react-msaview 9.1.0 → 9.2.0

package/dist/components/settings/MenuItemsForm.js

@@ -0,0 +1,80 @@
+import React, { useState } from 'react';
+import ArrowDropDown from '@mui/icons-material/ArrowDropDown';
+import ArrowRight from '@mui/icons-material/ArrowRight';
+import { Box, Button, Checkbox, FormControlLabel, MenuItem as MuiMenuItem, Radio, TextField, ToggleButton, ToggleButtonGroup, Typography, } from '@mui/material';
+function radios(items) {
+    return items.filter((i) => 'type' in i && i.type === 'radio');
+}
+function Caption({ children }) {
+    return (React.createElement(Typography, { variant: "caption", color: "text.secondary", sx: { mt: 1, display: 'block' } }, children));
+}
+function Segmented({ label, options, }) {
+    const value = options.findIndex(o => o.checked);
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Caption, null, label),
+        React.createElement(ToggleButtonGroup, { exclusive: true, fullWidth: true, size: "small", value: value, "aria-label": label, onChange: (_event, i) => {
+                if (i !== null) {
+                    options[i]?.onClick();
+                }
+            } }, options.map((o, i) => (React.createElement(ToggleButton, { key: String(o.label), value: i, disabled: o.disabled, title: o.helpText, sx: { textTransform: 'none', py: 0.25 } }, o.label))))));
+}
+// each option fires its own onClick, so picking the checked one again still
+// runs, which reopens a dialog like the custom gap threshold
+function Select({ label, options, }) {
+    const value = options.findIndex(o => o.checked);
+    return (React.createElement(TextField, { select: true, size: "small", fullWidth: true, label: label, value: value === -1 ? '' : value, sx: { mt: 1.5, '& .MuiInputBase-root': { typography: 'body2' } } }, options.map((o, i) => (React.createElement(MuiMenuItem, { key: String(o.label), value: i, disabled: o.disabled, dense: true, onClick: () => {
+            o.onClick();
+        } }, o.label)))));
+}
+// a short submenu opens in place under a caption, where every choice shows at
+// once; a long one, like the extra color schemes, folds behind a toggle
+const inlineUpTo = 8;
+function SubSection({ item }) {
+    const [open, setOpen] = useState(false);
+    if (!('subMenu' in item) || !Array.isArray(item.subMenu)) {
+        return null;
+    }
+    const label = String(item.label);
+    const display = 'display' in item ? item.display : undefined;
+    if (display) {
+        const options = radios(item.subMenu);
+        const rest = item.subMenu.filter(i => !options.includes(i));
+        const Control = display === 'segmented' ? Segmented : Select;
+        return (React.createElement(React.Fragment, null,
+            React.createElement(Control, { label: label, options: options }),
+            React.createElement(MenuItemsForm, { items: rest })));
+    }
+    if (item.subMenu.length <= inlineUpTo) {
+        return (React.createElement(React.Fragment, null,
+            React.createElement(Caption, null, label),
+            React.createElement(MenuItemsForm, { items: item.subMenu })));
+    }
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Button, { size: "small", color: "inherit", startIcon: open ? React.createElement(ArrowDropDown, null) : React.createElement(ArrowRight, null), onClick: () => {
+                setOpen(!open);
+            }, sx: { textTransform: 'none', justifyContent: 'flex-start', px: 0.5 } }, label),
+        open ? (React.createElement(Box, { sx: { pl: 2 } },
+            React.createElement(MenuItemsForm, { items: item.subMenu }))) : null));
+}
+export default function MenuItemsForm({ items }) {
+    return (React.createElement(Box, { sx: { display: 'flex', flexDirection: 'column' } }, items.map((item, i) => {
+        const key = 'label' in item ? String(item.label) : String(i);
+        if (!('label' in item)) {
+            return null;
+        }
+        if ('type' in item && item.type === 'subHeader') {
+            return React.createElement(Caption, { key: key }, item.label);
+        }
+        if ('subMenu' in item) {
+            return React.createElement(SubSection, { key: key, item: item });
+        }
+        const onClick = 'onClick' in item ? item.onClick : undefined;
+        if ('type' in item &&
+            (item.type === 'checkbox' || item.type === 'radio')) {
+            const Control = item.type === 'checkbox' ? Checkbox : Radio;
+            return (React.createElement(FormControlLabel, { key: key, disabled: item.disabled, control: React.createElement(Control, { size: "small", checked: item.checked, onChange: () => onClick?.(), sx: { py: 0.25 } }), label: item.label, slotProps: { typography: { variant: 'body2' } } }));
+        }
+        return (React.createElement(Button, { key: key, size: "small", disabled: item.disabled, onClick: () => onClick?.(), sx: { alignSelf: 'flex-start', textTransform: 'none' } }, item.label));
+    })));
+}
+//# sourceMappingURL=MenuItemsForm.js.map

package/dist/components/settings/MenuItemsForm.js.map

@@ -0,0 +1 @@
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package/dist/components/settings/SettingsPanel.d.ts

