react-msaview 6.1.1 → 6.2.1

package/dist/components/dialogs/ExportSVGDialog.js

@@ -1,18 +1,33 @@
 import React, { useState } from 'react';
 import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
-import { Alert, Button, DialogActions, DialogContent, FormControl, FormControlLabel, FormLabel, Radio, RadioGroup, Typography, useTheme, } from '@mui/material';
+import { Alert, Button, CircularProgress, DialogActions, DialogContent, FormControl, FormControlLabel, FormLabel, Radio, RadioGroup, Typography, useTheme, } from '@mui/material';
 import Checkbox2 from '../Checkbox2.js';
+// Run after the browser has painted. A requestAnimationFrame callback still
+// runs *before* the frame it was queued for, so one alone hands the main thread
+// to the render with the spinner not yet on screen; the second fires once that
+// frame is out.
+function afterPaint(fn) {
+    requestAnimationFrame(() => {
+        requestAnimationFrame(fn);
+    });
+}
 export default function ExportSVGDialog({ model, onClose, }) {
     const [includeMinimap, setIncludeMinimap] = useState(true);
     const [includeTracks, setIncludeTracks] = useState(true);
     const [exportType, setExportType] = useState('viewport');
     const [error, setError] = useState();
+    const [exporting, setExporting] = useState(false);
     const theme = useTheme();
-    const { totalWidth, totalHeight, treeAreaWidth, turnedOnTracks, totalTrackAreaHeight, } = model;
+    const { totalWidth, totalHeight, treeAreaWidth, turnedOnTracks, totalTrackAreaHeight, numColumns, leaves, showMsaLetters, } = model;
     const hasTracks = turnedOnTracks.length > 0;
     const entireWidth = totalWidth + treeAreaWidth;
     const entireHeight = totalHeight + (includeTracks ? totalTrackAreaHeight : 0);
-    const isLargeExport = exportType === 'entire' && (entireWidth > 10000 || entireHeight > 10000);
+    // the background is one raster image whatever its size, so what the figure
+    // actually costs is its residue letters: each is an svg element of its own.
+    // Past roughly this many the export runs to tens of seconds and can exhaust
+    // the tab's memory outright
+    const glyphs = showMsaLetters && exportType === 'entire' ? numColumns * leaves.length : 0;
+    const isLargeExport = glyphs > 100_000;
     return (React.createElement(Dialog, { onClose: () => {
             onClose();
         }, open: true, title: "Export SVG" },
@@ -37,28 +52,41 @@ export default function ExportSVGDialog({ model, onClose, }) {
                         React.createElement(FormControlLabel, { value: "entire", control: React.createElement(Radio, null), label: "Entire MSA" }),
                         React.createElement(FormControlLabel, { value: "viewport", control: React.createElement(Radio, null), label: "Current viewport only" })))),
             isLargeExport ? (React.createElement(Alert, { severity: "warning", style: { marginTop: 8 } },
-                "The entire MSA is very large (",
+                "The entire MSA is ",
                 Math.round(entireWidth),
                 "x",
                 Math.round(entireHeight),
-                " pixels). Export may be slow or fail.")) : null),
+                " pixels and draws",
+                ' ',
+                Math.round(glyphs / 1000),
+                "k residue letters, each its own SVG element. Export may be slow or fail \u2014 zooming out far enough to hide the letters exports the same alignment as an image instead.")) : null),
         React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                    void model
-                        .exportSVG({
-                        theme,
-                        includeMinimap: exportType === 'entire' ? false : includeMinimap,
-                        includeTracks: hasTracks && includeTracks,
-                        exportType,
-                    })
-                        .then(() => {
-                        onClose();
-                    })
-                        .catch((e) => {
-                        console.error(e);
-                        setError(e);
+            React.createElement(Button, { variant: "contained", color: "primary", 
+                // rendering runs on the main thread and a large figure holds it for
+                // seconds; without this the button stays live through the freeze and
+                // a second click starts a second export
+                disabled: exporting, startIcon: exporting ? React.createElement(CircularProgress, { size: 16, color: "inherit" }) : null, onClick: () => {
+                    setExporting(true);
+                    afterPaint(() => {
+                        void model
+                            .exportSVG({
+                            theme,
+                            includeMinimap,
+                            includeTracks: hasTracks && includeTracks,
+                            exportType,
+                        })
+                            .then(() => {
+                            onClose();
+                        })
+                            .catch((e) => {
+                            console.error(e);
+                            setError(e);
+                        })
+                            .finally(() => {
+                            setExporting(false);
+                        });
                     });
-                } }, "Submit"),
+                } }, exporting ? 'Exporting…' : 'Submit'),
             React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
                     onClose();
                 } }, "Cancel"))));

