react-msaview 6.0.0 → 6.1.0

package/dist/components/tracks/TrackBlocks.js

@@ -0,0 +1,65 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import { useCanvasAutorun } from '../../useCanvasAutorun.js';
+import { useColorContrast } from '../../useColorContrast.js';
+import { TrackResizeHandle } from '../ResizeHandles.js';
+import { drawTrackBlock } from './drawTracks.js';
+const TrackBlock = observer(function ({ model, track, offsetX, }) {
+    const { blockSize, colorScheme, highResScaleFactor } = model;
+    const { height, customColorScheme } = track.model;
+    const { theme, contrastScheme } = useColorContrast(customColorScheme ?? colorScheme);
+    const canvasWidth = blockSize * highResScaleFactor;
+    const canvasHeight = height * highResScaleFactor;
+    const ref = useCanvasAutorun({
+        draw: ctx => {
+            ctx.resetTransform();
+            ctx.clearRect(0, 0, canvasWidth, canvasHeight);
+            drawTrackBlock({ model, ctx, track, offsetX, theme, contrastScheme });
+        },
+        width: canvasWidth,
+        height: canvasHeight,
+        deps: [model, track, offsetX, theme, contrastScheme],
+    });
+    return (React.createElement("canvas", { ref: ref, width: canvasWidth, height: canvasHeight, style: {
+            position: 'absolute',
+            left: offsetX,
+            width: blockSize,
+            height,
+        } }));
+});
+/**
+ * The canvas blocks covering one track's row of the alignment. Every track kind
+ * shares this host: what differs between conservation, sequence logo and the
+ * Stockholm text tracks is which draw function `drawTrackBlock` dispatches to,
+ * not how the blocks are laid out or kept in sync with the horizontal scroll.
+ */
+const TrackBlocks = observer(function ({ model, track, }) {
+    // msaCanvasWidth, not msaAreaWidth: a track row is a legend for the columns
+    // directly below it, so it has to stop where the alignment canvas does rather
+    // than running on another 20px under the vertical scrollbar -- otherwise the
+    // last columns appear in the tracks but not in the alignment, and the hovered
+    // -column indicator (sized to the canvas) stops short of the track it crosses
+    const { blocksX, msaCanvasWidth, scrollX } = model;
+    const { kind, height, data } = track.model;
+    // a text track with no data draws nothing, and an empty row of its own would
+    // still take up vertical space
+    if (kind === 'text' && !data) {
+        return null;
+    }
+    return (React.createElement("div", { style: {
+            position: 'relative',
+            height,
+            width: msaCanvasWidth,
+            overflow: 'hidden',
+        } },
+        React.createElement("div", { style: {
+                position: 'absolute',
+                top: 0,
+                left: 0,
+                transform: `translateX(${scrollX}px)`,
+                willChange: 'transform',
+            } }, blocksX.map(bx => (React.createElement(TrackBlock, { key: bx, model: model, track: track, offsetX: bx })))),
+        React.createElement(TrackResizeHandle, { model: model, kind: kind })));
+});
+export default TrackBlocks;
+//# sourceMappingURL=TrackBlocks.js.map

package/dist/components/tracks/TrackBlocks.js.map

@@ -0,0 +1 @@
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package/dist/components/tracks/{renderTracksSvg.d.ts → drawTracks.d.ts}

@@ -1,3 +1,4 @@
+import type { ColumnCounts } from '../../columnCounts.ts';
 import type { MsaViewModel } from '../../model.ts';
 import type { BasicTrack } from '../../types.ts';
 import type { RenderCtx } from '../renderCtx.ts';
@@ -24,27 +25,38 @@ export declare function drawTextTrackContent({ ctx, data, colorScheme, contrastS
     offsetX: number;
     blockSize: number;
 }): void;
-export declare function renderConservationTrack({ model, ctx, track, offsetX, offsetY, trackHeight, blockSizeXOverride, highResScaleFactorOverride, }: {
-    model: MsaViewModel;
+export declare function drawSequenceLogo({ ctx, colStats, colorScheme, maxBits, textColor, colWidth, trackHeight, offsetX, blockSize, }: {
     ctx: RenderCtx;
-    track: BasicTrack;
-    offsetX: number;
-    offsetY: number;
+    colStats: ColumnCounts;
+    colorScheme: Record<string, string>;
+    maxBits: number;
+    textColor: string;
+    colWidth: number;
     trackHeight: number;
-    blockSizeXOverride?: number;
-    highResScaleFactorOverride?: number;
+    offsetX: number;
+    blockSize: number;
 }): void;
-export declare function renderTextTrack({ model, ctx, track, offsetX, offsetY, contrastScheme, theme, blockSizeXOverride, highResScaleFactorOverride, }: {
+/**
+ * Draw one track's content into a block of the alignment's column space, at
+ * `offsetY` within the ctx. Owns the transform, so both callers -- the live
+ * canvas blocks and the SVG export -- draw into the same coordinate space, and
+ * adding a track kind means a `kind`, a draw function above, and a case here.
+ */
+export declare function drawTrackBlock({ model, ctx, track, offsetX, offsetY, theme, contrastScheme, blockSizeXOverride, highResScaleFactorOverride, }: {
     model: MsaViewModel;
     ctx: RenderCtx;
     track: BasicTrack;
     offsetX: number;
-    offsetY: number;
-    contrastScheme: Record<string, string>;
+    offsetY?: number;
     theme: Theme;
+    contrastScheme: Record<string, string>;
     blockSizeXOverride?: number;
     highResScaleFactorOverride?: number;
 }): void;
+/**
+ * Every turned-on track stacked top to bottom, for the SVG export. The live
+ * view draws the same content one canvas block at a time -- see TrackBlocks.
+ */
 export declare function renderAllTracks({ model, ctx, offsetX, contrastScheme, theme, blockSizeXOverride, highResScaleFactorOverride, }: {
     model: MsaViewModel;
     ctx: RenderCtx;

