@datagrok-libraries/bio 5.52.0 → 5.52.2

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "friendlyName": "Datagrok bio library",
-  "version": "5.52.0",
+  "version": "5.52.2",
   "description": "Bio utilities, types supporting Macromolecule, Molecule3D data",
   "dependencies": {
     "@datagrok-libraries/chem-meta": "^1.2.7",

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

@@ -10,7 +10,10 @@ type MonomerPlacerProps = {
     fontCharWidth: number;
 };
 export declare const undefinedColor = "rgb(100,100,100)";
-export declare function hitBounds(bounds: number[], x: number): number | null;
+export declare const shiftedLeftPaddingText = "...";
+/** Be ware, this can return -1 meaning that hovering/clicking happened on the three dots
+ * and not on the monomer itself */
+export declare function hitBounds(bounds: number[], x: number, positionShiftPixels?: number): number | null;
 export declare class MonomerPlacer extends CellRendererBackBase<string> {
     monomerLengthLimit: number;
     private readonly propsProvider;
@@ -46,11 +49,12 @@ export declare class MonomerPlacer extends CellRendererBackBase<string> {
     private getCellMonomerLengthsForSeqValue;
     private getCellMonomerLengthsForSeqMsa;
     /** Returns seq position for pointer x */
-    getPosition(rowIdx: number, x: number, width: number): number | null;
+    getPosition(rowIdx: number, x: number, width: number, positionShiftPadding?: number): number | null;
     setMonomerLengthLimit(value: number): void;
     setSeparatorWidth(value: number): void;
     private padding;
     get positionShift(): number;
+    private _leftThreeDotsPadding;
     render(g: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, gridCell: DG.GridCell, _cellStyle: DG.GridCellStyle): void;
     onMouseMove(gridCell: DG.GridCell, e: MouseEvent): void;
 }

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":"AAIA,OAAO,KAAK,EAAE,MAAM,iBAAiB,CAAC;AAKtC,OAAO,EAAW,kBAAkB,EAA0C,MAAM,iBAAiB,CAAC;AAEtG,OAAO,EAAC,oBAAoB,EAAqB,MAAM,2BAA2B,CAAC;AACnF,OAAO,EAAC,OAAO,EAAC,MAAM,UAAU,CAAC;AAKjC,OAAO,EAAC,eAAe,EAAC,MAAM,gBAAgB,CAAC;AAM/C,KAAK,kBAAkB,GAAG;IACxB,cAAc,EAAE,MAAM,CAAC;IACvB,cAAc,EAAE,kBAAkB,CAAC;IACnC,IAAI,EAAE,MAAM,CAAC;IAAC,aAAa,EAAE,MAAM,CAAC;CACrC,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;AAED,qBAAa,aAAc,SAAQ,oBAAoB,CAAC,MAAM,CAAC;IAsBpD,kBAAkB,EAAE,MAAM;IACjC,OAAO,CAAC,QAAQ,CAAC,aAAa;IAtBhC,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,SAAS,CAAc;IAE/B,OAAO,CAAC,aAAa,CAAgC;IAErD,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;IA+B7C,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;WAmBpB,eAAe,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC,MAAM;;;;IAWzC,KAAK,IAAI,MAAM;IAIxB,SAAS,CAAC,aAAa,IAAI,eAAe,GAAG,IAAI;cAI9B,KAAK,IAAI,IAAI;IAWhC,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,2BAA2B;IAgCnC,OAAO,CAAC,gCAAgC;IAqBxC,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;IASnG,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;IA0I5C,WAAW,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,EAAE,CAAC,EAAE,UAAU,GAAG,IAAI;CAkDjE;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

