react-msaview 9.0.0 → 9.1.1

package/dist/renderToSvg.js

@@ -4,8 +4,7 @@ import { when } from 'mobx';
 import { visibleRowRange } from './components/getVisibleLeaves.js';
 import MinimapSVG from './components/minimap/MinimapSVG.js';
 import { legendRows } from './components/msa/legendRows.js';
-import { rasterImageHref, rasterSupported } from './components/msa/msaRaster.js';
-import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock.js';
+import { rasterApplies, rasterImageHref } from './components/msa/msaRaster.js';
 import { renderPersistentHighlights } from './components/msa/renderHighlights.js';
 import { renderMSABlock } from './components/msa/renderMSABlock.js';
 import { visibleColRange } from './components/msa/visibleColRange.js';
@@ -13,78 +12,15 @@ import { headerRunsAcross } from './components/rowpanels/headerLayout.js';
 import { renderRowPanels } from './components/rowpanels/renderRowPanel.js';
 import { renderAllTracks } from './components/tracks/drawTracks.js';
 import ScaleBarSVG from './components/tree/ScaleBarSVG.js';
-import { bracketGap, cladeHeight, cladeInGutter, cladeLabelHorizontal, cladeLabelOffset, } from './components/tree/cladeBrackets.js';
+import { cladeLabelBoxes } from './components/tree/cladeBrackets.js';
+import { ellipsize } from './components/tree/ellipsize.js';
 import { renderTreeCanvas } from './components/tree/renderTreeCanvas.js';
 import { renderTreeOverview } from './components/tree/renderTreeOverview.js';
 import { treeScaleBarHeight } from './constants.js';
+import { LEGEND_CHAR_W, LEGEND_FONT, LEGEND_PAD, LEGEND_ROW_H, LEGEND_SWATCH, LEGEND_TEXT_X, exportPageSize, getLayout, legendHeight, } from './exportLayout.js';
 import { measureTextCanvas } from './measureTextCanvas.js';
 import { renderToStaticMarkup, svgSafeColors } from './renderToStaticMarkup.js';
 import { outlineColor } from './util.js';
-// legend geometry, shared by the width calculation and the renderer so the
-// reserved column on the right exactly fits the drawn legends
-const LEGEND_PAD = 8;
-const LEGEND_ROW_H = 16;
-const LEGEND_SWATCH = 12;
-const LEGEND_FONT = 12;
-const LEGEND_CHAR_W = 7;
-// the width of a character as a fraction of the font size, close enough for a
-// sans-serif average
-const CHAR_WIDTH = 0.6;
-const LEGEND_MAX_W = 360;
-const LEGEND_TEXT_X = LEGEND_PAD + LEGEND_SWATCH + 6;
-function getLegendWidth(rows) {
-    const maxLen = rows.reduce((a, r) => Math.max(a, r.label.length), 0);
-    const w = LEGEND_TEXT_X + LEGEND_PAD + maxLen * LEGEND_CHAR_W;
-    return Math.min(LEGEND_MAX_W, Math.max(120, w));
-}
-function legendHeight(rows) {
-    return LEGEND_PAD * 2 + rows.length * LEGEND_ROW_H;
-}
-function getLayout(model, opts) {
-    const { scrollX, scrollY, totalWidth, totalHeight, effectiveTreeAreaWidth, rowPanelsWidth, rowPanelsHeaderHeight, totalTrackAreaHeight, minimapHeight, msaAreaHeight, msaCanvasWidth, showHorizontalScrollbar, treeOverviewHeight, treeScaleBar, } = model;
-    const trackHeight = opts.includeTracks ? totalTrackAreaHeight : 0;
-    // the minimap reflects the live viewport scroll position, so it's only
-    // meaningful for a viewport export, never for the entire alignment -- and
-    // only when the live view shows one at all, since a minimap over an alignment
-    // that already fits marks a viewport wider than the bar
-    const includeMinimap = opts.exportType === 'viewport' &&
-        !!opts.includeMinimap &&
-        showHorizontalScrollbar;
-    const rows = legendRows(model.legends);
-    const legendWidth = rows.length > 0 ? getLegendWidth(rows) : 0;
-    const topHeight = Math.max(includeMinimap ? minimapHeight : 0, rowPanelsHeaderHeight, treeOverviewHeight + (treeScaleBar ? treeScaleBarHeight : 0));
-    const gutterWidth = effectiveTreeAreaWidth + rowPanelsWidth;
-    // width stays content-only; the legend occupies an extra column added at the
-    // svg root in MsaSvg. The viewport export takes the alignment canvas's own
-    // size rather than the widget's -- the widget box also covers the header, the
