react-msaview 8.2.0 → 8.3.0

package/dist/columnCounts.d.ts

@@ -5,6 +5,7 @@ export declare class ColumnCounts {
     readonly totals: Uint32Array;
     private readonly slotTotals;
     constructor(numColumns: number);
+    /** tallies a row, counting the columns past a short row's end as gaps */
     addRow(row: string): void;
     add(col: number, letter: string): void;
     total(col: number): number;
@@ -32,10 +33,10 @@ export declare function residueSlotOfLetter(letter: string): number;
 export declare const numResidueSlots = 32;
 /**
  * Tally counts from alignment rows (gapped sequence strings, one per row). The
- * column count follows the longest row, matching what a per-column tally of
- * ragged input produces.
+ * column count defaults to the longest row, and a shorter row counts as gapped
+ * to the end.
  */
-export declare function columnCountsFromRows(rows: string[]): ColumnCounts;
+export declare function columnCountsFromRows(rows: string[], numColumns?: number): ColumnCounts;
 /**
  * Tally counts from column strings (one string per column, listing that
  * column's residues top to bottom). Convenient for tests and for callers that

package/dist/columnCounts.js

@@ -52,15 +52,21 @@ export class ColumnCounts {
         this.counts = new Uint32Array(numColumns * SLOTS);
         this.totals = new Uint32Array(numColumns);
     }
+    /** tallies a row, counting the columns past a short row's end as gaps */
     addRow(row) {
-        const { counts, totals, slotTotals } = this;
-        const n = Math.min(row.length, this.numColumns);
+        const { counts, totals, slotTotals, numColumns } = this;
+        const n = Math.min(row.length, numColumns);
         for (let col = 0; col < n; col++) {
             const slot = slotOf(row.charCodeAt(col));
             counts[col * SLOTS + slot]++;
             totals[col]++;
             slotTotals[slot]++;
         }
+        for (let col = n; col < numColumns; col++) {
+            counts[col * SLOTS + DASH]++;
+            totals[col]++;
+        }
+        slotTotals[DASH] += numColumns - n;
     }
     add(col, letter) {
         const slot = slotOf(letter.charCodeAt(0));
@@ -138,11 +144,10 @@ export function residueSlotOfLetter(letter) {
 export const numResidueSlots = SLOTS;
 /**
  * Tally counts from alignment rows (gapped sequence strings, one per row). The
- * column count follows the longest row, matching what a per-column tally of
- * ragged input produces.
+ * column count defaults to the longest row, and a shorter row counts as gapped
+ * to the end.
  */
-export function columnCountsFromRows(rows) {
-    const numColumns = rows.reduce((max, row) => Math.max(max, row.length), 0);
+export function columnCountsFromRows(rows, numColumns = rows.reduce((max, row) => Math.max(max, row.length), 0)) {
     const counts = new ColumnCounts(numColumns);
     for (const row of rows) {
         counts.addRow(row);

package/dist/columnCounts.js.map

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

@@ -4,6 +4,6 @@ import React from 'react';
  * cleared on unmount, since these live in dialogs the copy itself often closes.
  */
 export default function CopyButton({ text, label, }: {
-    text: string;
+    text: string | (() => string);
     label?: string;
 }): React.JSX.Element;

package/dist/components/CopyButton.js

@@ -12,7 +12,7 @@ export default function CopyButton({ text, label = 'Copy to clipboard', }) {
         clearTimeout(timer.current);
     }, []);
     return (React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-            copy(text);
+            copy(typeof text === 'string' ? text : text());
             setCopied(true);
             clearTimeout(timer.current);
             timer.current = setTimeout(() => {

package/dist/components/CopyButton.js.map

@@ -1 +1 @@
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+{"version":3,"file":"CopyButton.js","sourceRoot":"","sources":["../../src/components/CopyButton.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE1D,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AAEtC,OAAO,IAAI,MAAM,8BAA8B,CAAA;AAE/C;;;GAGG;AACH,MAAM,CAAC,OAAO,UAAU,UAAU,CAAC,EACjC,IAAI,EACJ,KAAK,GAAG,mBAAmB,GAI5B;IACC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,KAAK,GAAG,MAAM,CAAgC,SAAS,CAAC,CAAA;IAE9D,SAAS,CACP,GAAG,EAAE,CAAC,GAAG,EAAE;QACT,YAAY,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IAC7B,CAAC,EACD,EAAE,CACH,CAAA;IAED,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;YACZ,IAAI,CAAC,OAAO,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAC9C,SAAS,CAAC,IAAI,CAAC,CAAA;YACf,YAAY,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;YAC3B,KAAK,CAAC,OAAO,GAAG,UAAU,CAAC,GAAG,EAAE;gBAC9B,SAAS,CAAC,KAAK,CAAC,CAAA;YAClB,CAAC,EAAE,GAAG,CAAC,CAAA;QACT,CAAC,IAEA,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,CACpB,CACV,CAAA;AACH,CAAC"}

