react-msaview 9.1.0 → 9.2.0

package/dist/types.d.ts

@@ -5,7 +5,7 @@ export interface Accession {
     name: string;
     description: string;
 }
-export type TrackKind = 'text' | 'bar' | 'logo' | 'arc' | 'ruler';
+export type TrackKind = 'text' | 'bar' | 'logo' | 'arc' | 'ruler' | 'reference';
 /**
  * Which channel the color scheme paints. `fill` colors the cell a residue sits
  * in, `color` colors the letter itself, the same distinction a grammar of
@@ -21,11 +21,9 @@ export type ColorScheme = string | Required<Pick<ScaleSpec, 'map'>>;
 export interface BasicTrackModel {
     id: string;
     name: string;
-    associatedRowName?: string;
     height: number;
     kind: TrackKind;
     heightKey?: string;
-    defaultOff?: boolean;
 }
 export interface TextTrackModel extends BasicTrackModel {
     customColorScheme?: Record<string, string>;
@@ -170,6 +168,12 @@ export interface MappedStructure {
     id: string;
     kind?: 'experimental' | 'predicted';
     asymId?: string;
+    /**
+     * which id `asymId` is, the file's `label_asym_id` or the author's
+     * `auth_asym_id`. Unset reads as either, label first, which is right for the
+     * common entry whose two ids agree and wrong where they collide.
+     */
+    asymIdKind?: 'label' | 'auth';
     url?: string;
 }
 /**

package/dist/useWheelScroll.d.ts

@@ -1,8 +1,10 @@
-export declare function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom, }: {
+export declare function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, onZoomSettle, onWheelScroll, scrollZoom, }: {
     ref: React.RefObject<HTMLDivElement | null>;
     onScrollX?: (delta: number) => void;
     onScrollY?: (delta: number) => void;
     onZoom?: (scaleFactor: number, offsetX: number, offsetY: number) => void;
+    onZoomSettle?: () => void;
+    onWheelScroll?: (event: WheelEvent) => void;
     scrollZoom?: boolean;
 }): {
     onMouseDown: (event: React.MouseEvent) => void;