package/dist/components/tracks/drawTracks.js

@@ -0,0 +1,193 @@
+import { columnLogoStack } from '../../sequenceLogo.js';
+import { setFontSize } from '../../setFontSize.js';
+import { visibleColRange } from '../msa/visibleColRange.js';
+export function drawConservationBars({ ctx, values, color, colWidth, trackHeight, offsetX, blockSize, }) {
+    const { xStart, xEnd } = visibleColRange({
+        offsetX,
+        blockWidth: blockSize,
+        colWidth,
+    });
+    ctx.fillStyle = color;
+    for (let i = xStart; i < xEnd && i < values.length; i++) {
+        const value = values[i];
+        const barHeight = value * trackHeight;
+        const x = i * colWidth;
+        ctx.fillRect(x, trackHeight - barHeight, colWidth, barHeight);
+    }
+}
+// the bar-track values live on model getters (kept off the plain track object so
+// the live canvas autorun stays reactive); select the right one by track id
+export function barTrackValues(model, trackId) {
+    return trackId === 'property-conservation'
+        ? model.propertyConservation
+        : model.conservation;
+}
+export function drawTextTrackContent({ ctx, data, colorScheme, contrastScheme, bgColor, textColor, colWidth, rowHeight, offsetX, blockSize, }) {
+    const { xStart, xEnd } = visibleColRange({
+        offsetX,
+        blockWidth: blockSize,
+        colWidth,
+    });
+    const str = data?.slice(xStart, xEnd);
+    const drawLetters = rowHeight >= 10 && colWidth >= rowHeight / 2;
+    for (let i = 0; str && i < str.length; i++) {
+        const letter = str[i];
+        const upper = letter.toUpperCase();
+        const color = colorScheme[upper];
+        const x = (xStart + i) * colWidth;
+        const filled = bgColor && !!color;
+        if (filled) {
+            ctx.fillStyle = color;
+            ctx.fillRect(x, 0, colWidth, rowHeight);
+        }
+        if (drawLetters) {
+            // a letter on a colored tile needs the tile's contrast color; otherwise it
+            // sits on the plain background and takes the theme's text color
+            ctx.fillStyle = filled ? (contrastScheme[upper] ?? 'black') : textColor;
+            ctx.fillText(letter, x + colWidth / 2, rowHeight / 2 + 1);
+        }
+    }
+}
+// Cap height as a fraction of the font size. Every logo letter is scaled from
+// one reference font size to the height its frequency earns, and that scale is
+// only right if we know how tall the glyph actually draws. Measuring per letter
+// would be exact but `measureText` reports no vertical box in the SVG export
+// backend, so the ratio is a constant: the cap height of the sans-serif faces
+// both backends use, within a percent or two. It only has to be consistent --
+// the same ratio for every letter is what makes the slices sum to the stack
+// height instead of drifting apart.
+const CAP_HEIGHT_RATIO = 0.72;
+// letters below this many pixels are noise, and a stack that thin reads better
+// as the bar chart it approximates
+const MIN_LETTER_PX = 3;
+export function drawSequenceLogo({ ctx, colStats, colorScheme, maxBits, textColor, colWidth, trackHeight, offsetX, blockSize, }) {
+    const { xStart, xEnd } = visibleColRange({
+        offsetX,
+        blockWidth: blockSize,
+        colWidth,
+    });
+    const end = Math.min(xEnd, colStats.numColumns);
+    // one reference size for every glyph; each letter's own transform takes it
+    // from here to the height it earned, so the font is set once for the block
+    const referenceFontSize = trackHeight;
+    setFontSize(ctx, referenceFontSize);
+    ctx.textAlign = 'left';
+    ctx.textBaseline = 'alphabetic';
+    const capHeight = referenceFontSize * CAP_HEIGHT_RATIO;
+    for (let col = xStart; col < end; col++) {
+        const stack = columnLogoStack(colStats, col, maxBits);
+        if (stack.length === 0) {
+            continue;
+        }
+        const x = col * colWidth;
+        // stack up from the baseline: the array is ascending, so the tallest letter
