react-msaview 9.0.0 → 9.1.1

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

@@ -1,6 +1,5 @@
 import type { MsaViewModel } from '../../model.ts';
 import type { Theme } from '@mui/material';
-export declare const rasterTileSize = 512;
 export type RasterCanvas = HTMLCanvasElement | OffscreenCanvas;
 export interface RasterSpec {
     rowNames: string[];
@@ -39,7 +38,20 @@ export declare function rasterPixels({ spec, col0, row0, width, height, colStep,
     toPixel?: (css: string) => number;
     out?: Uint32Array;
 }): Uint32Array<ArrayBufferLike>;
-export declare function rasterSupported(): boolean;
+/**
+ * A canvas off the page, an OffscreenCanvas where there is one, with its 2d
+ * context, or undefined where the context fails `usable` (jsdom has none).
+ */
+export declare function makeOffscreenCanvas<Ctx>(width: number, height: number, usable: (ctx: unknown) => ctx is Ctx, settings?: CanvasRenderingContext2DSettings): {
+    canvas: RasterCanvas;
+    ctx: (CanvasRenderingContext2D | OffscreenCanvasRenderingContext2D | null | undefined) & Ctx;
+} | undefined;
+/**
+ * Whether the alignment background comes from the raster: true while the
+ * residue scheme fills the cells, with a 2d context that reads back, which
+ * jsdom lacks. renderMSABlock paints each cell otherwise.
+ */
+export declare function rasterApplies(model: Pick<MsaViewModel, 'cellFill'>): boolean;
 /**
  * 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

package/dist/components/msa/msaRaster.js

@@ -2,7 +2,7 @@ import { tileColorFn, tileColorTable } from './tileColor.js';
 // One raster tile holds this many cells on a side. A tile costs ~10ms to build
 // and ~1MB to hold, and is then drawn at any zoom for ~1ms, so the cache only
 // has to be large enough to cover a screen without thrashing.
-export const rasterTileSize = 512;
+const rasterTileSize = 512;
 const maxCachedTiles = 64;
 const maxThumbnailColumns = 2000;
 const maxColorCacheEntries = 4096;
@@ -164,16 +164,23 @@ function usableRasterCtx(ctx) {
         typeof c.clearRect === 'function' &&
         typeof c.fillRect === 'function');
 }
-function makeRasterCanvas(width, height) {
+/**
+ * A canvas off the page, an OffscreenCanvas where there is one, with its 2d
+ * context, or undefined where the context fails `usable` (jsdom has none).
+ */
+export function makeOffscreenCanvas(width, height, usable, settings) {
     const canvas = typeof OffscreenCanvas !== 'undefined'
         ? new OffscreenCanvas(width, height)
         : typeof document !== 'undefined'
             ? Object.assign(document.createElement('canvas'), { width, height })
             : undefined;
-    const ctx = canvas?.getContext('2d', { willReadFrequently: true });
-    return usableRasterCtx(ctx)
-        ? { canvas: canvas, ctx }
-        : undefined;
+    const ctx = canvas?.getContext('2d', settings);
+    return usable(ctx) ? { canvas: canvas, ctx } : undefined;
+}
+function makeRasterCanvas(width, height) {
+    return makeOffscreenCanvas(width, height, usableRasterCtx, {
+        willReadFrequently: true,
+    });
 }
 function paint(width, height, fill) {
     const made = makeRasterCanvas(width, height);
@@ -186,11 +193,14 @@ function paint(width, height, fill) {
     return made.canvas;
 }
 let supported;
-// jsdom, and any browser without a 2d context, has no raster to draw; the
-// per-cell painter in renderMSABlock stays the fallback
-export function rasterSupported() {
+/**
+ * Whether the alignment background comes from the raster: true while the
+ * residue scheme fills the cells, with a 2d context that reads back, which
+ * jsdom lacks. renderMSABlock paints each cell otherwise.
+ */
+export function rasterApplies(model) {
     supported ??= !!makeRasterCanvas(1, 1);
-    return supported;
+    return model.cellFill === 'residue' && supported;
 }
 const caches = new WeakMap();
 // Everything a cell's color depends on; a change to any of them starts a fresh

