react-msaview 5.4.1 → 5.6.0

package/dist/propertyConservation.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Per-column property conservation using Shannon entropy over physicochemical
+ * classes rather than exact residues. Returns 0-1 where 1 = every non-gap
+ * residue shares one property class. Mirrors the identity-conservation formula
+ * so the two tracks are directly comparable: (1 - H/Hmax) * (1 - gapFraction).
+ */
+export declare function calculatePropertyConservation(colStats: Record<string, number>[], colStatsSums: number[]): number[];

package/dist/propertyConservation.js

@@ -0,0 +1,66 @@
+// Disjoint physicochemical classes for the 20 standard amino acids. Property
+// conservation asks a different question than identity conservation: a column
+// can vary in exact residue yet stay within one property class (a conservative
+// substitution), which often marks a functionally constrained site that plain
+// identity conservation reports as variable.
+//
+// Histidine is grouped with the aromatics (it is only weakly/conditionally
+// positive at physiological pH); this mirrors common substitution-class schemes.
+const aminoPropertyClass = {
+    A: 'hydrophobic',
+    V: 'hydrophobic',
+    L: 'hydrophobic',
+    I: 'hydrophobic',
+    M: 'hydrophobic',
+    C: 'hydrophobic',
+    F: 'aromatic',
+    W: 'aromatic',
+    Y: 'aromatic',
+    H: 'aromatic',
+    K: 'positive',
+    R: 'positive',
+    D: 'negative',
+    E: 'negative',
+    S: 'polar',
+    T: 'polar',
+    N: 'polar',
+    Q: 'polar',
+    G: 'special',
+    P: 'special',
+};
+const numPropertyClasses = new Set(Object.values(aminoPropertyClass)).size;
+const maxPropertyEntropy = Math.log2(numPropertyClasses);
+/**
+ * Per-column property conservation using Shannon entropy over physicochemical
+ * classes rather than exact residues. Returns 0-1 where 1 = every non-gap
+ * residue shares one property class. Mirrors the identity-conservation formula
+ * so the two tracks are directly comparable: (1 - H/Hmax) * (1 - gapFraction).
+ */
+export function calculatePropertyConservation(colStats, colStatsSums) {
+    return colStats.map((stats, i) => {
+        const total = colStatsSums[i];
+        if (!total) {
+            return 0;
+        }
+        let nonGapTotal = 0;
+        const classCounts = {};
+        for (const [letter, count] of Object.entries(stats)) {
+            const cls = aminoPropertyClass[letter];
+            if (cls) {
+                classCounts[cls] = (classCounts[cls] ?? 0) + count;
+                nonGapTotal += count;
+            }
+        }
+        if (nonGapTotal === 0) {
+            return 0;
+        }
+        let entropy = 0;
+        for (const count of Object.values(classCounts)) {
+            const freq = count / nonGapTotal;
+            entropy -= freq * Math.log2(freq);
+        }
+        const gapFraction = (total - nonGapTotal) / total;
+        return Math.max(0, 1 - entropy / maxPropertyEntropy) * (1 - gapFraction);
+    });
+}
+//# sourceMappingURL=propertyConservation.js.map

package/dist/propertyConservation.js.map

@@ -0,0 +1 @@
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package/dist/renderToSvg.js