package/dist/components/DragHandle.js

@@ -2,6 +2,9 @@ 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 model's resizeHandleWidth feeds the layout, so a divider keeps its drawn
+// width and widens its target with this much invisible margin each side
+const hitSlop = 4;
 // The scroll thumbs (minimap, vertical scrollbar) and the resize dividers are
 // one widget -- press, drag along an axis, report the pixel delta -- differing
 // only in the affordance they present, so the variant carries the whole
@@ -38,7 +41,10 @@ export default function DragHandle({ axis, variant, getStart, onDrag, style, })
     const [hovered, setHovered] = useState(false);
     const { startDrag } = useDragScroll(axis, onDrag);
     const { fill, fillHovered, cursor, position, zIndex } = variants[variant];
-    return (React.createElement("div", { onMouseEnter: () => {
+    return (React.createElement("div", { ...(variant === 'resizer' && {
+            role: 'separator',
+            'aria-orientation': axis === 'x' ? 'vertical' : 'horizontal',
+        }), onMouseEnter: () => {
             setHovered(true);
         }, onMouseLeave: () => {
             setHovered(false);
@@ -50,6 +56,12 @@ export default function DragHandle({ axis, variant, getStart, onDrag, style, })
             cursor: cursor(axis),
             background: hovered ? fillHovered(theme) : fill(theme),
             ...style,
-        } }));
+        } }, variant === 'resizer' ? (React.createElement("div", { style: {
+            position: 'absolute',
+            zIndex: 101,
+            ...(axis === 'x'
+                ? { top: 0, bottom: 0, left: -hitSlop, right: -hitSlop }
+                : { left: 0, right: 0, top: -hitSlop, bottom: -hitSlop }),
+        } })) : null));
 }
 //# sourceMappingURL=DragHandle.js.map

package/dist/components/DragHandle.js.map

@@ -1 +1 @@
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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,+EAA+E;AAC/E,wEAAwE;AACxE,MAAM,OAAO,GAAG,CAAC,CAAA;AAEjB,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,gCACM,CAAC,OAAO,KAAK,SAAS,IAAI;YAC5B,IAAI,EAAE,WAAW;YACjB,kBAAkB,EAAE,IAAI,KAAK,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,YAAY;SAC7D,CAAC,EACF,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,IAEA,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,CACvB,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,GAAG;YACX,GAAG,CAAC,IAAI,KAAK,GAAG;gBACd,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,OAAO,EAAE,KAAK,EAAE,CAAC,OAAO,EAAE;gBACxD,CAAC,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,CAAC,OAAO,EAAE,CAAC;SAC5D,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC"}

package/dist/components/Loading.js

@@ -1,17 +1,11 @@
 import React from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary';
-import { Button, CircularProgress, Typography } from '@mui/material';
+import { Button } from '@mui/material';
 import { observer } from 'mobx-react';
 import MSAView from './MSAView.js';
+import StatusMessage from './StatusMessage.js';
 import ImportForm from './import/ImportForm.js';
-const LoadingSpinner = observer(function ({ model }) {
-    const { status } = model;
-    return (React.createElement("div", { style: { display: 'flex', alignItems: 'center', gap: 12, padding: 20 } },
-        React.createElement(CircularProgress, { size: 24 }),
-        React.createElement(Typography, { variant: "h6" }, status?.msg ?? 'Loading...'),
-        status?.onCancel ? (React.createElement(Button, { variant: "outlined", size: "small", onClick: () => status.onCancel?.() }, "Cancel")) : null));
-});
 const Reset = observer(function ({ model, error, }) {
     return (React.createElement("div", null,
         React.createElement(ErrorMessage, { error: error }),
@@ -20,9 +14,14 @@ const Reset = observer(function ({ model, error, }) {
             } }, "Return to import form")));
 });
 const Loading = observer(function ({ model }) {
-    const { isLoading, dataInitialized, error, resetCount, msaFilehandle, treeFilehandle, } = model;
-    const hasPendingFilehandle = !!(msaFilehandle || treeFilehandle);
-    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 })))));
+    const { isLoading, dataInitialized, data, error, resetCount, msaFilehandle, treeFilehandle, } = model;
+    const hasData = !!(data.msa || data.tree);
+    // a failed load keeps its filehandle, so the error outranks the spinner
+    const loading = !error && !!(msaFilehandle || treeFilehandle || isLoading);
+    return (React.createElement("div", null, React.createElement(ErrorBoundary, { key: resetCount, FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(StatusMessage, { model: model, variant: "page" })) : (React.createElement(MSAView, { model: model }))) : hasData ? (React.createElement(Reset, { model: model, error: error })) : (React.createElement(React.Fragment, null,
+        loading ? React.createElement(StatusMessage, { model: model, variant: "page" }) : null,
+        React.createElement("div", { style: { display: loading ? 'none' : undefined } },
+            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,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,aAAa,MAAM,oBAAqB,CAAA;AAC/C,OAAO,UAAU,MAAM,wBAAyB,CAAA;AAIhD,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,IAAI,EACJ,KAAK,EACL,UAAU,EACV,aAAa,EACb,cAAc,GACf,GAAG,KAAK,CAAA;IACT,MAAM,OAAO,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,IAAI,IAAI,CAAC,IAAI,CAAC,CAAA;IACzC,wEAAwE;IACxE,MAAM,OAAO,GAAG,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,aAAa,IAAI,cAAc,IAAI,SAAS,CAAC,CAAA;IAE1E,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,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAC,MAAM,GAAG,CAC/C,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACF,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CACZ,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CACtC,CAAC,CAAC,CAAC,CACF;QACG,OAAO,CAAC,CAAC,CAAC,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI;QAChE,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,EAAE;YACnD,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CACxB,CACL,CACJ,CACa,CACZ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/MSAViewer.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import type { MsaViewModel } from '../model.ts';
-import type { Cell, Clade, ColumnTrackSpec, Encoding, Highlight, Region, ResidueEncoding, ResidueMapping, RowPanelSpec, Viewport } from '../types.ts';
+import type { Cell, Clade, ColumnTrackSpec, Encoding, Highlight, Region, ResidueEncoding, ResidueMapping, RowPanelSpec, TreeOrder, TreeRoot, Viewport } from '../types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { ThemeOptions } from '@mui/material/styles';
 export interface MSAViewerProps {
@@ -62,6 +62,17 @@ export interface MSAViewerProps {
     autoTreeAreaWidth?: boolean;
     /** draw branch lengths (default true); false draws a cladogram */
     showBranchLen?: boolean;
+    /**
+     * the order each node's children draw in: `branchLength` (default,
+     * shortest first), `input` (as the file gives them), `ladderize` (fewest
+     * tips first) or `ladderizeReverse` (most tips first)
+     */
+    treeOrder?: TreeOrder;
+    /**
+     * reroot the tree: `midpoint`, or `{outgroup: [tip names]}` on the branch
+     * above those tips' common ancestor
+     */
+    treeRoot?: TreeRoot;
     /**
      * which channel `colorScheme` paints: `fill` (default) colors the background
      * of the cell a residue sits in, `color` colors the letter itself and leaves