package/dist/components/dialogs/ExportSVGDialog.js.map

@@ -1 +1 @@
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package/dist/components/getVisibleLeaves.d.ts

@@ -1,4 +1,12 @@
 import type { MsaViewModel } from '../model.ts';
+export declare function visibleRowRange({ model, offsetY, blockSizeY, }: {
+    model: MsaViewModel;
+    offsetY: number;
+    blockSizeY: number;
+}): {
+    yStart: number;
+    yEnd: number;
+};
 export declare function getVisibleLeaves({ model, offsetY, blockSizeY, }: {
     model: MsaViewModel;
     offsetY: number;

package/dist/components/getVisibleLeaves.js

@@ -1,9 +1,16 @@
-// The slice of leaves whose rows intersect a block of height blockSizeY at
-// vertical offset offsetY, padded by one row on each side.
+// The half-open range of rows [yStart, yEnd) whose leaves intersect a block of
+// height blockSizeY at vertical offset offsetY, padded by one row on each side.
+// Y-axis counterpart to visibleColRange.
+export function visibleRowRange({ model, offsetY, blockSizeY, }) {
+    const { rowHeight } = model;
+    return {
+        yStart: Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight)),
+        yEnd: Math.max(0, Math.ceil((offsetY + blockSizeY + rowHeight) / rowHeight)),
+    };
+}
+// The leaves in that range.
 export function getVisibleLeaves({ model, offsetY, blockSizeY, }) {
-    const { leaves, rowHeight } = model;
-    const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
-    const yEnd = Math.max(0, Math.ceil((offsetY + blockSizeY + rowHeight) / rowHeight));
-    return leaves.slice(yStart, yEnd);
+    const { yStart, yEnd } = visibleRowRange({ model, offsetY, blockSizeY });
+    return model.leaves.slice(yStart, yEnd);
 }
 //# sourceMappingURL=getVisibleLeaves.js.map

package/dist/components/getVisibleLeaves.js.map

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package/dist/components/minimap/Minimap.js

@@ -8,7 +8,7 @@ import { MINIMAP_BAR_HEIGHT, getMinimapLayout } from './minimapLayout.js';
 const Minimap = observer(function ({ model }) {
     const { minimapHeight, msaCanvasWidth, highResScaleFactor } = model;
     const theme = useTheme();
-    const { unit, s, w, polygonHeight, polygonPoints } = getMinimapLayout(model, msaCanvasWidth);
+    const { unit, s, w, polygonHeight, polygonPoints } = getMinimapLayout(model);
     // the whole alignment, sampled down to the bar: it says where the conserved
     // blocks and the gappy stretches are, which is what a scroll aims at
     const barWidth = Math.round(msaCanvasWidth * highResScaleFactor);

package/dist/components/minimap/Minimap.js.map

@@ -1 +1 @@
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package/dist/components/minimap/MinimapSVG.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
 import type { MsaViewModel } from '../../model.ts';
-declare const MinimapSVG: ({ model, width }: {
+import type { Theme } from '@mui/material';
+export default function MinimapSVG({ model, theme, }: {
     model: MsaViewModel;
-    width: number;
-}) => React.JSX.Element;
-export default MinimapSVG;
+    theme: Theme;
+}): React.JSX.Element;