+        // lands on top, which is the convention that makes a logo readable at a
+        // glance
+        let bottom = trackHeight;
+        for (const { letter, bits } of stack) {
+            const h = (bits / maxBits) * trackHeight;
+            if (h < MIN_LETTER_PX) {
+                bottom -= h;
+                continue;
+            }
+            const width = ctx.measureText(letter).width;
+            if (width === 0) {
+                bottom -= h;
+                continue;
+            }
+            ctx.fillStyle = colorScheme[letter] ?? textColor;
+            ctx.save();
+            // land the glyph's baseline on the bottom of its slice, then stretch it to
+            // fill the slice vertically and the column horizontally
+            ctx.translate(x, bottom);
+            ctx.scale(colWidth / width, h / capHeight);
+            ctx.fillText(letter, 0, 0);
+            ctx.restore();
+            bottom -= h;
+        }
+    }
+}
+/**
+ * Draw one track's content into a block of the alignment's column space, at
+ * `offsetY` within the ctx. Owns the transform, so both callers -- the live
+ * canvas blocks and the SVG export -- draw into the same coordinate space, and
+ * adding a track kind means a `kind`, a draw function above, and a case here.
+ */
+export function drawTrackBlock({ model, ctx, track, offsetX, offsetY = 0, theme, contrastScheme, blockSizeXOverride, highResScaleFactorOverride, }) {
+    const { blockSize, bgColor, colWidth, colStats, colorScheme: modelColorScheme, fontSize, rowHeight, alphabetMaxBits, highResScaleFactor, } = model;
+    const { id, kind, height: trackHeight, barColor, customColorScheme, data, } = track.model;
+    const blockSizeX = blockSizeXOverride ?? blockSize;
+    const k = highResScaleFactorOverride ?? highResScaleFactor;
+    const textColor = theme.palette.text.primary;
+    ctx.resetTransform();
+    ctx.scale(k, k);
+    ctx.translate(-offsetX, offsetY);
+    switch (kind) {
+        case 'bar': {
+            drawConservationBars({
+                ctx,
+                values: barTrackValues(model, id),
+                color: barColor ?? 'gray',
+                colWidth,
+                trackHeight,
+                offsetX,
+                blockSize: blockSizeX,
+            });
+            break;
+        }
+        case 'logo': {
+            drawSequenceLogo({
+                ctx,
+                colStats,
+                colorScheme: modelColorScheme,
+                maxBits: alphabetMaxBits,
+                textColor,
+                colWidth,
+                trackHeight,
+                offsetX,
+                blockSize: blockSizeX,
+            });
+            break;
+        }
+        case 'text': {
+            ctx.textAlign = 'center';
+            setFontSize(ctx, fontSize);
+            drawTextTrackContent({
+                ctx,
+                data,
+                colorScheme: customColorScheme ?? modelColorScheme,
+                contrastScheme,
+                bgColor,
+                textColor,
+                colWidth,
+                rowHeight,
+                offsetX,
+                blockSize: blockSizeX,
+            });
+            break;
+        }
+    }
+    ctx.resetTransform();
+}
+/**
+ * Every turned-on track stacked top to bottom, for the SVG export. The live
+ * view draws the same content one canvas block at a time -- see TrackBlocks.
+ */
+export function renderAllTracks({ model, ctx, offsetX, contrastScheme, theme, blockSizeXOverride, highResScaleFactorOverride, }) {
+    let currentY = 0;
+    for (const track of model.turnedOnTracks) {
+        drawTrackBlock({
+            model,
+            ctx,
+            track,
+            offsetX,
+            offsetY: currentY,
+            theme,
+            contrastScheme,
+            blockSizeXOverride,
+            highResScaleFactorOverride,
+        });
+        currentY += track.model.height;
+    }
+}
+//# sourceMappingURL=drawTracks.js.map