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

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

@@ -1,5 +1,8 @@
+import type { HierarchyNode } from '../../hierarchy.ts';
 import type { MsaViewModel } from '../../model.ts';
+import type { DomainBand, NodeWithIdsAndLength } from '../../types.ts';
 import type { RenderCtx } from '../renderCtx.ts';
+import type { SpanSource } from './drawFeatureSpans.ts';
 import type { Theme } from '@mui/material';
 export declare function renderBoxFeatureCanvasBlock({ model, theme, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }: {
     offsetX: number;
@@ -11,3 +14,9 @@ export declare function renderBoxFeatureCanvasBlock({ model, theme, offsetX, off
     blockSizeXOverride?: number;
     blockSizeYOverride?: number;
 }): void;
+/**
+ * The domain overlay's spans over `leaves`, in alignment pixels: filled rows,
+ * an underline bar, or thin sub-rows, as `domainUnderline` and
+ * `subFeatureRows` decide.
+ */
+export declare function domainOverlaySource(model: MsaViewModel, leaves: HierarchyNode<NodeWithIdsAndLength>[]): SpanSource<DomainBand>;

package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -3,7 +3,7 @@ import { contrastTextFn } from '../../util.js';
 import { getVisibleLeaves } from '../getVisibleLeaves.js';
 import { drawFeatureSpans, spanRows } from './drawFeatureSpans.js';
 export function renderBoxFeatureCanvasBlock({ model, theme, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
-    const { blockSize, rowHeight, highResScaleFactor, actuallyShowDomains, subFeatureRows, colWidth, featureColors, featureLabels, segmentLabels, showMsaLetters, domainUnderline, domainBands, } = model;
+    const { blockSize, rowHeight, highResScaleFactor, actuallyShowDomains } = model;
     if (!actuallyShowDomains) {
         return;
     }
@@ -13,6 +13,41 @@ export function renderBoxFeatureCanvasBlock({ model, theme, offsetX, offsetY, ct
     ctx.resetTransform();
     ctx.scale(k, k);
     ctx.translate(-offsetX, rowHeight / 2 - offsetY);
+    const source = domainOverlaySource(model, getVisibleLeaves({ model, offsetY, blockSizeY: by }));
+    const contrastText = contrastTextFn(theme);
+    if (model.cellFill === 'residue' && model.domainUnderline) {
+        // over residue colors a bar in a categorical color blends into the cells
+        // beside it, so a strip of the page background parts it from them
+        const { height } = source.layout;
+        const halo = theme.palette.background.default;
+        drawFeatureSpans({
+            ctx,
+            ...source,
+            layout: { ...source.layout, height: n => height(n) + barHalo },
+            colors: new Map([...source.colors.keys()].map(a => [a, { fill: halo, stroke: halo }])),
+            labelOf: undefined,
+            labelDrawn: undefined,
+            contrastText,
+            xMin: offsetX,
+            xMax: offsetX + bx,
+        });
+    }
+    drawFeatureSpans({
+        ctx,
+        ...source,
+        contrastText,
+        xMin: offsetX,
+        xMax: offsetX + bx,
+    });
+}
+const barHalo = 1.5;
+/**
+ * The domain overlay's spans over `leaves`, in alignment pixels: filled rows,
+ * an underline bar, or thin sub-rows, as `domainUnderline` and
+ * `subFeatureRows` decide.
+ */
+export function domainOverlaySource(model, leaves) {
+    const { rowHeight, subFeatureRows, colWidth, featureColors, featureLabels, segmentLabels, showMsaLetters, domainUnderline, domainBands, } = model;
     // the plain and underline modes give every band the same height; a sub-row
     // band is thinner, and how thin depends on how many lanes its row needs
     const barHeight = domainUnderline
@@ -28,9 +63,8 @@ export function renderBoxFeatureCanvasBlock({ model, theme, offsetX, offsetY, ct
     // whole band. Keyed by accession rather than drawn on row 0, because the rows
     // carrying the gene model are often not the first ones in the alignment
     const labelled = drawSegmentLabels ? new Set() : undefined;
-    drawFeatureSpans({
-        ctx,
-        rows: spanRows(getVisibleLeaves({ model, offsetY, blockSizeY: by }), domainBands),
+    return {
+        rows: spanRows(leaves, domainBands),
         layout: {
             // sub-rows are thin, but a row whose lanes would spill onto the row below
             // shares out the row height between them instead
@@ -53,9 +87,6 @@ export function renderBoxFeatureCanvasBlock({ model, theme, offsetX, offsetY, ct
                 ? segmentLabels.get(band.annotation.accession)
                 : undefined),
         labelDrawn: band => labelled?.add(band.annotation.accession),
-        contrastText: contrastTextFn(theme),
-        xMin: offsetX,
-        xMax: offsetX + bx,
-    });
+    };
 }
 //# sourceMappingURL=renderBoxFeatureCanvasBlock.js.map