@@ -0,0 +1,12 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+/**
+ * The settings whose effect the user watches as they change them, docked to
+ * the right of the alignment so nothing it opens covers the tree or the rows.
+ * Each section folds, and the browser remembers which ones the user folded.
+ */
+declare const SettingsPanel: ({ model, height, }: {
+    model: MsaViewModel;
+    height: number;
+}) => React.JSX.Element;
+export default SettingsPanel;

package/dist/components/settings/SettingsPanel.js

@@ -0,0 +1,92 @@
+import React, { useState } from 'react';
+import ArrowDropDown from '@mui/icons-material/ArrowDropDown';
+import ArrowRight from '@mui/icons-material/ArrowRight';
+import Close from '@mui/icons-material/Close';
+import { Box, ButtonBase, IconButton, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import { settingsPanelWidth } from '../../constants.js';
+import { annotationsSubMenu } from '../header/getAnnotationsMenu.js';
+import { alignmentSettingsItems, colorSettingsItems, gapsSubMenu, trackSettingsItems, treeSubMenu, } from '../header/menuBarItems.js';
+import MenuItemsForm from './MenuItemsForm.js';
+import TrackList from './TrackList.js';
+const collapsedKey = 'msaview-settings-collapsed';
+function readCollapsed() {
+    try {
+        const parsed = JSON.parse(localStorage.getItem(collapsedKey) ?? '[]');
+        return new Set(Array.isArray(parsed) ? parsed.map(String) : []);
+    }
+    catch {
+        return new Set();
+    }
+}
+function writeCollapsed(collapsed) {
+    try {
+        localStorage.setItem(collapsedKey, JSON.stringify([...collapsed]));
+    }
+    catch { }
+}
+function Section({ title, collapsed, onToggle, children, }) {
+    const Arrow = collapsed ? ArrowRight : ArrowDropDown;
+    return (React.createElement(Box, { sx: { px: 1.5, py: 1, borderBottom: 1, borderColor: 'divider' } },
+        React.createElement(ButtonBase, { "aria-expanded": !collapsed, onClick: onToggle, sx: { width: '100%', justifyContent: 'flex-start', ml: -0.75 } },
+            React.createElement(Arrow, { fontSize: "small", color: "action" }),
+            React.createElement(Typography, { variant: "overline", color: "text.secondary" }, title)),
+        collapsed ? null : children));
+}
+/**
+ * The settings whose effect the user watches as they change them, docked to
+ * the right of the alignment so nothing it opens covers the tree or the rows.
+ * Each section folds, and the browser remembers which ones the user folded.
+ */
+const SettingsPanel = observer(function ({ model, height, }) {
+    const { noTree, noDomains } = model;
+    const [collapsed, setCollapsed] = useState(readCollapsed);
+    const section = (title) => ({
+        title,
+        collapsed: collapsed.has(title),
+        onToggle: () => {
+            const next = new Set(collapsed);
+            if (!next.delete(title)) {
+                next.add(title);
+            }
+            writeCollapsed(next);
+            setCollapsed(next);
+        },
+    });
+    return (React.createElement(Box, { "data-testid": "settings_panel", sx: {
+            width: settingsPanelWidth,
+            height,
+            flexShrink: 0,
+            overflowY: 'auto',
+            borderLeft: 1,
+            borderColor: 'divider',
+            bgcolor: 'background.paper',
+        } },
+        React.createElement(Box, { sx: {
+                display: 'flex',
+                alignItems: 'center',
+                justifyContent: 'space-between',
+                px: 1.5,
+                pt: 0.5,
+            } },
+            React.createElement(Typography, { variant: "subtitle1" }, "Settings"),
+            React.createElement(IconButton, { "aria-label": "Close settings", onClick: () => {
+                    model.setSettingsOpen(false);
+                } },
+                React.createElement(Close, { fontSize: "small" }))),
+        React.createElement(Section, { ...section('Color') },
+            React.createElement(MenuItemsForm, { items: colorSettingsItems(model) })),
+        noTree ? null : (React.createElement(Section, { ...section('Tree') },
+            React.createElement(MenuItemsForm, { items: treeSubMenu(model) }))),
+        React.createElement(Section, { ...section('Alignment') },
+            React.createElement(MenuItemsForm, { items: alignmentSettingsItems(model) }),
+            React.createElement(MenuItemsForm, { items: gapsSubMenu(model) })),
+        noDomains ? null : (React.createElement(Section, { ...section('Annotations') },
+            React.createElement(MenuItemsForm, { items: annotationsSubMenu(model) }))),
+        React.createElement(Section, { ...section('Tracks') },
+            React.createElement(TrackList, { model: model }),
+            React.createElement(Box, { sx: { mt: 1, pt: 0.5, borderTop: 1, borderColor: 'divider' } },
+                React.createElement(MenuItemsForm, { items: trackSettingsItems(model) })))));
+});
+export default SettingsPanel;
+//# sourceMappingURL=SettingsPanel.js.map

