react-msaview 9.0.0 → 9.1.1

package/src/zoomSnapshot.ts

@@ -0,0 +1,80 @@
+import { calculateBlocks } from './calculateBlocks.ts'
+
+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
+}
+
+// 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: Viewport,
+  axis: 'x' | 'y',
+  scale: number,
+  marginFraction: number,
+) {
+  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: number[], have: number[]) =>
+  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: Viewport, withMargin: boolean) {
+  const m = withMargin ? margin : 0
+  return {
+    colWidth: view.colWidth,
+    rowHeight: view.rowHeight,
+    blocksX: blocksAt(view, 'x', 1, m),
+    blocksY: blocksAt(view, 'y', 1, m),
+  } satisfies ZoomSnapshot
+}
+
+export function zoomSnapshotScale(view: Viewport, snap: ZoomSnapshot) {
+  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: Viewport, snap: ZoomSnapshot) {
+  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)
+  )
+}

package/dist/components/header/ColorSchemeMenu.d.ts

@@ -1,12 +0,0 @@
-import React from 'react';
-import type { MsaViewModel } from '../../model.ts';
-export declare function colorSchemeMenuItems(model: MsaViewModel): {
-    readonly label: string;
-    readonly type: 'radio';
-    readonly checked: boolean;
-    readonly onClick: () => void;
-}[];
-declare const ColorSchemeMenu: ({ model }: {
-    model: MsaViewModel;
-}) => React.JSX.Element;
-export default ColorSchemeMenu;

package/dist/components/header/ColorSchemeMenu.js

@@ -1,37 +0,0 @@
-import React from 'react';
-import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-import Palette from '@mui/icons-material/Palette';
-import { observer } from 'mobx-react';
-import colorSchemes from '../../colorSchemes.js';
-// While a `customColorScheme` map is set, a checked Custom entry stands for it
-// and no named scheme is checked. Picking a named scheme clears the map.
-export function colorSchemeMenuItems(model) {
-    const { colorSchemeName, customColorScheme } = model;
-    const custom = customColorScheme
-        ? [
-            {
-                label: 'Custom',
-                type: 'radio',
-                checked: true,
-                onClick: () => { },
-            },
-        ]
-        : [];
-    return [
-        ...custom,
-        ...Object.keys(colorSchemes).map(option => ({
-            label: option,
-            type: 'radio',
-            checked: !customColorScheme && colorSchemeName === option,
-            onClick: () => {
-                model.setColorSchemeName(option);
-            },
-        })),
-    ];
-}
-const ColorSchemeMenu = observer(function ({ model }) {
-    return (React.createElement(CascadingMenuButton, { "data-testid": "color_scheme_menu", tooltip: "Color scheme", closeAfterItemClick: true, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: colorSchemeMenuItems(model) },
-        React.createElement(Palette, null)));
-});
-export default ColorSchemeMenu;
-//# sourceMappingURL=ColorSchemeMenu.js.map

package/dist/components/header/ColorSchemeMenu.js.map

@@ -1 +0,0 @@
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package/dist/components/header/FileMenu.js

@@ -1,66 +0,0 @@
-import React, { lazy } from 'react';
-import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-import AccountTree from '@mui/icons-material/AccountTree';
-import Assignment from '@mui/icons-material/Assignment';
-import FolderOpen from '@mui/icons-material/FolderOpen';
-import Menu from '@mui/icons-material/Menu';
-import PhotoCamera from '@mui/icons-material/PhotoCamera';
-import { observer } from 'mobx-react';
-import { getAnnotationsMenu } from './getAnnotationsMenu.js';
-const MetadataDialog = lazy(() => import('../dialogs/MetadataDialog.js'));
-const ExportSVGDialog = lazy(() => import('../dialogs/ExportSVGDialog.js'));
-const FileMenu = observer(({ model }) => {
-    return (React.createElement(CascadingMenuButton, { "data-testid": "file_menu", tooltip: "File", menuItems: [
-            {
-                label: 'Return to import form',
-                icon: FolderOpen,
-                onClick: () => {
-                    model.reset();
-                },
-            },
-            {
-                label: 'Metadata',
-                icon: Assignment,
-                onClick: () => {
-                    model.queueDialog(onClose => [
-                        MetadataDialog,
-                        {
-                            model,
-                            onClose,
-                        },
-                    ]);
-                },
-            },
-            {
-                label: 'Annotations',
-                type: 'subMenu',
-                subMenu: getAnnotationsMenu({
-                    model,
-                }),
-            },
-            {
-                label: 'Export tree (Newick)',
-                icon: AccountTree,
-                disabled: !!model.tree.noTree,
-                onClick: () => {
-                    model.exportNewick();
-                },
-            },
-            {
-                label: 'Export SVG',
-                icon: PhotoCamera,
-                onClick: () => {
-                    model.queueDialog(onClose => [
-                        ExportSVGDialog,
-                        {
-                            onClose,
-                            model,
-                        },
-                    ]);
-                },
-            },
-        ], anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' } },
-        React.createElement(Menu, null)));
-});
-export default FileMenu;
-//# sourceMappingURL=FileMenu.js.map