@@ -12,7 +12,13 @@ import { HelmTypes } from '../helm/consts';
 import { execMonomerHoverLinks } from '../monomer-works/monomer-hover';
 import * as operators from 'rxjs/operators';
 export const undefinedColor = 'rgb(100,100,100)';
-export function hitBounds(bounds, x) {
+export const shiftedLeftPaddingText = '...';
+/** Be ware, this can return -1 meaning that hovering/clicking happened on the three dots
+ * and not on the monomer itself */
+export function hitBounds(bounds, x, positionShiftPixels) {
+    if ((positionShiftPixels ?? 0) > 0 && x < (bounds[0] ?? 0) + positionShiftPixels)
+        return -1;
+    x -= positionShiftPixels ?? 0;
     let iterationCount = 100;
     let leftI = 0;
     let rightI = bounds.length - 1;
@@ -47,6 +53,7 @@ export class MonomerPlacer extends CellRendererBackBase {
         this._monomerStructureMap = {}; // caches the atomic structures of monomers
         this.sysMonomerLib = null;
         this.padding = 5;
+        this._leftThreeDotsPadding = 0;
         this.props = this.propsProvider();
         this._processedRows = DG.BitSet.create(this.tableCol.length);
         if (this.gridCol) {
@@ -137,7 +144,7 @@ export class MonomerPlacer extends CellRendererBackBase {
     }
     getSummedMonomerLengths(res) {
         const resSum = new Array(res.length + 1);
-        resSum[0] = 5; // padding
+        resSum[0] = this.padding; // padding
         for (let pos = 1; pos < resSum.length; pos++)
             resSum[pos] = resSum[pos - 1] + res[pos - 1];
         // due to implementation specifics and performance, resSum can have NaN s at the end for stuff that is not visible
@@ -252,13 +259,13 @@ export class MonomerPlacer extends CellRendererBackBase {
         return res; // first (and single) row of data
     }
     /** Returns seq position for pointer x */
-    getPosition(rowIdx, x, width) {
+    getPosition(rowIdx, x, width, positionShiftPadding) {
         const [_monomerMaxLengthList, monomerMaxLengthSumList] = this.getCellMonomerLengths(rowIdx, width);
         const sh = this.seqHelper.getSeqHandler(this.tableCol);
         const seqSS = sh.getSplitted(rowIdx);
         if (seqSS.length === 0)
             return null;
-        return hitBounds(monomerMaxLengthSumList, x);
+        return hitBounds(monomerMaxLengthSumList, x, positionShiftPadding);
     }
     setMonomerLengthLimit(value) {
         if (this.monomerLengthLimit != value) {
@@ -273,7 +280,8 @@ export class MonomerPlacer extends CellRendererBackBase {
         }
     }
     get positionShift() {
-        return Number.parseInt(this.tableCol?.tags[bioTAGS.positionShift] ?? '0') ?? 0;
+        const parsed = Number.parseInt(this.tableCol?.tags[bioTAGS.positionShift] ?? '0') ?? 0;
+        return isNaN(parsed) ? 0 : Math.max(parsed, 0);
     }
     render(g, x, y, w, h, gridCell, _cellStyle) {
         // for cases when we render it on somewhere other than grid, gridRow might be null or incorrect (set to 0).
@@ -339,7 +347,7 @@ export class MonomerPlacer extends CellRendererBackBase {
                 const splitterFunc = sh.getSplitter(splitLimit);
                 const seqSS = splitterFunc(((tempReferenceSequence != null) && (tempReferenceSequence != '')) ?
                     tempReferenceSequence : tempCurrentWord ?? '');
-                return wu.count(0).take(seqSS.length).map((posIdx) => seqSS.getOriginal(posIdx)).toArray();
+                return wu.count(0).take(seqSS.length).slice(positionShift).map((posIdx) => seqSS.getOriginal(posIdx)).toArray();
             })();
             const subParts = isRenderedOnGrid ? sh.getSplitted(rowIdx) : sh.splitter(value);
             if (!isRenderedOnGrid)
@@ -347,6 +355,10 @@ export class MonomerPlacer extends CellRendererBackBase {
             let drawStyle = DrawStyle.classic;
             if (aligned && aligned.includes('MSA') && units == NOTATION.SEPARATOR)
                 drawStyle = DrawStyle.MSA;
+            // if the sequence is rendered in shifted mode, we will also render three dots at start, indicating the shift
+            this._leftThreeDotsPadding = positionShift > 0 ? g.measureText(shiftedLeftPaddingText).width : 0;
+            // currently selected position to highlight
+            const selectedPosition = Number.parseInt(tableCol.getTag(bioTAGS.selectedPosition) ?? '-200');