package/dist/useWheelScroll.js

@@ -1,11 +1,13 @@
 import { useEffect, useRef, useState } from 'react';
-import { SCROLL_ZOOM_DIVISOR, getZoomNormalizer, normalizeWheelDelta, zoomFactorFromAccum, } from './wheelZoom.js';
-export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom, }) {
+import { WheelZoomSmoother } from './wheelZoom.js';
+const zoomSettleMs = 150;
+export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, onZoomSettle, onWheelScroll, scrollZoom, }) {
     const scheduled = useRef(false);
-    const zoomScheduled = useRef(false);
+    const zoomFrame = useRef(undefined);
+    const zoomSettle = useRef(undefined);
     const deltaX = useRef(0);
     const deltaY = useRef(0);
-    const zoomAccum = useRef(0);
+    const zoomSmoother = useRef(new WheelZoomSmoother());
     const zoomX = useRef(0);
     const zoomY = useRef(0);
     const lastZoomTime = useRef(null);
@@ -26,23 +28,26 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom,
                 !event.shiftKey &&
                 Math.abs(event.deltaY) >= Math.abs(event.deltaX);
             if (onZoom && (isCtrlZoom || isScrollZoom)) {
+                const zoom = onZoom;
                 const rect = curr.getBoundingClientRect();
-                // normalize away deltaMode (line/page), then divide by an adaptive
-                // factor so fine pinches and coarse notches feel consistent
-                const dY = normalizeWheelDelta(event.deltaY, event.deltaMode);
-                const divisor = isCtrlZoom ? getZoomNormalizer(dY) : SCROLL_ZOOM_DIVISOR;
-                zoomAccum.current += dY / divisor;
+                zoomSmoother.current.add(event.deltaY, event.deltaMode, isCtrlZoom);
                 zoomX.current = event.clientX - rect.left;
                 zoomY.current = event.clientY - rect.top;
-                if (!zoomScheduled.current) {
-                    zoomScheduled.current = true;
-                    requestAnimationFrame(now => {
+                if (zoomFrame.current === undefined) {
+                    lastZoomTime.current = null;
+                    const frame = (now) => {
                         const elapsed = lastZoomTime.current === null ? 16.67 : now - lastZoomTime.current;
                         lastZoomTime.current = now;
-                        onZoom(zoomFactorFromAccum(zoomAccum.current, Math.min(100, elapsed)), zoomX.current, zoomY.current);
-                        zoomAccum.current = 0;
-                        zoomScheduled.current = false;
-                    });
+                        zoom(zoomSmoother.current.step(Math.min(100, elapsed)), zoomX.current, zoomY.current);
+                        clearTimeout(zoomSettle.current);
+                        zoomSettle.current = setTimeout(() => {
+                            onZoomSettle?.();
+                        }, zoomSettleMs);
+                        zoomFrame.current = zoomSmoother.current.idle
+                            ? undefined
+                            : requestAnimationFrame(frame);
+                    };
+                    zoomFrame.current = requestAnimationFrame(frame);
                 }
                 event.preventDefault();
                 event.stopPropagation();
@@ -53,6 +58,7 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom,
             const consumeX = !!onScrollX && event.deltaX !== 0;
             const consumeY = !!onScrollY && event.deltaY !== 0;
             if (consumeX || consumeY) {
+                onWheelScroll?.(event);
                 if (onScrollX) {
                     deltaX.current += event.deltaX;
                 }
@@ -80,8 +86,21 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom,
         curr.addEventListener('wheel', onWheel, { passive: false });
         return () => {
             curr.removeEventListener('wheel', onWheel);
+            if (zoomFrame.current !== undefined) {
+                cancelAnimationFrame(zoomFrame.current);
+                zoomFrame.current = undefined;
+            }
+            clearTimeout(zoomSettle.current);
         };
-    }, [ref, onScrollX, onScrollY, onZoom, scrollZoom]);
+    }, [
+        ref,
+        onScrollX,
+        onScrollY,
+        onZoom,
+        onZoomSettle,
+        onWheelScroll,
+        scrollZoom,
+    ]);
     useEffect(() => {
         if (!mouseDragging) {
             return;

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package/dist/util.d.ts

@@ -23,3 +23,5 @@ export declare function len(a: {
     end: number;
     start: number;
 }): number;
+/** reads computeds so a reaction observes them, which keeps them cached */
+export declare function readComputed(..._values: unknown[]): void;

package/dist/util.js

@@ -127,4 +127,6 @@ export function computeRowInsertions(blanks, seq) {
 export function len(a) {
     return a.end - a.start;
 }
+/** reads computeds so a reaction observes them, which keeps them cached */
+export function readComputed(..._values) { }
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

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

@@ -1 +1 @@
-export declare const version = "9.1.0";
+export declare const version = "9.2.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '9.1.0';
+export const version = '9.2.0';
 //# sourceMappingURL=version.js.map

package/dist/wheelZoom.d.ts

@@ -1,4 +1,9 @@
-export declare const SCROLL_ZOOM_DIVISOR = 500;
+export declare const NOTCH_ZOOM = 1.25;
 export declare function normalizeWheelDelta(delta: number, mode: number): number;
-export declare function getZoomNormalizer(deltaY: number): 25 | 75 | 150 | 500;
-export declare function zoomFactorFromAccum(zoomAccum: number, elapsedMs: number): number;
+export declare class WheelZoomSmoother {
+    private continuous;
+    private pending;
+    add(deltaY: number, deltaMode: number, isPinch: boolean): void;
+    get idle(): boolean;
+    step(elapsedMs: number): number;
+}

