react-msaview 6.5.0 → 8.0.0

package/dist/components/msa/msaRaster.js

@@ -16,9 +16,8 @@ let scratch;
 const colorCache = new Map();
 /**
  * CSS color string -> the packed pixel an ImageData holds for it. Painting a 1x1
- * canvas and reading it back handles every form a color scheme can produce --
- * hex, rgb(), hsl(), named -- without a parser of our own, and the cache means
- * each distinct color is resolved once per session rather than once per cell.
+ * canvas and reading it back parses hex, rgb(), hsl() and named colors; the
+ * cache resolves each distinct color once per session.
  */
 export function cssColorToPixel(css) {
     const hit = colorCache.get(css);
@@ -42,21 +41,46 @@ export function cssColorToPixel(css) {
     colorCache.set(css, packed);
     return packed;
 }
+function cellPixelFn(spec, toPixel) {
+    const { columns, relativeTo, colorAt, bg, hover } = spec;
+    const bgPixel = toPixel(bg);
+    const hoverPixel = toPixel(hover);
+    const reference = relativeTo ? columns.get(relativeTo) : undefined;
+    return (name, col, letter) => {
+        if (reference && name !== relativeTo && letter === reference[col]) {
+            return hoverPixel;
+        }
+        const color = colorAt(col, letter);
+        return color === undefined ? bgPixel : toPixel(color);
+    };
+}
 /**
  * Packs a rectangle of the alignment into one pixel per cell, in `rowNames`
  * order, ready to hand to putImageData. Cells past the end of a row, and rows
- * with no sequence at all, stay transparent -- what the per-cell tile painter
- * also leaves behind.
+ * with no sequence, stay transparent, as in the per-cell painter.
  *
- * `colStep`/`rowStep` sample instead of covering, which is how the minimap fits
- * a whole alignment into a 12px bar.
+ * `colStep`/`rowStep` sample every nth cell, which fits a whole alignment into
+ * the minimap's 12px bar. `colSpan`/`rowSpan` average each block of that many
+ * cells into one pixel, so a zoom below a device pixel per column still shows
+ * every column's color without blending neighbouring rows.
  */
-export function rasterPixels({ spec, col0, row0, width, height, colStep = 1, rowStep = 1, toPixel = cssColorToPixel, }) {
-    const { rowNames, columns, relativeTo, colorAt, bg, hover } = spec;
-    const out = new Uint32Array(width * height);
-    const bgPixel = toPixel(bg);
-    const hoverPixel = toPixel(hover);
-    const reference = relativeTo ? columns.get(relativeTo) : undefined;
+export function rasterPixels({ spec, col0, row0, width, height, colStep = 1, rowStep = 1, colSpan = 1, rowSpan = 1, toPixel = cssColorToPixel, out = new Uint32Array(width * height), }) {
+    if (colSpan > 1 || rowSpan > 1) {
+        averagePixels({
+            spec,
+            col0,
+            row0,
+            width,
+            height,
+            colSpan,
+            rowSpan,
+            toPixel,
+            out,
+        });
+        return out;
+    }
+    const { rowNames, columns } = spec;
+    const cellPixel = cellPixelFn(spec, toPixel);
     for (let r = 0; r < height; r++) {
         const name = rowNames[row0 + r * rowStep];
         if (name === undefined) {
@@ -66,7 +90,6 @@ export function rasterPixels({ spec, col0, row0, width, height, colStep = 1, row
         if (!str) {
             continue;
         }
-        const isReference = name === relativeTo;
         const base = r * width;
         for (let c = 0; c < width; c++) {
             const col = col0 + c * colStep;
@@ -74,21 +97,64 @@ export function rasterPixels({ spec, col0, row0, width, height, colStep = 1, row
             if (letter === undefined) {
                 break;
             }
-            if (reference && !isReference && letter === reference[col]) {
-                out[base + c] = hoverPixel;
+            out[base + c] = cellPixel(name, col, letter);
+        }
+    }
+    return out;
+}