package/dist/components/tracks/drawTracks.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"drawTracks.js","sourceRoot":"","sources":["../../../src/components/tracks/drawTracks.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAA;AACvD,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAA;AAClD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAQ3D,MAAM,UAAU,oBAAoB,CAAC,EACnC,GAAG,EACH,MAAM,EACN,KAAK,EACL,QAAQ,EACR,WAAW,EACX,OAAO,EACP,SAAS,GASV;IACC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,SAAS;QACrB,QAAQ;KACT,CAAC,CAAA;IAEF,GAAG,CAAC,SAAS,GAAG,KAAK,CAAA;IACrB,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,IAAI,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACxD,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACxB,MAAM,SAAS,GAAG,KAAK,GAAG,WAAW,CAAA;QACrC,MAAM,CAAC,GAAG,CAAC,GAAG,QAAQ,CAAA;QACtB,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,WAAW,GAAG,SAAS,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;IAC/D,CAAC;AACH,CAAC;AAED,iFAAiF;AACjF,4EAA4E;AAC5E,MAAM,UAAU,cAAc,CAAC,KAAmB,EAAE,OAAe;IACjE,OAAO,OAAO,KAAK,uBAAuB;QACxC,CAAC,CAAC,KAAK,CAAC,oBAAoB;QAC5B,CAAC,CAAC,KAAK,CAAC,YAAY,CAAA;AACxB,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,EACnC,GAAG,EACH,IAAI,EACJ,WAAW,EACX,cAAc,EACd,OAAO,EACP,SAAS,EACT,QAAQ,EACR,SAAS,EACT,OAAO,EACP,SAAS,GAYV;IACC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,SAAS;QACrB,QAAQ;KACT,CAAC,CAAA;IACF,MAAM,GAAG,GAAG,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IACrC,MAAM,WAAW,GAAG,SAAS,IAAI,EAAE,IAAI,QAAQ,IAAI,SAAS,GAAG,CAAC,CAAA;IAEhE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,IAAI,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;QACtB,MAAM,KAAK,GAAG,MAAM,CAAC,WAAW,EAAE,CAAA;QAClC,MAAM,KAAK,GAAG,WAAW,CAAC,KAAK,CAAC,CAAA;QAChC,MAAM,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAA;QACjC,MAAM,MAAM,GAAG,OAAO,IAAI,CAAC,CAAC,KAAK,CAAA;QACjC,IAAI,MAAM,EAAE,CAAC;YACX,GAAG,CAAC,SAAS,GAAG,KAAM,CAAA;YACtB,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAA;QACzC,CAAC;QACD,IAAI,WAAW,EAAE,CAAC;YAChB,2EAA2E;YAC3E,gEAAgE;YAChE,GAAG,CAAC,SAAS,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,cAAc,CAAC,KAAK,CAAC,IAAI,OAAO,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;YACvE,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,QAAQ,GAAG,CAAC,EAAE,SAAS,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;QAC3D,CAAC;IACH,CAAC;AACH,CAAC;AAED,8EAA8E;AAC9E,+EAA+E;AAC/E,gFAAgF;AAChF,6EAA6E;AAC7E,8EAA8E;AAC9E,8EAA8E;AAC9E,4EAA4E;AAC5E,oCAAoC;AACpC,MAAM,gBAAgB,GAAG,IAAI,CAAA;AAC7B,+EAA+E;AAC/E,mCAAmC;AACnC,MAAM,aAAa,GAAG,CAAC,CAAA;AAEvB,MAAM,UAAU,gBAAgB,CAAC,EAC/B,GAAG,EACH,QAAQ,EACR,WAAW,EACX,OAAO,EACP,SAAS,EACT,QAAQ,EACR,WAAW,EACX,OAAO,EACP,SAAS,GAWV;IACC