package/dist/wheelZoom.js

@@ -1,43 +1,55 @@
-// Wheel / trackpad-pinch delta handling, adapted from @jbrowse/core's
-// util/wheelZoom (not yet in our pinned @jbrowse/core). Turns raw wheel deltas
-// into a per-frame zoom factor that feels consistent across fine trackpad
-// pinches and coarse mouse notches.
-// Fixed divisor for plain-wheel scroll-zoom mode, where deltas are big notches.
-export const SCROLL_ZOOM_DIVISOR = 500;
-// Cap the zoom change per millisecond so a burst of momentum-scroll events
-// coalesced into one frame can't jump the zoom level (0.2 per ~60fps frame).
-const MAX_ZOOM_RATE_PER_MS = 0.2 / 16.67;
-// Convert a wheel delta to pixels regardless of the browser's deltaMode; some
-// browsers/mice report lines or pages instead of pixels.
+// Chrome and Firefox encode a trackpad pinch as ctrl+wheel with
+// deltaY = -100 * ln(scale), so dividing by 100 tracks the fingers 1:1
+const PINCH_PX_PER_LOG = 100;
+// a plain scroll covers more pixels than a pinch for the same intent
+const SCROLL_PX_PER_LOG = 400;
+// a pixel delta at least this large counts as a wheel notch
+const NOTCH_MIN_PX = 40;
+export const NOTCH_ZOOM = 1.25;
+// the time constant a notch eases in over
+const NOTCH_TAU_MS = 60;
+// a burst of continuous events coalesced into one frame applies at most 2x
+const MAX_FRAME_LOG = Math.log(2);
+// the queue holds at most four notches, which caps a fast spin
+const MAX_PENDING_LOG = 4 * Math.log(NOTCH_ZOOM);
 export function normalizeWheelDelta(delta, mode) {
     if (mode === 1) {
-        return delta * 16; // DOM_DELTA_LINE
+        return delta * 16;
     }
     if (mode === 2) {
-        return delta * 100; // DOM_DELTA_PAGE
+        return delta * 100;
     }
-    return delta; // DOM_DELTA_PIXEL
+    return delta;
 }
-// Adaptive divisor: tiny pinch deltas zoom in larger steps, big mouse notches
-// in finer steps, so a trackpad pinch and a mouse wheel feel similar.
-export function getZoomNormalizer(deltaY) {
-    const abs = Math.abs(deltaY);
-    if (abs < 6) {
-        return 25;
+const clampAbs = (x, max) => Math.max(-max, Math.min(max, x));
+// Positive log zooms in. Feed every wheel event to add() and call step() once
+// per animation frame with the time since the last frame; step() returns the
+// multiplier for colWidth/rowHeight.
+export class WheelZoomSmoother {
+    continuous = 0;
+    pending = 0;
+    add(deltaY, deltaMode, isPinch) {
+        const px = normalizeWheelDelta(deltaY, deltaMode);
+        if (deltaMode !== 0 || Math.abs(px) >= NOTCH_MIN_PX) {
+            const notches = deltaMode !== 0 ? 1 : Math.min(Math.max(Math.abs(px) / 100, 1), 3);
+            this.pending = clampAbs(this.pending - Math.sign(px) * notches * Math.log(NOTCH_ZOOM), MAX_PENDING_LOG);
+        }
+        else {
+            this.continuous -= px / (isPinch ? PINCH_PX_PER_LOG : SCROLL_PX_PER_LOG);
+        }
     }
-    if (abs > 150) {
-        return 500;
+    get idle() {
+        return this.continuous === 0 && this.pending === 0;
     }
-    if (abs > 30) {
-        return 150;
+    step(elapsedMs) {
+        let eased = this.pending * (1 - Math.exp(-elapsedMs / NOTCH_TAU_MS));
+        if (Math.abs(this.pending - eased) < 0.005) {
+            eased = this.pending;
+        }
+        this.pending -= eased;
+        const log = clampAbs(this.continuous + eased, MAX_FRAME_LOG);
+        this.continuous = 0;
+        return Math.exp(log);
     }
-    return 75;
-}
-// Turn accumulated, normalized zoom intent into a colWidth/rowHeight multiplier.
-// Positive accum (wheel toward user) zooms out (factor < 1); negative zooms in.
-export function zoomFactorFromAccum(zoomAccum, elapsedMs) {
-    const max = MAX_ZOOM_RATE_PER_MS * elapsedMs;
-    const d = Math.max(-max, Math.min(max, zoomAccum));
-    return d > 0 ? 1 / (1 + d) : 1 - d;
 }
 //# sourceMappingURL=wheelZoom.js.map