package/dist/components/MSAViewer.js

@@ -53,7 +53,7 @@ function useModelReaction(model, key, handler) {
         }, { 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, }) {
+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, treeOrder, treeRoot, region, hideHeader, theme, onCellHover, onCellClick, onViewportChange, onModel, }) {
     const [model] = useState(() => MSAModelF().create({
         type: 'MsaView',
         ...(msa || tree || gff || rowData
@@ -88,6 +88,8 @@ function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle,
         ...(treeAreaWidth ? { treeAreaWidth } : {}),
         ...(autoTreeAreaWidth ? { autoTreeAreaWidth } : {}),
         ...(showBranchLen !== undefined ? { showBranchLen } : {}),
+        ...(treeOrder ? { treeOrder } : {}),
+        ...(treeRoot ? { treeRoot } : {}),
         ...(residueEncoding !== undefined
             ? { bgColor: residueEncoding === 'fill' }
             : {}),
@@ -141,6 +143,11 @@ function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle,
             model.setShowBranchLen(showBranchLen);
         }
     }, [model, showBranchLen]);
+    useEffect(() => {
+        if (treeOrder !== undefined) {
+            model.setTreeOrder(treeOrder);
+        }
+    }, [model, treeOrder]);
     useEffect(() => {
         if (residueEncoding !== undefined) {
             model.setBgColor(residueEncoding === 'fill');
@@ -159,6 +166,10 @@ function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle,
     useEffect(() => {
         model.setHighlights(JSON.parse(highlightsKey));
     }, [model, highlightsKey]);
+    const treeRootKey = JSON.stringify(treeRoot ?? null);
+    useEffect(() => {
+        model.setTreeRoot(JSON.parse(treeRootKey) ?? undefined);
+    }, [model, treeRootKey]);
     const cladesKey = JSON.stringify(clades ?? []);
     useEffect(() => {
         model.setClades(JSON.parse(cladesKey));

package/dist/components/MSAViewer.js.map

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package/dist/components/SequenceTextArea.d.ts

@@ -1,4 +1,15 @@
 import React from 'react';
+export declare const maxShownRecords = 100;
+export declare const maxShownChars = 200000;
+/**
+ * The first records of `rows` as FASTA, up to `maxShownRecords` records or
+ * `maxShownChars` characters, whichever comes first. A textarea holding every
+ * row of a large alignment freezes the page.
+ */
+export declare function fastaPreview(rows: [string, string][], showGaps: boolean): {
+    text: string;
+    hidden: number;
+};
 export default function SequenceTextArea({ str }: {
     str: [string, string][];
 }): React.JSX.Element;

