@datagrok-libraries/bio 6.0.3 → 6.0.6

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

@@ -0,0 +1 @@
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package/dist/src/utils/macromolecule-highlight.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/utils/macromolecule-highlight.js.map

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package/dist/src/utils/monomer-selection-dialog.d.ts.map

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package/dist/src/utils/monomer-selection-dialog.js.map

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package/dist/src/utils/monomer-ui.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/utils/monomer-ui.js.map

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package/dist/src/utils/seq-helper.d.ts.map

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package/dist/src/utils/seq-helper.js.map

@@ -0,0 +1 @@
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package/dist/src/utils/sequence-column-input.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/utils/sequence-column-input.js.map

@@ -0,0 +1 @@
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package/{src → dist/src}/utils/sequence-position-scroller.d.ts

@@ -43,6 +43,7 @@ export declare abstract class MSAHeaderTrack {
     protected title: string;
     protected tooltipEnabled: boolean;
     protected tooltipContent: ((position: number, monomer: string | null, data: Map<string, number>) => HTMLElement) | null;
+    protected getPositionName: (posIdx: number) => string;
     constructor(height?: number, minHeight?: number, title?: string);
     /**
      * Initialize the track with a canvas context
@@ -51,6 +52,8 @@ export declare abstract class MSAHeaderTrack {
     getMonomerAt(_x: number, _y: number, _position: number): string | null;
     enableTooltip(enabled: boolean): void;
     setTooltipContentGenerator(contentGenerator: (position: number, monomer: string | null, data: Map<string, number>) => HTMLElement): void;
+    /** Sets how the track names a position (0-based index), e.g. '111A' of a numbering scheme */
+    setPositionNameGetter(getter: (posIdx: number) => string): void;
     getTooltipContent(position: number, monomer: string | null): HTMLElement | null;
     /**
      * Get data for a specific position (to be implemented by subclasses)
@@ -136,6 +139,14 @@ export declare class MSAScrollingHeader {
     private onSelectionCallback;
     private trackButtons;
     private userSelectedTracks;
+    private positionNames;
+    private positionNamesSource;
+    private positionNamesNumbered;
+    private painted;
+    private readonly grid;
+    private readonly statusName;
+    private readonly keyDownListener;
+    private readonly overlayDrawSub;
     constructor(options: MSAHeaderOptions, gridColumn: DG.GridColumn);
     private determineVisibleTracks;
     private drawTrackButtons;
@@ -151,6 +162,15 @@ export declare class MSAScrollingHeader {
     private clearHoverStates;
     private redraw;
     setSelectionData(dataFrame: DG.DataFrame, seqColumn: DG.Column<string>, seqHandler: ISeqHandler, callback?: (position: number, monomer: string) => void): void;
+    /** Name of the position (0-based index) from the column's position labels or names, such as '111A' of a
+     * numbering scheme kept by an extracted region; the 1-based index when the column has none */
+    getPositionName(posIdx: number): string;
+    private updatePositionNames;
+    /** Readings `header tracks of <column>` and `header positions of <column>` (the ruler's names) and a
+     * `position <name> of <column> header` hit area over each position's WebLogo stack, as last painted */
+    private getStatus;
+    /** The ruler names the first position and the round ones: '10', 'N-20', but not the insertion '110A' */
+    private isLabeledPosition;
     setupTooltipHandling(): void;
     private handleTooltipMouseMove;
     private handleTooltipMouseLeave;

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

@@ -0,0 +1 @@
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package/{src → dist/src}/utils/sequence-position-scroller.js