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

@@ -1,10 +1,7 @@
 import type { MsaViewModel } from '../../model.ts';
 import type { RenderCtx } from '../renderCtx.ts';
 import type { Theme } from '@mui/material';
-export declare const highlightFill = "rgba(255,140,0,0.28)";
-export declare const highlightBorder = "rgba(210,90,0,0.95)";
 export declare const highlightRowFill = "rgba(255,140,0,0.18)";
-export declare const labelFontSize = 11;
 export declare const highlightLabelHeight: number;
 export interface LabelBox {
     left: number;
@@ -67,8 +64,8 @@ export declare function renderSelection({ ctx, model, offsetX, offsetY, height,
 }): void;
 /**
  * The overlay parts that come from the snapshot: the reference row's tint, a
- * bordered band per run of highlighted columns, the `highlights` layer and the
- * selected block. The live overlay draws these under its hover and click
+ * bordered band per run of highlighted columns and the `highlights` layer. The
+ * live overlay draws these under the selected block and its hover and click
  * bands; the SVG export draws only these.
  */
 export declare function renderPersistentHighlights({ ctx, model, theme, offsetX, offsetY, width, height, }: {

package/dist/components/msa/renderHighlights.js

@@ -2,10 +2,10 @@ import { setFontSize } from '../../setFontSize.js';
 import { referenceColor, selectionBorder, selectionFill, } from '../overlayColors.js';
 // a fill plus a solid border; the hover wash alone is invisible over clustalx
 // coloring
-export const highlightFill = 'rgba(255,140,0,0.28)';
-export const highlightBorder = 'rgba(210,90,0,0.95)';
+const highlightFill = 'rgba(255,140,0,0.28)';
+const highlightBorder = 'rgba(210,90,0,0.95)';
 export const highlightRowFill = 'rgba(255,140,0,0.18)';
-export const labelFontSize = 11;
+const labelFontSize = 11;
 const labelPad = 3;
 // the label box above a highlight band; tree blocks also check rows this far
 // outside themselves
@@ -137,8 +137,8 @@ export function renderSelection({ ctx, model, offsetX, offsetY, height, }) {
 }
 /**
  * The overlay parts that come from the snapshot: the reference row's tint, a
- * bordered band per run of highlighted columns, the `highlights` layer and the
- * selected block. The live overlay draws these under its hover and click
+ * bordered band per run of highlighted columns and the `highlights` layer. The
+ * live overlay draws these under the selected block and its hover and click
  * bands; the SVG export draws only these.
  */
 export function renderPersistentHighlights({ ctx, model, theme, offsetX, offsetY, width, height, }) {
@@ -157,6 +157,5 @@ export function renderPersistentHighlights({ ctx, model, theme, offsetX, offsetY
         ctx.strokeRect(x, 0, w, height);
     }
     renderHighlights({ ctx, model, theme, offsetX, offsetY, width, height });
-    renderSelection({ ctx, model, offsetX, offsetY, height });
 }
 //# sourceMappingURL=renderHighlights.js.map

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

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

@@ -1,7 +1,7 @@
 import type { MsaViewModel } from '../../model.ts';
 import type { RenderCtx } from '../renderCtx.ts';
 import type { Theme } from '@mui/material';
-export declare function renderMSABlock({ model, offsetX, offsetY, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, rasterTiles, }: {
+export declare function renderMSABlock({ model, offsetX, offsetY, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, rasterTiles, domains, }: {
     offsetX: number;
     offsetY: number;
     theme: Theme;
@@ -11,4 +11,9 @@ export declare function renderMSABlock({ model, offsetX, offsetY, ctx, theme, hi
     blockSizeXOverride?: number;
     blockSizeYOverride?: number;
     rasterTiles?: boolean;
+    /**
+     * draw the domain overlay too, over the cell colors and under the letters,
+     * which is the one order every cell fill reads right in
+     */
+    domains?: boolean;
 }): void;

