react-msaview 6.5.0 → 8.0.0

package/dist/colorSchemes.js

@@ -12,8 +12,7 @@ const dna = {
     T: red[500],
     U: red[500],
 };
-// annotated rather than asserted: the wide type is what lets a free-string
-// scheme name index this, and an annotation still checks the literal against it
+// Record<string, ...> so a free-string scheme name can index it
 const colorSchemes = {
     none: {},
     nucleotide: dna,

package/dist/colorSchemes.js.map

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

@@ -0,0 +1,28 @@
+import type { ColumnCounts } from './columnCounts.ts';
+export interface ColumnStats {
+    col: number;
+    total: number;
+    gaps: number;
+    gapFraction: number;
+    conservation: number;
+    propertyConservation: number | undefined;
+    consensusLetter: string;
+    consensusCount: number;
+    consensusFraction: number;
+    distribution: [string, number][];
+}
+/**
+ * Summarize one column: consensus residue and its identity fraction, the two
+ * conservation scores, gap fraction, and the non-gap residue distribution
+ * sorted by count. undefined past the end of the alignment or for a column with
+ * no sequences.
+ *
+ * A module-level function: a getter that reached the method through `this` made
+ * TypeScript infer the whole views object to type it, and fell back to `any`.
+ */
+export declare function columnStats({ col, colStats, conservation, propertyConservation, }: {
+    col: number;
+    colStats: ColumnCounts;
+    conservation: number[];
+    propertyConservation: number[];
+}): ColumnStats | undefined;

package/dist/columnStats.js

@@ -0,0 +1,34 @@
+/**
+ * Summarize one column: consensus residue and its identity fraction, the two
+ * conservation scores, gap fraction, and the non-gap residue distribution
+ * sorted by count. undefined past the end of the alignment or for a column with
+ * no sequences.
+ *
+ * A module-level function: a getter that reached the method through `this` made
+ * TypeScript infer the whole views object to type it, and fell back to `any`.
+ */
+export function columnStats({ col, colStats, conservation, propertyConservation, }) {
+    if (col >= colStats.numColumns) {
+        return undefined;
+    }
+    const total = colStats.total(col);
+    if (!total) {
+        return undefined;
+    }
+    const gaps = colStats.gapCount(col);
+    const distribution = colStats.residueEntries(col).sort((a, b) => b[1] - a[1]);
+    const consensus = distribution[0];
+    return {
+        col,
+        total,
+        gaps,
+        gapFraction: gaps / total,
+        conservation: conservation[col] ?? 0,
+        propertyConservation: propertyConservation[col],
+        consensusLetter: consensus?.[0] ?? '',
+        consensusCount: consensus?.[1] ?? 0,
+        consensusFraction: consensus ? consensus[1] / total : 0,
+        distribution,
+    };
+}
+//# sourceMappingURL=columnStats.js.map

package/dist/columnStats.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"columnStats.js","sourceRoot":"","sources":["../src/columnStats.ts"],"names":[],"mappings":"AAeA;;;;;;;;GAQG;AACH,MAAM,UAAU,WAAW,CAAC,EAC1B,GAAG,EACH,QAAQ,EACR,YAAY,EACZ,oBAAoB,GAMrB;IACC,IAAI,GAAG,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAC;QAC/B,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,KAAK,GAAG,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACjC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,IAAI,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;IACnC,MAAM,YAAY,GAAG,QAAQ,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7E,MAAM,SAAS,GAAG,YAAY,CAAC,CAAC,CAAC,CAAA;IACjC,OAAO;QACL,GAAG;QACH,KAAK;QACL,IAAI;QACJ,WAAW,EAAE,IAAI,GAAG,KAAK;QACzB,YAAY,EAAE,YAAY,CAAC,GAAG,CAAC,IAAI,CAAC;QACpC,oBAAoB,EAAE,oBAAoB,CAAC,GAAG,CAAC;QAC/C,eAAe,EAAE,SAAS,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE;QACrC,cAAc,EAAE,SAAS,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;QACnC,iBAAiB,EAAE,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;QACvD,YAAY;KACb,CAAA;AACH,CAAC"}