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,eAAe,CAAC;QACvC,OAAO;QACP,UAAU,EAAE,SAAS;QACrB,QAAQ;KACT,CAAC,CAAA;IACF,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,QAAQ,CAAC,UAAU,CAAC,CAAA;IAE/C,2EAA2E;IAC3E,2EAA2E;IAC3E,MAAM,iBAAiB,GAAG,WAAW,CAAA;IACrC,WAAW,CAAC,GAAG,EAAE,iBAAiB,CAAC,CAAA;IACnC,GAAG,CAAC,SAAS,GAAG,MAAM,CAAA;IACtB,GAAG,CAAC,YAAY,GAAG,YAAY,CAAA;IAC/B,MAAM,SAAS,GAAG,iBAAiB,GAAG,gBAAgB,CAAA;IAEtD,KAAK,IAAI,GAAG,GAAG,MAAM,EAAE,GAAG,GAAG,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;QACxC,MAAM,KAAK,GAAG,eAAe,CAAC,QAAQ,EAAE,GAAG,EAAE,OAAO,CAAC,CAAA;QACrD,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvB,SAAQ;QACV,CAAC;QACD,MAAM,CAAC,GAAG,GAAG,GAAG,QAAQ,CAAA;QACxB,4EAA4E;QAC5E,wEAAwE;QACxE,SAAS;QACT,IAAI,MAAM,GAAG,WAAW,CAAA;QACxB,KAAK,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,IAAI,KAAK,EAAE,CAAC;YACrC,MAAM,CAAC,GAAG,CAAC,IAAI,GAAG,OAAO,CAAC,GAAG,WAAW,CAAA;YACxC,IAAI,CAAC,GAAG,aAAa,EAAE,CAAC;gBACtB,MAAM,IAAI,CAAC,CAAA;gBACX,SAAQ;YACV,CAAC;YACD,MAAM,KAAK,GAAG,GAAG,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,KAAK,CAAA;YAC3C,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;gBAChB,MAAM,IAAI,CAAC,CAAA;gBACX,SAAQ;YACV,CAAC;YACD,GAAG,CAAC,SAAS,GAAG,WAAW,CAAC,MAAM,CAAC,IAAI,SAAS,CAAA;YAChD,GAAG,CAAC,IAAI,EAAE,CAAA;YACV,2EAA2E;YAC3E,wDAAwD;YACxD,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,MAAM,CAAC,CAAA;YACxB,GAAG,CAAC,KAAK,CAAC,QAAQ,GAAG,KAAK,EAAE,CAAC,GAAG,SAAS,CAAC,CAAA;YAC1C,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;YAC1B,GAAG,CAAC,OAAO,EAAE,CAAA;YACb,MAAM,IAAI,CAAC,CAAA;QACb,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,cAAc,CAAC,EAC7B,KAAK,EACL,GAAG,EACH,KAAK,EACL,OAAO,EACP,OAAO,GAAG,CAAC,EACX,KAAK,EACL,cAAc,EACd,kBAAkB,EAClB,0BAA0B,GAW3B;IACC,MAAM,EACJ,SAAS,EACT,OAAO,EACP,QAAQ,EACR,QAAQ,EACR,WAAW,EAAE,gBAAgB,EAC7B,QAAQ,EACR,SAAS,EACT,eAAe,EACf,kBAAkB,GACnB,GAAG,KAAK,CAAA;IACT,MAAM,EACJ,EAAE,EACF,IAAI,EACJ,MAAM,EAAE,WAAW,EACnB,QAAQ,EACR,iBAAiB,EACjB,IAAI,GACL,GAAG,KAAK,CAAC,KAAK,CAAA;IACf,MAAM,UAAU,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAClD,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAC1D,MAAM,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAA;IAE5C,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;IAEhC,QAAQ,IAAI,EAAE,CAAC;QACb,KAAK,KAAK,EAAE,CAAC;YACX,oBAAoB,CAAC;gBACnB,GAAG;gBACH,MAAM,EAAE,cAAc,CAAC,KAAK,EAAE,EAAE,CAAC;gBACjC,KAAK,EAAE,QAAQ,IAAI,MAAM;gBACzB,QAAQ;gBACR,WAAW;gBACX,OAAO;gBACP,SAAS,EAAE,UAAU;aACtB,CAAC,CAAA;YACF,MAAK;QACP,CAAC;QACD,KAAK,MAAM,EAAE,CAAC;YACZ,gBAAgB,CAAC;gBACf,GAAG;gBACH,QAAQ;gBACR,WAAW,EAAE,gBAAgB;gBAC7B,OAAO,EAAE,eAAe;gBA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package/dist/components/tree/TreeCanvas.js