package/dist/components/msa/renderMSABlock.js

@@ -1,20 +1,25 @@
+import { zoomFrameMaxLetters } from '../../constants.js';
 import { setFontSize } from '../../setFontSize.js';
 import { adjustColorForContrast, contrastTextFn } from '../../util.js';
 import { getVisibleLeaves } from '../getVisibleLeaves.js';
 import { domainBandCursor } from './domainBandCursor.js';
+import { renderBoxFeatureCanvasBlock } from './renderBoxFeatureCanvasBlock.js';
 import { tileColorFn } from './tileColor.js';
 import { visibleColRange } from './visibleColRange.js';
-export function renderMSABlock({ model, offsetX, offsetY, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, rasterTiles, }) {
-    const { colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, actuallyShowDomains, bgColor, } = model;
+export function renderMSABlock({ model, offsetX, offsetY, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, rasterTiles, domains, }) {
+    const { colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, cellFill, bgColor, } = model;
     const k = highResScaleFactorOverride ?? highResScaleFactor;
     const bx = blockSizeXOverride ?? blockSize;
     const by = blockSizeYOverride ?? blockSize;
-    ctx.resetTransform();
-    ctx.scale(k, k);
-    ctx.translate(-offsetX, rowHeight / 2 - offsetY);
-    ctx.textAlign = 'center';
-    ctx.textBaseline = 'alphabetic';
-    setFontSize(ctx, fontSize, !bgColor);
+    const setup = () => {
+        ctx.resetTransform();
+        ctx.scale(k, k);
+        ctx.translate(-offsetX, rowHeight / 2 - offsetY);
+        ctx.textAlign = 'center';
+        ctx.textBaseline = 'alphabetic';
+        setFontSize(ctx, fontSize, !bgColor);
+    };
+    setup();
     const { xStart, xEnd } = visibleColRange({
         offsetX,
         blockWidth: bx,
@@ -25,7 +30,7 @@ export function renderMSABlock({ model, offsetX, offsetY, ctx, theme, highResSca
     const referenceSeq = relativeTo
         ? columns.get(relativeTo)?.slice(xStart, xEnd)
         : null;
-    drawTilesAndText({
+    const cells = {
         model,
         ctx,
         theme,
@@ -33,13 +38,34 @@ export function renderMSABlock({ model, offsetX, offsetY, ctx, theme, highResSca
         xEnd,
         visibleLeaves,
         referenceSeq,
-        // when domains are shown the background tiles come from
+        // when the domains fill the cells the background comes from
         // renderBoxFeatureCanvasBlock, so only the letters are drawn here
-        drawTiles: !actuallyShowDomains,
+        drawTiles: cellFill !== 'domain',
         // ...and when the caller has already laid the raster down, the tiles are
         // there but nothing here has to paint them
         rasterTiles,
-    });
+        letters: model.showMsaLetters &&
+            (!model.wheelZooming ||
+                (bx * by) / (colWidth * rowHeight) <= zoomFrameMaxLetters),
+    };
+    if (domains) {
+        drawTilesAndText({ ...cells, pass: 'tiles' });
+        renderBoxFeatureCanvasBlock({
+            model,
+            theme,
+            ctx,
+            offsetX,
+            offsetY,
+            highResScaleFactorOverride,
+            blockSizeXOverride,
+            blockSizeYOverride,
+        });
+        setup();
+        drawTilesAndText({ ...cells, pass: 'letters' });
+    }
+    else {
+        drawTilesAndText({ ...cells, pass: 'both' });
+    }
     drawInsertionIndicators({
         model,
         ctx,
@@ -49,11 +75,12 @@ export function renderMSABlock({ model, offsetX, offsetY, ctx, theme, highResSca
     });
     ctx.resetTransform();
 }
-function drawTilesAndText({ model, ctx, theme, visibleLeaves, xStart, xEnd, referenceSeq, drawTiles, rasterTiles, }) {
-    const { bgColor, columns, colWidth, rowHeight, fontSize, relativeTo, showMsaLetters, subFeatureRows, domainUnderline, domainBandsByStart, featureColors, } = model;
+function drawTilesAndText({ model, ctx, theme, visibleLeaves, xStart, xEnd, referenceSeq, drawTiles, rasterTiles, letters: lettersOn, pass, }) {
+    const { bgColor, columns, colWidth, rowHeight, fontSize, relativeTo, subFeatureRows, domainUnderline, domainBandsByStart, featureColors, } = model;
     const tiles = drawTiles && bgColor;
-    const paintTiles = tiles && !rasterTiles;
-    if (paintTiles || showMsaLetters) {
+    const paintTiles = tiles && !rasterTiles && pass !== 'letters';
+    const letters = lettersOn && pass !== 'tiles';
+    if (paintTiles || letters) {
         const tileColor = tileColorFn(model);
         // Domain fills come from a categorical palette with no fixed lightness, and
         // a dynamic scheme colors a cell from its column, so a readable letter color
@@ -91,7 +118,7 @@ function drawTilesAndText({ model, ctx, theme, visibleLeaves, xStart, xEnd, refe
                             : color || theme.palette.background.default;
                         ctx.fillRect(x, tileY, colWidth, rowHeight);
                     }
-                    if (showMsaLetters) {
+                    if (letters) {
                         const covering = bandAt(col);
                         ctx.fillStyle = covering
                             ? // on top of a domain box: contrast against the box fill