+function averagePixels({ spec, col0, row0, width, height, colSpan, rowSpan, toPixel, out, }) {
+    const { rowNames, columns } = spec;
+    const cellPixel = cellPixelFn(spec, toPixel);
+    const cells = colSpan * rowSpan;
+    const rShift = littleEndian ? 0 : 24;
+    const gShift = littleEndian ? 8 : 16;
+    const bShift = littleEndian ? 16 : 8;
+    const aShift = littleEndian ? 24 : 0;
+    const names = [];
+    const strs = [];
+    for (let r = 0; r < height; r++) {
+        names.length = 0;
+        strs.length = 0;
+        for (let dr = 0; dr < rowSpan; dr++) {
+            const name = rowNames[row0 + r * rowSpan + dr];
+            const str = name === undefined ? undefined : columns.get(name);
+            if (name !== undefined && str) {
+                names.push(name);
+                strs.push(str);
             }
-            else {
-                const color = colorAt(col, letter);
-                out[base + c] = color === undefined ? bgPixel : toPixel(color);
+        }
+        const base = r * width;
+        for (let c = 0; c < width; c++) {
+            // premultiplied, so a cell past the end of a row dilutes the alpha of its
+            // pixel rather than darkening its color
+            let sumR = 0;
+            let sumG = 0;
+            let sumB = 0;
+            let sumA = 0;
+            for (let i = 0; i < strs.length; i++) {
+                const str = strs[i];
+                const name = names[i];
+                for (let dc = 0; dc < colSpan; dc++) {
+                    const col = col0 + c * colSpan + dc;
+                    const letter = str[col];
+                    if (letter === undefined) {
+                        break;
+                    }
+                    const p = cellPixel(name, col, letter);
+                    const a = (p >>> aShift) & 255;
+                    sumR += ((p >>> rShift) & 255) * a;
+                    sumG += ((p >>> gShift) & 255) * a;
+                    sumB += ((p >>> bShift) & 255) * a;
+                    sumA += a;
+                }
             }
+            out[base + c] =
+                sumA === 0
+                    ? 0
+                    : packRgba(Math.round(sumR / sumA), Math.round(sumG / sumA), Math.round(sumB / sumA), Math.round(sumA / cells));
         }
     }
-    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 &&
@@ -109,13 +175,13 @@ function makeRasterCanvas(width, height) {
         ? { canvas: canvas, ctx }
         : undefined;
 }
-function paint(pixels, width, height) {
+function paint(width, height, fill) {
     const made = makeRasterCanvas(width, height);
     if (!made) {
         return undefined;
     }
     const image = made.ctx.createImageData(width, height);
-    new Uint32Array(image.data.buffer).set(pixels);
+    fill(new Uint32Array(image.data.buffer));
     made.ctx.putImageData(image, 0, 0);
     return made.canvas;
 }
@@ -127,8 +193,8 @@ export function rasterSupported() {
     return supported;
 }
 const caches = new WeakMap();
-// Everything a cell's color depends on. A change to any of them makes every
-// cached tile stale, which a fresh cache expresses without tracking which.
+// Everything a cell's color depends on; a change to any of them starts a fresh
+// cache.
 function rasterKeys(model, theme) {
     return [
         model.columns,
@@ -163,8 +229,16 @@ function getCache(model, theme) {
     caches.set(model, next);
     return next;
 }
-function getTile(cache, tileRow, tileCol) {
-    const key = `${tileRow}_${tileCol}`;
+// Cells averaged into one tile pixel along an axis: the smallest power of two
+// that brings a pixel back to at least one device pixel. Powers of two keep the
+// number of distinct tile sets a zoom sweep builds to a handful.
+function cellsPerPixel(devicePixelsPerCell) {
+    return devicePixelsPerCell >= 1
+        ? 1
+        : 2 ** Math.ceil(Math.log2(1 / devicePixelsPerCell));
+}