@@ -8,7 +8,7 @@ import TreeCanvasBlock from './TreeCanvasBlock.js';
 import { padding } from './renderTreeCanvas.js';
 const TreeCanvas = observer(function ({ model }) {
     const ref = useRef(null);
-    const { treeWidth, height, blocksY, treeAreaWidth } = model;
+    const { treeWidth, height, blocksY, treeAreaWidth, scrollY } = model;
     const onScrollY = useCallback((d) => {
         model.doScrollY(d);
     }, [model]);
@@ -50,7 +50,13 @@ const TreeCanvas = observer(function ({ model }) {
             position: 'relative',
             width: treeWidth + padding,
         } },
-        blocksY.map(block => (React.createElement(TreeCanvasBlock, { key: block, model: model, offsetY: block }))),
+        React.createElement("div", { style: {
+                position: 'absolute',
+                top: 0,
+                left: 0,
+                transform: `translateY(${scrollY}px)`,
+                willChange: 'transform',
+            } }, blocksY.map(block => (React.createElement(TreeCanvasBlock, { key: block, model: model, offsetY: block })))),
         React.createElement("canvas", { ref: mouseoverRef, width: treeAreaWidth, height: height, style: {
                 position: 'absolute',
                 top: 0,

package/dist/components/tree/TreeCanvas.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvas.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAA;AACxD,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpE,OAAO,eAAe,MAAM,sBAAuB,CAAA;AACnD,OAAO,EAAE,OAAO,EAAE,MAAM,uBAAuB,CAAA;AAI/C,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACpE,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,GAAG,cAAc,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,CAAA;IAErE,MAAM,YAAY,GAAG,gBAAgB,CAAC;QACpC,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,IAAI,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;gBACnB,MAAM,EACJ,SAAS,EACT,aAAa,EAAE,CAAC,EAChB,MAAM,EAAE,CAAC,EACT,OAAO,EAAE,EAAE,EACX,QAAQ,EACR,iBAAiB,EACjB,iBAAiB,GAClB,GAAG,KAAK,CAAA;gBACT,GAAG,CAAC,cAAc,EAAE,CAAA;gBACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;gBAEzB,oEAAoE;gBACpE,6DAA6D;gBAC7D,MAAM,OAAO,GAAG,CAAC,KAAa,EAAE,EAAE;oBAChC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,GAAG,EAAE,EAAE,CAAC,EAAE,SAAS,CAAC,CAAA;gBACvD,CAAC,CAAA;gBAED,IAAI,iBAAiB,KAAK,SAAS,EAAE,CAAC;oBACpC,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;oBAC9B,OAAO,CAAC,iBAAiB,CAAC,CAAA;gBAC5B,CAAC;gBAED,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;gBAC9B,KAAK,MAAM,KAAK,IAAI,iBAAiB,EAAE,CAAC;oBACtC,OAAO,CAAC,KAAK,CAAC,CAAA;gBAChB,CAAC;gBACD,IACE,QAAQ,KAAK,SAAS;oBACtB,QAAQ,KAAK,iBAAiB;oBAC9B,CAAC,iBAAiB,CAAC,QAAQ,CAAC,QAAQ,CAAC,EACrC,CAAC;oBACD,OAAO,CAAC,QAAQ,CAAC,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;QACD,KAAK,EAAE,aAAa;QACpB,MAAM;QACN,IAAI,EAAE,CAAC,KAAK,CAAC;KACd,CAAC,CAAA;IAEF,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,WAAW,EACxB,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,KAAK,CAAC,EAAE;YACpB,KAAK,CAAC,cAAc,EAAE,CAAA;QACxB,CAAC,EACD,KAAK,EAAE;YACL,MAAM;YACN,QAAQ,EAAE,UAAU;YACpB,KAAK,EAAE,SAAS,GAAG,OAAO;SAC3B;QAID,6BACE,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,CAAC;gBACP,SAAS,EAAE,cAAc,OAAO,KAAK;gBACrC,UAAU,EAAE,WAAW;aACxB,IAEA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACpB,oBAAC,eAAe,IAAC,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,GAAI,CAC9D,CAAC,CACE;QACN,gCACE,GAAG,EAAE,YAAY,EACjB,KAAK,EAAE,aAAa,EACpB,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,CAAC;gBACP,KAAK,EAAE,aAAa;gBACpB,MAAM;gBACN,MAAM,EAAE,IAAI;gBACZ,aAAa,EAAE,MAAM;aACtB,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/tree/TreeCanvasBlock.js

@@ -2,6 +2,7 @@ import React, { useState } from 'react';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { createPortal } from 'react-dom';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import TreeBranchMenu from './TreeBranchMenu.js';
 import TreeNodeMenu from './TreeNodeMenu.js';
@@ -35,7 +36,7 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const [branchMenu, setBranchMenu] = useState();
     const [nodeMenu, setNodeMenu] = useState();
     const { clickMap, hovered, hitTest, onMouseMove, onMouseLeave } = useTreeHover({ model, offsetY });
-    const { scrollY, treeAreaWidth, blockSize, highResScaleFactor } = model;
+    const { treeAreaWidth, blockSize, highResScaleFactor } = model;
     const width = treeAreaWidth + padding;
     const height = blockSize;
     const canvasWidth = width * highResScaleFactor;
@@ -59,7 +60,7 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const style = {
         width,
         height,
-        top: scrollY + offsetY,
+        top: offsetY,
         left: 0,
         position: 'absolute',
     };
@@ -93,11 +94,13 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
             } }),
         hovered && !hovered.branch ? (React.createElement("div", { className: classes.hover, style: {
                 left: hovered.minX,
-                top: hovered.minY + scrollY,
+                top: hovered.minY,
                 width: hovered.maxX - hovered.minX,
                 height: hovered.maxY - hovered.minY,
             } })) : null,
-        hovered ? (React.createElement("div", { className: classes.tooltip, style: { left: hovered.clientX + 12, top: hovered.clientY + 12 } }, hovered.name)) : null));
+        hovered
+            ? createPortal(React.createElement("div", { className: classes.tooltip, style: { left: hovered.clientX + 12, top: hovered.clientY + 12 } }, hovered.name), document.body)
+            : null));
 });
 export default TreeCanvasBlock;
 //# sourceMappingURL=TreeCanvasBlock.js.map