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

@@ -1 +1 @@
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package/dist/components/msa/renderMSAMouseover.js

@@ -1,5 +1,5 @@
 import { clickColor, hoverColor, multiRowHoverColor } from '../overlayColors.js';
-import { renderPersistentHighlights } from './renderHighlights.js';
+import { renderPersistentHighlights, renderSelection, } from './renderHighlights.js';
 export function renderMouseover({ ctx, model, theme, }) {
     const { mouseCol, colWidth, msaCanvasWidth: width, height, rowHeight, scrollX, scrollY, mouseRow, mouseClickRow, mouseClickCol, highResScaleFactor, hoveredRowIndices, } = model;
     ctx.resetTransform();
@@ -22,6 +22,7 @@ export function renderMouseover({ ctx, model, theme, }) {
         width,
         height,
     });
+    renderSelection({ ctx, model, offsetX: -scrollX, offsetY: -scrollY, height });
     // every tip under a hovered tree node stays lit
     ctx.fillStyle = multiRowHoverColor;
     for (const rowIndex of hoveredRowIndices) {

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

@@ -1 +1 @@
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+{"version":3,"file":"renderMSAMouseover.js","sourceRoot":"","sources":["../../../src/components/msa/renderMSAMouseover.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,kBAAkB,EAAE,MAAM,qBAAqB,CAAA;AAChF,OAAO,EACL,0BAA0B,EAC1B,eAAe,GAChB,MAAM,uBAAuB,CAAA;AAK9B,MAAM,UAAU,eAAe,CAAC,EAC9B,GAAG,EACH,KAAK,EACL,KAAK,GAKN;IACC,MAAM,EACJ,QAAQ,EACR,QAAQ,EACR,cAAc,EAAE,KAAK,EACrB,MAAM,EACN,SAAS,EACT,OAAO,EACP,OAAO,EACP,QAAQ,EACR,aAAa,EACb,aAAa,EACb,kBAAkB,EAClB,iBAAiB,GAClB,GAAG,KAAK,CAAA;IACT,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,GAAG,kBAAkB,EAAE,MAAM,GAAG,kBAAkB,CAAC,CAAA;IAC5E,GAAG,CAAC,KAAK,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAA;IAEjD,8EAA8E;IAC9E,oEAAoE;IACpE,MAAM,OAAO,GAAG,CAAC,KAAa,EAAE,EAAE;QAChC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,GAAG,OAAO,EAAE,KAAK,EAAE,SAAS,CAAC,CAAA;IAChE,CAAC,CAAA;IACD,MAAM,OAAO,GAAG,CAAC,KAAa,EAAE,EAAE;QAChC,GAAG,CAAC,QAAQ,CAAC,KAAK,GAAG,QAAQ,GAAG,OAAO,EAAE,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAA;IAC/D,CAAC,CAAA;IAED,0BAA0B,CAAC;QACzB,GAAG;QACH,KAAK;QACL,KAAK;QACL,OAAO,EAAE,CAAC,OAAO;QACjB,OAAO,EAAE,CAAC,OAAO;QACjB,KAAK;QACL,MAAM;KACP,CAAC,CAAA;IACF,eAAe,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,OAAO,EAAE,OAAO,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,CAAC,CAAA;IAE7E,gDAAgD;IAChD,GAAG,CAAC,SAAS,GAAG,kBAAkB,CAAA;IAClC,KAAK,MAAM,QAAQ,IAAI,iBAAiB,EAAE,CAAC;QACzC,OAAO,CAAC,QAAQ,CAAC,CAAA;IACnB,CAAC;IAED,GAAG,CAAC,SAAS,GAAG,UAAU,CAAA;IAC1B,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;QAC3B,OAAO,CAAC,QAAQ,CAAC,CAAA;IACnB,CAAC;IACD,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;QAC3B,OAAO,CAAC,QAAQ,CAAC,CAAA;IACnB,CAAC;IACD,GAAG,CAAC,SAAS,GAAG,UAAU,CAAA;IAC1B,IAAI,aAAa,KAAK,SAAS,EAAE,CAAC;QAChC,OAAO,CAAC,aAAa,CAAC,CAAA;IACxB,CAAC;IACD,IAAI,aAAa,KAAK,SAAS,EAAE,CAAC;QAChC,OAAO,CAAC,aAAa,CAAC,CAAA;IACxB,CAAC;AACH,CAAC"}