@@ -8,123 +8,153 @@ import { renderMSABlock } from "./components/msa/renderMSABlock.js";
 import { renderAllTracks } from "./components/tracks/renderTracksSvg.js";
 import { renderTreeCanvas } from "./components/tree/renderTreeCanvas.js";
 import { colorContrast } from "./util.js";
-export async function renderToSvg(model, opts) {
-    await when(() => model.dataInitialized);
-    const { width, height, scrollX, scrollY, totalTrackAreaHeight, minimapHeight, } = model;
-    const { exportType, theme, includeTracks } = opts;
-    const trackHeight = includeTracks ? totalTrackAreaHeight : 0;
+// domain-legend geometry, shared by the width calculation and the renderer so
+// the reserved column on the right exactly fits the drawn legend
+const LEGEND_PAD = 8;
+const LEGEND_ROW_H = 16;
+const LEGEND_SWATCH = 12;
+const LEGEND_FONT = 12;
+const LEGEND_CHAR_W = 7;
+function getLegendWidth(model) {
+    const names = model.visibleDomainTypes.map(d => d.name);
+    const maxLen = Math.max(0, ...names.map(n => n.length));
+    const w = LEGEND_PAD * 2 + LEGEND_SWATCH + 6 + maxLen * LEGEND_CHAR_W;
+    return Math.min(360, Math.max(120, w));
+}
+function getLayout(model, opts) {
+    const { width, height, scrollX, scrollY, totalWidth, totalHeight, treeAreaWidth, totalTrackAreaHeight, minimapHeight, } = 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
-    const includeMinimap = exportType === 'viewport' && !!opts.includeMinimap;
-    if (exportType === 'entire') {
-        return render({
-            width: model.totalWidth + model.treeAreaWidth,
-            height: model.totalHeight + trackHeight,
-            contentHeight: model.totalHeight,
+    const includeMinimap = opts.exportType === 'viewport' && !!opts.includeMinimap;
+    const legendWidth = model.actuallyShowDomains && model.visibleDomainTypes.length > 0
+        ? getLegendWidth(model)
+        : 0;
+    // width stays content-only (the renderers derive msaAreaWidth from it); the
+    // legend occupies an extra column added at the svg root in MsaSvg
+    return opts.exportType === 'entire'
+        ? {
+            width: totalWidth + treeAreaWidth,
+            height: totalHeight + trackHeight,
+            contentHeight: totalHeight,
             trackHeight,
-            theme,
-            model,
-            offsetY: 0,
             offsetX: 0,
+            offsetY: 0,
             includeMinimap,
-            includeTracks,
-        });
-    }
-    return render({
-        width,
-        height: height + (includeMinimap ? minimapHeight : 0) + trackHeight,
-        contentHeight: height,
-        trackHeight,
-        theme,
-        model,
-        offsetY: -scrollY,
-        offsetX: -scrollX,
-        includeMinimap,
-        includeTracks,
-    });
+            legendWidth,
+        }
+        : {
+            width,
+            height: height + (includeMinimap ? minimapHeight : 0) + trackHeight,
+            contentHeight: height,
+            trackHeight,
+            offsetX: -scrollX,
+            offsetY: -scrollY,
+            includeMinimap,
+            legendWidth,
+        };
 }
-async function render({ width, height, contentHeight, trackHeight, offsetX, offsetY, theme, model, includeMinimap, includeTracks, }) {
+export async function renderToSvg(model, opts) {
+    await when(() => model.dataInitialized);
     const { Context } = await import('@jbrowse/svgcanvas');
+    return renderToStaticMarkup(React.createElement(MsaSvg, { model: model, theme: opts.theme, Context: Context, layout: getLayout(model, opts) }));
+}
+function MsaSvg({ model, theme, Context, layout, }) {
+    const { width, height, trackHeight, includeMinimap, legendWidth } = layout;
     const { treeAreaWidth, minimapHeight } = model;
-    const content = (React.createElement(React.Fragment, null,
-        includeTracks && trackHeight > 0 ? (React.createElement(TrackRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, msaAreaWidth: width - treeAreaWidth, trackHeight: trackHeight })) : null,