package/dist/components/SequenceTextArea.js

@@ -1,7 +1,8 @@
 import React, { useState } from 'react';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { TextField } from '@mui/material';
+import { Button, TextField } from '@mui/material';
 import { getUngappedSequence } from 'msa-parsers';
+import { saveAs } from '../vendor/fileSaver.js';
 import Checkbox2 from './Checkbox2.js';
 import CopyButton from './CopyButton.js';
 const useStyles = makeStyles()(theme => ({
@@ -14,24 +15,55 @@ const useStyles = makeStyles()(theme => ({
         margin: 4,
     },
 }));
+export const maxShownRecords = 100;
+export const maxShownChars = 200_000;
+function fastaRecord([name, seq], showGaps) {
+    return `>${name}\n${showGaps ? seq : getUngappedSequence(seq)}`;
+}
+function isAllGaps(seq) {
+    return !/[^.-]/.test(seq);
+}
+/**
+ * The first records of `rows` as FASTA, up to `maxShownRecords` records or
+ * `maxShownChars` characters, whichever comes first. A textarea holding every
+ * row of a large alignment freezes the page.
+ */
+export function fastaPreview(rows, showGaps) {
+    const shown = [];
+    let chars = 0;
+    for (const row of rows) {
+        if (shown.length >= maxShownRecords || chars >= maxShownChars) {
+            break;
+        }
+        const record = fastaRecord(row, showGaps);
+        shown.push(record);
+        chars += record.length + 1;
+    }
+    return { text: shown.join('\n'), hidden: rows.length - shown.length };
+}
 export default function SequenceTextArea({ str }) {
     const { classes } = useStyles();
     const [showGaps, setShowGaps] = useState(false);
     const [showEmpty, setShowEmpty] = useState(false);
-    const disp = str
-        .map(([s1, s2]) => [s1, showGaps ? s2 : getUngappedSequence(s2)])
-        .filter(([, s2]) => showEmpty || !!s2)
-        .map(([s1, s2]) => `>${s1}\n${s2}`)
-        .join('\n');
+    const rows = showEmpty
+        ? str
+        : str.filter(([, seq]) => (showGaps ? !!seq : !isAllGaps(seq)));
+    const { text, hidden } = fastaPreview(rows, showGaps);
+    const fullText = () => rows.map(row => fastaRecord(row, showGaps)).join('\n');
     return (React.createElement(React.Fragment, null,
-        React.createElement(CopyButton, { text: disp }),
+        React.createElement(CopyButton, { text: fullText }),
+        React.createElement(Button, { onClick: () => {
+                saveAs(new Blob([fullText()], { type: 'text/plain' }), 'sequences.fasta');
+            } }, "Download"),
         React.createElement(Checkbox2, { label: "Show gaps", checked: showGaps, onChange: () => {
                 setShowGaps(!showGaps);
             } }),
         React.createElement(Checkbox2, { label: "Show empty", checked: showEmpty, onChange: () => {
                 setShowEmpty(!showEmpty);
             } }),
-        React.createElement(TextField, { variant: "outlined", multiline: true, className: classes.dialogContent, minRows: 5, maxRows: 10, fullWidth: true, value: disp, slotProps: {
+        React.createElement(TextField, { variant: "outlined", multiline: true, className: classes.dialogContent, minRows: 5, maxRows: 10, fullWidth: true, value: text, helperText: hidden > 0
+                ? `Showing ${rows.length - hidden} of ${rows.length.toLocaleString()} sequences. ${hidden.toLocaleString()} more are in the copy and the download.`
+                : undefined, slotProps: {
                 input: {
                     readOnly: true,
                     className: classes.textAreaFont,

package/dist/components/SequenceTextArea.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SequenceTextArea.js","sourceRoot":"","sources":["../../src/components/SequenceTextArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAA;AAEjD,OAAO,EAAE,MAAM,EAAE,MAAM,wBAAwB,CAAA;AAC/C,OAAO,SAAS,MAAM,gBAAiB,CAAA;AACvC,OAAO,UAAU,MAAM,iBAAkB,CAAA;AAEzC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;QACzB,QAAQ,EAAE,YAAY;KACvB;IACD,aAAa,EAAE;QACb,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,QAAQ;QACzC,MAAM,EAAE,CAAC;KACV;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,CAAC,MAAM,eAAe,GAAG,GAAG,CAAA;AAClC,MAAM,CAAC,MAAM,aAAa,GAAG,OAAO,CAAA;AAEpC,SAAS,WAAW,CAAC,CAAC,IAAI,EAAE,GAAG,CAAmB,EAAE,QAAiB;IACnE,OAAO,IAAI,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,mBAAmB,CAAC,GAAG,CAAC,EAAE,CAAA;AACjE,CAAC;AAED,SAAS,SAAS,CAAC,GAAW;IAC5B,OAAO,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;AAC3B,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,YAAY,CAAC,IAAwB,EAAE,QAAiB;IACtE,MAAM,KAAK,GAAa,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,IAAI,KAAK,CAAC,MAAM,IAAI,eAAe,IAAI,KAAK,IAAI,aAAa,EAAE,CAAC;YAC9D,MAAK;QACP,CAAC;QACD,MAAM,MAAM,GAAG,WAAW,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;QACzC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAClB,KAAK,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,CAAA;IAC5B,CAAC;IACD,OAAO,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;AACvE,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,gBAAgB,CAAC,EAAE,GAAG,EAA+B;IAC3E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC/C,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEjD,MAAM,IAAI,GAAG,SAAS;QACpB,CAAC,CAAC,GAAG;QACL,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;IACjE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,YAAY,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;IACrD,MAAM,QAAQ,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,WAAW,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;IAC7E,OAAO,CACL;QACE,oBAAC,UAAU,IAAC,IAAI,EAAE,QAAQ,GAAI;QAC9B,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;gBACZ,MAAM,CACJ,IAAI,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC,EAAE,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,EAC9C,iBAAiB,CAClB,CAAA;YACH,CAAC,eAGM;QACT,oBAAC,SAAS,IACR,KAAK,EAAC,WAAW,EACjB,OAAO,EAAE,QAAQ,EACjB,QAAQ,EAAE,GAAG,EAAE;gBACb,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;YACxB,CAAC,GACD;QACF,oBAAC,SAAS,IACR,KAAK,EAAC,YAAY,EAClB,OAAO,EAAE,SAAS,EAClB,QAAQ,EAAE,GAAG,EAAE;gBACb,YAAY,CAAC,CAAC,SAAS,CAAC,CAAA;YAC1B,CAAC,GACD;QACF,oBAAC,SAAS,IACR,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,SAAS,QACT,KAAK,EAAE,IAAI,EACX,UAAU,EACR,MAAM,GAAG,CAAC;gBACR,CAAC,CAAC,WAAW,IAAI,CAAC,MAAM,GAAG,MAAM,OAAO,IAAI,CAAC,MAAM,CAAC,cAAc,EAAE,eAAe,MAAM,CAAC,cAAc,EAAE,yCAAyC;gBACnJ,CAAC,CAAC,SAAS,EAEf,SAAS,EAAE;gBACT,KAAK,EAAE;oBACL,QAAQ,EAAE,IAAI;oBACd,SAAS,EAAE,OAAO,CAAC,YAAY;iBAChC;aACF,GACD,CACD,CACJ,CAAA;AACH,CAAC"}