package/dist/components/minimap/MinimapSVG.js

@@ -1,15 +1,21 @@
 import React from 'react';
-import { observer } from 'mobx-react';
+import { scrollbarThumbFill } from '../DragHandle.js';
+import { canvasHref, msaThumbnail } from '../msa/msaRaster.js';
 import { MINIMAP_BAR_HEIGHT, getMinimapLayout } from './minimapLayout.js';
-const MinimapSVG = observer(({ model, width }) => {
-    const { s, w, polygonPoints } = getMinimapLayout(model, width);
-    const fillColor = 'rgb(66, 119, 127)';
-    const fillOpacity = 0.3;
+// The static counterpart to Minimap, for the SVG export. renderToSvg drives it
+// through renderToStaticMarkup, so it reads the model once and never re-renders
+// -- no observer wrapper.
+export default function MinimapSVG({ model, theme, }) {
+    const { msaCanvasWidth } = model;
+    const { s, w, polygonPoints } = getMinimapLayout(model);
+    // the same downsampled alignment the live minimap draws behind its thumb;
+    // undefined wherever a canvas cannot be read back, leaving a bare outline
+    const href = canvasHref(msaThumbnail({ model, theme, height: MINIMAP_BAR_HEIGHT }));
     return (React.createElement(React.Fragment, null,
-        React.createElement("rect", { x: 0, y: 0, width: width, height: MINIMAP_BAR_HEIGHT, stroke: "#555", fill: "none" }),
-        React.createElement("rect", { x: Math.max(0, s), y: 0, width: w, height: MINIMAP_BAR_HEIGHT, fill: fillColor, fillOpacity: fillOpacity, stroke: "#555" }),
+        href ? (React.createElement("image", { href: href, x: 0, y: 0, width: msaCanvasWidth, height: MINIMAP_BAR_HEIGHT, preserveAspectRatio: "none" })) : null,
+        React.createElement("rect", { x: 0, y: 0, width: msaCanvasWidth, height: MINIMAP_BAR_HEIGHT, stroke: "#555", fill: "none" }),
+        React.createElement("rect", { x: Math.max(0, s), y: 0, width: w, height: MINIMAP_BAR_HEIGHT, fill: scrollbarThumbFill, stroke: "#555" }),
         React.createElement("g", { transform: `translate(0 ${MINIMAP_BAR_HEIGHT})` },
-            React.createElement("polygon", { fill: fillColor, fillOpacity: fillOpacity, points: polygonPoints }))));
-});
-export default MinimapSVG;
+            React.createElement("polygon", { fill: scrollbarThumbFill, points: polygonPoints }))));
+}
 //# sourceMappingURL=MinimapSVG.js.map

package/dist/components/minimap/MinimapSVG.js.map

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package/dist/components/minimap/minimapLayout.d.ts

@@ -1,15 +1,12 @@
 import type { MsaViewModel } from '../../model.ts';
 export declare const MINIMAP_BAR_HEIGHT = 12;
 /**
- * Viewport-rectangle and trapezoid geometry for a minimap drawn `minimapWidth`
- * pixels wide, shared by the interactive Minimap and the static MinimapSVG.
- *
- * The width is a parameter rather than read off the model because the two
- * differ: on screen the minimap sits over the alignment canvas, while the SVG
- * export lays the whole figure out on its own grid. What the rectangle *marks*
- * is always the on-screen viewport, so that part comes from the model.
+ * Viewport-rectangle and trapezoid geometry for the minimap, shared by the
+ * interactive Minimap and the static MinimapSVG. Both span the alignment canvas
+ * exactly -- a minimap drawn a different width than the columns it maps puts
+ * its viewport rectangle over the wrong ones.
  */
-export declare function getMinimapLayout(model: MsaViewModel, minimapWidth: number): {
+export declare function getMinimapLayout(model: MsaViewModel): {
     unit: number;
     s: number;
     w: number;