package/dist/wheelZoom.js.map

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

@@ -0,0 +1,29 @@
+export interface ZoomSnapshot {
+    colWidth: number;
+    rowHeight: number;
+    blocksX: number[];
+    blocksY: number[];
+}
+interface Viewport {
+    colWidth: number;
+    rowHeight: number;
+    scrollX: number;
+    scrollY: number;
+    msaAreaWidth: number;
+    msaAreaHeight: number;
+    totalWidth: number;
+    totalHeight: number;
+    blockSize: number;
+}
+export declare function takeZoomSnapshot(view: Viewport, withMargin: boolean): {
+    colWidth: number;
+    rowHeight: number;
+    blocksX: number[];
+    blocksY: number[];
+};
+export declare function zoomSnapshotScale(view: Viewport, snap: ZoomSnapshot): {
+    sx: number;
+    sy: number;
+};
+export declare function zoomSnapshotCovers(view: Viewport, snap: ZoomSnapshot): boolean;
+export {};

package/dist/zoomSnapshot.js

@@ -0,0 +1,47 @@
+import { calculateBlocks } from './calculateBlocks.js';
+// past this stretch the scaled letters blur enough to redraw
+const maxStretch = 2;
+// a redraw covers this fraction of the viewport again on each side, so a zoom
+// out shrinks it for a few frames before it runs out of picture
+const margin = 0.2;
+function blocksAt(view, axis, scale, marginFraction) {
+    const size = axis === 'x' ? view.msaAreaWidth : view.msaAreaHeight;
+    const pos = -(axis === 'x' ? view.scrollX : view.scrollY);
+    const map = axis === 'x' ? view.totalWidth : view.totalHeight;
+    const pad = size * marginFraction;
+    return calculateBlocks({
+        viewportSize: (size + 2 * pad) / scale,
+        viewportPos: (pos - pad) / scale,
+        mapSize: map / scale,
+        blockSize: view.blockSize,
+    });
+}
+const within = (need, have) => need.length === 0 ||
+    (have.length > 0 && need[0] >= have[0] && need.at(-1) <= have.at(-1));
+// a gesture starts from the blocks already drawn, and each redraw during it
+// adds the margin
+export function takeZoomSnapshot(view, withMargin) {
+    const m = withMargin ? margin : 0;
+    return {
+        colWidth: view.colWidth,
+        rowHeight: view.rowHeight,
+        blocksX: blocksAt(view, 'x', 1, m),
+        blocksY: blocksAt(view, 'y', 1, m),
+    };
+}
+export function zoomSnapshotScale(view, snap) {
+    return {
+        sx: view.colWidth / snap.colWidth,
+        sy: view.rowHeight / snap.rowHeight,
+    };
+}
+// whether the blocks drawn at the snapshot, stretched to the current cell
+// size, still fill the viewport sharply enough
+export function zoomSnapshotCovers(view, snap) {
+    const { sx, sy } = zoomSnapshotScale(view, snap);
+    return (sx <= maxStretch &&
+        sy <= maxStretch &&
+        within(blocksAt(view, 'x', sx, 0), snap.blocksX) &&
+        within(blocksAt(view, 'y', sy, 0), snap.blocksY));
+}
+//# sourceMappingURL=zoomSnapshot.js.map