package/dist/components/DragHandle.d.ts

@@ -1,8 +1,9 @@
 import React from 'react';
+import type { Theme } from '@mui/material';
 export declare const scrollbarThumbFill = "rgba(66,119,127,0.3)";
 declare const variants: Record<'thumb' | 'resizer', {
-    fill: string;
-    fillHovered: string;
+    fill: (theme: Theme) => string;
+    fillHovered: (theme: Theme) => string;
     cursor: (axis: 'x' | 'y') => string;
     position: React.CSSProperties['position'];
     zIndex?: number;

package/dist/components/DragHandle.js

@@ -1,4 +1,5 @@
 import React, { useState } from 'react';
+import { useTheme } from '@mui/material';
 import { useDragScroll } from '../useDragScroll.js';
 export const scrollbarThumbFill = 'rgba(66,119,127,0.3)';
 // The scroll thumbs (minimap, vertical scrollbar) and the resize dividers are
@@ -7,15 +8,19 @@ export const scrollbarThumbFill = 'rgba(66,119,127,0.3)';
 // difference rather than a second copy of the drag wiring.
 const variants = {
     thumb: {
-        fill: scrollbarThumbFill,
-        fillHovered: 'rgba(66,119,127,0.6)',
+        fill: () => scrollbarThumbFill,
+        fillHovered: () => 'rgba(66,119,127,0.6)',
         cursor: () => 'pointer',
         position: 'absolute',
         zIndex: 100,
     },
     resizer: {
-        fill: 'rgba(200,200,200)',
-        fillHovered: 'rgba(150,150,150)',
+        fill: theme => theme.palette.mode === 'dark'
+            ? theme.palette.grey[800]
+            : 'rgba(200,200,200)',
+        fillHovered: theme => theme.palette.mode === 'dark'
+            ? theme.palette.grey[600]
+            : 'rgba(150,150,150)',
         cursor: axis => (axis === 'x' ? 'ew-resize' : 'ns-resize'),
         position: 'relative',
     },
@@ -29,6 +34,7 @@ const variants = {
  * on every render.
  */
 export default function DragHandle({ axis, variant, getStart, onDrag, style, }) {
+    const theme = useTheme();
     const [hovered, setHovered] = useState(false);
     const { startDrag } = useDragScroll(axis, onDrag);
     const { fill, fillHovered, cursor, position, zIndex } = variants[variant];
@@ -42,7 +48,7 @@ export default function DragHandle({ axis, variant, getStart, onDrag, style, })
             position,
             zIndex,
             cursor: cursor(axis),
-            background: hovered ? fillHovered : fill,
+            background: hovered ? fillHovered(theme) : fill(theme),
             ...style,
         } }));
 }