package/dist/components/minimap/minimapLayout.js

@@ -1,20 +1,19 @@
 export const MINIMAP_BAR_HEIGHT = 12;
 /**
- * Viewport-rectangle and trapezoid geometry for a minimap drawn `minimapWidth`
- * pixels wide, shared by the interactive Minimap and the static MinimapSVG.
- *
- * The width is a parameter rather than read off the model because the two
- * differ: on screen the minimap sits over the alignment canvas, while the SVG
- * export lays the whole figure out on its own grid. What the rectangle *marks*
- * is always the on-screen viewport, so that part comes from the model.
+ * Viewport-rectangle and trapezoid geometry for the minimap, shared by the
+ * interactive Minimap and the static MinimapSVG. Both span the alignment canvas
+ * exactly -- a minimap drawn a different width than the columns it maps puts
+ * its viewport rectangle over the wrong ones.
  */
-export function getMinimapLayout(model, minimapWidth) {
+export function getMinimapLayout(model) {
     const { scrollX, minimapHeight, totalWidth, msaCanvasWidth } = model;
-    const unit = totalWidth > 0 ? minimapWidth / totalWidth : 0;
+    const unit = totalWidth > 0 ? msaCanvasWidth / totalWidth : 0;
     const s = -scrollX * unit;
-    const w = Math.max(msaCanvasWidth * unit, 20);
+    // the rectangle marks the visible slice of the alignment, so it can never be
+    // wider than the bar itself
+    const w = Math.min(msaCanvasWidth, Math.max(msaCanvasWidth * unit, 20));
     const polygonHeight = minimapHeight - MINIMAP_BAR_HEIGHT;
-    const polygonPoints = `${s + w},0 ${s},0 0,${polygonHeight} ${minimapWidth},${polygonHeight}`;
+    const polygonPoints = `${s + w},0 ${s},0 0,${polygonHeight} ${msaCanvasWidth},${polygonHeight}`;
     return { unit, s, w, polygonHeight, polygonPoints };
 }
 //# sourceMappingURL=minimapLayout.js.map

package/dist/components/minimap/minimapLayout.js.map

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package/dist/components/msa/msaRaster.d.ts

@@ -1,7 +1,7 @@
 import type { MsaViewModel } from '../../model.ts';
 import type { Theme } from '@mui/material';
 export declare const rasterTileSize = 512;
-type RasterCanvas = HTMLCanvasElement | OffscreenCanvas;
+export type RasterCanvas = HTMLCanvasElement | OffscreenCanvas;
 export interface RasterSpec {
     rowNames: string[];
     columns: Map<string, string>;
@@ -50,6 +50,37 @@ export declare function drawMsaRaster({ ctx, model, theme, offsetX, offsetY, }:
     offsetX: number;
     offsetY: number;
 }): void;
+/**
+ * A raster canvas as a PNG data URI, for embedding in the SVG export.
+ *
+ * toDataURL is the synchronous read-back and only the DOM canvas has it, so an
+ * OffscreenCanvas -- which is what the tile and thumbnail caches hold wherever
+ * it exists -- gets copied onto one first. Returns undefined wherever the
+ * read-back is unavailable (jsdom) rather than throwing, which is the signal to
+ * fall back to drawing the thing in vector.
+ */
+export declare function canvasHref(canvas: RasterCanvas | undefined): string | undefined;
+/**
+ * The alignment rectangle [col0, col0+numCols) x [row0, row0+numRows) as a PNG
+ * data URI, for the SVG export.
+ *
+ * SVG has no blit, so the export cannot reuse the tile cache the live canvas
+ * draws from: one <image> is the whole background instead. That is the
+ * difference between an export that scales and one that does not -- the vector
+ * path emits a <rect> per cell, and a 200x500 alignment exhausts the heap
+ * building them.
+ *
+ * Returns undefined wherever a canvas cannot be read back (jsdom, notably),
+ * which is the signal to keep the per-cell path.
+ */
+export declare function rasterImageHref({ model, theme, col0, row0, numCols, numRows, }: {
+    model: MsaViewModel;
+    theme: Theme;
+    col0: number;
+    row0: number;
+    numCols: number;
+    numRows: number;
+}): string | undefined;
 /**
  * The whole alignment sampled down to a strip small enough to sit behind the
  * minimap thumb, cached alongside the block tiles because it goes stale under
@@ -60,4 +91,3 @@ export declare function msaThumbnail({ model, theme, height, }: {
     theme: Theme;
     height: number;
 }): RasterCanvas | undefined;
-export {};