             const visibleSeqLength = Math.min(subParts.length, splitLimit);
             for (let posIdx = positionShift; posIdx < visibleSeqLength; ++posIdx) {
                 const om = posIdx < subParts.length ? subParts.getOriginal(posIdx) : sh.defaultGapOriginal;
@@ -365,12 +377,22 @@ export class MonomerPlacer extends CellRendererBackBase {
                     color: color, pivot: 0, left: true, transparencyRate: 1.0, separator: separator, last: last,
                     drawStyle: drawStyle, maxWord: maxLengthWordsSum, wordIdx: posIdx - positionShift, gridCell: gridCell,
                     referenceSequence: referenceSequence, maxLengthOfMonomer: maxLengthOfMonomer,
-                    monomerTextSizeMap: this._monomerLengthMap, logger: this.logger
+                    monomerTextSizeMap: this._monomerLengthMap, logger: this.logger,
+                    selectedPosition: isNaN(selectedPosition) || selectedPosition < 1 ? undefined : selectedPosition - positionShift,
                 };
-                printLeftOrCentered(g, om, x + this.padding, y, w, h, opts);
+                printLeftOrCentered(g, om, x + this.padding + this._leftThreeDotsPadding, y, w, h, opts);
                 if (minDistanceRenderer > w)
                     break;
             }
+            if (positionShift > 0) {
+                const opts = {
+                    color: undefinedColor, pivot: 0, left: true, transparencyRate: 1.0, separator: separator, last: false,
+                    drawStyle: drawStyle, maxWord: maxLengthWordsSum, wordIdx: 0, gridCell: gridCell,
+                    maxLengthOfMonomer: maxLengthOfMonomer,
+                    monomerTextSizeMap: this._monomerLengthMap, logger: this.logger,
+                };
+                printLeftOrCentered(g, shiftedLeftPaddingText, x + this.padding, y, w, h, opts);
+            }
         }
         catch (err) {
             const [errMsg, errStack] = errInfo(err);
@@ -388,6 +410,7 @@ export class MonomerPlacer extends CellRendererBackBase {
             return;
         // if (gridCell.cell.column.getTag(bioTAGS.aligned) !== ALIGNMENT.SEQ_MSA)
         //   return;
+        const positionShift = this.positionShift;
         const gridCellBounds = gridCell.bounds;
         // const value: any = gridCell.cell.value;
         //
@@ -397,16 +420,17 @@ export class MonomerPlacer extends CellRendererBackBase {
         //   maxLengthWordsSum[posI] = maxLengthWordsSum[posI - 1] + maxLengthWords[posI];
         // const maxIndex = maxLengthWords.length;
         const argsX = e.offsetX - gridCell.gridColumn.left + (gridCell.gridColumn.left - gridCellBounds.x);
-        const left = this.getPosition(gridCell.tableRowIndex, argsX, gridCellBounds.width);
+        const leftPadding = positionShift > 0 && (this._leftThreeDotsPadding ?? 0) > 0 ? this._leftThreeDotsPadding : 0;
+        const left = this.getPosition(gridCell.tableRowIndex, argsX, gridCellBounds.width, leftPadding);
         this.logger.debug(`${logPrefix}, start, argsX: ${argsX}, left: ${left}`);
         const sh = this.seqHelper.getSeqHandler(this.tableCol);
         const seqSS = sh.getSplitted(gridCell.tableRowIndex);
-        if (left !== null && left + this.positionShift < seqSS.length) {
+        if (left !== null && left >= 0 && left + positionShift < seqSS.length) {
             const alphabet = sh.alphabet ?? ALPHABET.UN;
             const seqMonomer = {
                 position: left,
                 biotype: alphabet === ALPHABET.RNA || alphabet === ALPHABET.DNA ? HelmTypes.NUCLEOTIDE : HelmTypes.AA,
-                symbol: seqSS.getCanonical(left + this.positionShift),
+                symbol: seqSS.getCanonical(left + positionShift),
             };
             const tooltipElements = [];
             let monomerDiv = this._monomerStructureMap[seqMonomer.symbol];
@@ -422,8 +446,10 @@ export class MonomerPlacer extends CellRendererBackBase {
             execMonomerHoverLinks(gridCell, seqMonomer);
         }
         else {
-            //
-            ui.tooltip.hide();
+            if (left === -1)
+                ui.tooltip.show(ui.divText(`${Math.min(positionShift, seqSS.length)} hidden monomers`), e.x + 16, e.y + 16);
+            else
+                ui.tooltip.hide();
             execMonomerHoverLinks(gridCell, null);
         }
     }