package/dist/components/DragHandle.js.map

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+{"version":3,"file":"DragHandle.js","sourceRoot":"","sources":["../../src/components/DragHandle.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,OAAO,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAA;AAInD,MAAM,CAAC,MAAM,kBAAkB,GAAG,sBAAsB,CAAA;AAExD,8EAA8E;AAC9E,+EAA+E;AAC/E,wEAAwE;AACxE,2DAA2D;AAC3D,MAAM,QAAQ,GASV;IACF,KAAK,EAAE;QACL,IAAI,EAAE,GAAG,EAAE,CAAC,kBAAkB;QAC9B,WAAW,EAAE,GAAG,EAAE,CAAC,sBAAsB;QACzC,MAAM,EAAE,GAAG,EAAE,CAAC,SAAS;QACvB,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,GAAG;KACZ;IACD,OAAO,EAAE;QACP,IAAI,EAAE,KAAK,CAAC,EAAE,CACZ,KAAK,CAAC,OAAO,CAAC,IAAI,KAAK,MAAM;YAC3B,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;YACzB,CAAC,CAAC,mBAAmB;QACzB,WAAW,EAAE,KAAK,CAAC,EAAE,CACnB,KAAK,CAAC,OAAO,CAAC,IAAI,KAAK,MAAM;YAC3B,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC;YACzB,CAAC,CAAC,mBAAmB;QACzB,MAAM,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,KAAK,GAAG,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,WAAW,CAAC;QAC1D,QAAQ,EAAE,UAAU;KACrB;CACF,CAAA;AAED;;;;;;;GAOG;AACH,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,IAAI,EACJ,OAAO,EACP,QAAQ,EACR,MAAM,EACN,KAAK,GAON;IACC,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,EAAE,SAAS,EAAE,GAAG,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;IACjD,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAA;IAEzE,OAAO,CACL,6BACE,YAAY,EAAE,GAAG,EAAE;YACjB,UAAU,CAAC,IAAI,CAAC,CAAA;QAClB,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;YACjB,UAAU,CAAC,KAAK,CAAC,CAAA;QACnB,CAAC,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,SAAS,CAAC,KAAK,EAAE,QAAQ,EAAE,CAAC,CAAA;QAC9B,CAAC,EACD,KAAK,EAAE;YACL,QAAQ;YACR,MAAM;YACN,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC;YACpB,UAAU,EAAE,OAAO,CAAC,CAAC,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC;YACtD,GAAG,KAAK;SACT,GACD,CACH,CAAA;AACH,CAAC"}

package/dist/components/Loading.js

@@ -26,9 +26,9 @@ const Reset = observer(function ({ model, error, }) {
             } }, "Return to import form")));
 });
 const Loading = observer(function ({ model }) {
-    const { isLoading, dataInitialized, error, msaFilehandle, treeFilehandle } = model;
+    const { isLoading, dataInitialized, error, resetCount, msaFilehandle, treeFilehandle, } = model;
     const hasPendingFilehandle = !!(msaFilehandle || treeFilehandle);
-    return (React.createElement("div", null, React.createElement(ErrorBoundary, { FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(MSAView, { model: model }))) : error ? (React.createElement(Reset, { model: model, error: error })) : hasPendingFilehandle || isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(ImportForm, { model: model })))));
+    return (React.createElement("div", null, React.createElement(ErrorBoundary, { key: resetCount, FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(MSAView, { model: model }))) : error ? (React.createElement(Reset, { model: model, error: error })) : hasPendingFilehandle || isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(ImportForm, { model: model })))));
 });
 export default Loading;
 //# sourceMappingURL=Loading.js.map

package/dist/components/Loading.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../src/components/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,gCAAgC,CAAA;AAC9D,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,UAAU,MAAM,wBAAyB,CAAA;AAIhD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC1E,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,OAAO,CACL,6BACE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,EAAE,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;QAEtE,6BACE,KAAK,EAAC,IAAI,EACV,MAAM,EAAC,IAAI,EACX,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,4BAA4B;YAElC,mCACG,0DAA0D,CACrD;YACR,gCACE,EAAE,EAAC,IAAI,EACP,EAAE,EAAC,IAAI,EACP,CAAC,EAAC,IAAI,EACN,MAAM,EAAC,MAAM,EACb,WAAW,EAAC,GAAG,EACf,IAAI,EAAC,MAAM,GACX;YACF,8BACE,CAAC,EAAC,yBAAyB,EAC3B,MAAM,EAAC,SAAS,EAChB,WAAW,EAAC,GAAG,EACf,IAAI,EAAC,MAAM,EACX,aAAa,EAAC,OAAO,EACrB,KAAK,EAAE;oBACL,SAAS,EAAE,4BAA4B;oBACvC,eAAe,EAAE,QAAQ;iBAC1B,GACD,CACE;QACN,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,IAAE,MAAM,EAAE,GAAG,IAAI,YAAY,CAAc;QAClE,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC,CAClB,oBAAC,MAAM,IACL,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,aAG3B,CACV,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAC/B,KAAK,EACL,KAAK,GAIN;IACC,OAAO,CACL;QACE,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,KAAK,EAAE,CAAA;YACf,CAAC,4BAGM,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EACJ,SAAS,EACT,eAAe,EACf,KAAK,EACL,UAAU,EACV,aAAa,EACb,cAAc,GACf,GAAG,KAAK,CAAA;IACT,MAAM,oBAAoB,GAAG,CAAC,CAAC,CAAC,aAAa,IAAI,cAAc,CAAC,CAAA;IAEhE,OAAO,CACL,iCAIE,oBAAC,aAAa,IACZ,GAAG,EAAE,UAAU,EACf,iBAAiB,EAAE,CAAC,CAAC,EAAE,CAAC,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,GAAI,IAE9D,eAAe,CAAC,CAAC,CAAC,CACjB,SAAS,CAAC,CAAC,CAAC,CACV,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACF,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAGV,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CACtC,CAAC,CAAC,CAAC,oBAAoB,IAAI,SAAS,CAAC,CAAC,CAAC,CACtC,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,CACF,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC7B,CACa,CACZ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/MSAView.js