-    // resize handle and the scrollbars, and rendering that box exports rows and
-    // columns the scrollbars hide on screen
-    return opts.exportType === 'entire'
-        ? {
-            width: totalWidth + gutterWidth,
-            msaAreaWidth: totalWidth,
-            height: totalHeight + trackHeight + topHeight,
-            contentHeight: totalHeight,
-            trackHeight,
-            topHeight,
-            offsetX: 0,
-            offsetY: 0,
-            includeMinimap,
-            legendWidth,
-        }
-        : {
-            width: msaCanvasWidth + gutterWidth,
-            msaAreaWidth: msaCanvasWidth,
-            height: msaAreaHeight + topHeight + trackHeight,
-            contentHeight: msaAreaHeight,
-            trackHeight,
-            topHeight,
-            offsetX: -scrollX,
-            offsetY: -scrollY,
-            includeMinimap,
-            legendWidth,
-        };
-}
 export async function renderToSvg(model, opts) {
     // dataInitialized stays false while the model holds a load error, so waiting
     // on it alone would never settle
@@ -99,27 +35,26 @@ export async function renderToSvg(model, opts) {
     // into the page as strings.
     const layers = new Map();
     const markup = renderToStaticMarkup(React.createElement(MsaSvg, { model: model, theme: opts.theme, Context: Context, layout: getLayout(model, opts), layers: layers }));
+    // innerHTML serializes as HTML, and an XML parser rejects its  
     return svgSafeColors(markup.replaceAll(/<g data-layer="([^"]+)"><\/g>/g, (match, id) => {
         const ctx = layers.get(id);
         return ctx ? `<g id="${id}">${ctx.getSvg().innerHTML}</g>` : match;
-    }));
+    })).replaceAll('&nbsp;', '&#160;');
 }
 function MsaSvg({ model, theme, Context, layout, layers, }) {
     const { width, trackHeight, includeMinimap, legendWidth, topHeight } = layout;
     const { effectiveTreeAreaWidth, rowPanelsWidth } = model;
-    const totalWidth = width + legendWidth;
+    const { width: totalWidth, height } = exportPageSize(model, layout);
     const legendTop = topHeight;
-    // a short alignment with many legend entries has a key taller than its rows,
-    // and the page has to hold the whole key
-    const height = legendWidth > 0
-        ? Math.max(layout.height, legendTop + legendHeight(legendRows(model.legends)))
-        : layout.height;
     const props = { Context, model, theme, layout, layers };
     const body = (React.createElement(React.Fragment, null,
         trackHeight > 0 ? React.createElement(TrackRendering, { ...props }) : null,
         React.createElement("g", { transform: trackHeight > 0 ? `translate(0 ${trackHeight})` : undefined },
             React.createElement(CoreRendering, { ...props }))));
-    return (React.createElement("svg", { width: totalWidth, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: `0 0 ${totalWidth} ${height}` },
+    return (React.createElement("svg", { width: totalWidth, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: `0 0 ${totalWidth} ${height}`, 
+        // the canvas layers name sans-serif on each glyph; the legend, labels
+        // and headers inherit it here instead of an editor's default serif
+        fontFamily: "sans-serif" },
         React.createElement("rect", { width: "100%", height: "100%", fill: theme.palette.background.default }),
         topHeight > 0 ? (React.createElement(React.Fragment, null,
             includeMinimap ? (React.createElement("g", { id: "minimap-panel", transform: `translate(${effectiveTreeAreaWidth + rowPanelsWidth} 0)` },
@@ -171,49 +106,27 @@ function RowPanelHeadersSVG({ model, theme, bandHeight, }) {
         const center = effectiveTreeAreaWidth + panel.offsetX + panel.width / 2;
         const x = across ? center : center + size / 3;
         const room = across ? panel.width : y - LEGEND_PAD;
-        const maxChars = Math.floor(room / (size * CHAR_WIDTH));
         return size < 5 ? null : (React.createElement("text", { key: panel.id, x: x, y: y, ...(across
                 ? { textAnchor: 'middle' }