package/dist/components/StatusMessage.d.ts

@@ -0,0 +1,12 @@
+import React from 'react';
+import type { MsaViewModel } from '../model.ts';
+/**
+ * The model's status line with its Cancel button: a spinner and a heading in
+ * place of the view while it loads, or a line in the header afterwards, which
+ * disappears when there is no status.
+ */
+declare const StatusMessage: ({ model, variant, }: {
+    model: MsaViewModel;
+    variant: 'page' | 'header';
+}) => React.JSX.Element | null;
+export default StatusMessage;

package/dist/components/StatusMessage.js

@@ -0,0 +1,43 @@
+import React from 'react';
+import { LoadingEllipses } from '@jbrowse/core/ui';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
+import { Button, CircularProgress, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+const useStyles = makeStyles()({
+    page: {
+        display: 'flex',
+        alignItems: 'center',
+        gap: 12,
+        padding: 20,
+    },
+    header: {
+        display: 'flex',
+        alignItems: 'center',
+        gap: 4,
+        margin: 'auto',
+        marginLeft: 10,
+    },
+});
+/**
+ * The model's status line with its Cancel button: a spinner and a heading in
+ * place of the view while it loads, or a line in the header afterwards, which
+ * disappears when there is no status.
+ */
+const StatusMessage = observer(function ({ model, variant, }) {
+    const { status } = model;
+    const { classes } = useStyles();
+    if (variant === 'header' && !status) {
+        return null;
+    }
+    const message = status?.msg ?? 'Loading...';
+    const onCancel = status?.onCancel;
+    return (React.createElement("div", { className: classes[variant] },
+        variant === 'page' ? (React.createElement(React.Fragment, null,
+            React.createElement(CircularProgress, { size: 24 }),
+            React.createElement(Typography, { variant: "h6" }, message))) : (React.createElement(LoadingEllipses, { message: message, component: "span" })),
+        onCancel ? (React.createElement(Button, { variant: variant === 'page' ? 'outlined' : 'text', size: "small", onClick: () => {
+                onCancel();
+            } }, "Cancel")) : null));
+});
+export default StatusMessage;
+//# sourceMappingURL=StatusMessage.js.map

package/dist/components/StatusMessage.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"StatusMessage.js","sourceRoot":"","sources":["../../src/components/StatusMessage.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,MAAM,EAAE,gBAAgB,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACpE,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,OAAO,EAAE,MAAM;QACf,UAAU,EAAE,QAAQ;QACpB,GAAG,EAAE,EAAE;QACP,OAAO,EAAE,EAAE;KACZ;IACD,MAAM,EAAE;QACN,OAAO,EAAE,MAAM;QACf,UAAU,EAAE,QAAQ;QACpB,GAAG,EAAE,CAAC;QACN,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF;;;;GAIG;AACH,MAAM,aAAa,GAAG,QAAQ,CAAC,UAAU,EACvC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,IAAI,OAAO,KAAK,QAAQ,IAAI,CAAC,MAAM,EAAE,CAAC;QACpC,OAAO,IAAI,CAAA;IACb,CAAC;IACD,MAAM,OAAO,GAAG,MAAM,EAAE,GAAG,IAAI,YAAY,CAAA;IAC3C,MAAM,QAAQ,GAAG,MAAM,EAAE,QAAQ,CAAA;IACjC,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,OAAO,CAAC;QAC7B,OAAO,KAAK,MAAM,CAAC,CAAC,CAAC,CACpB;YACE,oBAAC,gBAAgB,IAAC,IAAI,EAAE,EAAE,GAAI;YAC9B,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,IAAE,OAAO,CAAc,CAC9C,CACJ,CAAC,CAAC,CAAC,CACF,oBAAC,eAAe,IAAC,OAAO,EAAE,OAAO,EAAE,SAAS,EAAC,MAAM,GAAG,CACvD;QACA,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,MAAM,IACL,OAAO,EAAE,OAAO,KAAK,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,MAAM,EACjD,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,QAAQ,EAAE,CAAA;YACZ,CAAC,aAGM,CACV,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,aAAa,CAAA"}

package/dist/components/Track.js

@@ -80,7 +80,7 @@ const Track = observer(function ({ model, track, }) {
     }, [model]);
     useWheelScroll({ ref, onScrollX });
     const { classes } = useStyles();
-    const { hover, onMouseMove, onMouseLeave } = useTrackHover({
+    const { anchor, onMouseMove, onMouseLeave } = useTrackHover({
         model,
         tooltip: showColumnStats,
     });
@@ -95,8 +95,8 @@ const Track = observer(function ({ model, track, }) {
                 onMouseLeave();
             } },
             React.createElement(track.ReactComponent, { model: model, track: track }),
-            hover ? (React.createElement(BaseTooltip, { clientPoint: { x: hover.x, y: hover.y + 15 } },
-                React.createElement(TrackTooltipContent, { model: model, track: track, col: hover.col }))) : null)));
+            anchor ? (React.createElement(BaseTooltip, { clientPoint: anchor.clientPoint },
+                React.createElement(TrackTooltipContent, { model: model, track: track, col: anchor.value }))) : null)));
 });
 export default Track;
 //# sourceMappingURL=Track.js.map