package/dist/components/header/FileMenu.js.map

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package/dist/components/header/GappynessSlider.js.map

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package/dist/components/header/GoToBox.js

@@ -1,31 +0,0 @@
-import React, { useState } from 'react';
-import { Autocomplete, TextField } from '@mui/material';
-import { observer } from 'mobx-react';
-import { findableRowNames, goTo, rowNameSuggestions } from './goTo.js';
-const label = 'Go to row or column';
-// MUI 9 hands renderInput `slotProps`; MUI 7, which every released JBrowse host
-// serves, hands it `inputProps` and no `slotProps` at all
-export function labelledInput(params) {
-    const { slotProps, inputProps } = params;
-    return slotProps
-        ? {
-            slotProps: {
-                ...slotProps,
-                htmlInput: { ...slotProps.htmlInput, 'aria-label': label },
-            },
-        }
-        : { inputProps: { ...inputProps, 'aria-label': label } };
-}
-const GoToBox = observer(function ({ model }) {
-    const [missed, setMissed] = useState(false);
-    const names = findableRowNames(model);
-    return names.length > 1 || model.numColumns > 0 ? (React.createElement(Autocomplete, { freeSolo: true, size: "small", options: names, filterOptions: (options, { inputValue }) => rowNameSuggestions(options, inputValue), value: null, blurOnSelect: true, onInputChange: () => {
-            setMissed(false);
-        }, onChange: (_, text) => {
-            if (text) {
-                setMissed(!goTo(model, text));
-            }
-        }, style: { width: 180, margin: 'auto 8px' }, renderInput: params => (React.createElement(TextField, { ...params, error: missed, placeholder: label, title: "A row name, a column number, or name:residue", ...labelledInput(params) })) })) : null;
-});
-export default GoToBox;
-//# sourceMappingURL=GoToBox.js.map

package/dist/components/header/GoToBox.js.map

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package/dist/components/header/MSASettingsMenu.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import type { MsaViewModel } from '../../model.ts';
-declare const MSASettingsMenu: ({ model }: {
-    model: MsaViewModel;
-}) => React.JSX.Element;
-export default MSASettingsMenu;

package/dist/components/header/MSASettingsMenu.js

@@ -1,11 +0,0 @@
-import React from 'react';
-import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-import Tune from '@mui/icons-material/Tune';
-import { observer } from 'mobx-react';
-import { msaSettingsMenuItems } from './settingsMenuItems.js';
-const MSASettingsMenu = observer(function ({ model }) {
-    return (React.createElement(CascadingMenuButton, { "data-testid": "msa_settings_menu", tooltip: "Alignment settings", closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: msaSettingsMenuItems(model) },
-        React.createElement(Tune, null)));
-});
-export default MSASettingsMenu;
-//# sourceMappingURL=MSASettingsMenu.js.map

package/dist/components/header/MSASettingsMenu.js.map

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package/dist/components/header/ScrollZoomIcons.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import type { SvgIconProps } from '@mui/material/SvgIcon';
-export declare function MouseScroll(props: SvgIconProps): React.JSX.Element;
-export declare function MouseZoomBoth(props: SvgIconProps): React.JSX.Element;
-export declare function MouseZoomHorizontal(props: SvgIconProps): React.JSX.Element;
-export declare function MouseZoomVertical(props: SvgIconProps): React.JSX.Element;