-                : { transform: `rotate(-90 ${x} ${y})` }), fontSize: size, fill: theme.palette.text.primary }, panel.header.length > maxChars
-            ? `${panel.header.slice(0, Math.max(1, maxChars - 1))}…`
-            : panel.header));
+                : { transform: `rotate(-90 ${x} ${y})` }), fontSize: size, fill: theme.palette.text.primary }, ellipsize(t => measureTextCanvas(t, size), panel.header, room)
+            .text));
     })));
 }
-// A label past the room it has, cut to what fits with an ellipsis. The measure
-// is the one cladeGutterWidth sizes the gutter with, so a label the gutter
-// holds keeps every character.
-function clipCladeLabel(label, room, fontSize) {
-    const width = measureTextCanvas(label, fontSize);
-    if (width <= room) {
-        return label;
-    }
-    const fits = Math.floor((label.length * room) / width);
-    return `${label.slice(0, Math.max(1, fits - 1))}…`;
-}
 // Each bracket's label in the gutter beside its bar, where the live view puts
 // it (see CladeLabels). The canvas layer draws the bar; a label longer than the
 // gutter or the clade is clipped, since text that overruns runs off the figure.
+// cladeGutterWidth sizes the gutter with the same measureTextCanvas, so a label
+// the gutter holds keeps every character.
 function CladeLabelsSVG({ model, theme, offsetY, }) {
-    const { resolvedClades, cladeGutterWidth, rowHeight, effectiveTreeAreaWidth, fontSize, } = model;
-    if (cladeGutterWidth === 0) {
-        return null;
-    }
-    const gutterLeft = effectiveTreeAreaWidth - cladeGutterWidth;
-    return (React.createElement("g", { id: "clade-labels" }, resolvedClades.map((clade, index) => {
-        const { label, markColor, rows } = clade;
-        if (!label || !cladeInGutter(clade)) {
-            return null;
-        }
-        const left = gutterLeft + cladeLabelOffset(clade);
-        const top = rows[0] * rowHeight - offsetY;
-        const height = cladeHeight(clade, rowHeight);
-        const horizontal = cladeLabelHorizontal(clade, rowHeight, fontSize);
-        const room = horizontal
-            ? effectiveTreeAreaWidth - left - bracketGap
-            : height;
-        const x = horizontal ? left : left + fontSize;
-        const y = horizontal ? top + height / 2 + fontSize / 3 : top + height;
-        return (React.createElement("text", { key: `${rows[0]}-${rows[1]}-${index}`, x: x, y: y, transform: horizontal ? undefined : `rotate(-90 ${x} ${y})`, fontSize: fontSize, fill: markColor ?? theme.palette.text.primary }, clipCladeLabel(label, room, fontSize)));
+    const { fontSize } = model;
+    const boxes = cladeLabelBoxes(model);
+    return boxes.length === 0 ? null : (React.createElement("g", { id: "clade-labels" }, boxes.map(box => {
+        const top = box.top - offsetY;
+        const x = box.horizontal ? box.left : box.left + fontSize;
+        const y = box.horizontal
+            ? top + box.height / 2 + fontSize / 3
+            : top + box.height;
+        return (React.createElement("text", { key: box.key, x: x, y: y, transform: box.horizontal ? undefined : `rotate(-90 ${x} ${y})`, fontSize: fontSize, fill: box.color ?? theme.palette.text.primary }, ellipsize(t => measureTextCanvas(t, fontSize), box.label, box.horizontal ? box.width : box.height).text));
     })));
 }
 // the color keys drawn as a reserved column to the right of the alignment,
@@ -223,16 +136,14 @@ function LegendSVG({ model, theme, width, }) {
     const boxHeight = legendHeight(rows);
     // the column is capped at LEGEND_MAX_W, so a name too long for it has to be
     // clipped here -- text that overruns the reserved width runs off the figure
-    const maxChars = Math.floor((width - LEGEND_TEXT_X - LEGEND_PAD) / LEGEND_CHAR_W);
+    const room = width - LEGEND_TEXT_X - LEGEND_PAD;
     return (React.createElement("g", null,
         React.createElement("rect", { x: 0, y: 0, width: width - 4, height: boxHeight, fill: theme.palette.background.paper, stroke: theme.palette.divider, rx: 2 }),