package/dist/components/Track.js.map

@@ -1 +1 @@
-{"version":3,"file":"Track.js","sourceRoot":"","sources":["../../src/components/Track.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElE,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,iBAAiB,MAAM,mCAAmC,CAAA;AACjE,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC1D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AACrD,OAAO,mBAAmB,MAAM,iCAAkC,CAAA;AAClE,OAAO,EAAE,aAAa,EAAE,MAAM,2BAA2B,CAAA;AAKzD,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA+B,CAAC,CAAC,CAAA;AAE3E,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,MAAM,EAAE;QACN,OAAO,EAAE,CAAC;KACX;IACD,0EAA0E;IAC1E,2EAA2E;IAC3E,6EAA6E;IAC7E,4EAA4E;IAC5E,8DAA8D;IAC9D,GAAG,EAAE;QACH,OAAO,EAAE,MAAM;QACf,oBAAoB,EAAE;YACpB,SAAS,EAAE,kBAAkB,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE;SACrD;KACF;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,UAAU,GAAG,QAAQ,CAAC,SAAS,UAAU,CAAC,EAC9C,KAAK,EACL,KAAK,GAIN;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAqB,CAAA;IAC7D,MAAM,SAAS,GAAG,GAAG,EAAE;QACrB,WAAW,CAAC,SAAS,CAAC,CAAA;IACxB,CAAC,CAAA;IACD,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,aAAa,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC5D,MAAM,EACJ,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,GACxB,GAAG,KAAK,CAAA;IACT,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,gBAAgB,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IAEnD,OAAO,CAIL,6BACE,KAAK,EAAE;YACL,KAAK;YACL,MAAM;YACN,UAAU,EAAE,CAAC;YACb,OAAO,EAAE,MAAM;YACf,UAAU,EAAE,YAAY;YACxB,cAAc,EAAE,UAAU;YAC1B,GAAG,EAAE,CAAC;YACN,QAAQ,EAAE,gBAAgB;SAC3B;QAED,8BACE,KAAK,EAAE,IAAI,EACX,KAAK,EAAE;gBACL,QAAQ,EAAE,QAAQ;gBAClB,YAAY,EAAE,UAAU;gBACxB,UAAU,EAAE,QAAQ;aACrB,IAEA,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAClB;QACP,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,MAAM,gBACb,GAAG,IAAI,aAAa,EAChC,KAAK,EAAE;gBACL,KAAK,EAAE,gBAAgB;gBACvB,MAAM,EAAE,gBAAgB;gBACxB,UAAU,EAAE,CAAC;aACd,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,WAAW,CAAC,KAAK,CAAC,aAAa,CAAC,CAAA;YAClC,CAAC;YAED,oBAAC,iBAAiB,OAAG,CACV;QACZ,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,IAAI,IACH,QAAQ,EAAE,QAAQ,EAClB,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE;gBACZ,SAAS,EAAE,CAAA;YACb,CAAC;YAED,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;oBACjC,SAAS,EAAE,CAAA;gBACb,CAAC,iBAGQ;YACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,eAAe;wBACf,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE;qBAChC,CAAC,CAAA;oBACF,SAAS,EAAE,CAAA;gBACb,CAAC,eAGQ,CACN,CACR,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,MAAM,EAAE,iBAAiB,EAAE,cAAc,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,MAAM,EACJ,KAAK,EAAE,EAAE,MAAM,EAAE,GAClB,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,cAAc,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,CAAA;IAClC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,YAAY,EAAE,GAAG,aAAa,CAAC;QACzD,KAAK;QACL,OAAO,EAAE,eAAe;KACzB,CAAC,CAAA;IAEF,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE,MAAM,EAAE;QAC5C,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI;QAG1C,6BACE,KAAK,EAAE,EAAE,KAAK,EAAE,cAAc,GAAG,iBAAiB,EAAE,UAAU,EAAE,CAAC,EAAE,GACnE;QACF,6BACE,GAAG,EAAE,GAAG,iBACK,SAAS,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EACtC,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;oBAChB,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,OAAO,CAAC,CAAA;gBACjC,CAAC;YACH,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,YAAY,EAAE,CAAA;YAChB,CAAC;YAED,oBAAC,KAAK,CAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI;YACnD,KAAK,CAAC,CAAC,CAAC,CACP,oBAAC,WAAW,IAAC,WAAW,EAAE,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC,GAAG,EAAE,EAAE;gBACvD,oBAAC,mBAAmB,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,GAAI,CACvD,CACf,CAAC,CAAC,CAAC,IAAI,CACJ,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,KAAK,CAAA"}