+function getTile({ cache, tileRow, tileCol, colSpan, rowSpan, }) {
+    const key = `${colSpan}_${rowSpan}_${tileRow}_${tileCol}`;
     const hit = cache.tiles.get(key);
     if (hit) {
         // re-inserting makes this the newest entry: a Map iterates in insertion
@@ -173,14 +247,25 @@ function getTile(cache, tileRow, tileCol) {
         cache.tiles.set(key, hit);
         return hit;
     }
-    const col0 = tileCol * rasterTileSize;
-    const row0 = tileRow * rasterTileSize;
-    const width = Math.min(rasterTileSize, cache.numColumns - col0);
-    const height = Math.min(rasterTileSize, cache.numRows - row0);
+    const col0 = tileCol * rasterTileSize * colSpan;
+    const row0 = tileRow * rasterTileSize * rowSpan;
+    const width = Math.min(rasterTileSize, Math.ceil((cache.numColumns - col0) / colSpan));
+    const height = Math.min(rasterTileSize, Math.ceil((cache.numRows - row0) / rowSpan));
     if (width <= 0 || height <= 0) {
         return undefined;
     }
-    const canvas = paint(rasterPixels({ spec: cache.spec, col0, row0, width, height }), width, height);
+    const canvas = paint(width, height, out => {
+        rasterPixels({
+            spec: cache.spec,
+            col0,
+            row0,
+            width,
+            height,
+            colSpan,
+            rowSpan,
+            out,
+        });
+    });
     if (!canvas) {
         return undefined;
     }
@@ -196,30 +281,35 @@ function getTile(cache, tileRow, tileCol) {
 /**
  * Paints the alignment background of one MSA block from cached
  * one-pixel-per-cell tiles. The tiles do not depend on the zoom level, so a zoom
- * frame costs a handful of drawImage calls instead of a fillRect per visible
- * cell -- which ran to 885ms per block at the minimum column width.
+ * frame costs a handful of drawImage calls. A fillRect per visible cell measured
+ * 885ms per block at the minimum column width.
+ *
+ * Below a device pixel per cell the tiles average cells together, per axis.
+ * The browser's image smoothing blurs both axes, which turns every row
+ * boundary into a gradient at fit-to-width, where only the columns are narrow.
  */
 export function drawMsaRaster({ ctx, model, theme, offsetX, offsetY, }) {
     const { colWidth, rowHeight, blockSize, highResScaleFactor } = model;
     const cache = getCache(model, theme);
+    const colSpan = cellsPerPixel(colWidth * highResScaleFactor);
+    const rowSpan = cellsPerPixel(rowHeight * highResScaleFactor);
     ctx.resetTransform();
     ctx.scale(highResScaleFactor, highResScaleFactor);
     ctx.translate(-offsetX, -offsetY);
-    // below a pixel per cell a tile carries more cells than the block has room
-    // for, so let the browser downsample it rather than letting whichever cell
-    // landed last win
-    ctx.imageSmoothingEnabled = colWidth < 1 || rowHeight < 1;
-    const tileWidth = rasterTileSize * colWidth;
-    const tileHeight = rasterTileSize * rowHeight;
+    ctx.imageSmoothingEnabled = false;
+    const pixelWidth = colWidth * colSpan;
+    const pixelHeight = rowHeight * rowSpan;
+    const tileWidth = rasterTileSize * pixelWidth;
+    const tileHeight = rasterTileSize * pixelHeight;
     const firstCol = Math.max(0, Math.floor(offsetX / tileWidth));
     const lastCol = Math.floor((offsetX + blockSize) / tileWidth);
     const firstRow = Math.max(0, Math.floor(offsetY / tileHeight));
     const lastRow = Math.floor((offsetY + blockSize) / tileHeight);
     for (let tileRow = firstRow; tileRow <= lastRow; tileRow++) {
         for (let tileCol = firstCol; tileCol <= lastCol; tileCol++) {
-            const tile = getTile(cache, tileRow, tileCol);
+            const tile = getTile({ cache, tileRow, tileCol, colSpan, rowSpan });
             if (tile) {
-                ctx.drawImage(tile, 0, 0, tile.width, tile.height, tileCol * tileWidth, tileRow * tileHeight, tile.width * colWidth, tile.height * rowHeight);