package/dist/components/tree/TreeCanvasBlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,YAAY,EAAE,MAAM,WAAW,CAAA;AAExC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,cAAc,MAAM,qBAAsB,CAAA;AACjD,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,EAAE,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACjE,OAAO,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAA;AAIhD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,QAAQ,EAAE,OAAO;QACjB,aAAa,EAAE,MAAM;QACrB,MAAM,EAAE,KAAK;QACb,eAAe,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;QACxC,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;QACjC,OAAO,EAAE,SAAS;QAClB,YAAY,EAAE,CAAC;QACf,QAAQ,EAAE,EAAE;QACZ,UAAU,EAAE,QAAQ;QACpB,QAAQ,EAAE,GAAG;QACb,QAAQ,EAAE,QAAQ;QAClB,YAAY,EAAE,UAAU;KACzB;IACD,KAAK,EAAE;QACL,QAAQ,EAAE,UAAU;QACpB,aAAa,EAAE,MAAM;QACrB,MAAM,EAAE,GAAG;QACX,UAAU,EAAE,iBAAiB;KAC9B;CACF,CAAC,CAAC,CAAA;AASH,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,EAAY,CAAA;IACxD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAY,CAAA;IACpD,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,GAC7D,YAAY,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAA;IAElC,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAC9D,MAAM,KAAK,GAAG,aAAa,GAAG,OAAO,CAAA;IACrC,MAAM,MAAM,GAAG,SAAS,CAAA;IAExB,MAAM,WAAW,GAAG,KAAK,GAAG,kBAAkB,CAAA;IAC9C,MAAM,YAAY,GAAG,MAAM,GAAG,kBAAkB,CAAA;IAChD,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,WAAW,EAAE,YAAY,CAAC,CAAA;YAC9C,gBAAgB,CAAC;gBACf,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,QAAQ;gBACR,KAAK;aACN,CAAC,CAAA;QACJ,CAAC;QACD,KAAK,EAAE,WAAW;QAClB,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,CAAC,KAAK,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,CAAC;KACxC,CAAC,CAAA;IAEF,MAAM,KAAK,GAAG;QACZ,KAAK;QACL,MAAM;QACN,GAAG,EAAE,OAAO;QACZ,IAAI,EAAE,CAAC;QACP,QAAQ,EAAE,UAAU;KACZ,CAAA;IAEV,OAAO,CACL;QACG,UAAU,CAAC,CAAC,CAAC,CACZ,oBAAC,cAAc,IACb,IAAI,EAAE,UAAU,EAChB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,aAAa,CAAC,SAAS,CAAC,CAAA;YAC1B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,YAAY,IACX,IAAI,EAAE,QAAQ,EACd,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,WAAW,CAAC,SAAS,CAAC,CAAA;YACxB,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAER,gCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,YAAY,EACpB,KAAK,EAAE,EAAE,GAAG,KAAK,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,EAC5D,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,WAAW,CAAC,KAAK,CAAC,CAAA;YACpB,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,YAAY,EAAE,CAAA;YAChB,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;gBAC5B,IAAI,KAAK,EAAE,CAAC;oBACV,MAAM,IAAI,GAAG;wBACX,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,EAAE,EAAE,KAAK,CAAC,EAAE;wBACZ,IAAI,EAAE,KAAK,CAAC,IAAI;qBACjB,CAAA;oBACD,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;wBACjB,aAAa,CAAC,IAAI,CAAC,CAAA;oBACrB,CAAC;yBAAM,CAAC;wBACN,WAAW,CAAC,IAAI,CAAC,CAAA;oBACnB,CAAC;gBACH,CAAC;YACH,CAAC,GACD;QAGD,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAC5B,6BACE,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE;gBACL,IAAI,EAAE,OAAO,CAAC,IAAI;gBAClB,GAAG,EAAE,OAAO,CAAC,IAAI;gBACjB,KAAK,EAAE,OAAO,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI;gBAClC,MAAM,EAAE,OAAO,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI;aACpC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAKP,OAAO;YACN,CAAC,CAAC,YAAY,CACV,6BACE,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,KAAK,EAAE,EAAE,IAAI,EAAE,OAAO,CAAC,OAAO,GAAG,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,OAAO,GAAG,EAAE,EAAE,IAE/D,OAAO,CAAC,IAAI,CACT,EACN,QAAQ,CAAC,IAAI,CACd;YACH,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/tree/renderTreeCanvas.js