package/dist/zoomSnapshot.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "9.1.0",
+  "version": "9.2.0",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -37,23 +37,23 @@
     "react-dom": ">=16.8.0"
   },
   "devDependencies": {
-    "@jbrowse/core": "^5.0.0-beta.9",
-    "@jbrowse/mobx-state-tree": "^6.6.1",
-    "@mui/icons-material": "^9.4.0",
-    "@mui/material": "^9.4.0",
-    "@types/node": "^26.6.2",
+    "@jbrowse/core": "^5.0.0-beta.15",
+    "@jbrowse/mobx-state-tree": "^6.9.0",
+    "@mui/icons-material": "^9.5.0",
+    "@mui/material": "^9.5.0",
+    "@types/node": "^26.6.5",
     "esbuild": "^0.28.2",
-    "mobx": "^7.0.3",
+    "mobx": "^7.0.6",
     "mobx-react": "^10.0.2",
-    "react": "^19.3.0",
-    "react-dom": "^19.3.0"
+    "react": "^19.3.1",
+    "react-dom": "^19.3.1"
   },
   "dependencies": {
     "@gmod/newick": "^1.0.3",
-    "@jbrowse/svgcanvas": "9.1.0",
+    "@jbrowse/svgcanvas": "9.2.0",
     "colord": "^2.10.0",
     "flatbush": "^4.6.2",
-    "msa-parsers": "9.1.0"
+    "msa-parsers": "9.2.0"
   },
   "scripts": {
     "clean": "rimraf dist bundle",

package/src/blosum62.ts

@@ -0,0 +1,45 @@
+// BLOSUM62 (Henikoff & Henikoff 1992), shared by the neighbor-joining tree and
+// the blosum62_dynamic color scheme
+
+// prettier-ignore
+const BLOSUM62_KEYS = 'ARNDCQEGHILKMFPSTWYVBZX*'
+// prettier-ignore
+const BLOSUM62_DATA = [
+  [ 4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0,-2,-1, 0,-4],
+  [-1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3,-1, 0,-1,-4],
+  [-2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3, 3, 0,-1,-4],
+  [-2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3, 4, 1,-1,-4],
+  [ 0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4],
+  [-1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2, 0, 3,-1,-4],
+  [-1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2, 1, 4,-1,-4],
+  [ 0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3,-1,-2,-1,-4],
+  [-2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3, 0, 0,-1,-4],
+  [-1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3,-3,-3,-1,-4],
+  [-1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1,-4,-3,-1,-4],
+  [-1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2, 0, 1,-1,-4],
+  [-1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1,-3,-1,-1,-4],
+  [-2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1,-3,-3,-1,-4],
+  [-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2,-2,-1,-2,-4],
+  [ 1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2, 0, 0, 0,-4],
+  [ 0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0,-1,-1, 0,-4],
+  [-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3,-4,-3,-2,-4],
+  [-2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1,-3,-2,-1,-4],
+  [ 0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4,-3,-2,-1,-4],
+  [-2,-1, 3, 4,-3, 0, 1,-1, 0,-3,-4, 0,-3,-3,-2, 0,-1,-4,-3,-3, 4, 1,-1,-4],
+  [-1, 0, 0, 1,-3, 3, 4,-2, 0,-3,-3, 1,-1,-3,-1, 0,-1,-3,-2,-2, 1, 4,-1,-4],
+  [ 0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-1,-1,-1,-4],
+  [-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4, 1],
+]
+
+export const NUM_SYMBOLS = BLOSUM62_KEYS.length
+export const BLOSUM62 = Int8Array.from(BLOSUM62_DATA.flat())
+
+// charCode -> row/column in BLOSUM62, -1 for anything the matrix does not name.
+// On a 120x800 alignment a Map keyed by upper-cased character took 2.6s to
+// build a tree, against 0.34s for this table.
+export const symbolOfCode = new Int8Array(128).fill(-1)
+for (let i = 0; i < NUM_SYMBOLS; i++) {
+  const key = BLOSUM62_KEYS[i]!
+  symbolOfCode[key.charCodeAt(0)] = i
+  symbolOfCode[key.toLowerCase().charCodeAt(0)] = i
+}