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

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

@@ -27,6 +27,7 @@ export declare const PrintOptionsDefaults: {
         [key: string]: TextMetrics;
     };
     /** */ logger?: ILogger;
+    selectedPosition?: 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

@@ -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;CACtB,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,CAkER"}
+{"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,CAsER"}

package/src/utils/cell-renderer.js

@@ -32,6 +32,7 @@ export const PrintOptionsDefaults = new class {
         /** Max length of a monomer */ this.maxLengthOfMonomer = null;
         /** Map of monomers' text sizes */ this.monomerTextSizeMap = {};
         /** */ this.logger = undefined;
+        this.selectedPosition = undefined;
     }
 }();
 /** A function that prints a string aligned to left or centered.
@@ -85,6 +86,10 @@ export function printLeftOrCentered(g, s, x, y, w, h, options) {
     }
     /** Draw color part at {@link dx1}, and gray part at {@link dx2}. */
     function draw(dx1, dx2) {
+        if (opts.selectedPosition === opts.wordIdx + 1) {
+            g.fillStyle = 'rgba(60, 177, 115, 0.2)'; // green for selected position
+            g.fillRect(x + dx1, y, maxColorTextSize, h);
+        }
         const drawColor = colorCode ? opts.color : blackColor;
         g.fillStyle = drawColor;
         g.globalAlpha = opts.transparencyRate;

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

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

@@ -27,7 +27,8 @@ export declare enum TAGS {
     positionNames = ".positionNames",
     positionLabels = ".positionLabels",
     regions = ".regions",
-    positionShift = ".positionShift"
+    positionShift = ".positionShift",
+    selectedPosition = ".selectedPosition"
 }
 export { TAGS as BioTags };
 export declare const positionSeparator: string;

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

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

@@ -27,6 +27,7 @@ export var TAGS;
     TAGS["positionLabels"] = ".positionLabels";
     TAGS["regions"] = ".regions";
     TAGS["positionShift"] = ".positionShift";
+    TAGS["selectedPosition"] = ".selectedPosition";
 })(TAGS || (TAGS = {}));
 export { TAGS as BioTags };
 export const positionSeparator = ', ';

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

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

@@ -0,0 +1,109 @@
+/**
+ * MSAHeader.ts - Interactive MSA Header Component
+ * This module provides functionality for an interactive MSA (Multiple Sequence Alignment) header
+ * with position markers, slider navigation, and position selection.
+ */
+interface WindowRange {
+    start: number;
+    end: number;
+}
+interface MSAHeaderOptions {
+    canvas: HTMLCanvasElement;
+    totalPositions?: number;
+    positionWidth?: number;
+    headerHeight?: number;
+    sliderHeight?: number;
+    currentPosition?: number;
+    windowStartPosition?: number;
+    cellBackground?: boolean;
+    sliderColor?: string;
+    x?: number;
+    y?: number;
+    width?: number;
+    height?: number;
+    onPositionChange?: (position: number, range: WindowRange) => void;
+}
+interface Preventable {
+    preventDefault: () => void;
+}
+export declare class MSAScrollingHeader {
+    private config;
+    private state;
+    private canvas;
+    private ctx;
+    private eventElement;
+    /**
+     * Constructor for the MSA Header
+     * @param {MSAHeaderOptions} options - Configuration options
+     */
+    constructor(options: MSAHeaderOptions);
+    /**
+     * Initialize the component
+     */
+    private init;
+    get isValid(): boolean;
+    draw(x: number, y: number, w: number, h: number, currentPos: number, scrollerStart: number, preventable: Preventable): void;
+    getCoords(e: MouseEvent): {
+        x: number;
+        y: number;
+    };
+    isInHeaderArea(e: MouseEvent): boolean;
+    get positionWidth(): number;
+    set positionWidth(value: number);
+    isInSliderArea(e: MouseEvent): boolean;
+    get sliderWidth(): number;
+    isInSliderDraggableArea(e: MouseEvent): boolean;
+    /**
+     * Handle mouse down (start dragging)
+     * @param {MouseEvent} e - Mouse event
+     */
+    private handleMouseDown;
+    private handleMouseWheel;
+    /**
+     * Handle mouse move (dragging)
+     * @param {MouseEvent} e - Mouse event
+     */
+    private handleMouseMove;
+    private handleKeyDown;
+    /**
+     * Handle mouse up (end dragging)
+     */
+    private handleMouseUp;
+    /**
+     * Handle slider drag
+     * @param {number} x - X position of mouse
+     */
+    private handleSliderDrag;
+    get headerHeight(): number;
+    /** Soft setting of header hight, without redrawing or update event
+     * @param {number} value - New header height
+     */
+    set headerHeight(value: number);
+    /**
+     * Handle click on positions
+     * @param {MouseEvent} e - Mouse event
+     */
+    private handleClick;
+    /**
+     * Get the current window range
+     * @return {WindowRange} Object with start and end properties
+     */
+    getWindowRange(): WindowRange;
+    /**
+     * Update configuration
+     * @param {MSAHeaderOptions} newConfig - New configuration options
+     */
+    updateConfig(newConfig: Partial<MSAHeaderOptions>): void;
+    /**
+     * Get current position
+     * @return {number} Current position
+     */
+    getCurrentPosition(): number;
+    /**
+     * Set current position
+     * @param {number} position - New position
+     */
+    setCurrentPosition(position: number): void;
+}
+export {};
+//# sourceMappingURL=sequence-position-scroller.d.ts.map