         rows.map((row, i) => {
             const y = LEGEND_PAD + i * LEGEND_ROW_H;
             return (React.createElement("g", { key: row.key },
                 row.color ? (React.createElement("rect", { x: LEGEND_PAD, y: y, width: LEGEND_SWATCH, height: LEGEND_SWATCH, fill: row.color, stroke: outlineColor(row.color) })) : null,
-                React.createElement("text", { x: row.color ? LEGEND_TEXT_X : LEGEND_PAD, y: y + LEGEND_SWATCH - 1, fontSize: LEGEND_FONT, fontWeight: row.color ? undefined : 'bold', fill: theme.palette.text.primary }, row.label.length > maxChars
-                    ? `${row.label.slice(0, Math.max(1, maxChars - 1))}…`
-                    : row.label)));
+                React.createElement("text", { x: row.color ? LEGEND_TEXT_X : LEGEND_PAD, y: y + LEGEND_SWATCH - 1, fontSize: LEGEND_FONT, fontWeight: row.color ? undefined : 'bold', fill: theme.palette.text.primary }, ellipsize(t => t.length * LEGEND_CHAR_W, row.label, room).text)));
         })));
 }
 function CoreRendering({ model, theme, layout, Context, layers }) {
@@ -262,18 +173,6 @@ function CoreRendering({ model, theme, layout, Context, layers }) {
     }
     const raster = rasterBackground({ model, theme, layout });
     const msaCtx = new Context(msaAreaWidth, contentHeight);
-    renderBoxFeatureCanvasBlock({
-        model,
-        theme,
-        ctx: msaCtx,
-        offsetX,
-        offsetY,
-        // the overlay culls bands to this width; without it the export falls back
-        // to the on-screen 500px block size and drops every band past it
-        blockSizeXOverride: msaAreaWidth,
-        blockSizeYOverride: contentHeight,
-        highResScaleFactorOverride: 1,
-    });
     renderMSABlock({
         model,
         theme,
@@ -284,6 +183,7 @@ function CoreRendering({ model, theme, layout, Context, layers }) {
         blockSizeYOverride: contentHeight,
         highResScaleFactorOverride: 1,
         rasterTiles: !!raster,
+        domains: true,
     });
     msaCtx.resetTransform();
     renderPersistentHighlights({
@@ -302,9 +202,8 @@ function CoreRendering({ model, theme, layout, Context, layers }) {
         React.createElement(ClipGroup, { panelId: "msa-panel", clipId: `msa-${id}`, width: msaAreaWidth, height: contentHeight, transform: `translate(${effectiveTreeAreaWidth + rowPanelsWidth} 0)`, ctx: msaCtx, layers: layers, underlay: raster })));
 }
 /**
- * The alignment background as a single <image>, under the live canvas's
- * conditions: no domain overlay boxes, background coloring on, and a canvas
- * that reads back.
+ * The alignment background as a single <image>, wherever the live canvas
+ * draws the raster.
  *
  * The vector path's <rect> per cell exhausts the heap on a real alignment. The
  * image is one pixel per cell, and image-rendering keeps the upscaled cell
@@ -312,8 +211,8 @@ function CoreRendering({ model, theme, layout, Context, layers }) {
  */
 function rasterBackground({ model, theme, layout, }) {
     const { contentHeight, offsetX, offsetY, msaAreaWidth } = layout;
-    const { colWidth, rowHeight, actuallyShowDomains, bgColor } = model;
-    if (actuallyShowDomains || !bgColor || !rasterSupported()) {
+    const { colWidth, rowHeight } = model;
+    if (!rasterApplies(model)) {
         return undefined;
     }
     const { xStart, xEnd } = visibleColRange({
@@ -369,7 +268,8 @@ function TrackLabelsSVG({ model, theme, }) {
         const top = turnedOnTracks
             .slice(0, i)
             .reduce((acc, t) => acc + t.model.height, 0);
-        return { id, name, size, baseline: top + height / 2 + size / 3 };
+        // pinned to the top of the track, as the live view's flex row pins it
+        return { id, name, size, baseline: top + size * 0.8 };
     });
     return (React.createElement(React.Fragment, null, labels.map(({ id, name, size, baseline }) => {
         return size < 5 ? null : (React.createElement("text", { key: id, x: effectiveTreeAreaWidth - 4, y: baseline, fontSize: size, textAnchor: "end", fill: theme.palette.text.primary }, name));