+{"version":3,"file":"Track.js","sourceRoot":"","sources":["../../src/components/Track.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAElE,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,iBAAiB,MAAM,mCAAmC,CAAA;AACjE,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC1D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AACrD,OAAO,mBAAmB,MAAM,iCAAkC,CAAA;AAClE,OAAO,EAAE,aAAa,EAAE,MAAM,2BAA2B,CAAA;AAKzD,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA+B,CAAC,CAAC,CAAA;AAE3E,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,MAAM,EAAE;QACN,OAAO,EAAE,CAAC;KACX;IACD,0EAA0E;IAC1E,2EAA2E;IAC3E,6EAA6E;IAC7E,4EAA4E;IAC5E,8DAA8D;IAC9D,GAAG,EAAE;QACH,OAAO,EAAE,MAAM;QACf,oBAAoB,EAAE;YACpB,SAAS,EAAE,kBAAkB,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE;SACrD;KACF;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,UAAU,GAAG,QAAQ,CAAC,SAAS,UAAU,CAAC,EAC9C,KAAK,EACL,KAAK,GAIN;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAqB,CAAA;IAC7D,MAAM,SAAS,GAAG,GAAG,EAAE;QACrB,WAAW,CAAC,SAAS,CAAC,CAAA;IACxB,CAAC,CAAA;IACD,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,aAAa,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IAC5D,MAAM,EACJ,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,GACxB,GAAG,KAAK,CAAA;IACT,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,gBAAgB,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IAEnD,OAAO,CAIL,6BACE,KAAK,EAAE;YACL,KAAK;YACL,MAAM;YACN,UAAU,EAAE,CAAC;YACb,OAAO,EAAE,MAAM;YACf,UAAU,EAAE,YAAY;YACxB,cAAc,EAAE,UAAU;YAC1B,GAAG,EAAE,CAAC;YACN,QAAQ,EAAE,gBAAgB;SAC3B;QAED,8BACE,KAAK,EAAE,IAAI,EACX,KAAK,EAAE;gBACL,QAAQ,EAAE,QAAQ;gBAClB,YAAY,EAAE,UAAU;gBACxB,UAAU,EAAE,QAAQ;aACrB,IAEA,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAClB;QACP,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,MAAM,gBACb,GAAG,IAAI,aAAa,EAChC,KAAK,EAAE;gBACL,KAAK,EAAE,gBAAgB;gBACvB,MAAM,EAAE,gBAAgB;gBACxB,UAAU,EAAE,CAAC;aACd,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,WAAW,CAAC,KAAK,CAAC,aAAa,CAAC,CAAA;YAClC,CAAC;YAED,oBAAC,iBAAiB,OAAG,CACV;QACZ,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,IAAI,IACH,QAAQ,EAAE,QAAQ,EAClB,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE;gBACZ,SAAS,EAAE,CAAA;YACb,CAAC;YAED,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;oBACjC,SAAS,EAAE,CAAA;gBACb,CAAC,iBAGQ;YACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,eAAe;wBACf,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE;qBAChC,CAAC,CAAA;oBACF,SAAS,EAAE,CAAA;gBACb,CAAC,eAGQ,CACN,CACR,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,MAAM,EAAE,iBAAiB,EAAE,cAAc,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACpE,MAAM,EACJ,KAAK,EAAE,EAAE,MAAM,EAAE,GAClB,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,cAAc,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,CAAA;IAClC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,YAAY,EAAE,GAAG,aAAa,CAAC;QAC1D,KAAK;QACL,OAAO,EAAE,eAAe;KACzB,CAAC,CAAA;IAEF,OAAO,CACL,6BAAK,SAAS,EAAE,OAAO,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE,MAAM,EAAE;QAC5C,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI;QAG1C,6BACE,KAAK,EAAE,EAAE,KAAK,EAAE,cAAc,GAAG,iBAAiB,EAAE,UAAU,EAAE,CAAC,EAAE,GACnE;QACF,6BACE,GAAG,EAAE,GAAG,iBACK,SAAS,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EACtC,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;oBAChB,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,OAAO,CAAC,CAAA;gBACjC,CAAC;YACH,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,YAAY,EAAE,CAAA;YAChB,CAAC;YAED,oBAAC,KAAK,CAAC,cAAc,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI;YACnD,MAAM,CAAC,CAAC,CAAC,CACR,oBAAC,WAAW,IAAC,WAAW,EAAE,MAAM,CAAC,WAAW;gBAC1C,oBAAC,mBAAmB,IAClB,KAAK,EAAE,KAAK,EACZ,KAAK,EAAE,KAAK,EACZ,GAAG,EAAE,MAAM,CAAC,KAAK,GACjB,CACU,CACf,CAAC,CAAC,CAAC,IAAI,CACJ,CACF,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,KAAK,CAAA"}

