScores(table, col, ref, scoring, seqHelper) {
     const refSplitted = refUh.getSplitted(0); // ref is at 0
     const scoresCol = scoring === SCORE.IDENTITY ? calculateIdentity(refSplitted, splitSeqDf) :
         scoring === SCORE.SIMILARITY ? await calculateSimilarity(refSplitted, splitSeqDf, seqHelper) : null;
-    if (scoresCol === null)
+    if (scoresCol == null)
         throw new Error(`In bio library: Unknown sequence scoring method: ${scoring}`);
     scoresCol.name = table.columns.getUnusedName(scoresCol.name);
     table.columns.add(scoresCol);

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

	@@ -1 +1 @@
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package/src/utils/macromolecule-highlight.d.ts ADDED Viewed

@@ -0,0 +1,87 @@
+import * as DG from 'datagrok-api/dg';
+/** Custom event id for toggling monomer highlights in macromolecule grid cells (HELM renderer
+ *  and generic sequence renderer). Payload: {@link MacromoleculeHighlightEventArgs}. Fire via
+ *  {@link grok.events.fireCustomEvent} or the convenience helpers in this module. */
+export declare const MACROMOLECULE_HIGHLIGHT_EVENT_ID = "bio-macromolecule-monomer-highlight";
+/** Slot name on `column.temp` where per-row monomer highlights are stored by the macromolecule
+ *  cell renderers. Shape: `Map<rowIdx, MacromoleculeHighlightEntry>`. */
+export declare const MACROMOLECULE_HIGHLIGHT_TEMP = "bio.macromolecule.highlightMonomers";
+/** Forced alpha (0..1) applied to every highlight color — solid colors are not allowed. */
+export declare const MACROMOLECULE_HIGHLIGHT_ALPHA = 0.4;
+/** Default fill color (translucent yellow) as a DG.Color ARGB int. The alpha component of the
+ *  input is ignored by the renderer and replaced with {@link MACROMOLECULE_HIGHLIGHT_ALPHA}. */
+export declare const DEFAULT_MACROMOLECULE_HIGHLIGHT_FILL: number;
+/** Default stroke color (amber) as a DG.Color ARGB int. */
+export declare const DEFAULT_MACROMOLECULE_HIGHLIGHT_STROKE: number;
+/** A single highlight record stored in `column.temp[MACROMOLECULE_HIGHLIGHT_TEMP]`, keyed by
+ *  row index. */
+export type MacromoleculeHighlightEntry = {
+    /** 0-based monomer indices to highlight for this row.
+     *  - HELM renderer: indices into `editor.m.atoms` of the rendered molecule.
+     *  - Generic sequence renderer: 0-based position in the split sequence. */
+    monomers: number[];
+    /** DG.Color ARGB integer for the marker fill. Alpha is always replaced with
+     *  {@link MACROMOLECULE_HIGHLIGHT_ALPHA}. Falls back to {@link DEFAULT_MACROMOLECULE_HIGHLIGHT_FILL}. */
+    fillColor?: number;
+    /** DG.Color ARGB integer for the marker outline (HELM renderer ring stroke). Alpha is always
+     *  replaced with {@link MACROMOLECULE_HIGHLIGHT_ALPHA}. Falls back to
+     *  {@link DEFAULT_MACROMOLECULE_HIGHLIGHT_STROKE}. Ignored by background-painting renderers. */
+    strokeColor?: number;
+};
+export type MacromoleculeHighlightEventArgs = {
+    /** Match by dataframe name. Optional — if omitted, `tableId` or no filter is used. */
+    tableName?: string;
+    /** Match by dataframe id. Optional. */
+    tableId?: string;
+    /** Name of the macromolecule column. */
+    columnName: string;
+    /** Row index in the dataframe (as stored, i.e. `gridCell.tableRowIndex`). */