package/dist/components/msa/msaRaster.js

@@ -85,23 +85,28 @@ export function rasterPixels({ spec, col0, row0, width, height, colStep = 1, row
     }
     return out;
 }
+// Getting a context object back is not the same as getting one that can do
+// this: the headless render shim hands back a context carrying only measureText,
+// which a truthiness test accepts and putImageData then does not survive. Name
+// the methods the raster actually calls, so every caller degrades together.
+function usableRasterCtx(ctx) {
+    const c = ctx;
+    return (!!c &&
+        typeof c.createImageData === 'function' &&
+        typeof c.putImageData === 'function' &&
+        typeof c.getImageData === 'function' &&
+        typeof c.clearRect === 'function' &&
+        typeof c.fillRect === 'function');
+}
 function makeRasterCanvas(width, height) {
-    if (typeof OffscreenCanvas !== 'undefined') {
-        const canvas = new OffscreenCanvas(width, height);
-        const ctx = canvas.getContext('2d', { willReadFrequently: true });
-        return ctx
-            ? { canvas: canvas, ctx: ctx }
+    const canvas = typeof OffscreenCanvas !== 'undefined'
+        ? new OffscreenCanvas(width, height)
+        : typeof document !== 'undefined'
+            ? Object.assign(document.createElement('canvas'), { width, height })
             : undefined;
-    }
-    if (typeof document === 'undefined') {
-        return undefined;
-    }
-    const canvas = document.createElement('canvas');
-    canvas.width = width;
-    canvas.height = height;
-    const ctx = canvas.getContext('2d', { willReadFrequently: true });
-    return ctx
-        ? { canvas: canvas, ctx: ctx }
+    const ctx = canvas?.getContext('2d', { willReadFrequently: true });
+    return usableRasterCtx(ctx)
+        ? { canvas: canvas, ctx }
         : undefined;
 }
 function paint(pixels, width, height) {
@@ -221,6 +226,79 @@ export function drawMsaRaster({ ctx, model, theme, offsetX, offsetY, }) {
     ctx.resetTransform();
     ctx.imageSmoothingEnabled = true;
 }
+/**
+ * A raster canvas as a PNG data URI, for embedding in the SVG export.
+ *
+ * toDataURL is the synchronous read-back and only the DOM canvas has it, so an
+ * OffscreenCanvas -- which is what the tile and thumbnail caches hold wherever
+ * it exists -- gets copied onto one first. Returns undefined wherever the
+ * read-back is unavailable (jsdom) rather than throwing, which is the signal to
+ * fall back to drawing the thing in vector.
+ */
+export function canvasHref(canvas) {
+    if (!canvas || typeof document === 'undefined') {
+        return undefined;
+    }
+    try {
+        if (canvas instanceof HTMLCanvasElement) {
+            return canvas.toDataURL('image/png');
+        }
+        const out = document.createElement('canvas');
+        out.width = canvas.width;
+        out.height = canvas.height;
+        const ctx = out.getContext('2d');
+        if (typeof ctx?.drawImage !== 'function') {
+            return undefined;
+        }
+        ctx.drawImage(canvas, 0, 0);
+        return out.toDataURL('image/png');
+    }
+    catch {
+        return undefined;
+    }
+}
+// A canvas much past this many pixels fails to allocate, and the browser's own
+// per-side limit is lower still, so a raster bigger than either samples down.
+// The result is still drawn across the same rectangle -- it loses cell-exact
+// detail at a size where no figure could show it anyway.
+const maxImagePixels = 64e6;
+const maxImageSide = 16384;
+/**
+ * The alignment rectangle [col0, col0+numCols) x [row0, row0+numRows) as a PNG
+ * data URI, for the SVG export.
+ *
+ * SVG has no blit, so the export cannot reuse the tile cache the live canvas
+ * draws from: one <image> is the whole background instead. That is the
+ * difference between an export that scales and one that does not -- the vector
+ * path emits a <rect> per cell, and a 200x500 alignment exhausts the heap
+ * building them.
+ *
+ * Returns undefined wherever a canvas cannot be read back (jsdom, notably),
+ * which is the signal to keep the per-cell path.
+ */
+export function rasterImageHref({ model, theme, col0, row0, numCols, numRows, }) {
+    if (numCols <= 0 || numRows <= 0 || typeof document === 'undefined') {
+        return undefined;
+    }
+    const cache = getCache(model, theme);
+    let step = 1;
+    while (Math.ceil(numCols / step) * Math.ceil(numRows / step) > maxImagePixels ||
+        Math.ceil(numCols / step) > maxImageSide ||
+        Math.ceil(numRows / step) > maxImageSide) {
+        step *= 2;
+    }
+    const width = Math.ceil(numCols / step);
+    const height = Math.ceil(numRows / step);
+    return canvasHref(paint(rasterPixels({
+        spec: cache.spec,
+        col0,
+        row0,
+        width,
+        height,
+        colStep: step,
+        rowStep: step,
+    }), width, height));
+}
 /**
  * The whole alignment sampled down to a strip small enough to sit behind the
  * minimap thumb, cached alongside the block tiles because it goes stale under