package/dist/renderToSvg.js.map

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

@@ -12,6 +12,7 @@ export interface TreeNode {
     length?: number;
     children?: TreeNode[];
 }
+export declare function preorder<N extends TreeNode>(root: N, parents?: Map<N, N>): N[];
 /**
  * The tree rooted on the branch above `target`, `offset` up from it, or at the
  * middle of that branch without one. Where the root has two children, their

package/dist/rerootTree.js

@@ -1,16 +1,15 @@
-function preorder(root) {
+export function preorder(root, parents) {
     const order = [];
-    const parents = new Map();
     const stack = [root];
     while (stack.length > 0) {
         const node = stack.pop();
         order.push(node);
         for (const child of (node.children ?? [])) {
-            parents.set(child, node);
+            parents?.set(child, node);
             stack.push(child);
         }
     }
-    return { order, parents };
+    return order;
 }
 function hasLengths(order) {
     return order.some(n => n.length !== undefined);
@@ -34,7 +33,8 @@ function mergedSibling(root, target) {
  * branches join.
  */
 export function rerootTree(root, target, offset) {
-    const { order, parents } = preorder(root);
+    const parents = new Map();
+    const order = preorder(root, parents);
     if (!parents.has(target)) {
         return root;
     }
@@ -87,7 +87,8 @@ export function rerootTree(root, target, offset) {
  * counts branches.
  */
 export function midpointRoot(root) {
-    const { order, parents } = preorder(root);
+    const parents = new Map();
+    const order = preorder(root, parents);
     const tips = order.filter(n => !n.children?.length);
     if (tips.length < 2) {
         return root;

package/dist/rerootTree.js.map

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

@@ -0,0 +1,12 @@
+import type { MsaViewModel } from './model.ts';
+/**
+ * A reader for the color the active scheme gives a row's residue, as hex, for a
+ * host that paints another view, such as a structure, with the alignment's own
+ * colors. `seqPos` is 1-based, like `structureResidue`. The reader returns
+ * undefined where the scheme leaves the residue uncolored, the row lacks it, or
+ * its column is hidden.
+ *
+ * Build it inside a reaction: a new scheme, a hidden gap column or a collapsed
+ * clade then re-runs the caller.
+ */
+export declare function schemeResidueColor(model: MsaViewModel): (rowName: string, seqPos: number) => string | undefined;

package/dist/schemeResidueColor.js

@@ -0,0 +1,33 @@
+import { colord } from 'colord';
+import { tileColorFn } from './components/msa/tileColor.js';
+/**
+ * A reader for the color the active scheme gives a row's residue, as hex, for a
+ * host that paints another view, such as a structure, with the alignment's own
+ * colors. `seqPos` is 1-based, like `structureResidue`. The reader returns
+ * undefined where the scheme leaves the residue uncolored, the row lacks it, or
+ * its column is hidden.
+ *
+ * Build it inside a reaction: a new scheme, a hidden gap column or a collapsed
+ * clade then re-runs the caller.
+ */
+export function schemeResidueColor(model) {
+    const colorAt = tileColorFn(model);
+    const { columns } = model;
+    const hexes = new Map();
+    const toHex = (color) => {
+        if (!hexes.has(color)) {
+            const parsed = colord(color);
+            hexes.set(color, parsed.isValid() ? parsed.toHex() : undefined);
+        }
+        return hexes.get(color);
+    };
+    return (rowName, seqPos) => {
+        const col = model.seqPosToVisibleCol(rowName, seqPos - 1);
+        const letter = col === undefined ? undefined : columns.get(rowName)?.[col];
+        const color = col === undefined || letter === undefined
+            ? undefined
+            : colorAt(col, letter);
+        return color === undefined ? undefined : toHex(color);
+    };
+}
+//# sourceMappingURL=schemeResidueColor.js.map

package/dist/schemeResidueColor.js.map

@@ -0,0 +1 @@
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package/dist/similarityColors.d.ts