package/dist/components/header/ScrollZoomIcons.js

@@ -1,35 +0,0 @@
-import React from 'react';
-import SvgIcon from '@mui/material/SvgIcon';
-// Mouse glyphs with outward arrows on the axes a wheel zoom scales.
-// @mui/icons-material ships only the plain `Mouse`, and three variants that
-// differ only in their arrows have to share one body to stay apart at 24px.
-// The body's inner subpath runs the opposite sweep, which punches the hole the
-// wheel bar sits in.
-const BODY = 'M12 5a4 4 0 0 0-4 4v6a4 4 0 0 0 8 0V9a4 4 0 0 0-4-4zm0 2a2 2 0 0 1 2 2v6a2 2 0 0 1-4 0V9a2 2 0 0 1 2-2z';
-const WHEEL = 'M11.2 8.6h1.6v3.2h-1.6z';
-const LEFT = 'M.4 12 5 15V9z';
-const RIGHT = 'M23.6 12 19 9v6z';
-const UP = 'M12 .4 15 4H9z';
-const DOWN = 'M12 23.6 9 20h6z';
-function MouseZoom({ arrows, ...rest }) {
-    return (React.createElement(SvgIcon, { ...rest },
-        React.createElement("path", { d: BODY }),
-        React.createElement("path", { d: WHEEL }),
-        arrows.map(d => (React.createElement("path", { key: d, d: d })))));
-}
-// the bare body, for a wheel that scrolls. @mui/icons-material's own `Mouse` is
-// a solid silhouette, which would jump to a different drawing when the menu
-// changes the mode.
-export function MouseScroll(props) {
-    return React.createElement(MouseZoom, { ...props, arrows: [] });
-}
-export function MouseZoomBoth(props) {
-    return React.createElement(MouseZoom, { ...props, arrows: [LEFT, RIGHT, UP, DOWN] });
-}
-export function MouseZoomHorizontal(props) {
-    return React.createElement(MouseZoom, { ...props, arrows: [LEFT, RIGHT] });
-}
-export function MouseZoomVertical(props) {
-    return React.createElement(MouseZoom, { ...props, arrows: [UP, DOWN] });
-}
-//# sourceMappingURL=ScrollZoomIcons.js.map

package/dist/components/header/ScrollZoomIcons.js.map

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package/dist/components/header/TreeSettingsMenu.js

@@ -1,42 +0,0 @@
-import React from 'react';
-import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-import AccountTree from '@mui/icons-material/AccountTree';
-import { observer } from 'mobx-react';
-import { maxNeighborJoiningRows } from '../../constants.js';
-import { treeSettingsMenuItems } from './settingsMenuItems.js';
-const TreeSettingsMenu = observer(function ({ model, }) {
-    const { rows } = model;
-    const tooManyRows = rows.length > maxNeighborJoiningRows;
-    return (React.createElement(CascadingMenuButton, { "data-testid": "tree_settings_menu", tooltip: "Tree settings", closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: [
-            ...treeSettingsMenuItems(model),
-            ...(rows.length >= 2
-                ? [
-                    {
-                        label: 'Advanced',
-                        type: 'subMenu',
-                        subMenu: [
-                            {
-                                // the label shows the cap before a click would freeze the tab
-                                label: tooManyRows
-                                    ? `Calculate neighbor joining tree (over ${maxNeighborJoiningRows} rows, use FastTree)`
-                                    : 'Calculate neighbor joining tree (BLOSUM62)',
-                                disabled: tooManyRows,
-                                onClick: () => {
-                                    try {
-                                        model.calculateNeighborJoiningTreeFromMSA();
-                                    }
-                                    catch (e) {
-                                        console.error('Failed to calculate NJ tree:', e);
-                                        model.setError(e);
-                                    }
-                                },
-                            },
-                        ],
-                    },
-                ]
-                : []),
-        ] },
-        React.createElement(AccountTree, null)));
-});
-export default TreeSettingsMenu;
-//# sourceMappingURL=TreeSettingsMenu.js.map

package/dist/components/header/TreeSettingsMenu.js.map

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package/dist/components/header/ZoomMenu.js