@@ -7,16 +7,26 @@ import Header from './header/Header.js';
 import Minimap from './minimap/Minimap.js';
 import MSAPanel from './msa/MSAPanel.js';
 import { clickColor, hoverColor } from './overlayColors.js';
+import RowPanelHeaders from './rowpanels/RowPanelHeaders.js';
+import RowPanels from './rowpanels/RowPanels.js';
+import TreeOverview from './tree/TreeOverview.js';
 import TreePanel from './tree/TreePanel.js';
 import TreeRuler from './tree/TreeRuler.js';
+// 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
+// resize handle, so the minimap starts exactly where the alignment canvas does.
 const TopArea = observer(function ({ model }) {
-    const { showHorizontalScrollbar } = model;
+    const { showHorizontalScrollbar, showTreeOverview, resizeHandleWidth } = model;
     return (React.createElement("div", { style: { display: 'flex' } },
-        React.createElement(TreeRuler, { model: model }),
+        React.createElement("div", { style: { flexShrink: 0 } },
+            showTreeOverview ? React.createElement(TreeOverview, { model: model }) : null,
+            React.createElement(TreeRuler, { model: model })),
+        React.createElement(RowPanelHeaders, { model: model }),
+        React.createElement("div", { style: { width: resizeHandleWidth, flexShrink: 0 } }),
         showHorizontalScrollbar ? React.createElement(Minimap, { model: model }) : null));
 });
 const TrackColumnIndicator = observer(function ({ model, }) {
-    const { mouseCol, mouseClickCol, colWidth, scrollX, treeAreaWidth, resizeHandleWidth, totalTrackAreaHeight, msaCanvasWidth, } = model;
+    const { mouseCol, mouseClickCol, colWidth, scrollX, treeAreaWidth, rowPanelsWidth, resizeHandleWidth, totalTrackAreaHeight, msaCanvasWidth, } = model;
     // hovered column, then the pinned one, matching the alignment's own overlay
     const bands = [
         { col: mouseCol, color: hoverColor },
@@ -24,7 +34,7 @@ const TrackColumnIndicator = observer(function ({ model, }) {
     ];
     return (React.createElement("div", { style: {
             position: 'absolute',
-            left: treeAreaWidth + resizeHandleWidth,
+            left: treeAreaWidth + rowPanelsWidth + resizeHandleWidth,
             top: 0,
             width: msaCanvasWidth,
             height: totalTrackAreaHeight,
@@ -53,6 +63,7 @@ const MainArea = observer(function ({ model }) {
     const { showVerticalScrollbar } = model;
     return (React.createElement("div", { style: { display: 'flex' } },
         React.createElement(TreePanel, { model: model }),
+        React.createElement(RowPanels, { model: model }),
         React.createElement(VerticalResizeHandle, { model: model }),
         React.createElement(MSAPanel, { model: model }),
         showVerticalScrollbar ? React.createElement(VerticalScrollbar, { model: model }) : null));
@@ -64,10 +75,10 @@ const View = observer(function ({ model }) {
         React.createElement(MainArea, { model: model })));
 });
 const MSAView = observer(function ({ model }) {
-    const { height, viewInitialized, DialogComponent, DialogProps } = model;
+    const { height, hideHeader, viewInitialized, DialogComponent, DialogProps } = model;
     return (React.createElement("div", null, viewInitialized ? (React.createElement(React.Fragment, null,
         React.createElement("div", { style: { height, overflow: 'hidden' } },
-            React.createElement(Header, { model: model }),
+            hideHeader ? null : React.createElement(Header, { model: model }),
             React.createElement(View, { model: model })),
         React.createElement(HorizontalResizeHandle, { model: model }),
         DialogComponent ? (React.createElement(Suspense, { fallback: null },