package/dist/components/msa/tileColor.js

@@ -7,6 +7,10 @@ export function tileColorFn(model) {
         const { colClustalX } = model;
         return (col, letter) => colClustalX[col][letter];
     }
+    if (dynamicColorSchemeName === 'blosum62_dynamic') {
+        const { colSimilarity } = model;
+        return (col, letter) => colSimilarity[col][letter];
+    }
     if (dynamicColorSchemeName === 'percent_identity_dynamic') {
         const { colConsensus } = model;
         return (col, letter) => {
@@ -25,6 +29,9 @@ export function tileColorTable(model) {
     if (dynamicColorSchemeName === 'clustalx_protein_dynamic') {
         return model.colClustalX;
     }
+    if (dynamicColorSchemeName === 'blosum62_dynamic') {
+        return model.colSimilarity;
+    }
     if (dynamicColorSchemeName === 'percent_identity_dynamic') {
         return model.colConsensus;
     }

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

@@ -1 +1 @@
-{"version":3,"file":"tileColor.js","sourceRoot":"","sources":["../../../src/components/msa/tileColor.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,0EAA0E;AAC1E,cAAc;AACd,MAAM,UAAU,WAAW,CAAC,KAAmB;IAC7C,MAAM,EAAE,sBAAsB,EAAE,GAAG,KAAK,CAAA;IACxC,IAAI,sBAAsB,KAAK,0BAA0B,EAAE,CAAC;QAC1D,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;QAC7B,OAAO,CAAC,GAAW,EAAE,MAAc,EAAE,EAAE,CAAC,WAAW,CAAC,GAAG,CAAE,CAAC,MAAM,CAAC,CAAA;IACnE,CAAC;IACD,IAAI,sBAAsB,KAAK,0BAA0B,EAAE,CAAC;QAC1D,MAAM,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;QAC9B,OAAO,CAAC,GAAW,EAAE,MAAc,EAAE,EAAE;YACrC,MAAM,SAAS,GAAG,YAAY,CAAC,GAAG,CAAE,CAAA;YACpC,OAAO,MAAM,KAAK,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;QAClE,CAAC,CAAA;IACH,CAAC;IACD,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC7B,OAAO,CAAC,IAAY,EAAE,MAAc,EAAE,EAAE,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;AAC9D,CAAC;AAED,gFAAgF;AAChF,+EAA+E;AAC/E,gEAAgE;AAChE,MAAM,UAAU,cAAc,CAAC,KAAmB;IAChD,MAAM,EAAE,sBAAsB,EAAE,GAAG,KAAK,CAAA;IACxC,IAAI,sBAAsB,KAAK,0BAA0B,EAAE,CAAC;QAC1D,OAAO,KAAK,CAAC,WAAW,CAAA;IAC1B,CAAC;IACD,IAAI,sBAAsB,KAAK,0BAA0B,EAAE,CAAC;QAC1D,OAAO,KAAK,CAAC,YAAY,CAAA;IAC3B,CAAC;IACD,OAAO,KAAK,CAAC,WAAW,CAAA;AAC1B,CAAC"}
+{"version":3,"file":"tileColor.js","sourceRoot":"","sources":["../../../src/components/msa/tileColor.ts"],"names":[],"mappings":"AAEA,8EAA8E;AAC9E,0EAA0E;AAC1E,cAAc;AACd,MAAM,UAAU,WAAW,CAAC,KAAmB;IAC7C,MAAM,EAAE,sBAAsB,EAAE,GAAG,KAAK,CAAA;IACxC,IAAI,sBAAsB,KAAK,0BAA0B,EAAE,CAAC;QAC1D,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;QAC7B,OAAO,CAAC,GAAW,EAAE,MAAc,EAAE,EAAE,CAAC,WAAW,CAAC,GAAG,CAAE,CAAC,MAAM,CAAC,CAAA;IACnE,CAAC;IACD,IAAI,sBAAsB,KAAK,kBAAkB,EAAE,CAAC;QAClD,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;QAC/B,OAAO,CAAC,GAAW,EAAE,MAAc,EAAE,EAAE,CAAC,aAAa,CAAC,GAAG,CAAE,CAAC,MAAM,CAAC,CAAA;IACrE,CAAC;IACD,IAAI,sBAAsB,KAAK,0BAA0B,EAAE,CAAC;QAC1D,MAAM,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;QAC9B,OAAO,CAAC,GAAW,EAAE,MAAc,EAAE,EAAE;YACrC,MAAM,SAAS,GAAG,YAAY,CAAC,GAAG,CAAE,CAAA;YACpC,OAAO,MAAM,KAAK,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;QAClE,CAAC,CAAA;IACH,CAAC;IACD,MAAM,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC7B,OAAO,CAAC,IAAY,EAAE,MAAc,EAAE,EAAE,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;AAC9D,CAAC;AAED,gFAAgF;AAChF,+EAA+E;AAC/E,gEAAgE;AAChE,MAAM,UAAU,cAAc,CAAC,KAAmB;IAChD,MAAM,EAAE,sBAAsB,EAAE,GAAG,KAAK,CAAA;IACxC,IAAI,sBAAsB,KAAK,0BAA0B,EAAE,CAAC;QAC1D,OAAO,KAAK,CAAC,WAAW,CAAA;IAC1B,CAAC;IACD,IAAI,sBAAsB,KAAK,kBAAkB,EAAE,CAAC;QAClD,OAAO,KAAK,CAAC,aAAa,CAAA;IAC5B,CAAC;IACD,IAAI,sBAAsB,KAAK,0BAA0B,EAAE,CAAC;QAC1D,OAAO,KAAK,CAAC,YAAY,CAAA;IAC3B,CAAC;IACD,OAAO,KAAK,CAAC,WAAW,CAAA;AAC1B,CAAC"}