@@ -9,6 +9,7 @@
 import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
+import { TAGS as bioTAGS } from './macromolecule/consts';
 import { HelmTypes } from '../helm/consts';
 import { buildCompositionTable } from './composition-table';
 // WebLogo Constants
@@ -63,6 +64,7 @@ export class MSAHeaderTrack {
         this.title = '';
         this.tooltipEnabled = false;
         this.tooltipContent = null;
+        this.getPositionName = (posIdx) => `${posIdx + 1}`;
         this.height = height;
         this.defaultHeight = height;
         this.minHeight = minHeight;
@@ -83,6 +85,10 @@ export class MSAHeaderTrack {
     setTooltipContentGenerator(contentGenerator) {
         this.tooltipContent = contentGenerator;
     }
+    /** Sets how the track names a position (0-based index), e.g. '111A' of a numbering scheme */
+    setPositionNameGetter(getter) {
+        this.getPositionName = getter;
+    }
     getTooltipContent(position, monomer) {
         if (!this.tooltipEnabled || !this.tooltipContent)
             return null;
@@ -173,7 +179,7 @@ export class WebLogoTrack extends MSAHeaderTrack {
     }
     createTooltipContent(position, monomer, data) {
         const tooltipRows = [];
-        tooltipRows.push(ui.divText(`Position: ${position + 1}`, {
+        tooltipRows.push(ui.divText(`Position: ${this.getPositionName(position)}`, {
             style: { fontWeight: 'bold', marginBottom: '6px', fontSize: '13px' }
         }));
         if (monomer) {
@@ -451,6 +457,7 @@ const LAYOUT_CONSTANTS = {
     DEFAULT_TRACK_HEIGHT: 45,
     MIN_TRACK_HEIGHT: 35,
     ANNOTATION_TRACK_HEIGHT: 20,
+    POSITION_LABEL_GAP: 4,
 };
 // STRICT HEIGHT THRESHOLDS - All pixel-perfect and deterministic
 const HEIGHT_THRESHOLDS = {
@@ -490,6 +497,11 @@ export class MSAScrollingHeader {
         // Track button state
         this.trackButtons = [];
         this.userSelectedTracks = null;
+        this.positionNames = [];
+        this.positionNamesSource = null;
+        this.positionNamesNumbered = true;
+        this.painted = null;
+        this.keyDownListener = (e) => this.handleKeyDown(e);
         this.config = {
             x: options.x || 0,
             y: options.y || 0,
@@ -510,6 +522,13 @@ export class MSAScrollingHeader {
         this.eventElement = ui.div();
         this.eventElement.style.position = 'absolute';
         this.config.canvas.parentElement?.appendChild(this.eventElement);
+        this.grid = gridColumn.grid;
+        // the grid paints only the headers on screen and draw() shows the element again, so a scrolled-away
+        // header does not leave its element over other columns
+        this.overlayDrawSub = this.grid.onBeforeDrawOverlay.subscribe(() => this.eventElement.style.display = 'none');
+        this.statusName = `msa-header ${gridColumn.name}`;
+        // older platforms have no status providers
+        this.grid.addStatusProvider?.(this.statusName, () => this.getStatus());
         this.state = { isDragging: false, dragStartX: 0, dragMode: 'none', dragStartWindowPosition: 1, dragOccurred: false };
         this.setupEventListeners();
         this.init();
@@ -734,6 +753,9 @@ export class MSAScrollingHeader {
         }
     }
     redraw() {
+        // the header scrolled away since the redraw was requested
+        if (this.eventElement.style.display === 'none')
+            return;
         this.draw(this.config.x, this.config.y, this.config.width, this.config.height, this.config.currentPosition, this.config.windowStartPosition, { preventDefault: () => { } }, this.seqColumn?.name);
     }
     setSelectionData(dataFrame, seqColumn, seqHandler, callback) {
@@ -742,6 +764,60 @@ export class MSAScrollingHeader {
         this.seqHandler = seqHandler;
         this.onSelectionCallback = callback || null;
     }
+    /** Name of the position (0-based index) from the column's position labels or names, such as '111A' of a
+     * numbering scheme kept by an extracted region; the 1-based index when the column has none */
+    getPositionName(posIdx) {
+        return this.positionNames[posIdx] || `${posIdx + 1}`;
+    }
+    updatePositionNames() {
+        const namesTag = this.seqColumn?.getTag(bioTAGS.positionNames) ?? '';
+        const labelsTag = this.seqColumn?.getTag(bioTAGS.positionLabels) ?? '';
+        const source = `${namesTag}\n${labelsTag}`;
+        if (source === this.positionNamesSource)
+            return;
+        this.positionNamesSource = source;
+        const split = (tag) => tag ? tag.split(',').map((p) => p.trim()) : [];
+        const names = split(namesTag);
+        const labels = split(labelsTag);
+        this.positionNames = Array.from({ length: Math.max(names.length, labels.length) }, (_, i) => labels[i] || names[i]);
+        this.positionNamesNumbered = this.positionNames.length === 0 || this.positionNames.some((n) => /\d/.test(n));
+    }
+    /** Readings `header tracks of <column>` and `header positions of <column>` (the ruler's names) and a