+    const totalWidth = width + legendWidth;
+    const legendTop = includeMinimap ? minimapHeight : 0;
+    const body = (React.createElement(React.Fragment, null,
+        trackHeight > 0 ? (React.createElement(TrackRendering, { Context: Context, model: model, theme: theme, layout: layout })) : null,
         React.createElement("g", { transform: trackHeight > 0 ? `translate(0 ${trackHeight})` : undefined },
-            React.createElement(CoreRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, offsetY: offsetY, msaAreaWidth: width - treeAreaWidth, contentHeight: contentHeight }))));
-    return renderToStaticMarkup(React.createElement(SvgWrapper, { width: width, height: height }, includeMinimap ? (React.createElement(React.Fragment, null,
-        React.createElement("g", { transform: `translate(${treeAreaWidth} 0)` },
-            React.createElement(MinimapSVG, { model: model })),
-        React.createElement("g", { transform: `translate(0 ${minimapHeight})` }, content))) : (content)));
+            React.createElement(CoreRendering, { Context: Context, model: model, theme: theme, layout: layout }))));
+    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} ${height}` },
+        React.createElement("rect", { width: "100%", height: "100%", fill: "white" }),
+        includeMinimap ? (React.createElement(React.Fragment, null,
+            React.createElement("g", { transform: `translate(${treeAreaWidth} 0)` },
+                React.createElement(MinimapSVG, { model: model })),
+            React.createElement("g", { transform: `translate(0 ${minimapHeight})` }, body))) : (body),
+        legendWidth > 0 ? (React.createElement("g", { transform: `translate(${width} ${legendTop})` },
+            React.createElement(LegendSVG, { model: model, width: legendWidth }))) : null));
+}
+// the domain color key drawn as a reserved column to the right of the
+// alignment, mirroring the on-screen DomainLegend overlay
+function LegendSVG({ model, width }) {
+    const { visibleDomainTypes, fillPalette, strokePalette } = model;
+    const boxHeight = LEGEND_PAD * 2 + visibleDomainTypes.length * LEGEND_ROW_H;
+    return (React.createElement("g", null,
+        React.createElement("rect", { x: 0, y: 0, width: width - 4, height: boxHeight, fill: "white", stroke: "#ccc", rx: 2 }),
+        visibleDomainTypes.map((d, i) => {
+            const y = LEGEND_PAD + i * LEGEND_ROW_H;
+            return (React.createElement("g", { key: d.accession },
+                React.createElement("rect", { x: LEGEND_PAD, y: y, width: LEGEND_SWATCH, height: LEGEND_SWATCH, fill: fillPalette[d.accession], stroke: strokePalette[d.accession] }),
+                React.createElement("text", { x: LEGEND_PAD + LEGEND_SWATCH + 6, y: y + LEGEND_SWATCH - 1, fontSize: LEGEND_FONT }, d.name)));
+        })));
 }
-function CoreRendering({ model, theme, msaAreaWidth, contentHeight, offsetX, offsetY, Context, }) {
+function CoreRendering({ model, theme, layout, Context, }) {
+    const { contentHeight, offsetX, offsetY, width } = layout;
     const { treeAreaWidth, colorScheme, id } = model;
-    const clipId1 = `tree-${id}`;
-    const clipId2 = `msa-${id}`;
+    const msaAreaWidth = width - treeAreaWidth;
     const contrastScheme = colorContrast(colorScheme, theme);
-    const ctx1 = new Context(treeAreaWidth, contentHeight);
-    const ctx2 = new Context(msaAreaWidth, contentHeight);
-    renderBoxFeatureCanvasBlock({
-        ctx: ctx2,
-        offsetX,
-        offsetY,
+    const treeCtx = new Context(treeAreaWidth, contentHeight);
+    renderTreeCanvas({
         model,
+        theme,
+        ctx: treeCtx,
+        offsetY,
         blockSizeYOverride: contentHeight,
         highResScaleFactorOverride: 1,
     });
-    renderTreeCanvas({
+    const msaCtx = new Context(msaAreaWidth, contentHeight);