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

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package/src/utils/sequence-position-scroller.js

@@ -0,0 +1,394 @@
+/* eslint-disable max-len */
+/**
+ * MSAHeader.ts - Interactive MSA Header Component
+ * This module provides functionality for an interactive MSA (Multiple Sequence Alignment) header
+ * with position markers, slider navigation, and position selection.
+ */
+import * as ui from 'datagrok-api/ui';
+export class MSAScrollingHeader {
+    /**
+     * Constructor for the MSA Header
+     * @param {MSAHeaderOptions} options - Configuration options
+     */
+    constructor(options) {
+        this.canvas = null;
+        this.ctx = null;
+        // Default configuration with required fields
+        this.config = {
+            x: options.x || 0,
+            y: options.y || 0,
+            width: options.width || 0,
+            height: options.height || 0,
+            windowStartPosition: options.windowStartPosition || 1,
+            positionWidth: options.positionWidth || 15,
+            totalPositions: options.totalPositions || 5000,
+            headerHeight: options.headerHeight || 50,
+            sliderHeight: options.sliderHeight || 8,
+            currentPosition: options.currentPosition || 1,
+            cellBackground: options.cellBackground !== undefined ? options.cellBackground : true,
+            sliderColor: options.sliderColor || 'rgba(220, 220, 220, 0.4)',
+            onPositionChange: options.onPositionChange || ((_, __) => { }),
+            ...options // Override defaults with any provided options
+        };
+        this.eventElement = ui.div();
+        this.eventElement.style.position = 'absolute';
+        this.config.canvas.parentElement?.appendChild(this.eventElement);
+        // Internal state
+        this.state = {
+            isDragging: false,
+            dragStartX: 0
+        };
+        this.init();
+    }
+    /**
+     * Initialize the component
+     */
+    init() {
+        // Get canvas and context
+        this.canvas = this.config.canvas;
+        if (!this.canvas) {
+            console.error(`canvas not found.`);
+            return;
+        }
+        const context = this.canvas.getContext('2d');
+        if (!context) {
+            console.error('Failed to get 2D context from canvas');
+            return;
+        }
+        this.ctx = context;
+        // Add event listeners
+        this.eventElement.addEventListener('mousedown', this.handleMouseDown.bind(this));
+        this.eventElement.addEventListener('mousemove', this.handleMouseMove.bind(this));
+        this.eventElement.addEventListener('mouseup', this.handleMouseUp.bind(this));
+        this.eventElement.addEventListener('mouseleave', this.handleMouseUp.bind(this));
+        this.eventElement.addEventListener('click', this.handleClick.bind(this));
+        this.eventElement.addEventListener('wheel', this.handleMouseWheel.bind(this));
+        window.addEventListener('keydown', this.handleKeyDown.bind(this));
+    }
+    get isValid() {
+        return !!this.canvas && !!this.ctx && this.config.height >= this.config.headerHeight;
+    }
+    draw(x, y, w, h, currentPos, scrollerStart, preventable) {
+        // soft internal update
+        if (this.config.x != x || this.config.y != y || this.config.width != w || this.config.height != h || this.config.currentPosition != currentPos || this.config.windowStartPosition != scrollerStart)
+            Object.assign(this.config, { x, y, width: w, height: h, currentPosition: currentPos, windowStartPosition: scrollerStart });
+        if (!this.isValid) {
+            this.eventElement.style.display = 'none';
+            return;
+        }
+        this.ctx.save();
+        // Clear canvas
+        this.ctx.clearRect(x, y, w, h);
+        this.ctx.translate(x, y);
+        this.ctx.rect(0, 0, w, h);
+        this.ctx.clip();
+        // Calculate dimensions
+        const canvasWidth = w;
+        const canvasHeight = h;
+        const topPadding = 5;
+        const posIndexTop = topPadding;
+        const sliderTop = this.config.headerHeight - this.config.sliderHeight;
+        // Draw the full sequence slider bar (very subtle gray bar)
+        this.ctx.fillStyle = this.config.sliderColor;
+        this.ctx.fillRect(0, sliderTop, canvasWidth, this.config.sliderHeight);
+        const visiblePositionsN = Math.floor(this.config.width / this.config.positionWidth);
+        const windowStart = Math.max(1, this.config.windowStartPosition);
+        // Calculate slider position on the bar
+        const totalSliderRange = this.config.totalPositions - visiblePositionsN;
+        const sliderStartPX = totalSliderRange <= 0 ? 0 :