@@ -139,7 +139,7 @@ function renderNodeBubbles({ ctx, clickMap, offsetY, model, tipX, maxDepthToLeaf
     });
 }
 function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepthToLeaf, blockSizeYOverride, collapsedSet, }) {
-    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, noTree, labelWidthMap, } = model;
+    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, noTree, labelWidthMap, labelWidthScale, } = model;
     const by = blockSizeYOverride ?? blockSize;
     // labels only exist for leaves, which are laid out top to bottom, so take the
     // same slice the MSA renderer uses instead of walking every tip per block
@@ -167,7 +167,10 @@ function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepth
             if (!noTree) {
                 xp = getNodeX(node, showBranchLen, tipX, maxDepthToLeaf) ?? 0;
             }
-            const width = labelWidthMap.get(name) ?? ctx.measureText(displayName).width;
+            const measured = labelWidthMap.get(name);
+            const width = measured === undefined
+                ? ctx.measureText(displayName).width
+                : measured * labelWidthScale;
             ctx.fillStyle = theme.palette.text.primary;
             if (labelsAlignRight) {
                 const smallPadding = 2;

package/dist/components/tree/renderTreeCanvas.js.map

@@ -1 +1 @@
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package/dist/constants.d.ts

@@ -14,6 +14,9 @@ export declare const segmentFeatureTypes: Set<string>;
 export declare const segmentShades: string[];
 export declare const defaultDrawMsaLetters = true;
 export declare const defaultScrollZoom = false;
+export declare const minLetterRowHeight = 8;
+export declare const minLetterColWidth = 5;
+export declare const labelReferenceFontSize = 16;
 export declare const minColWidth = 0.2;
 export declare const minRowHeight = 1;
 export declare const maxCellSize = 80;

package/dist/constants.js

@@ -28,6 +28,14 @@ export const segmentFeatureTypes = new Set([
 export const segmentShades = ['#9fb6d4', '#d4dcea'];
 export const defaultDrawMsaLetters = true;
 export const defaultScrollZoom = false;
+// Cell size floors for drawing residue letters and tree labels. Below these a
+// 500px block holds thousands of glyphs, and fillText -- which no sprite atlas
+// beats, measured -- dominates every zoom frame.
+export const minLetterRowHeight = 8;
+export const minLetterColWidth = 5;
+// Tree labels are measured once at this size and scaled to the current font
+// size, so a vertical zoom never re-measures the tree.
+export const labelReferenceFontSize = 16;
 // Zoom limits, px per cell. maxCellSize caps both smooth zoom and the stepwise
 // zoom-in buttons (which otherwise grow unbounded). minColWidth/minRowHeight are
 // the smooth-zoom floors.

package/dist/constants.js.map

@@ -1 +1 @@
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package/dist/model/DataModel.d.ts

@@ -40,8 +40,5 @@ export declare function DataModelF(): import("@jbrowse/mobx-state-tree").IModelT
      */
     setGFF(gff?: string): void;
 }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
-    tree: string | undefined;
-    msa: string | undefined;
-    treeMetadata: string | undefined;
-    gff: string | undefined;
+    [k: string]: string | undefined;
 }>;

package/dist/model/DataModel.js

@@ -52,15 +52,13 @@ export function DataModelF() {
             self.gff = gff;
         },
     }))
-        .postProcessSnapshot(snap => {
-        const { tree, msa, treeMetadata, gff } = snap;
-        const max = 50_000;
-        return {
-            tree: tree && tree.length > max ? undefined : tree,
-            msa: msa && msa.length > max ? undefined : msa,
-            treeMetadata: treeMetadata && treeMetadata.length > max ? undefined : treeMetadata,
-            gff: gff && gff.length > max ? undefined : gff,
-        };
-    });
+        .postProcessSnapshot(snap => 
+    // a large document is dropped from the snapshot rather than inlined
+    // into a session or a shared URL, and every field here holds one, so
+    // the rule is the same for all of them
+    Object.fromEntries(Object.entries(snap).map(([key, text]) => [
+        key,
+        text && text.length > 50_000 ? undefined : text,
+    ])));
 }
 //# sourceMappingURL=DataModel.js.map

package/dist/model/DataModel.js.map

@@ -1 +1 @@
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