+    rowIdx: number;
+    /** 0-based monomer indices to highlight. Pass `null` or `[]` to clear the row. */
+    monomers: number[] | null;
+    /** Optional DG.Color ARGB int for the marker fill. Alpha is forced to
+     *  {@link MACROMOLECULE_HIGHLIGHT_ALPHA} to prevent solid colors. Ignored when clearing. */
+    fillColor?: number;
+    /** Optional DG.Color ARGB int for the marker outline (HELM ring). Alpha is forced to
+     *  {@link MACROMOLECULE_HIGHLIGHT_ALPHA}. Ignored when clearing. */
+    strokeColor?: number;
+};
+/** Optional color overrides accepted by the utility helpers (DG.Color ARGB ints). */
+export type MacromoleculeHighlightColors = {
+    fillColor?: number;
+    strokeColor?: number;
+};
+/** Converts a DG.Color ARGB int to an `rgba(r,g,b,alpha)` CSS string. The input's alpha is
+ *  discarded — the fixed {@link MACROMOLECULE_HIGHLIGHT_ALPHA} is used unless an explicit
+ *  override is passed (renderers may use a smaller alpha for backgrounds). */
+export declare function macromoleculeHighlightColorToCss(color: number, alpha?: number): string;
+/** Common input for the highlight helpers: accepts either a dataframe instance or its
+ *  identifying name/id, plus either a column instance or its name. */
+export type MacromoleculeHighlightTarget = {
+    table?: DG.DataFrame;
+    tableName?: string;
+    tableId?: string;
+    column?: DG.Column;
+    columnName?: string;
+};
+/** Fires the macromolecule highlight event. Updates on the renderer side are applied
+ *  asynchronously via the platform's custom-event bus; visible cells in the target column will
+ *  be repainted. */
+export declare function fireMacromoleculeHighlight(args: MacromoleculeHighlightEventArgs): void;
+/** Highlight the given monomers in a single row. Replaces any previous highlight for that row.
+ *  Optional `colors` override the defaults. */
+export declare function setMacromoleculeMonomerHighlight(target: MacromoleculeHighlightTarget, rowIdx: number, monomers: number[], colors?: MacromoleculeHighlightColors): void;
+/** Clear the highlight for a single row. */
+export declare function clearMacromoleculeMonomerHighlight(target: MacromoleculeHighlightTarget, rowIdx: number): void;
+/** Per-row entry for {@link setMacromoleculeMonomerHighlights}: either `null` (clear), a plain
+ *  monomer array (use defaults), or an object bundling monomers with optional color overrides. */
+export type MacromoleculeHighlightRowSpec = null | number[] | ({
+    monomers: number[];
+} & MacromoleculeHighlightColors);
+/** Set highlights for many rows at once. Each value is either `null` (clear that row), an
+ *  array of monomer indices (use default colors), or `{monomers, fillColor?, strokeColor?}`. */
+export declare function setMacromoleculeMonomerHighlights(target: MacromoleculeHighlightTarget, rowHighlights: Map<number, MacromoleculeHighlightRowSpec> | Record<number, MacromoleculeHighlightRowSpec>): void;
+/** Clears all highlights stored on the column by re-firing a clear event for every currently-
+ *  highlighted row. */
+export declare function clearAllMacromoleculeMonomerHighlights(target: MacromoleculeHighlightTarget): void;
+//# sourceMappingURL=macromolecule-highlight.d.ts.map