+     * `position <name> of <column> header` hit area over each position's WebLogo stack, as last painted */
+    getStatus() {
+        if (!this.painted || !this.seqColumn || this.eventElement.style.display === 'none')
+            return {};
+        const { x, y, tracks, webLogo, positions, labels } = this.painted;
+        // a scrolled column passes under the frozen ones
+        let left = 0;
+        const frozenColumns = this.grid.props.frozenColumns ?? 0;
+        if (this.gridColumn.idx >= frozenColumns) {
+            for (let i = 0; i < frozenColumns; i++) {
+                const frozen = this.grid.columns.byIndex(i);
+                left += frozen?.visible ? frozen.width : 0;
+            }
+        }
+        const right = this.grid.canvas.clientWidth;
+        const col = this.seqColumn.name;
+        const hitAreas = {};
+        if (webLogo) {
+            for (const p of positions) {
+                if (x + p.x >= left && x + p.x + p.width <= right)
+                    hitAreas[`position ${p.name} of ${col} header`] = { x: x + p.x, y: y + webLogo.y, width: p.width, height: webLogo.height };
+            }
+        }
+        const shownLabels = labels.filter((l) => x + l.x >= left && x + l.x <= right).map((l) => l.name);
+        return { hitAreas, values: { [`header tracks of ${col}`]: tracks.join(', '), [`header positions of ${col}`]: shownLabels.join(', ') } };
+    }
+    /** The ruler names the first position and the round ones: '10', 'N-20', but not the insertion '110A' */
+    isLabeledPosition(posIdx) {
+        if (posIdx === 0)
+            return true;
+        if (!this.positionNamesNumbered)
+            return (posIdx + 1) % 10 === 0;
+        const number = /^\D*(\d+)$/.exec(this.getPositionName(posIdx));
+        return !!number && Number(number[1]) % 10 === 0;
+    }
     setupTooltipHandling() {
         this.eventElement.addEventListener('mousemove', this.handleTooltipMouseMove.bind(this));
         this.eventElement.addEventListener('mouseleave', this.handleTooltipMouseLeave.bind(this));
@@ -834,7 +910,7 @@ export class MSAScrollingHeader {
     handleTooltipMouseLeave() {
         this.hideTooltip();
         this.clearHoverStates();
-        window.requestAnimationFrame(() => this.draw(this.config.x, this.config.y, this.config.width, this.config.height, this.config.currentPosition, this.config.windowStartPosition, { preventDefault: () => { } }, this.seqColumn?.name));
+        window.requestAnimationFrame(() => this.redraw());
     }
     hideTooltip() {
         this.currentHoverPosition = -1;
@@ -851,6 +927,9 @@ export class MSAScrollingHeader {
             this.eventElement.style.display = 'none';
             return;
         }
+        this.updatePositionNames();
+        const painted = { x, y, tracks: [], webLogo: null, positions: [], labels: [] };
+        this.painted = painted;
         this.ctx.save();
         this.ctx.clearRect(x, y, w, h);
         this.ctx.translate(x, y);
@@ -872,10 +951,16 @@ export class MSAScrollingHeader {
                 visibleTracks.push({ id, track });
         });
         let currentY = tracksEndY;
-        for (const { track } of visibleTracks) {
+        for (const { id, track } of visibleTracks) {
             const trackHeight = track.getHeight();
             const trackStartY = currentY - trackHeight;
             track.draw(0, trackStartY, w, trackHeight, this.config.windowStartPosition, this.config.positionWidth, this.config.totalPositions, this.config.currentPosition);
+            // a track without data for the window hides itself while drawing
+            if (track.isVisible()) {
+                painted.tracks.unshift(track.getTitle());
+                if (id === 'weblogo')
+                    painted.webLogo = { y: trackStartY, height: trackHeight };
+            }
             visibleTrackPositions.unshift({ y: trackStartY, height: trackHeight });
             currentY = trackStartY - LAYOUT_CONSTANTS.TRACK_GAP;
         }
@@ -921,6 +1006,19 @@ export class MSAScrollingHeader {
         const visiblePositionsN = Math.floor(width / positionWidth);
         const posIndexTop = y + LAYOUT_CONSTANTS.TOP_PADDING;
         this.drawSlider(x, sliderTop, width);
+        this.ctx.font = FONTS.POSITION_LABELS;
+        const labelHalfWidth = (position) => this.ctx.measureText(this.getPositionName(position - 1)).width / 2;
+        // a name wider than its cell stays inside the header at the edges
+        const labelCenterX = (position, halfWidth) => Math.min(Math.max(x + (position - windowStart + 0.5) * positionWidth, x + halfWidth), x + width - halfWidth);
+        const labelGap = LAYOUT_CONSTANTS.POSITION_LABEL_GAP;
+        // the current position's label wins over the ones it would overlap
+        const currentVisible = currentPosition >= windowStart && currentPosition < windowStart + visiblePositionsN &&
+            currentPosition <= totalPositions;