+                ctx.drawImage(tile, 0, 0, tile.width, tile.height, tileCol * tileWidth, tileRow * tileHeight, tile.width * pixelWidth, tile.height * pixelHeight);
             }
         }
     }
@@ -229,12 +319,11 @@ export function drawMsaRaster({ ctx, model, theme, offsetX, offsetY, }) {
 /**
  * A raster canvas as a PNG data URI, for embedding in the SVG export.
  *
- * toDataURL is the synchronous read-back. The DOM canvas has it, and so does a
- * node canvas standing in for OffscreenCanvas headlessly; a browser
- * OffscreenCanvas -- which is what the tile and thumbnail caches hold wherever
- * it exists -- gets copied onto a DOM canvas 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.
+ * toDataURL is the synchronous read-back. The DOM canvas and a headless node
+ * canvas have it; a browser OffscreenCanvas, which the tile and thumbnail
+ * caches hold where it exists, is copied onto a DOM canvas first. Returns
+ * undefined where read-back is unavailable (jsdom), and the caller then draws
+ * in vector.
  */
 export function canvasHref(canvas) {
     if (!canvas) {
@@ -261,52 +350,63 @@ export function canvasHref(canvas) {
         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.
+// A canvas much past this many pixels fails to allocate, and the browser's
+// per-side limit is lower still, so a larger raster averages down per axis and
+// is drawn across the same rectangle. An alignment that hits the limit on
+// columns alone keeps every row.
 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.
+ * SVG has no blit, so the export draws the whole background as one <image>. 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.
+ * Returns undefined where a canvas cannot be read back (jsdom), and the caller
+ * then keeps 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;
+    let colSpan = 1;
+    let rowSpan = 1;
+    while (Math.ceil(numCols / colSpan) > maxImageSide) {
+        colSpan *= 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));
+    while (Math.ceil(numRows / rowSpan) > maxImageSide) {
+        rowSpan *= 2;
+    }
+    while (Math.ceil(numCols / colSpan) * Math.ceil(numRows / rowSpan) >
+        maxImagePixels) {
+        if (numCols / colSpan >= numRows / rowSpan) {
+            colSpan *= 2;
+        }
+        else {
+            rowSpan *= 2;
+        }
+    }
+    const width = Math.ceil(numCols / colSpan);
+    const height = Math.ceil(numRows / rowSpan);
+    return canvasHref(paint(width, height, out => {
+        rasterPixels({
+            spec: cache.spec,
+            col0,
+            row0,
+            width,
+            height,
+            colSpan,
+            rowSpan,
+            out,
+        });
+    }));
 }
 /**
- * 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
- * exactly the same conditions.
+ * The whole alignment sampled down to a strip behind the minimap thumb, cached
+ * with the block tiles since the same keys invalidate both.
  */
 export function msaThumbnail({ model, theme, height, }) {
     const cache = getCache(model, theme);
@@ -323,15 +423,18 @@ export function msaThumbnail({ model, theme, height, }) {
         const h = Math.ceil(numRows / rowStep);
         cache.thumbnail = {
             height,
-            canvas: paint(rasterPixels({
-                spec: cache.spec,
-                col0: 0,
-                row0: 0,
-                width: w,
-                height: h,
-                colStep,
-                rowStep,
-            }), w, h),
+            canvas: paint(w, h, out => {
+                rasterPixels({
+                    spec: cache.spec,
+                    col0: 0,
+                    row0: 0,
+                    width: w,
+                    height: h,
+                    colStep,
+                    rowStep,
+                    out,
+                });
+            }),
         };
     }
     return cache.thumbnail.canvas;

