@datagrok-libraries/bio 5.63.6 → 5.64.0

package/src/monomer-works/types.js

@@ -10,6 +10,13 @@ export function setMolGraph(dict, libKey, value) {
         pt = dict[libKey.polymerType] = {};
     pt[libKey.symbol] = value;
 }
+/** Role of an entry in a HELM RNA splitted sequence (sugar, base, phosphate). */
+export var NucleotideRole;
+(function (NucleotideRole) {
+    NucleotideRole[NucleotideRole["SUGAR"] = 0] = "SUGAR";
+    NucleotideRole[NucleotideRole["BASE"] = 1] = "BASE";
+    NucleotideRole[NucleotideRole["PHOSPHATE"] = 2] = "PHOSPHATE";
+})(NucleotideRole || (NucleotideRole = {}));
 export class MonomerMap extends Map {
     constructor(entries) {
         super(entries);

package/src/monomer-works/types.js.map

@@ -1 +1 @@
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+{"version":3,"file":"types.js","sourceRoot":"","sources":["types.ts"],"names":[],"mappings":"AAmEA,MAAM,UAAU,WAAW,CAAC,IAAwB,EAAE,MAAqB;IACzE,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;AACnD,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,IAAwB,EAAE,MAAqB;IACzE,OAAO,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;AACrD,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,IAAwB,EAAE,MAAqB,EAAE,KAAe;IAC1F,IAAI,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC;IAClC,IAAI,CAAC,EAAE;QACL,EAAE,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,GAAG,EAAE,CAAC;IACrC,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,KAAK,CAAC;AAC5B,CAAC;AAwCD,iFAAiF;AACjF,MAAM,CAAN,IAAY,cAIX;AAJD,WAAY,cAAc;IACxB,qDAAS,CAAA;IACT,mDAAQ,CAAA;IACR,6DAAa,CAAA;AACf,CAAC,EAJW,cAAc,KAAd,cAAc,QAIzB;AAID,MAAM,OAAO,UAAW,SAAQ,GAA4B;IAC1D,YAAY,OAA4C;QACtD,KAAK,CAAC,OAAO,CAAC,CAAC;IACjB,CAAC;CACF;AAED,kDAAkD;AAClD,MAAM,OAAO,cAAc;IACzB,YACkB,OAAe,EACf,QAAoB;QADpB,YAAO,GAAP,OAAO,CAAQ;QACf,aAAQ,GAAR,QAAQ,CAAY;IACnC,CAAC;IAEJ,MAAM,CAAC,WAAW,KAAK,OAAO,IAAI,cAAc,CAAC,EAAE,EAAE,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;CAC9E"}