@@ -1,37 +0,0 @@
-import React from 'react';
-import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-import MoreVert from '@mui/icons-material/MoreVert';
-import RestartAlt from '@mui/icons-material/RestartAlt';
-import { observer } from 'mobx-react';
-const ZoomMenu = observer(function ({ model }) {
-    return (React.createElement(CascadingMenuButton, { tooltip: "Fit / zoom options", menuItems: [
-            {
-                label: 'Fit both vertically/horizontally',
-                onClick: () => {
-                    model.fit();
-                },
-            },
-            {
-                label: 'Fit vertically',
-                onClick: () => {
-                    model.fitVertically();
-                },
-            },
-            {
-                label: 'Fit horizontally',
-                onClick: () => {
-                    model.fitHorizontally();
-                },
-            },
-            {
-                label: 'Reset zoom to default',
-                icon: RestartAlt,
-                onClick: () => {
-                    model.resetZoom();
-                },
-            },
-        ] },
-        React.createElement(MoreVert, null)));
-});
-export default ZoomMenu;
-//# sourceMappingURL=ZoomMenu.js.map

package/dist/components/header/ZoomMenu.js.map

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package/dist/components/header/goTo.d.ts

@@ -1,20 +0,0 @@
-import type { MsaViewModel } from '../../model.ts';
-export declare function findableRowNames(model: MsaViewModel): string[];
-export declare function rowNameSuggestions(names: string[], input: string, limit?: number): string[];
-/**
- * The visible row and column a "Go to" entry names: a row by its name, the
- * column the ruler numbers N, or residue N of a row written `name:N`. A name
- * is tried whole first, so a row called `chr1:100` stays reachable.
- */
-export declare function resolveGoTo(model: MsaViewModel, text: string): {
-    row: number;
-    col?: undefined;
-} | {
-    row: number | undefined;
-    col: number;
-} | {
-    row?: undefined;
-    col: number;
-} | undefined;
-/** centers the view on the entry's target and lights it; false if none */
-export declare function goTo(model: MsaViewModel, text: string): boolean;

package/dist/components/header/goTo.js.map

@@ -1 +0,0 @@
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package/dist/components/header/settingsMenuItems.d.ts

@@ -1,4 +0,0 @@
-import type { MsaViewModel } from '../../model.ts';
-import type { MenuItem } from '@jbrowse/core/ui/Menu';
-export declare function msaSettingsMenuItems(model: MsaViewModel): MenuItem[];
-export declare function treeSettingsMenuItems(model: MsaViewModel): MenuItem[];