+            windowStart / (this.config.totalPositions) * (canvasWidth - this.sliderWidth);
+        const sliderLengthPX = totalSliderRange <= 0 ? canvasWidth :
+            this.sliderWidth;
+        // Draw slider window (darker rectangle)
+        this.ctx.fillStyle = 'rgba(150, 150, 150, 0.5)';
+        this.ctx.fillRect(sliderStartPX, sliderTop, sliderLengthPX, this.config.sliderHeight);
+        if (this.config.currentPosition >= 1 && this.config.currentPosition <= this.config.totalPositions) {
+            // Calculate the position of the current selection as a proportion of total sequence
+            const currentPositionRatio = (this.config.currentPosition - 1) / (this.config.totalPositions - 1);
+            const notchX = Math.round(currentPositionRatio * canvasWidth);
+            // Draw a 3px thick vertical green marker at this position
+            this.ctx.fillStyle = '#3CB173'; // Same green as the cell highlight
+            this.ctx.fillRect(notchX - 1, // Center the 3px marker on the calculated position
+            sliderTop - 2, // Extend the marker 2px above the scrollbar
+            3, // 3px width as requested
+            this.config.sliderHeight + 4 // Make the marker taller than the scrollbar
+            );
+        }
+        // Draw position marks and indices
+        for (let i = 0; i < visiblePositionsN; i++) {
+            const position = windowStart + i;
+            if (position > this.config.totalPositions)
+                break;
+            const x = i * this.config.positionWidth;
+            const cellWidth = this.config.positionWidth;
+            const cellCenterX = x + cellWidth / 2;
+            // Draw cell background for monospace appearance
+            if (this.config.cellBackground) {
+                // Very light alternating cell background
+                this.ctx.fillStyle = i % 2 === 0 ? 'rgba(248, 248, 248, 0.3)' : 'rgba(242, 242, 242, 0.2)';
+                this.ctx.fillRect(x, posIndexTop, cellWidth, Math.min(this.config.headerHeight - topPadding, canvasHeight - posIndexTop) - this.config.sliderHeight);
+                // Cell borders - very light vertical lines
+                this.ctx.strokeStyle = 'rgba(220, 220, 220, 0.7)';
+                this.ctx.beginPath();
+                this.ctx.moveTo(x, posIndexTop);
+                this.ctx.lineTo(x, Math.min(this.config.headerHeight, canvasHeight) - this.config.sliderHeight);
+                this.ctx.stroke();
+            }
+            // Draw position dot for every position - centered in cell
+            this.ctx.fillStyle = '#999999';
+            this.ctx.beginPath();
+            this.ctx.arc(cellCenterX, posIndexTop * 2, 1, 0, Math.PI * 2);
+            this.ctx.fill();
+            // Draw position number for every 10th position, on the current position and also make sure that the number is not obstructed by some other numbers
+            if (position === this.config.currentPosition || ((position === 1 || position % 10 === 0) && Math.abs(position - this.config.currentPosition) > 1)) {
+                this.ctx.fillStyle = '#333333';
+                this.ctx.font = '12px monospace';
+                this.ctx.textAlign = 'center';
+                this.ctx.textBaseline = 'middle';
+                this.ctx.fillText(position.toString(), cellCenterX, posIndexTop * 4);
+            }
+            // Highlight current selected position with square marker
+            // if current is outside the range, draw it at the end
+            if (position === this.config.currentPosition) {
+                // Draw filled background with 50% opacity
+                this.ctx.fillStyle = 'rgba(60, 177, 115, 0.2)';
+                this.ctx.fillRect(x, 0, cellWidth, sliderTop);
+            }
+        }
+        this.ctx.restore();
+        // Prevent default behavior if in header area
+        preventable.preventDefault();
+        this.eventElement.style.display = 'block';
+        this.eventElement.style.left = `${this.config.x}px`;
+        this.eventElement.style.top = `${this.config.y}px`;
+        this.eventElement.style.width = `${this.config.width}px`;
+        this.eventElement.style.height = `${this.config.height}px`;
+    }
+    getCoords(e) {
+        const rect = this.canvas.getBoundingClientRect();
+        const x = e.clientX - rect.left - this.config.x;
+        const y = e.clientY - rect.top - this.config.y;
+        return { x, y };
+    }
+    isInHeaderArea(e) {
+        const { x, y } = this.getCoords(e);
+        return x >= 0 && x <= this.config.width && y >= 0 && y <= this.config.headerHeight;
+    }
+    get positionWidth() {
+        return this.config.positionWidth;
+    }
+    set positionWidth(value) {
+        this.config.positionWidth = value;
+    }