package/dist/components/MSAView.js.map

@@ -1 +1 @@
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package/dist/components/MSAViewer.d.ts

@@ -1,7 +1,9 @@
 import React from 'react';
-import type { ColumnTrackSpec, Highlight } from '../types.ts';
+import type { MsaViewModel } from '../model.ts';
+import type { Cell, Clade, ColumnTrackSpec, Encoding, Highlight, Region, ResidueEncoding, ResidueMapping, RowPanelSpec, Viewport } from '../types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
-interface MSAViewerProps {
+import type { ThemeOptions } from '@mui/material/styles';
+export interface MSAViewerProps {
     msa?: string;
     tree?: string;
     gff?: string;
@@ -14,6 +16,10 @@ interface MSAViewerProps {
     colWidth?: number;
     /** initial per-row pixel height */
     rowHeight?: number;
+    /**
+     * hide columns at least this percent gaps (default 100, i.e. hide nothing)
+     */
+    allowedGappyness?: number;
     /** alignment columns (0-based) to highlight with a persistent overlay */
     highlightColumns?: number[];
     /**
@@ -22,16 +28,75 @@ interface MSAViewerProps {
      * for whole rows, each with an optional `label` and `color`
      */
     highlights?: Highlight[];
+    /**
+     * clades of the tree with a mark drawn over them: `{mrca, tips, mark}` or
+     * `{range, tips, mark}`, where `mark` is `highlight`, `bracket`, `collapse`
+     * or `focus` (see docs/layers.md)
+     */
+    clades?: Clade[];
     /** row name to diff every other row against (matches render as ".") */
     relativeTo?: string;
     /** tracks supplied as data: per-column bar values or a text row (see docs/layers.md) */
     columnTracks?: ColumnTrackSpec[];
+    /** which residue of which structure each row's residues are (see docs/layers.md) */
+    residueMappings?: ResidueMapping[];
+    /** extra fields per row name, such as a lineage or a host (see docs/layers.md) */
+    rowData?: Record<string, Record<string, string>>;
+    /**
+     * what the viewer's marks read from a table: `{channel, field, scale?}`,
+     * where `channel` is `tipLabel`, `rowTint` or `branch` over `rowData`, or
+     * `featureFill` or `featureLabel` over the annotations (see docs/layers.md)
+     */
+    encodings?: Encoding[];
+    /**
+     * panels between the tree and the alignment, one cell per row:
+     * `{kind: 'strip', field, scale?, width?, header?}` colors each row by a
+     * `rowData` field (see docs/layers.md)
+     */
+    rowPanels?: RowPanelSpec[];
     /** draw the phylogenetic tree (default true); false leaves a labels-only gutter */
     drawTree?: boolean;
     /** fixed width (px) of the tree/label area */
     treeAreaWidth?: number;
     /** auto-size the tree/label area to the labels (used when drawTree is false) */
     autoTreeAreaWidth?: boolean;
+    /** draw branch lengths (default true); false draws a cladogram */
+    showBranchLen?: boolean;
+    /**
+     * which channel `colorScheme` paints: `fill` (default) colors the background
+     * of the cell a residue sits in, `color` colors the letter itself and leaves
+     * the background plain, which lets a domain overlay mark each span with a bar
+     * under the row and the residue colors show through
+     */
+    residueEncoding?: ResidueEncoding;
+    /**
+     * a span to zoom and scroll to once the alignment loads, and again whenever
+     * it changes: `{row, start, end}` in residues of that row, or `{start, end}`
+     * in columns, 1-based and inclusive
+     */
+    region?: Region;
+    /** leave out the toolbar, for a page drawing its own controls */
+    hideHeader?: boolean;
+    /**
+     * 'light' (default), 'dark', or MUI theme options (palette, typography)
+     * merged over the JBrowse theme
+     */
+    theme?: 'light' | 'dark' | ThemeOptions;
+    /** the cell under the pointer, or undefined when it leaves the alignment */
+    onCellHover?: (cell: Cell | undefined) => void;
+    /** the cell a click pinned, or undefined when a click clears it */
+    onCellClick?: (cell: Cell | undefined) => void;
+    /** the alignment columns on screen, after every scroll, zoom and resize */
+    onViewportChange?: (viewport: Viewport | undefined) => void;
+    /**
+     * the model the viewer built, for the model API; called again with the new
+     * model when msa, tree, gff or a filehandle changes
+     */
+    onModel?: (model: MsaViewModel) => void;
 }
-export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, highlightColumns, highlights, relativeTo, columnTracks, drawTree, treeAreaWidth, autoTreeAreaWidth, }: MSAViewerProps): React.JSX.Element;
-export {};
+/**
+ * A new alignment, tree or annotation file needs a new model, so the viewer
+ * remounts when one of those props changes and keeps its model across every
+ * other change.
+ */
+export default function MSAViewer(props: MSAViewerProps): React.JSX.Element;