package/dist/components/settings/SettingsPanel.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"SettingsPanel.js","sourceRoot":"","sources":["../../../src/components/settings/SettingsPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,aAAa,MAAM,mCAAmC,CAAA;AAC7D,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,KAAK,MAAM,2BAA2B,CAAA;AAC7C,OAAO,EAAE,GAAG,EAAE,UAAU,EAAE,UAAU,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACvE,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAA;AACvD,OAAO,EAAE,kBAAkB,EAAE,MAAM,iCAAiC,CAAA;AACpE,OAAO,EACL,sBAAsB,EACtB,kBAAkB,EAClB,WAAW,EACX,kBAAkB,EAClB,WAAW,GACZ,MAAM,2BAA2B,CAAA;AAClC,OAAO,aAAa,MAAM,oBAAqB,CAAA;AAC/C,OAAO,SAAS,MAAM,gBAAiB,CAAA;AAIvC,MAAM,YAAY,GAAG,4BAA4B,CAAA;AAEjD,SAAS,aAAa;IACpB,IAAI,CAAC;QACH,MAAM,MAAM,GAAY,IAAI,CAAC,KAAK,CAChC,YAAY,CAAC,OAAO,CAAC,YAAY,CAAC,IAAI,IAAI,CAC3C,CAAA;QACD,OAAO,IAAI,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;IACjE,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,GAAG,EAAU,CAAA;IAC1B,CAAC;AACH,CAAC;AAED,SAAS,cAAc,CAAC,SAAsB;IAC5C,IAAI,CAAC;QACH,YAAY,CAAC,OAAO,CAAC,YAAY,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,CAAA;IACpE,CAAC;IAAC,MAAM,CAAC,CAAA,CAAC;AACZ,CAAC;AAED,SAAS,OAAO,CAAC,EACf,KAAK,EACL,SAAS,EACT,QAAQ,EACR,QAAQ,GAMT;IACC,MAAM,KAAK,GAAG,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,aAAa,CAAA;IACpD,OAAO,CACL,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC,EAAE,YAAY,EAAE,CAAC,EAAE,WAAW,EAAE,SAAS,EAAE;QAClE,oBAAC,UAAU,qBACM,CAAC,SAAS,EACzB,OAAO,EAAE,QAAQ,EACjB,EAAE,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,cAAc,EAAE,YAAY,EAAE,EAAE,EAAE,CAAC,IAAI,EAAE;YAE9D,oBAAC,KAAK,IAAC,QAAQ,EAAC,OAAO,EAAC,KAAK,EAAC,QAAQ,GAAG;YACzC,oBAAC,UAAU,IAAC,OAAO,EAAC,UAAU,EAAC,KAAK,EAAC,gBAAgB,IAClD,KAAK,CACK,CACF;QACZ,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,QAAQ,CACxB,CACP,CAAA;AACH,CAAC;AAED;;;;GAIG;AACH,MAAM,aAAa,GAAG,QAAQ,CAAC,UAAU,EACvC,KAAK,EACL,MAAM,GAIP;IACC,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IACnC,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,CAAC,aAAa,CAAC,CAAA;IACzD,MAAM,OAAO,GAAG,CAAC,KAAa,EAAE,EAAE,CAAC,CAAC;QAClC,KAAK;QACL,SAAS,EAAE,SAAS,CAAC,GAAG,CAAC,KAAK,CAAC;QAC/B,QAAQ,EAAE,GAAG,EAAE;YACb,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,CAAA;YAC/B,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC;gBACxB,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjB,CAAC;YACD,cAAc,CAAC,IAAI,CAAC,CAAA;YACpB,YAAY,CAAC,IAAI,CAAC,CAAA;QACpB,CAAC;KACF,CAAC,CAAA;IACF,OAAO,CACL,oBAAC,GAAG,mBACU,gBAAgB,EAC5B,EAAE,EAAE;YACF,KAAK,EAAE,kBAAkB;YACzB,MAAM;YACN,UAAU,EAAE,CAAC;YACb,SAAS,EAAE,MAAM;YACjB,UAAU,EAAE,CAAC;YACb,WAAW,EAAE,SAAS;YACtB,OAAO,EAAE,kBAAkB;SAC5B;QAED,oBAAC,GAAG,IACF,EAAE,EAAE;gBACF,OAAO,EAAE,MAAM;gBACf,UAAU,EAAE,QAAQ;gBACpB,cAAc,EAAE,eAAe;gBAC/B,EAAE,EAAE,GAAG;gBACP,EAAE,EAAE,GAAG;aACR;YAED,oBAAC,UAAU,IAAC,OAAO,EAAC,WAAW,eAAsB;YACrD,oBAAC,UAAU,kBACE,gBAAgB,EAC3B,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,eAAe,CAAC,KAAK,CAAC,CAAA;gBAC9B,CAAC;gBAED,oBAAC,KAAK,IAAC,QAAQ,EAAC,OAAO,GAAG,CACf,CACT;QACN,oBAAC,OAAO,OAAK,OAAO,CAAC,OAAO,CAAC;YAC3B,oBAAC,aAAa,IAAC,KAAK,EAAE,kBAAkB,CAAC,KAAK,CAAC,GAAI,CAC3C;QACT,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACf,oBAAC,OAAO,OAAK,OAAO,CAAC,MAAM,CAAC;YAC1B,oBAAC,aAAa,IAAC,KAAK,EAAE,WAAW,CAAC,KAAK,CAAC,GAAI,CACpC,CACX;QACD,oBAAC,OAAO,OAAK,OAAO,CAAC,WAAW,CAAC;YAC/B,oBAAC,aAAa,IAAC,KAAK,EAAE,sBAAsB,CAAC,KAAK,CAAC,GAAI;YACvD,oBAAC,aAAa,IAAC,KAAK,EAAE,WAAW,CAAC,KAAK,CAAC,GAAI,CACpC;QACT,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAClB,oBAAC,OAAO,OAAK,OAAO,CAAC,aAAa,CAAC;YACjC,oBAAC,aAAa,IAAC,KAAK,EAAE,kBAAkB,CAAC,KAAK,CAAC,GAAI,CAC3C,CACX;QACD,oBAAC,OAAO,OAAK,OAAO,CAAC,QAAQ,CAAC;YAC5B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;YAC3B,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,EAAE,WAAW,EAAE,SAAS,EAAE;gBAC/D,oBAAC,aAAa,IAAC,KAAK,EAAE,kBAAkB,CAAC,KAAK,CAAC,GAAI,CAC/C,CACE,CACN,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,aAAa,CAAA"}