+    isInSliderArea(e) {
+        const { y } = this.getCoords(e);
+        const sliderTop = this.config.headerHeight - this.config.sliderHeight;
+        return y > sliderTop && y < sliderTop + this.config.sliderHeight;
+    }
+    get sliderWidth() {
+        const pseudoPositionWidth = this.config.width / this.config.totalPositions;
+        const w = pseudoPositionWidth * (this.config.width / this.config.positionWidth);
+        return Math.max(w, 20);
+    }
+    isInSliderDraggableArea(e) {
+        const { x, y } = this.getCoords(e);
+        const sliderTop = this.config.headerHeight - this.config.sliderHeight;
+        const startSeqX = this.config.windowStartPosition;
+        const pseudoPositionWidth = (this.config.width - this.sliderWidth) / this.config.totalPositions;
+        const startSliderXPX = (startSeqX - 1) * pseudoPositionWidth;
+        const endSliderXPX = startSliderXPX + this.sliderWidth;
+        return y > sliderTop && y < sliderTop + this.config.sliderHeight && x >= startSliderXPX && x < endSliderXPX;
+    }
+    /**
+     * Handle mouse down (start dragging)
+     * @param {MouseEvent} e - Mouse event
+     */
+    handleMouseDown(e) {
+        if (!this.isValid)
+            return;
+        const { x } = this.getCoords(e);
+        if (this.isInSliderDraggableArea(e)) {
+            this.state.isDragging = true;
+            this.state.dragStartX = x;
+            this.handleSliderDrag(x);
+            e.preventDefault();
+            e.stopPropagation();
+            e.stopImmediatePropagation();
+        }
+    }
+    handleMouseWheel(e) {
+        if (!this.isValid)
+            return;
+        if (this.isInHeaderArea(e)) {
+            e.preventDefault();
+            e.stopPropagation();
+            e.stopImmediatePropagation();
+            // Determine scroll direction and amount
+            // Use deltaX if available (for horizontal scrolling devices)
+            // otherwise use deltaY with shift key for horizontal scroll
+            const delta = e.shiftKey ? Math.sign(e.deltaY) : Math.sign(e.deltaX || e.deltaY);
+            // Move by 1 position or more for faster scrolling (optional)
+            const scrollSpeed = e.shiftKey ? 3 : 1; // Faster scrolling with shift
+            const newStartPosition = this.config.windowStartPosition + (delta * scrollSpeed);
+            // Clamp to valid range
+            const visiblePositions = Math.floor(this.config.width / this.config.positionWidth);
+            const maxStart = this.config.totalPositions - visiblePositions + 1;
+            this.config.windowStartPosition = Math.max(1, Math.min(maxStart, newStartPosition));
+            if (typeof this.config.onPositionChange === 'function')
+                this.config.onPositionChange(this.config.currentPosition, this.getWindowRange());
+        }
+    }
+    /**
+     * Handle mouse move (dragging)
+     * @param {MouseEvent} e - Mouse event
+     */
+    handleMouseMove(e) {
+        if (!this.state.isDragging || !this.isValid)
+            return;
+        const rect = this.canvas.getBoundingClientRect();
+        const x = e.clientX - rect.left - this.config.x;
+        this.handleSliderDrag(x);
+        e.preventDefault();
+        e.stopPropagation();
+        e.stopImmediatePropagation();
+    }
+    handleKeyDown(e) {
+        if (!this.isValid || this.config.currentPosition < 1)
+            return;
+        if (e.key === 'ArrowLeft' || e.key === 'ArrowRight') {
+            e.preventDefault();
+            e.stopPropagation();
+            e.stopImmediatePropagation();
+            // Determine scroll direction
+            const delta = e.key === 'ArrowLeft' ? -1 : 1;
+            const newPosition = Math.min(Math.max(this.config.currentPosition + delta, 1), this.config.totalPositions);
+            if (newPosition === this.config.currentPosition)
+                return;
+            this.config.currentPosition = newPosition;
+            // make sure that the cureent position is visible
+            const visiblePositions = Math.floor(this.config.width / this.config.positionWidth);
+            const start = this.config.windowStartPosition;
+            const end = start + visiblePositions - 1;
+            if (newPosition < start || newPosition > end) {
+                if (delta < 0)
+                    this.config.windowStartPosition = newPosition;
+                else
+                    this.config.windowStartPosition = Math.max(1, newPosition - visiblePositions + 1);
+            }
+        }
+        else if (e.key === 'Escape') {
+            // reset the current position
+            this.config.currentPosition = -2;
+            e.preventDefault();
+            e.stopPropagation();
+            e.stopImmediatePropagation();