package/dist/components/MSAViewer.js

@@ -1,17 +1,72 @@
-import React, { useEffect, useState } from 'react';
+import React, { useEffect, useRef, useState } from 'react';
 import { createJBrowseTheme } from '@jbrowse/core/ui/theme';
 import useMeasure from '@jbrowse/core/util/useMeasure';
+import { destroy, isAlive } from '@jbrowse/mobx-state-tree';
 import { ThemeProvider } from '@mui/material/styles';
+import { compareStructural, reaction, when } from 'mobx';
 import MSAModelF from '../model.js';
 import Loading from './Loading.js';
-const theme = createJBrowseTheme();
-export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, highlightColumns, highlights, relativeTo, columnTracks, drawTree, treeAreaWidth, autoTreeAreaWidth, }) {
-    // lazy initializer: the model is created exactly once from the initial props
-    // (a stable MST instance — not a value safe to recompute, so not useMemo)
+function resolveTheme(theme) {
+    return createJBrowseTheme(theme === 'dark'
+        ? { palette: { mode: 'dark' } }
+        : typeof theme === 'object'
+            ? theme
+            : undefined);
+}
+function sameSource(a, b) {
+    return (a.msa === b.msa &&
+        a.tree === b.tree &&
+        a.gff === b.gff &&
+        JSON.stringify([a.msaFilehandle, a.treeFilehandle, a.gffFilehandle]) ===
+            JSON.stringify([b.msaFilehandle, b.treeFilehandle, b.gffFilehandle]));
+}
+/**
+ * A new alignment, tree or annotation file needs a new model, so the viewer
+ * remounts when one of those props changes and keeps its model across every
+ * other change.
+ */
+export default function MSAViewer(props) {
+    const { msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle } = props;
+    const source = {
+        msa,
+        tree,
+        gff,
+        msaFilehandle,
+        treeFilehandle,
+        gffFilehandle,
+    };
+    const [shown, setShown] = useState({ source, generation: 0 });
+    if (!sameSource(shown.source, source)) {
+        setShown({ source, generation: shown.generation + 1 });
+    }
+    return React.createElement(Viewer, { key: shown.generation, ...props });
+}
+function useModelReaction(model, key, handler) {
+    const latest = useRef(handler);
+    useEffect(() => {
+        latest.current = handler;
+    });
+    const listening = !!handler;
+    useEffect(() => listening
+        ? reaction(() => model[key], value => {
+            latest.current?.(value);
+        }, { equals: compareStructural })
+        : undefined, [model, key, listening]);
+}
+function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, allowedGappyness, highlightColumns, highlights, clades, relativeTo, columnTracks, residueMappings, rowData, encodings, rowPanels, drawTree, residueEncoding, treeAreaWidth, autoTreeAreaWidth, showBranchLen, region, hideHeader, theme, onCellHover, onCellClick, onViewportChange, onModel, }) {
     const [model] = useState(() => MSAModelF().create({
         type: 'MsaView',
-        ...(msa || tree || gff
-            ? { data: { msa: msa ?? '', tree: tree ?? '', gff } }
+        ...(msa || tree || gff || rowData
+            ? {
+                data: {
+                    msa: msa ?? '',
+                    tree: tree ?? '',
+                    gff,
+                    // the row table is stored as this JSON string, which is what a