package/dist/components/renderCtx.d.ts

@@ -4,4 +4,4 @@
  * SVG export) satisfy this, so renderers can be typed against it without an
  * `as any` cast at the SVG-export boundary.
  */
-export type RenderCtx = Pick<CanvasRenderingContext2D, 'arc' | 'beginPath' | 'clearRect' | 'closePath' | 'fill' | 'fillRect' | 'fillStyle' | 'fillText' | 'font' | 'lineTo' | 'lineWidth' | 'measureText' | 'moveTo' | 'quadraticCurveTo' | 'resetTransform' | 'restore' | 'save' | 'scale' | 'setLineDash' | 'stroke' | 'strokeRect' | 'strokeStyle' | 'textAlign' | 'textBaseline' | 'translate'>;
+export type RenderCtx = Pick<CanvasRenderingContext2D, 'arc' | 'beginPath' | 'closePath' | 'fill' | 'fillRect' | 'fillStyle' | 'fillText' | 'font' | 'lineTo' | 'lineWidth' | 'measureText' | 'moveTo' | 'quadraticCurveTo' | 'resetTransform' | 'restore' | 'save' | 'scale' | 'setLineDash' | 'stroke' | 'strokeRect' | 'strokeStyle' | 'textAlign' | 'textBaseline' | 'translate'>;

package/dist/components/rowpanels/RowPanelBlock.js

@@ -1,7 +1,7 @@
 import React from 'react';
 import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
-import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { useCanvasTheme } from '../../darkReader.js';
 import { featureField, featureName } from '../../featureFields.js';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import { useHoverAnchor } from '../useHoverAnchor.js';
@@ -35,7 +35,7 @@ function hoverLines({ model, panel, name, x, }) {
 }
 const RowPanelBlock = observer(function ({ model, panel, offsetY, }) {
     const { anchor, hoverAt, clearAnchor } = useHoverAnchor();
-    const theme = useTheme();
+    const theme = useCanvasTheme();
     const { blockSize, highResScaleFactor, rowHeight } = model;
     const width = panel.width;
     const height = blockSize;