package/dist/components/VerticalScrollbar.js

@@ -10,7 +10,12 @@ const VerticalScrollbar = observer(({ model }) => {
     const onDrag = useCallback((delta, startScroll) => {
         model.setScrollY(startScroll - delta / unit);
     }, [model, unit]);
-    return (React.createElement("div", { style: {
+    return (React.createElement("div", { onMouseDown: event => {
+            if (event.button === 0 && event.target === event.currentTarget) {
+                const y = event.clientY - event.currentTarget.getBoundingClientRect().top;
+                model.setScrollY(-y / unit + msaAreaHeight / 2);
+            }
+        }, style: {
             position: 'relative',
             width,
             height: msaAreaHeight,

package/dist/components/VerticalScrollbar.js.map

@@ -1 +1 @@
-{"version":3,"file":"VerticalScrollbar.js","sourceRoot":"","sources":["../../src/components/VerticalScrollbar.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,OAAO,CAAA;AAE1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,UAAU,MAAM,iBAAkB,CAAA;AAIzC,MAAM,KAAK,GAAG,EAAE,CAAA;AAEhB,MAAM,iBAAiB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACxE,MAAM,EAAE,aAAa,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACrD,MAAM,IAAI,GAAG,aAAa,GAAG,WAAW,CAAA;IACxC,MAAM,CAAC,GAAG,CAAC,OAAO,GAAG,IAAI,CAAA;IACzB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,GAAG,aAAa,CAAC,GAAG,IAAI,CAAA;IAE3C,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,KAAK,CAAC,UAAU,CAAC,WAAW,GAAG,KAAK,GAAG,IAAI,CAAC,CAAA;IAC9C,CAAC,EACD,CAAC,KAAK,EAAE,IAAI,CAAC,CACd,CAAA;IAED,OAAO,CACL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,KAAK;YACL,MAAM,EAAE,aAAa;YACrB,UAAU,EAAE,gBAAgB;YAC5B,SAAS,EAAE,gBAAgB;YAC3B,SAAS,EAAE,YAAY;SACxB;QAED,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,OAAO,EACf,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,OAAO,EAC7B,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;gBACL,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gBACnB,IAAI,EAAE,CAAC;gBACP,SAAS,EAAE,YAAY;gBACvB,KAAK;gBACL,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;aAC5B,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AACF,eAAe,iBAAiB,CAAA"}
+{"version":3,"file":"VerticalScrollbar.js","sourceRoot":"","sources":["../../src/components/VerticalScrollbar.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,OAAO,CAAA;AAE1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,UAAU,MAAM,iBAAkB,CAAA;AAIzC,MAAM,KAAK,GAAG,EAAE,CAAA;AAEhB,MAAM,iBAAiB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACxE,MAAM,EAAE,aAAa,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACrD,MAAM,IAAI,GAAG,aAAa,GAAG,WAAW,CAAA;IACxC,MAAM,CAAC,GAAG,CAAC,OAAO,GAAG,IAAI,CAAA;IACzB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,GAAG,aAAa,CAAC,GAAG,IAAI,CAAA;IAE3C,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,KAAK,CAAC,UAAU,CAAC,WAAW,GAAG,KAAK,GAAG,IAAI,CAAC,CAAA;IAC9C,CAAC,EACD,CAAC,KAAK,EAAE,IAAI,CAAC,CACd,CAAA;IAED,OAAO,CACL,6BACE,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,IAAI,KAAK,CAAC,MAAM,KAAK,KAAK,CAAC,aAAa,EAAE,CAAC;gBAC/D,MAAM,CAAC,GACL,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,aAAa,CAAC,qBAAqB,EAAE,CAAC,GAAG,CAAA;gBACjE,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,aAAa,GAAG,CAAC,CAAC,CAAA;YACjD,CAAC;QACH,CAAC,EACD,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,KAAK;YACL,MAAM,EAAE,aAAa;YACrB,UAAU,EAAE,gBAAgB;YAC5B,SAAS,EAAE,gBAAgB;YAC3B,SAAS,EAAE,YAAY;SACxB;QAED,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,OAAO,EACf,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,OAAO,EAC7B,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;gBACL,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;gBACnB,IAAI,EAAE,CAAC;gBACP,SAAS,EAAE,YAAY;gBACvB,KAAK;gBACL,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;aAC5B,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AACF,eAAe,iBAAiB,CAAA"}

package/dist/components/dialogs/ExportSVGDialog.d.ts

@@ -1,6 +1,7 @@
 import React from 'react';
 import type { MsaViewModel } from '../../model.ts';
-export default function ExportSVGDialog({ model, onClose, }: {
+declare const ExportSVGDialog: ({ model, onClose, }: {
     model: MsaViewModel;
     onClose: () => void;
-}): React.JSX.Element;
+}) => React.JSX.Element;
+export default ExportSVGDialog;

package/dist/components/dialogs/ExportSVGDialog.js

@@ -1,6 +1,7 @@
 import React, { useState } from 'react';
 import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
 import { Alert, Button, CircularProgress, DialogActions, DialogContent, FormControl, FormControlLabel, FormLabel, Radio, RadioGroup, Typography, useTheme, } from '@mui/material';
+import { observer } from 'mobx-react';
 import Checkbox2 from '../Checkbox2.js';
 // Run after the browser has painted. A requestAnimationFrame callback still
 // runs *before* the frame it was queued for, so one alone hands the main thread
@@ -11,7 +12,7 @@ function afterPaint(fn) {
         requestAnimationFrame(fn);
     });
 }
-export default function ExportSVGDialog({ model, onClose, }) {
+const ExportSVGDialog = observer(function ({ model, onClose, }) {
     const [includeMinimap, setIncludeMinimap] = useState(true);
     const [includeTracks, setIncludeTracks] = useState(true);
     const [exportType, setExportType] = useState('viewport');
@@ -92,5 +93,6 @@ export default function ExportSVGDialog({ model, onClose, }) {
             React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
                     onClose();
                 } }, "Cancel"))));
-}
+});
+export default ExportSVGDialog;
 //# sourceMappingURL=ExportSVGDialog.js.map