+                    // shared URL and the size limit already cover
+                    ...(rowData ? { treeMetadata: JSON.stringify(rowData) } : {}),
+                },
+            }
             : {}),
         ...(msaFilehandle ? { msaFilehandle } : {}),
         ...(treeFilehandle ? { treeFilehandle } : {}),
@@ -20,21 +75,159 @@ export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandl
         ...(height ? { height } : {}),
         ...(colWidth ? { colWidth } : {}),
         ...(rowHeight ? { rowHeight } : {}),
+        ...(allowedGappyness !== undefined ? { allowedGappyness } : {}),
         ...(highlightColumns ? { highlightColumns } : {}),
         ...(highlights ? { highlights } : {}),
+        ...(clades ? { clades } : {}),
         ...(relativeTo ? { relativeTo } : {}),
         ...(columnTracks ? { columnTracks } : {}),
+        ...(residueMappings ? { residueMappings } : {}),
+        ...(encodings ? { encodings } : {}),
+        ...(rowPanels ? { rowPanels } : {}),
         ...(drawTree !== undefined ? { drawTree } : {}),
         ...(treeAreaWidth ? { treeAreaWidth } : {}),
         ...(autoTreeAreaWidth ? { autoTreeAreaWidth } : {}),
+        ...(showBranchLen !== undefined ? { showBranchLen } : {}),
+        ...(residueEncoding !== undefined
+            ? { bgColor: residueEncoding === 'fill' }
+            : {}),
     }));
+    const destroyTimer = useRef(undefined);
     const [ref, { width }] = useMeasure();
     useEffect(() => {
         if (width) {
             model.setWidth(width);
         }
     }, [model, width]);
-    return (React.createElement(ThemeProvider, { theme: theme },
+    // Each effect depends only on its own prop, so a change made inside the
+    // viewer survives the host's next render.
+    useEffect(() => {
+        if (height !== undefined) {
+            model.setHeight(height);
+        }
+    }, [model, height]);
+    useEffect(() => {
+        if (colorScheme !== undefined) {
+            model.setColorSchemeName(colorScheme);
+        }
+    }, [model, colorScheme]);
+    useEffect(() => {
+        if (colWidth !== undefined) {
+            model.setColWidth(colWidth);
+        }
+    }, [model, colWidth]);
+    useEffect(() => {
+        if (rowHeight !== undefined) {
+            model.setRowHeight(rowHeight);
+        }
+    }, [model, rowHeight]);
+    useEffect(() => {
+        if (allowedGappyness !== undefined) {
+            model.setAllowedGappyness(allowedGappyness);
+        }
+    }, [model, allowedGappyness]);
+    useEffect(() => {
+        if (drawTree !== undefined) {
+            model.setDrawTree(drawTree);
+        }
+    }, [model, drawTree]);
+    useEffect(() => {
+        if (treeAreaWidth !== undefined) {
+            model.setTreeAreaWidth(treeAreaWidth);
+        }
+    }, [model, treeAreaWidth]);
+    useEffect(() => {
+        if (showBranchLen !== undefined) {
+            model.setShowBranchLen(showBranchLen);
+        }
+    }, [model, showBranchLen]);
+    useEffect(() => {
+        if (residueEncoding !== undefined) {
+            model.setBgColor(residueEncoding === 'fill');
+        }
+    }, [model, residueEncoding]);
+    useEffect(() => {
+        model.setHideHeader(!!hideHeader);
+    }, [model, hideHeader]);
+    // unguarded, so removing the prop turns the reference diff off
+    useEffect(() => {