+    renderBoxFeatureCanvasBlock({
         model,
+        ctx: msaCtx,
+        offsetX,
         offsetY,
-        ctx: ctx1,
-        theme,
         blockSizeYOverride: contentHeight,
         highResScaleFactorOverride: 1,
     });
     renderMSABlock({
         model,
         theme,
-        offsetY,
-        offsetX,
+        ctx: msaCtx,
         contrastScheme,
-        ctx: ctx2,
+        offsetX,
+        offsetY,
         blockSizeXOverride: msaAreaWidth,
         blockSizeYOverride: contentHeight,
         highResScaleFactorOverride: 1,
     });
     return (React.createElement(React.Fragment, null,
-        React.createElement("defs", null,
-            React.createElement("clipPath", { id: clipId1 },
-                React.createElement("rect", { x: 0, y: 0, width: treeAreaWidth, height: contentHeight })),
-            React.createElement("clipPath", { id: clipId2 },
-                React.createElement("rect", { x: 0, y: 0, width: msaAreaWidth, height: contentHeight }))),
-        React.createElement(ClipGroup, { clipId: clipId1, html: ctx1.getSvg().innerHTML }),
-        React.createElement(ClipGroup, { clipId: clipId2, transform: `translate(${treeAreaWidth} 0)`, html: ctx2.getSvg().innerHTML })));
-}
-// Wraps SVG markup produced by a svgcanvas Context in a clipped group. The
-// markup is injected verbatim since it's already serialized SVG, not React.
-function ClipGroup({ clipId, html, transform, }) {
-    return (React.createElement("g", { clipPath: `url(#${clipId})`, transform: transform, dangerouslySetInnerHTML: { __html: html } }));
+        React.createElement(ClipGroup, { clipId: `tree-${id}`, width: treeAreaWidth, height: contentHeight, ctx: treeCtx }),
+        React.createElement(ClipGroup, { clipId: `msa-${id}`, width: msaAreaWidth, height: contentHeight, transform: `translate(${treeAreaWidth} 0)`, ctx: msaCtx })));
 }
-function TrackRendering({ model, theme, msaAreaWidth, trackHeight, offsetX, Context, }) {
+function TrackRendering({ model, theme, layout, Context, }) {
+    const { trackHeight, offsetX, width } = layout;
     const { treeAreaWidth, colorScheme, id } = model;
-    const clipId = `tracks-${id}`;
+    const msaAreaWidth = width - treeAreaWidth;
     const contrastScheme = colorContrast(colorScheme, theme);
     const ctx = new Context(msaAreaWidth, trackHeight);
     renderAllTracks({
         model,
         ctx,
-        offsetX,
         contrastScheme,
+        offsetX,
         blockSizeXOverride: msaAreaWidth,
         highResScaleFactorOverride: 1,
     });
     return (React.createElement("g", { transform: `translate(${treeAreaWidth} 0)` },
+        React.createElement(ClipGroup, { clipId: `tracks-${id}`, width: msaAreaWidth, height: trackHeight, ctx: ctx })));
+}
+// Clips a svgcanvas Context to its box and injects its markup verbatim (it is
+// already serialized SVG, not React).
+function ClipGroup({ clipId, width, height, transform, ctx, }) {
+    return (React.createElement(React.Fragment, null,
         React.createElement("defs", null,
             React.createElement("clipPath", { id: clipId },
-                React.createElement("rect", { x: 0, y: 0, width: msaAreaWidth, height: trackHeight }))),
-        React.createElement(ClipGroup, { clipId: clipId, html: ctx.getSvg().innerHTML })));
-}
-function SvgWrapper({ width, height, children, }) {
-    return (React.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: `0 0 ${width} ${height}` },
-        React.createElement("rect", { width: "100%", height: "100%", fill: "white" }),
-        children));
+                React.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
+        React.createElement("g", { clipPath: `url(#${clipId})`, transform: transform, 
+            // eslint-disable-next-line @eslint-react/dom-no-dangerously-set-innerhtml
+            dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML } })));
 }
 //# sourceMappingURL=renderToSvg.js.map