package/src/colorSchemes.ts

@@ -79,6 +79,7 @@ const colorSchemes: Record<string, Record<string, string>> = {
   },
 
   percent_identity_dynamic: {},
+  blosum62_dynamic: {},
   // https://github.com/biotite-dev/biotite/blob/8c460972f8ab904312f130dfb80f3efc8c9bd7c5/src/biotite/sequence/graphics/color_schemes/flower.json
   flower: {
     A: '#b18a51',

package/src/components/Loading.tsx

@@ -10,6 +10,7 @@ import StatusMessage from './StatusMessage.tsx'
 import ImportForm from './import/ImportForm.tsx'
 
 import type { MsaViewModel } from '../model.ts'
+import type { ToolbarSlots } from './header/Header.tsx'
 
 const Reset = observer(function ({
   model,
@@ -36,7 +37,10 @@ const Reset = observer(function ({
   )
 })
 
-const Loading = observer(function ({ model }: { model: MsaViewModel }) {
+const Loading = observer(function ({
+  model,
+  ...slots
+}: { model: MsaViewModel } & ToolbarSlots) {
   const {
     isLoading,
     dataInitialized,
@@ -64,7 +68,7 @@ const Loading = observer(function ({ model }: { model: MsaViewModel }) {
           isLoading ? (
             <StatusMessage model={model} variant="page" />
           ) : (
-            <MSAView model={model} />
+            <MSAView model={model} {...slots} />
           )
         ) : hasData ? (
           <Reset model={model} error={error} />

package/src/components/MSAView.tsx

@@ -14,11 +14,13 @@ import MSAPanel from './msa/MSAPanel.tsx'
 import { clickColor, hoverColor, selectionFill } from './overlayColors.ts'
 import RowPanelHeaders from './rowpanels/RowPanelHeaders.tsx'
 import RowPanels from './rowpanels/RowPanels.tsx'
+import SettingsPanel from './settings/SettingsPanel.tsx'
 import TreeOverview from './tree/TreeOverview.tsx'
 import TreePanel from './tree/TreePanel.tsx'
 import TreeRuler from './tree/TreeRuler.tsx'
 
 import type { MsaViewModel } from '../model.ts'
+import type { ToolbarSlots } from './header/Header.tsx'
 
 // The band above the panels: the tree overview and scale bar, the strip
 // headers, and the minimap over the alignment. The spacer stands in for the
@@ -139,17 +141,32 @@ const View = observer(function ({ model }: { model: MsaViewModel }) {
   )
 })
 
-const MSAView = observer(function ({ model }: { model: MsaViewModel }) {
-  const { height, hideHeader, viewInitialized, DialogComponent, DialogProps } =
-    model
+const MSAView = observer(function ({
+  model,
+  ...slots
+}: { model: MsaViewModel } & ToolbarSlots) {
+  const {
+    height,
+    headerHeight,
+    hideHeader,
+    settingsOpen,
+    viewInitialized,
+    DialogComponent,
+    DialogProps,
+  } = model
 
   return (
     <div>
       {viewInitialized ? (
         <>
           <div style={{ height, overflow: 'clip' }}>
-            {hideHeader ? null : <Header model={model} />}
-            <View model={model} />
+            {hideHeader ? null : <Header model={model} {...slots} />}
+            <div style={{ display: 'flex' }}>
+              <View model={model} />
+              {settingsOpen ? (
+                <SettingsPanel model={model} height={height - headerHeight} />
+              ) : null}
+            </div>
           </div>
           <HorizontalResizeHandle model={model} />