package/dist/components/msa/msaRaster.js.map

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package/dist/{renderTestEnv.d.ts → headlessRenderEnv.d.ts}

@@ -1,6 +1,6 @@
 /**
- * jsdom shims for the SVG-export tests. Test-only -- nothing in the viewer
- * imports this.
+ * DOM shims for driving `renderToSvg` outside a browser -- the SVG-export
+ * tests, the README figure generator, and react-msaview-cli all need them.
  *
  * jsdom implements neither DOMMatrix nor a canvas 2D context, and
  * `@jbrowse/svgcanvas` needs both: it tracks the current transform as a real
@@ -12,7 +12,7 @@
  * leaves the rest undefined -- every emitted transform then carries `NaN` in its
  * x components, which no assertion on a drawn x-position can survive.
  */
-export declare class TestDOMMatrix {
+export declare class HeadlessDOMMatrix {
     a: number;
     b: number;
     c: number;
@@ -20,24 +20,26 @@ export declare class TestDOMMatrix {
     e: number;
     f: number;
     constructor(init?: number[]);
-    multiply(o: TestDOMMatrix): TestDOMMatrix;
-    translate(x: number, y?: number): TestDOMMatrix;
-    scale(x: number, y?: number): TestDOMMatrix;
+    multiply(o: HeadlessDOMMatrix): HeadlessDOMMatrix;
+    translate(x: number, y?: number): HeadlessDOMMatrix;
+    scale(x: number, y?: number): HeadlessDOMMatrix;
 }
-export declare class TestDOMPoint {
+export declare class HeadlessDOMPoint {
     x: number;
     y: number;
     constructor(x?: number, y?: number);
-    matrixTransform(m: TestDOMMatrix): TestDOMPoint;
+    matrixTransform(m: HeadlessDOMMatrix): HeadlessDOMPoint;
 }
 /**
- * Install the shims. Call from `beforeAll` in any test that exports SVG.
+ * Install the shims, into `globalThis` by default. A Node caller that builds
+ * its own jsdom passes that window instead, because Node has no global
+ * HTMLCanvasElement to patch.
  *
  * `measureText` reports 0.6em per character, close enough to a real sans-serif
- * average for layout assertions and, more usefully, exactly predictable: a test
- * can compute the width a renderer will see rather than hardcoding a number
+ * average for layout and, more usefully, exactly predictable: a caller can
+ * compute the width a renderer will see rather than hardcoding a number
  * measured from one machine's fonts.
  */
-export declare function installRenderTestEnv(): void;
+export declare function installHeadlessRenderEnv(win?: unknown): void;
 /** the per-character width factor `measureText` above reports */
-export declare const TEST_CHAR_WIDTH_RATIO = 0.6;
+export declare const CHAR_WIDTH_RATIO = 0.6;