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

@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"cell-renderer-monomer-placer.d.ts","sourceRoot":"","sources":["cell-renderer-monomer-placer.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAW,kBAAkB,EAA0C,MAAM,iBAAiB,CAAC;AAEtG,OAAO,EAAC,oBAAoB,EAAC,MAAM,2BAA2B,CAAC;AAC/D,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAMjC,OAAO,EAAC,eAAe,EAAC,MAAM,0BAA0B,CAAC;AAWzD,KAAK,kBAAkB,GAAG;IACxB,cAAc,EAAE,MAAM,CAAC;IACvB,cAAc,EAAE,kBAAkB,CAAC;IACnC,IAAI,EAAE,MAAM,CAAC;IACb,aAAa,EAAE,MAAM,CAAC;CACvB,CAAC;AAEF,eAAO,MAAM,cAAc,qBAAqB,CAAC;AAEjD,eAAO,MAAM,sBAAsB,QAAQ,CAAC;AAE5C;mCACmC;AACnC,wBAAgB,SAAS,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,MAAM,EAAE,mBAAmB,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAwBlG;AAiBD,qBAAa,aAAc,SAAQ,oBAAoB,CAAC,MAAM,CAAC;IAqCpD,kBAAkB,EAAE,MAAM;IACjC,OAAO,CAAC,QAAQ,CAAC,aAAa;IArChC,OAAO,CAAC,QAAQ,CAAa;IAC7B,OAAO,CAAC,kBAAkB,CAA2B;IAGrD,OAAO,KAAK,cAAc,GAAwE;IAC3F,KAAK,EAAE,kBAAkB,CAAC;IACjC,OAAO,CAAC,cAAc,CAAY;IAClC,OAAO,CAAC,6BAA6B,CAAa;IAE3C,iBAAiB,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;KAAE,CAAM;IACvD,oBAAoB,EAAE;QAAE,CAAC,GAAG,EAAE,MAAM,GAAG,WAAW,CAAA;KAAE,CAAM;IAEjE,OAAO,CAAC,eAAe,CAAkC;IACzD,OAAO,CAAC,iBAAiB,CAAa;IACtC,OAAO,CAAC,WAAW,CAAc;IAEjC,OAAO,CAAC,WAAW,CAAgD;IAEnE,OAAO,CAAC,SAAS,CAAc;IAE/B,OAAO,CAAC,aAAa,CAAgC;IAErD,gFAAgF;IAChF,OAAO,CAAC,mBAAmB,CAAmC;IAE9D,OAAO,CAAC,qBAAqB;IAM7B,sEAAsE;gBAEpE,OAAO,EAAE,EAAE,CAAC,UAAU,GAAG,IAAI,EAC7B,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,EAC3B,MAAM,EAAE,OAAO,EACR,kBAAkB,EAAE,MAAM,EAChB,aAAa,EAAE,MAAM,kBAAkB;IA2C1D,OAAO,CAAC,yBAAyB;IAwBjC,OAAO,CAAC,2BAA2B;IAKnC,OAAO,CAAC,+BAA+B;IAsE1B,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAsBlC,OAAO,CAAC,oBAAoB;IAqB5B,OAAO,CAAC,kBAAkB;IAU1B,OAAO,CAAC,uBAAuB;WAiBjB,eAAe,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC,MAAM;;;;IAWzC,KAAK,IAAI,MAAM;IAIxB,SAAS,CAAC,aAAa,IAAI,eAAe,GAAG,IAAI;cAI9B,KAAK,IAAI,IAAI;IAYhC,SAAS,CAAC,cAAc,IAAI,IAAI;IAIhC,qGAAqG;IAC9F,qBAAqB,CAAC,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,CAAC;IAmBpF,OAAO,CAAC,uBAAuB;IAgB/B,OAAO,CAAC,gCAAgC;IAqBxC,OAAO,CAAC,2BAA2B;IAgCnC,OAAO,CAAC,8BAA8B;IAoDtC,yCAAyC;IAClC,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,oBAAoB,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI;IAWnG,qBAAqB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAO1C,iBAAiB,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI;IAO7C,OAAO,CAAC,OAAO,CAAa;IAE5B,IAAI,aAAa,IAAI,MAAM,CAG1B;IAED,OAAO,CAAC,qBAAqB,CAAa;IAE1C,MAAM,CAAC,CAAC,EAAE,wBAAwB,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAC5E,QAAQ,EAAE,EAAE,CAAC,QAAQ,EAAE,UAAU,EAAE,EAAE,CAAC,aAAa;IA8NrD,OAAO,CAAC,4BAA4B;IAI3B,WAAW,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,EAAE,CAAC,EAAE,UAAU,GAAG,IAAI;CAiFjE;AAED,wBAAgB,eAAe,CAC7B,IAAI,EAAE,EAAE,CAAC,IAAI,GAAG,IAAI,GAAG,SAAS,EAAE,CAAC,EAAE,wBAAwB,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,GAC/F,MAAM,CAER"}

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

@@ -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;
@@ -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

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

@@ -72,6 +72,8 @@ export declare const splitterAsFastaSimple: SplitterFunc;
  * @return {SplitterFunc}
  */
 export declare function getSplitterWithSeparator(separator: string, limit?: number | undefined): SplitterFunc;
+export declare const RNA_HELM_TRIPLET_MONOMER_REG: RegExp;
+export declare const RNA_HELM_TERMINAL_PHOSPHATELESS_MONOMER_REG: RegExp;
 /** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA).
  * Only for linear polymers, does not split RNA for ribose and phosphate monomers.
  * EG byciclic helm: PEPTIDE1{F}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[Cys_Bn].[meG].[Phe_3Cl].[dD].T.[dI].T.[dK].[aG].[3Pal].[xiIle].[meD].[Ala_tBu]}|PEPTIDE3{L.[Pro_4Me3OH].S.[NMe2Abz].Q.[3Pal].[xiIle].[D-Hyp].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].N.[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0