@@ -0,0 +1,11 @@
+import type { ColumnCounts } from './columnCounts.ts';
+/**
+ * The amino acids of a column shaded by BLOSUM62 similarity. Letters the matrix
+ * does not name, such as U, O and J, count for nothing and take no shade.
+ */
+export declare function blosum62ColumnColors(counts: ColumnCounts, col: number): Record<string, string>;
+/**
+ * Nucleotides and anything else without a substitution matrix: a residue's
+ * similarity is the fraction of the rest of its column that equals it.
+ */
+export declare function identityColumnColors(counts: ColumnCounts, col: number): Record<string, string>;

package/dist/similarityColors.js

@@ -0,0 +1,90 @@
+// Similarity shading, after biotite's plot_alignment_similarity_based and
+// Jalview's BLOSUM62 score scheme. Each residue takes a shade of one hue by how
+// similar it is, on average, to the other residues of its column.
+import { BLOSUM62, NUM_SYMBOLS, symbolOfCode } from './blosum62.js';
+import { letterOfResidueSlot, numResidueSlots } from './columnCounts.js';
+const AMINO_ACIDS = 20;
+const HUE = 240;
+const SATURATION = 50;
+const LIGHTEST = 96;
+const DARKEST = 40;
+// BLOSUM62 scaled per row to 0..1 over the twenty amino acids, so a residue's
+// own score is 1 and its worst substitution 0. Not symmetric, like biotite's.
+const normalized = new Float32Array(NUM_SYMBOLS * NUM_SYMBOLS);
+for (let a = 0; a < NUM_SYMBOLS; a++) {
+    let min = Infinity;
+    let max = -Infinity;
+    for (let b = 0; b < AMINO_ACIDS; b++) {
+        const score = BLOSUM62[a * NUM_SYMBOLS + b];
+        min = Math.min(min, score);
+        max = Math.max(max, score);
+    }
+    for (let b = 0; b < NUM_SYMBOLS; b++) {
+        const scaled = (BLOSUM62[a * NUM_SYMBOLS + b] - min) / (max - min);
+        normalized[a * NUM_SYMBOLS + b] = Math.min(Math.max(scaled, 0), 1);
+    }
+}
+// residue slot -> row of the matrix, -1 for a letter the matrix does not name
+const symbolOfSlot = Int8Array.from({ length: numResidueSlots }, (_, slot) => {
+    const letter = letterOfResidueSlot(slot);
+    return letter.length === 1 ? symbolOfCode[letter.charCodeAt(0)] : -1;
+});
+function shade(similarity) {
+    const lightness = Math.round(LIGHTEST - (LIGHTEST - DARKEST) * similarity);
+    return `hsl(${HUE}, ${SATURATION}%, ${lightness}%)`;
+}
+/**
+ * Shades each residue of one column by its mean similarity to the column's
+ * other residues, gaps left out of the mean. A column of fewer than two counted
+ * residues has nothing to compare and colors nothing.
+ */
+function shadeColumn(counts, col, measure) {
+    const { counted, shaded, score } = measure;
+    const present = [];
+    let total = 0;
+    counts.forEachResidue(col, (slot, count) => {
+        if (counted(slot)) {
+            present.push([slot, count]);
+            total += count;
+        }
+    });
+    const colors = {};
+    if (total < 2) {
+        return colors;
+    }
+    for (const [a] of present) {
+        if (shaded(a)) {
+            let sum = -score(a, a);
+            for (const [b, count] of present) {
+                sum += count * score(a, b);
+            }
+            colors[letterOfResidueSlot(a)] = shade(sum / (total - 1));
+        }
+    }
+    return colors;
+}
+const blosum62 = {
+    counted: slot => symbolOfSlot[slot] >= 0,
+    shaded: slot => symbolOfSlot[slot] < AMINO_ACIDS,
+    score: (a, b) => normalized[symbolOfSlot[a] * NUM_SYMBOLS + symbolOfSlot[b]],
+};
+const identity = {
+    counted: () => true,
+    shaded: () => true,
+    score: (a, b) => (a === b ? 1 : 0),
+};
+/**
+ * The amino acids of a column shaded by BLOSUM62 similarity. Letters the matrix
+ * does not name, such as U, O and J, count for nothing and take no shade.
+ */
+export function blosum62ColumnColors(counts, col) {
+    return shadeColumn(counts, col, blosum62);
+}
+/**
+ * Nucleotides and anything else without a substitution matrix: a residue's
+ * similarity is the fraction of the rest of its column that equals it.
+ */
+export function identityColumnColors(counts, col) {
+    return shadeColumn(counts, col, identity);
+}
+//# sourceMappingURL=similarityColors.js.map

package/dist/similarityColors.js.map

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