package/dist/components/header/settingsMenuItems.js

@@ -1,127 +0,0 @@
-import { treeOrders } from '../../constants.js';
-function radio(label, checked, onClick) {
-    return { label, type: 'radio', checked, onClick };
-}
-const treeOrderLabels = {
-    branchLength: 'By branch length',
-    input: 'As written',
-    ladderize: 'Ladderize, small clades first',
-    ladderizeReverse: 'Ladderize, large clades first',
-};
-function outgroupLabel(outgroup) {
-    const [first, ...rest] = outgroup;
-    return rest.length === 0
-        ? `Outgroup ${first}`
-        : `Outgroup ${first} … ${rest.at(-1)}`;
-}
-function toggle(label, checked, set) {
-    return {
-        label,
-        type: 'checkbox',
-        checked,
-        onClick: () => {
-            set(!checked);
-        },
-    };
-}
-// the only place in the UI to turn a hidden track back on
-function tracksSubMenu(model) {
-    const shown = new Set(model.turnedOnTracks.map(t => t.model.id));
-    return model.tracks.map(({ model: { id, name } }) => toggle(name, shown.has(id), () => {
-        model.toggleTrack(id);
-    }));
-}
-export function msaSettingsMenuItems(model) {
-    const { drawMsaLetters, hideGaps, bgColor, showColumnStats } = model;
-    return [
-        {
-            label: 'Tracks',
-            type: 'subMenu',
-            subMenu: tracksSubMenu(model),
-        },
-        { type: 'divider' },
-        toggle('Show track values on hover', showColumnStats, arg => {
-            model.setShowColumnStats(arg);
-        }),
-        toggle('Draw letters', drawMsaLetters, arg => {
-            model.setDrawMsaLetters(arg);
-        }),
-        // inverted: bgColor colors the tile, and off colors the letter
-        toggle('Color letters, not cells', !bgColor, arg => {
-            model.setBgColor(!arg);
-        }),
-        toggle('Hide gappy columns', hideGaps, arg => {
-            model.setHideGaps(arg);
-        }),
-    ];
-}
-export function treeSettingsMenuItems(model) {
-    const { drawTree, showBranchLen, labelsAlignRight, drawNodeBubbles, drawNodeLabels, drawLabels, treeAreaWidth, showTreeOverview, treeOrder, treeRoot, rotated, } = model;
-    return [
-        {
-            label: 'Order',
-            type: 'subMenu',
-            subMenu: [
-                ...treeOrders.map(order => radio(treeOrderLabels[order], treeOrder === order, () => {
-                    model.setTreeOrder(order);
-                })),
-                { type: 'divider' },
-                {
-                    label: 'Undo rotations',
-                    disabled: rotated.length === 0,
-                    onClick: () => {
-                        model.clearRotated();
-                    },
-                },
-            ],
-        },
-        {
-            label: 'Root',
-            type: 'subMenu',
-            subMenu: [
-                radio('As written', treeRoot === undefined, () => {
-                    model.setTreeRoot(undefined);
-                }),
-                radio('Midpoint', treeRoot === 'midpoint', () => {
-                    model.setTreeRoot('midpoint');
-                }),
-                // "Reroot here" in a node's menu sets the outgroup, so this only
-                // reports it
-                ...(typeof treeRoot === 'object'
-                    ? [
-                        {
-                            ...radio(outgroupLabel(treeRoot.outgroup), true, () => { }),
-                            disabled: true,
-                        },
-                    ]
-                    : []),
-            ],
-        },
-        { type: 'divider' },
-        toggle('Show branch length', showBranchLen, arg => {
-            model.setShowBranchLen(arg);
-        }),
-        toggle('Show tree', drawTree, arg => {
-            model.setDrawTree(arg);
-        }),
-        toggle('Draw bubbles on tree branches', drawNodeBubbles, arg => {
-            model.setDrawNodeBubbles(arg);
-        }),
-        toggle('Draw internal node labels', drawNodeLabels, arg => {
-            model.setDrawNodeLabels(arg);
-        }),
-        toggle('Show tree overview', showTreeOverview, arg => {
-            model.setShowTreeOverview(arg);
-        }),
-        toggle('Tree labels align right', labelsAlignRight, arg => {
-            model.setLabelsAlignRight(arg);
-        }),
-        toggle('Draw labels', drawLabels, arg => {
-            model.setDrawLabels(arg);
-        }),
-        toggle('Fit tree area to labels and tree', treeAreaWidth === undefined, arg => {
-            model.setTreeAreaWidth(arg ? undefined : model.effectiveTreeAreaWidth);
-        }),
-    ];
-}
-//# sourceMappingURL=settingsMenuItems.js.map

package/dist/components/header/settingsMenuItems.js.map

@@ -1 +0,0 @@
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package/src/components/header/ColorSchemeMenu.tsx

@@ -1,56 +0,0 @@
-import React from 'react'
-
-import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton'
-import Palette from '@mui/icons-material/Palette'
-import { observer } from 'mobx-react'
-
-import colorSchemes from '../../colorSchemes.ts'
-
-import type { MsaViewModel } from '../../model.ts'
-
-// While a `customColorScheme` map is set, a checked Custom entry stands for it
-// and no named scheme is checked. Picking a named scheme clears the map.
-export function colorSchemeMenuItems(model: MsaViewModel) {
-  const { colorSchemeName, customColorScheme } = model
-  const custom = customColorScheme
-    ? [
-        {
-          label: 'Custom',
-          type: 'radio',
-          checked: true,
-          onClick: () => {},
-        } as const,
-      ]
-    : []
-  return [
-    ...custom,
-    ...Object.keys(colorSchemes).map(
-      option =>
-        ({
-          label: option,
-          type: 'radio',
-          checked: !customColorScheme && colorSchemeName === option,
-          onClick: () => {
-            model.setColorSchemeName(option)
-          },
-        }) as const,
-    ),
-  ]
-}
-
-const ColorSchemeMenu = observer(function ({ model }: { model: MsaViewModel }) {
-  return (
-    <CascadingMenuButton
-      data-testid="color_scheme_menu"
-      tooltip="Color scheme"
-      closeAfterItemClick
-      anchorOrigin={{ vertical: 'bottom', horizontal: 'left' }}
-      transformOrigin={{ vertical: 'top', horizontal: 'left' }}
-      menuItems={colorSchemeMenuItems(model)}
-    >
-      <Palette />
-    </CascadingMenuButton>
-  )
-})
-
-export default ColorSchemeMenu