package/src/utils/macromolecule/utils.d.ts.map

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

@@ -305,6 +305,10 @@ export function getSplitterWithSeparator(separator, limit = undefined) {
         }
     };
 }
+// this scary thing is a pattern for matching HELM RNA notation with most complex cases like [Sug(smt)]([NNs])[pm()].
+export const RNA_HELM_TRIPLET_MONOMER_REG = /^((?:[^\[\]()]|\[[^\[\]]*\])+)\(((?:[^\[\]()]|\[[^\[\]]*\])+)\)((?:[^\[\]()]|\[[^\[\]]*\])+)$/;
+// this one matches the terminal phosphate-less monomer in RNA HELM notation, e.g. [dR](A) or [R](A)
+export const RNA_HELM_TERMINAL_PHOSPHATELESS_MONOMER_REG = /^((?:[^\[\]()]|\[[^\[\]]*\])+)\(((?:[^\[\]()]|\[[^\[\]]*\])+)\)$/;
 /** Splits Helm string to monomers, but does not replace monomer names to other notation (e.g. for RNA).
  * Only for linear polymers, does not split RNA for ribose and phosphate monomers.
  * EG byciclic helm: PEPTIDE1{F}|PEPTIDE2{[dI].[Trp_Ome].[Asp_OMe].[Cys_Bn].[meG].[Phe_3Cl].[dD].T.[dI].T.[dK].[aG].[3Pal].[xiIle].[meD].[Ala_tBu]}|PEPTIDE3{L.[Pro_4Me3OH].S.[NMe2Abz].Q.[3Pal].[xiIle].[D-Hyp].[Ala_tBu].[dI].[Trp_Ome].[Asp_OMe].N.[meG].[Phe_34diCl].[Phe_34diCl]}$PEPTIDE2,PEPTIDE2,16:R2-1:R1|PEPTIDE3,PEPTIDE3,16:R2-1:R1|PEPTIDE3,PEPTIDE2,10:R3-1:R3|PEPTIDE1,PEPTIDE2,1:R2-9:R3$$$V2.0
@@ -323,10 +327,22 @@ export const splitterAsHelm = (seq) => {
     // since we removed }|, need to add } to last part
     for (let i = 0; i < spList.length - 1; i++)
         spList[i] = spList[i] + '}';
-    const mListSplit = spList
-        .map((sp) => (sp.match(/(?<=\{).+(?=})/)?.[0]?.split('.') ?? [])
-        .map((m) => cleanupHelmSymbol(m)));
     const polymerTypes = spList.map((sp) => sp.replace(/\d{1,2}\{.+\}/, ''));
+    const mListSplit = spList
+        .map((sp, i) => (sp.match(/(?<=\{).+(?=})/)?.[0]?.split('.') ?? [])
+        .flatMap((m, k, fList) => {
+        if (polymerTypes[i] === "RNA" /* PolymerTypes.RNA */) {
+            const match = RNA_HELM_TRIPLET_MONOMER_REG.exec(m);
+            if (match != null)
+                return [cleanupHelmSymbol(match[1]), cleanupHelmSymbol(match[2]), cleanupHelmSymbol(match[3])];
+            if (k === fList.length - 1) { // if its the last monomer, it can be phosphate-less, so try to match it with another regex
+                const terminalMatch = RNA_HELM_TERMINAL_PHOSPHATELESS_MONOMER_REG.exec(m);
+                if (terminalMatch != null)
+                    return [cleanupHelmSymbol(terminalMatch[1]), cleanupHelmSymbol(terminalMatch[2])];
+            }
+        }
+        return [cleanupHelmSymbol(m)];
+    }));
     const res = new HelmSplitted(mListSplit, connectionsPart ?? '', polymerTypes, GapOriginals[NOTATION.HELM]);
     return res;
 };

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

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

@@ -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

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