package/dist/renderToSvg.js.map

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

@@ -13,9 +13,12 @@ export interface TextTrackModel extends BasicTrackModel {
     customColorScheme?: Record<string, string>;
     data?: string;
 }
+export interface BarTrackModel extends BasicTrackModel {
+    barColor?: string;
+}
 export interface BasicTrack {
     ReactComponent: React.FC<any>;
-    model: TextTrackModel;
+    model: TextTrackModel & BarTrackModel;
 }
 export interface Node {
     children?: Node[];

package/dist/{webpack.js → umd.js}

@@ -3,4 +3,4 @@ export { default as MSAView } from "./components/Loading.js";
 export { default as MSAModelF } from "./model.js";
 export * from 'react-dom/client';
 export { React };
-//# sourceMappingURL=webpack.js.map
+//# sourceMappingURL=umd.js.map

package/dist/umd.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"umd.js","sourceRoot":"","sources":["../src/umd.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,KAAK,MAAM,OAAO,CAAA;AAE9B,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA;AAEpE,cAAc,kBAAkB,CAAA;AAEhC,OAAO,EAAE,KAAK,EAAE,CAAA"}

package/dist/useCanvasAutorun.d.ts

@@ -0,0 +1,2 @@
+import type React from 'react';
+export declare function useCanvasAutorun(draw: (ctx: CanvasRenderingContext2D) => void, deps: React.DependencyList): React.RefObject<HTMLCanvasElement | null>;

package/dist/useCanvasAutorun.js

@@ -0,0 +1,23 @@
+import { useEffect, useRef } from 'react';
+import { autorun } from 'mobx';
+// Wires a canvas ref to a mobx autorun: grabs the 2d context once the canvas
+// mounts and re-runs `draw` whenever any observable it reads changes. Collapses
+// the getContext/null-guard/autorun-dispose boilerplate repeated by every
+// canvas block host. `deps` controls when the effect (and thus the context
+// lookup) is torn down and re-created, matching a normal useEffect dep array.
+export function useCanvasAutorun(draw, deps) {
+    const ref = useRef(null);
+    // the autorun tracks its own observable reads, so `draw` is intentionally not
+    // a dependency; `deps` alone controls when the effect re-subscribes
+    useEffect(() => {
+        const ctx = ref.current?.getContext('2d');
+        return ctx
+            ? autorun(() => {
+                draw(ctx);
+            })
+            : undefined;
+        // eslint-disable-next-line @eslint-react/exhaustive-deps
+    }, deps);
+    return ref;
+}
+//# sourceMappingURL=useCanvasAutorun.js.map

package/dist/useCanvasAutorun.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"useCanvasAutorun.js","sourceRoot":"","sources":["../src/useCanvasAutorun.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAGzC,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9B,6EAA6E;AAC7E,gFAAgF;AAChF,0EAA0E;AAC1E,2EAA2E;AAC3E,8EAA8E;AAC9E,MAAM,UAAU,gBAAgB,CAC9B,IAA6C,EAC7C,IAA0B;IAE1B,MAAM,GAAG,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAC3C,8EAA8E;IAC9E,oEAAoE;IACpE,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,EAAE,UAAU,CAAC,IAAI,CAAC,CAAA;QACzC,OAAO,GAAG;YACR,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE;gBACX,IAAI,CAAC,GAAG,CAAC,CAAA;YACX,CAAC,CAAC;YACJ,CAAC,CAAC,SAAS,CAAA;QACb,yDAAyD;IAC3D,CAAC,EAAE,IAAI,CAAC,CAAA;IACR,OAAO,GAAG,CAAA;AACZ,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "5.4.1";
+export declare const version = "5.6.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '5.4.1';
+export const version = '5.6.0';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "5.4.1",
+  "version": "5.6.0",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -35,23 +35,22 @@
     "react-dom": ">=16.8.0"
   },
   "devDependencies": {
-    "@types/node": "^25.9.4"
+    "@types/node": "^26.1.1",
+    "esbuild": "^0.28.1"
   },
   "dependencies": {
-    "@mui/icons-material": "^7.3.11",
-    "@mui/material": "^7.3.11",
     "colord": "^2.9.3",
     "flatbush": "^4.6.2",
-    "@jbrowse/svgcanvas": "5.4.1",
-    "msa-parsers": "5.4.1"
+    "msa-parsers": "5.6.0",
+    "@jbrowse/svgcanvas": "5.6.0"
   },
   "scripts": {
     "clean": "rimraf dist bundle",
     "watch": "pnpm build:esm --watch",
     "format": "prettier --write .",
     "build:esm": "tsc --project tsconfig.build.json",
-    "build:bundle": "webpack",
-    "build": "pnpm clean && pnpm build:esm && pnpm build:bundle",
+    "build:umd": "node esbuild.mjs",
+    "build": "pnpm clean && pnpm build:esm && pnpm build:umd",
     "statedocs": "rm -rf apidocs && mkdir apidocs && node --experimental-strip-types docgen/generateStateModelDocs.ts",
     "poststatedocs": "pnpm format",
     "test": "vitest"