package/src/utils/macromolecule-highlight.d.ts.map ADDED Viewed

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package/src/utils/macromolecule-highlight.js ADDED Viewed

@@ -0,0 +1,87 @@
+import * as grok from 'datagrok-api/grok';
+import * as DG from 'datagrok-api/dg';
+/** Custom event id for toggling monomer highlights in macromolecule grid cells (HELM renderer
+ *  and generic sequence renderer). Payload: {@link MacromoleculeHighlightEventArgs}. Fire via
+ *  {@link grok.events.fireCustomEvent} or the convenience helpers in this module. */
+export const MACROMOLECULE_HIGHLIGHT_EVENT_ID = 'bio-macromolecule-monomer-highlight';
+/** Slot name on `column.temp` where per-row monomer highlights are stored by the macromolecule
+ *  cell renderers. Shape: `Map<rowIdx, MacromoleculeHighlightEntry>`. */
+export const MACROMOLECULE_HIGHLIGHT_TEMP = 'bio.macromolecule.highlightMonomers';
+/** Forced alpha (0..1) applied to every highlight color — solid colors are not allowed. */
+export const MACROMOLECULE_HIGHLIGHT_ALPHA = 0.4;
+/** Default fill color (translucent yellow) as a DG.Color ARGB int. The alpha component of the
+ *  input is ignored by the renderer and replaced with {@link MACROMOLECULE_HIGHLIGHT_ALPHA}. */
+export const DEFAULT_MACROMOLECULE_HIGHLIGHT_FILL = DG.Color.argb(255, 255, 220, 0);
+/** Default stroke color (amber) as a DG.Color ARGB int. */
+export const DEFAULT_MACROMOLECULE_HIGHLIGHT_STROKE = DG.Color.argb(255, 230, 140, 0);
+/** Converts a DG.Color ARGB int to an `rgba(r,g,b,alpha)` CSS string. The input's alpha is
+ *  discarded — the fixed {@link MACROMOLECULE_HIGHLIGHT_ALPHA} is used unless an explicit
+ *  override is passed (renderers may use a smaller alpha for backgrounds). */
+export function macromoleculeHighlightColorToCss(color, alpha) {
+    return `rgba(${DG.Color.r(color)},${DG.Color.g(color)},${DG.Color.b(color)},${alpha ?? MACROMOLECULE_HIGHLIGHT_ALPHA})`;
+}
+function resolveTarget(t) {
+    const columnName = t.columnName ?? t.column?.name;
+    if (!columnName)
+        throw new Error('MacromoleculeHighlight: columnName (or column) must be provided.');
+    const tableName = t.tableName ?? t.table?.name;
+    const tableId = t.tableId ?? t.table?.id;
+    return { tableName, tableId, columnName };
+}
+/** Fires the macromolecule highlight event. Updates on the renderer side are applied
+ *  asynchronously via the platform's custom-event bus; visible cells in the target column will
+ *  be repainted. */
+export function fireMacromoleculeHighlight(args) {
+    grok.events.fireCustomEvent(MACROMOLECULE_HIGHLIGHT_EVENT_ID, args);
+}
+/** Highlight the given monomers in a single row. Replaces any previous highlight for that row.
+ *  Optional `colors` override the defaults. */
+export function setMacromoleculeMonomerHighlight(target, rowIdx, monomers, colors) {
+    const { tableName, tableId, columnName } = resolveTarget(target);
+    fireMacromoleculeHighlight({
+        tableName, tableId, columnName, rowIdx, monomers,
+        fillColor: colors?.fillColor, strokeColor: colors?.strokeColor,
+    });
+}
+/** Clear the highlight for a single row. */
+export function clearMacromoleculeMonomerHighlight(target, rowIdx) {
+    const { tableName, tableId, columnName } = resolveTarget(target);
+    fireMacromoleculeHighlight({ tableName, tableId, columnName, rowIdx, monomers: null });
+}
+/** Set highlights for many rows at once. Each value is either `null` (clear that row), an
+ *  array of monomer indices (use default colors), or `{monomers, fillColor?, strokeColor?}`. */
+export function setMacromoleculeMonomerHighlights(target, rowHighlights) {
+    const { tableName, tableId, columnName } = resolveTarget(target);
+    const entries = rowHighlights instanceof Map ?
+        Array.from(rowHighlights.entries()) :
+        Object.entries(rowHighlights).map(([k, v]) => [Number(k), v]);
+    for (const [rowIdx, spec] of entries) {
+        if (spec == null) {
+            fireMacromoleculeHighlight({ tableName, tableId, columnName, rowIdx, monomers: null });
+        }
+        else if (Array.isArray(spec)) {
+            fireMacromoleculeHighlight({ tableName, tableId, columnName, rowIdx, monomers: spec });
+        }
+        else {
+            fireMacromoleculeHighlight({
+                tableName, tableId, columnName, rowIdx,
+                monomers: spec.monomers, fillColor: spec.fillColor, strokeColor: spec.strokeColor,
+            });
+        }
+    }
+}
+/** Clears all highlights stored on the column by re-firing a clear event for every currently-
+ *  highlighted row. */
+export function clearAllMacromoleculeMonomerHighlights(target) {
+    const { tableName, tableId, columnName } = resolveTarget(target);
+    const col = target.column ?? target.table?.columns.byName(columnName);
+    if (!col)
+        return;
+    const map = col.temp[MACROMOLECULE_HIGHLIGHT_TEMP];
+    if (!map || map.size === 0)
+        return;
+    const rows = Array.from(map.keys());
+    for (const rowIdx of rows)
+        fireMacromoleculeHighlight({ tableName, tableId, columnName, rowIdx, monomers: null });
+}
+//# sourceMappingURL=macromolecule-highlight.js.map

package/src/utils/macromolecule-highlight.js.map ADDED Viewed

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package/src/utils/monomer-selection-dialog.js CHANGED Viewed

@@ -91,7 +91,7 @@ export class MonomerSelectionWidget {
                     this.renderTags();
                     this.updateCountLabel();
                 }
-            });
+            }, 'Remove');
             removeBtn.style.marginLeft = '4px';
             removeBtn.style.cursor = 'pointer';
             const tag = ui.div([ui.span([symbol]), removeBtn], {

package/src/utils/monomer-selection-dialog.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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