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

@@ -1 +1 @@
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package/dist/components/msa/packDomainLanes.d.ts

@@ -0,0 +1,20 @@
+/**
+ * Assigns each of one row's bands a lane: the first lane whose last band ends
+ * before this one starts, so only bands that actually overlap stack. A row of
+ * adjacent exons packs into a single lane; a family with a domain nested inside
+ * it takes two.
+ *
+ * Packing runs left to right, but the result keeps the input's largest-first
+ * paint order. `laneCount` is the row's depth, which the renderer divides the
+ * row height by so a deep stack stays inside its own row.
+ *
+ * The coordinates are whatever the caller packs in: alignment columns for the
+ * overlay, residue positions for a `features` row panel.
+ */
+export declare function packDomainLanes<T extends {
+    startCol: number;
+    endCol: number;
+}>(bands: T[]): (T & {
+    lane: number;
+    laneCount: number;
+})[];

package/dist/components/msa/packDomainLanes.js

@@ -0,0 +1,33 @@
+/**
+ * Assigns each of one row's bands a lane: the first lane whose last band ends
+ * before this one starts, so only bands that actually overlap stack. A row of
+ * adjacent exons packs into a single lane; a family with a domain nested inside
+ * it takes two.
+ *
+ * Packing runs left to right, but the result keeps the input's largest-first
+ * paint order. `laneCount` is the row's depth, which the renderer divides the
+ * row height by so a deep stack stays inside its own row.
+ *
+ * The coordinates are whatever the caller packs in: alignment columns for the
+ * overlay, residue positions for a `features` row panel.
+ */
+export function packDomainLanes(bands) {
+    const laneEnds = [];
+    const lanes = new Array(bands.length);
+    const byStart = bands
+        .map((_, i) => i)
+        .sort((a, b) => bands[a].startCol - bands[b].startCol);
+    for (const i of byStart) {
+        const { startCol, endCol } = bands[i];
+        const found = laneEnds.findIndex(end => end <= startCol);
+        const lane = found === -1 ? laneEnds.length : found;
+        laneEnds[lane] = endCol;
+        lanes[i] = lane;
+    }
+    return bands.map((band, i) => ({
+        ...band,
+        lane: lanes[i],
+        laneCount: laneEnds.length,
+    }));
+}
+//# sourceMappingURL=packDomainLanes.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"packDomainLanes.js","sourceRoot":"","sources":["../../../src/components/msa/packDomainLanes.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,eAAe,CAC7B,KAAU;IAEV,MAAM,QAAQ,GAAa,EAAE,CAAA;IAC7B,MAAM,KAAK,GAAG,IAAI,KAAK,CAAS,KAAK,CAAC,MAAM,CAAC,CAAA;IAC7C,MAAM,OAAO,GAAG,KAAK;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;SAChB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE,CAAC,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAE,CAAC,QAAQ,CAAC,CAAA;IAE1D,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;QACxB,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACtC,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,QAAQ,CAAC,CAAA;QACxD,MAAM,IAAI,GAAG,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAA;QACnD,QAAQ,CAAC,IAAI,CAAC,GAAG,MAAM,CAAA;QACvB,KAAK,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;IACjB,CAAC;IAED,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;QAC7B,GAAG,IAAI;QACP,IAAI,EAAE,KAAK,CAAC,CAAC,CAAE;QACf,SAAS,EAAE,QAAQ,CAAC,MAAM;KAC3B,CAAC,CAAC,CAAA;AACL,CAAC"}

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

@@ -1,9 +1,11 @@
 import type { MsaViewModel } from '../../model.ts';
 import type { RenderCtx } from '../renderCtx.ts';
-export declare function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }: {
+import type { Theme } from '@mui/material';
+export declare function renderBoxFeatureCanvasBlock({ model, theme, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }: {
     offsetX: number;
     offsetY: number;
     model: MsaViewModel;
+    theme: Theme;
     ctx: RenderCtx;
     highResScaleFactorOverride?: number;
     blockSizeXOverride?: number;