package/src/colorSchemes.docs.test.ts

@@ -0,0 +1,55 @@
+import { readFileSync } from 'node:fs'
+
+import { expect, test } from 'vitest'
+
+import colorSchemes from './colorSchemes.ts'
+
+// Guard against doc drift: every color-scheme name listed in the JS embedding
+// docs (USAGE.md) must be a real registered scheme, so a rename or removal in
+// colorSchemes.ts can't silently leave a dead name in the docs that users copy.
+// (Subset check only — a registered scheme may intentionally go undocumented.)
+test('color schemes listed in USAGE.md all exist', () => {
+  const registered = new Set(Object.keys(colorSchemes))
+  const usage = readFileSync(
+    new URL('../../../USAGE.md', import.meta.url),
+    'utf8',
+  )
+
+  const section = /## Color schemes\n([\s\S]*?)\n## /.exec(usage)?.[1]
+  expect(section, 'could not find the "## Color schemes" section').toBeTruthy()
+
+  // drop the bold labels (**Protein:**, **Dynamic (per-column):**, …), leaving
+  // just the comma-separated scheme names
+  const names = section!.replace(/\*\*[^*]+\*\*/g, '').match(/[a-z][a-z0-9_]+/g)
+  expect(names?.length).toBeGreaterThan(0)
+
+  const unknown = names!.filter(name => !registered.has(name))
+  expect(
+    unknown,
+    `documented but not registered: ${unknown.join(', ')}`,
+  ).toEqual([])
+})
+
+// Same guard for the R package docs, whose color_scheme names pass straight
+// through as colorSchemeName with no remapping — a name that isn't registered
+// silently renders with no coloring.
+test('color schemes listed in the R README all exist', () => {
+  const registered = new Set(Object.keys(colorSchemes))
+  const readme = readFileSync(
+    new URL('../../r-msaview/README.md', import.meta.url),
+    'utf8',
+  )
+
+  const section = /## Color schemes\n([\s\S]*?)\n## /.exec(readme)?.[1]
+  expect(section, 'could not find the "## Color schemes" section').toBeTruthy()
+
+  // names are backtick-quoted, e.g. `jalview_taylor`
+  const names = [...section!.matchAll(/`([a-z][a-z0-9_]+)`/g)].map(m => m[1])
+  expect(names.length).toBeGreaterThan(0)
+
+  const unknown = names.filter(name => !registered.has(name))
+  expect(
+    unknown,
+    `documented but not registered: ${unknown.join(', ')}`,
+  ).toEqual([])
+})

package/src/colorSchemes.ts

@@ -6,8 +6,19 @@ import { transform } from './util.ts'
 
 extend([namesPlugin])
 
+// standard A/C/G/T(/U) coloring, shared by the `jbrowse_dna` and `nucleotide`
+// scheme names
+const dna = {
+  A: green[500],
+  C: blue[500],
+  G: orange[500],
+  T: red[500],
+  U: red[500],
+}
+
 const colorSchemes = {
   none: {},
+  nucleotide: dna,
   clustal: {
     G: 'orange',
     P: 'orange',
@@ -135,13 +146,7 @@ const colorSchemes = {
     T: '#19cc19',
     U: '#19cc19',
   },
-  jbrowse_dna: {
-    A: green[500],
-    C: blue[500],
-    G: orange[500],
-    T: red[500],
-    U: red[500],
-  },
+  jbrowse_dna: dna,
   jalview_buried: {
     A: '#00a35c',
     R: '#00fc03',