npm - @datagrok-libraries/bio - Versions diffs - 6.0.4 → 6.0.6 - Mend

@datagrok-libraries/bio 6.0.4 → 6.0.6

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 (604) hide show

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

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

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

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package/dist/src/utils/monomer-ui.js.map ADDED Viewed

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

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

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package/dist/src/utils/sequence-column-input.d.ts.map ADDED Viewed

@@ -0,0 +1 @@

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package/dist/src/utils/sequence-column-input.js.map ADDED Viewed

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package/{src → dist/src}/utils/sequence-position-scroller.d.ts RENAMED Viewed

@@ -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 ADDED Viewed

@@ -0,0 +1 @@

+ 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package/{src → dist/src}/utils/sequence-position-scroller.js RENAMED Viewed

@@ -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