+        model.drawRelativeTo(relativeTo);
+    }, [model, relativeTo]);
+    // keyed by content, since a host computing a layer inline passes a new array
+    // on every render
+    const highlightsKey = JSON.stringify(highlights ?? []);
+    useEffect(() => {
+        model.setHighlights(JSON.parse(highlightsKey));
+    }, [model, highlightsKey]);
+    const cladesKey = JSON.stringify(clades ?? []);
+    useEffect(() => {
+        model.setClades(JSON.parse(cladesKey));
+    }, [model, cladesKey]);
+    const columnTracksKey = JSON.stringify(columnTracks ?? []);
+    useEffect(() => {
+        model.setColumnTracks(JSON.parse(columnTracksKey));
+    }, [model, columnTracksKey]);
+    const residueMappingsKey = JSON.stringify(residueMappings ?? []);
+    useEffect(() => {
+        model.setResidueMappings(JSON.parse(residueMappingsKey));
+    }, [model, residueMappingsKey]);
+    const rowDataKey = JSON.stringify(rowData ?? {});
+    useEffect(() => {
+        const table = JSON.parse(rowDataKey);
+        // an empty table leaves whatever the snapshot or a filehandle loaded
+        if (Object.keys(table).length) {
+            model.setRowData(table);
+        }
+    }, [model, rowDataKey]);
+    const encodingsKey = JSON.stringify(encodings ?? []);
+    useEffect(() => {
+        model.setEncodings(JSON.parse(encodingsKey));
+    }, [model, encodingsKey]);
+    const rowPanelsKey = JSON.stringify(rowPanels ?? []);
+    useEffect(() => {
+        model.setRowPanels(JSON.parse(rowPanelsKey));
+    }, [model, rowPanelsKey]);
+    const highlightColumnsKey = JSON.stringify(highlightColumns ?? null);
+    useEffect(() => {
+        model.setHighlightedColumns(JSON.parse(highlightColumnsKey) ?? undefined);
+    }, [model, highlightColumnsKey]);
+    const regionKey = JSON.stringify(region ?? null);
+    useEffect(() => {
+        const target = JSON.parse(regionKey);
+        return target
+            ? when(() => model.viewInitialized && model.numColumns > 0, () => {
+                model.zoomToRegion(target);
+            })
+            : undefined;
+    }, [model, regionKey]);
+    useModelReaction(model, 'hoveredCell', onCellHover);
+    useModelReaction(model, 'clickedCell', onCellClick);
+    useModelReaction(model, 'viewport', onViewportChange);
+    const latestOnModel = useRef(onModel);
+    useEffect(() => {
+        latestOnModel.current = onModel;
+    });
+    useEffect(() => {
+        latestOnModel.current?.(model);
+    }, [model]);
+    // destroy releases the model's matchMedia listener and fetches. It waits a
+    // tick because StrictMode remounts with the same state, and the remount's
+    // effect cancels it.
+    useEffect(() => {
+        if (destroyTimer.current !== undefined) {
+            clearTimeout(destroyTimer.current);
+            destroyTimer.current = undefined;
+        }
+        return () => {
+            destroyTimer.current = setTimeout(() => {
+                destroyTimer.current = undefined;
+                if (isAlive(model)) {
+                    destroy(model);
+                }
+            });
+        };
+    }, [model]);
+    return (React.createElement(ThemeProvider, { theme: resolveTheme(theme) },
         React.createElement("div", { ref: ref },
             React.createElement(Loading, { model: model }))));
 }