+        }
+        else
+            return;
+        if (typeof this.config.onPositionChange === 'function')
+            this.config.onPositionChange(this.config.currentPosition, this.getWindowRange());
+    }
+    /**
+     * Handle mouse up (end dragging)
+     */
+    handleMouseUp() {
+        this.state.isDragging = false;
+    }
+    /**
+     * Handle slider drag
+     * @param {number} x - X position of mouse
+     */
+    handleSliderDrag(x) {
+        if (!this.isValid)
+            return;
+        const sliderWidth = this.sliderWidth;
+        // Calculate the position based on the drag position
+        const canvasWidth = this.config.width - sliderWidth;
+        const normalizedX = Math.max(0, Math.min(this.config.width, x));
+        // this shows how many positions are in one pixel
+        const pseudoPositionWidth = canvasWidth / this.config.totalPositions;
+        const fittedPositions = Math.floor(this.config.width / this.config.positionWidth);
+        // we add these positions so that it feels like we are grabbing the slider by its center
+        this.config.windowStartPosition = Math.max(1, Math.min(Math.round((normalizedX - sliderWidth / 2) / pseudoPositionWidth), this.config.totalPositions - fittedPositions + 1));
+        // Call callback if defined
+        if (typeof this.config.onPositionChange === 'function')
+            this.config.onPositionChange(this.config.currentPosition, this.getWindowRange());
+    }
+    get headerHeight() {
+        return this.config.headerHeight;
+    }
+    /** Soft setting of header hight, without redrawing or update event
+     * @param {number} value - New header height
+     */
+    set headerHeight(value) {
+        this.config.headerHeight = value;
+    }
+    /**
+     * Handle click on positions
+     * @param {MouseEvent} e - Mouse event
+     */
+    handleClick(e) {
+        if (!this.isValid)
+            return;
+        // Get calculated coordinates
+        const { x, y } = this.getCoords(e);
+        const sliderTop = this.config.headerHeight - this.config.sliderHeight;
+        if (y < sliderTop && y >= 0) {
+            // Calculate which position was clicked
+            const cellWidth = this.config.positionWidth;
+            const clickedCellIndex = Math.round(x / cellWidth - 0.5);
+            // Calculate actual position in sequence
+            const windowStart = this.config.windowStartPosition;
+            const clickedPosition = windowStart + clickedCellIndex;
+            // Update current position if valid
+            if (clickedPosition >= 1 && clickedPosition <= this.config.totalPositions) {
+                this.config.currentPosition = clickedPosition;
+                // Call callback if defined
+                if (typeof this.config.onPositionChange === 'function')
+                    this.config.onPositionChange(this.config.currentPosition, this.getWindowRange());
+            }
+        }
+    }
+    /**
+     * Get the current window range
+     * @return {WindowRange} Object with start and end properties
+     */
+    getWindowRange() {
+        return {
+            start: this.config.windowStartPosition,
+            end: Math.min(this.config.totalPositions, this.config.windowStartPosition + Math.floor(this.config.width / this.config.positionWidth))
+        };
+    }
+    /**
+     * Update configuration
+     * @param {MSAHeaderOptions} newConfig - New configuration options
+     */
+    updateConfig(newConfig) {
+        // Update config with new values
+        Object.assign(this.config, newConfig);
+        // Ensure current position is still valid
+        this.config.currentPosition = Math.min(this.config.currentPosition, this.config.totalPositions);
+        // Call callback if defined
+        if (typeof this.config.onPositionChange === 'function')
+            this.config.onPositionChange(this.config.currentPosition, this.getWindowRange());
+    }
+    /**
+     * Get current position
+     * @return {number} Current position
+     */
+    getCurrentPosition() {
+        return this.config.currentPosition;
+    }
+    /**
+     * Set current position
+     * @param {number} position - New position
+     */
+    setCurrentPosition(position) {
+        // Clamp to valid range
+        this.config.currentPosition = Math.max(1, Math.min(this.config.totalPositions, position));
+        // Call callback if defined
+        if (typeof this.config.onPositionChange === 'function')
+            this.config.onPositionChange(this.config.currentPosition, this.getWindowRange());
+    }
+}
+//# sourceMappingURL=sequence-position-scroller.js.map

package/src/utils/sequence-position-scroller.js.map

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