+        const currentHalfWidth = currentVisible ? labelHalfWidth(currentPosition) : 0;
+        const currentLabel = currentVisible ?
+            { centerX: labelCenterX(currentPosition, currentHalfWidth), halfWidth: currentHalfWidth } : null;
+        let lastLabelRight = -Infinity;
+        const painted = this.painted;
         for (let i = 0; i < visiblePositionsN; i++) {
             const position = windowStart + i;
             if (position > totalPositions)
@@ -928,6 +1026,8 @@ export class MSAScrollingHeader {
             const posX = x + (i * positionWidth);
             const cellWidth = positionWidth;
             const cellCenterX = posX + cellWidth / 2;
+            const name = this.getPositionName(position - 1);
+            painted.positions.push({ name, x: posX, width: cellWidth });
             if (this.config.cellBackground) {
                 this.ctx.fillStyle = i % 2 === 0 ? 'rgba(248, 248, 248, 0.3)' : 'rgba(242, 242, 242, 0.2)';
                 this.ctx.fillRect(posX, y, cellWidth, height);
@@ -942,14 +1042,21 @@ export class MSAScrollingHeader {
             this.ctx.beginPath();
             this.ctx.arc(cellCenterX, posIndexTop + 5, 1, 0, Math.PI * 2);
             this.ctx.fill();
-            // Draw position number
-            if (position === currentPosition || ((position === 1 || position % 10 === 0) &&
-                Math.abs(position - currentPosition) > 1)) {
-                this.ctx.fillStyle = COLORS.TITLE_TEXT;
-                this.ctx.font = FONTS.POSITION_LABELS;
-                this.ctx.textAlign = 'center';
-                this.ctx.textBaseline = 'middle';
-                this.ctx.fillText(position.toString(), cellCenterX, posIndexTop + 15);
+            // Draw position name
+            const isCurrent = position === currentPosition;
+            if (isCurrent || (Math.abs(position - currentPosition) > 1 && this.isLabeledPosition(position - 1))) {
+                const halfWidth = labelHalfWidth(position);
+                const labelX = labelCenterX(position, halfWidth);
+                if (isCurrent || (labelX - halfWidth > lastLabelRight + labelGap && (!currentLabel ||
+                    Math.abs(labelX - currentLabel.centerX) > halfWidth + currentLabel.halfWidth + labelGap))) {
+                    this.ctx.fillStyle = COLORS.TITLE_TEXT;
+                    this.ctx.font = FONTS.POSITION_LABELS;
+                    this.ctx.textAlign = 'center';
+                    this.ctx.textBaseline = 'middle';
+                    this.ctx.fillText(name, labelX, posIndexTop + 15);
+                    lastLabelRight = labelX + halfWidth;
+                    painted.labels.push({ name, x: labelX });
+                }
             }
             // Highlight current selected position
             if (position === currentPosition) {
@@ -1048,7 +1155,7 @@ export class MSAScrollingHeader {
         this.eventElement.addEventListener('click', this.handleSelectionClick.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));
+        window.addEventListener('keydown', this.keyDownListener);
     }
     handleSelectionClick(e) {
         if (this.state.dragOccurred)
@@ -1138,6 +1245,7 @@ export class MSAScrollingHeader {
     addTrack(id, track) {
         if (this.ctx)
             track.init(this.ctx);
+        track.setPositionNameGetter((posIdx) => this.getPositionName(posIdx));
         this.tracks.set(id, track);
     }
     removeTrack(id) {
@@ -1152,13 +1260,7 @@ export class MSAScrollingHeader {
             updater(track);
     }
     get isValid() {
-        const gc = this.gridColumn;
-        const g = gc?.grid;
-        const minScroll = g?.horzScroll?.min || 0;
-        const maxScroll = g?.horzScroll?.max || 1e7;
-        return !!this.canvas && !!this.ctx &&
-            this.config.height >= HEIGHT_THRESHOLDS.WITH_TITLE() &&
-            g && (between(gc.left ?? 0, minScroll, maxScroll) || between(gc.right ?? Infinity, minScroll, maxScroll)); // check that the column is actually visible
+        return !!this.canvas && !!this.ctx && this.config.height >= HEIGHT_THRESHOLDS.WITH_TITLE();
     }
     handleMouseDown(e) {
         if (!this.isValid)
@@ -1223,8 +1325,10 @@ export class MSAScrollingHeader {
         e.stopImmediatePropagation();
     }
     detach() {
+        this.overlayDrawSub.unsubscribe();
+        this.grid.removeStatusProvider?.(this.statusName);
         this.eventElement.remove(); // all event listeners are removed along with the element
-        window.removeEventListener('keydown', this.handleKeyDown.bind(this));
+        window.removeEventListener('keydown', this.keyDownListener);
     }
     handleKeyDown(e) {
         if (!this.isValid || this.config.currentPosition < 1)
@@ -1352,7 +1456,4 @@ export class MSAScrollingHeader {
         };
     }
 }
-function between(value, min, max) {
-    return value >= min && value <= max;
-}
 //# sourceMappingURL=sequence-position-scroller.js.map