package/dist/components/{header/FileMenu.d.ts → settings/TrackList.d.ts}

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

package/dist/components/settings/TrackList.js

@@ -0,0 +1,58 @@
+import React, { useState } from 'react';
+import { Box, Button, Checkbox, FormControlLabel, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
+function trackGroups(model) {
+    const computed = new Set(model.computedTrackModels.map(t => t.model.id));
+    const computedEntries = [];
+    const alignmentEntries = [];
+    const referenceEntries = [];
+    for (const { model: t } of model.tracks) {
+        const entries = t.kind === 'reference'
+            ? referenceEntries
+            : computed.has(t.id)
+                ? computedEntries
+                : alignmentEntries;
+        entries.push({ id: t.id, label: t.name });
+    }
+    return [
+        { title: 'Computed from the alignment', entries: computedEntries },
+        { title: 'Alignment annotations', entries: alignmentEntries },
+        { title: 'Reference row', entries: referenceEntries },
+    ].filter(g => g.entries.length > 0);
+}
+// a filter box shows once the list is long enough to need one
+const filterFrom = 10;
+const TrackList = observer(function ({ model }) {
+    const [filter, setFilter] = useState('');
+    const shown = new Set(model.turnedOnTracks.map(t => t.model.id));
+    const all = trackGroups(model);
+    const needle = filter.trim().toLowerCase();
+    const groups = all
+        .map(g => ({
+        ...g,
+        entries: g.entries.filter(e => e.label.toLowerCase().includes(needle)),
+    }))
+        .filter(g => g.entries.length > 0);
+    const matching = groups.flatMap(g => g.entries.map(e => e.id));
+    const long = all.reduce((n, g) => n + g.entries.length, 0) >= filterFrom;
+    return (React.createElement(React.Fragment, null,
+        long ? (React.createElement(React.Fragment, null,
+            React.createElement(TextField, { size: "small", placeholder: "Filter tracks", value: filter, onChange: event => {
+                    setFilter(event.target.value);
+                }, fullWidth: true }),
+            React.createElement(Box, { sx: { display: 'flex' } },
+                React.createElement(Button, { size: "small", onClick: () => {
+                        model.setTracksShown(matching, true);
+                    } }, "Show all"),
+                React.createElement(Button, { size: "small", onClick: () => {
+                        model.setTracksShown(matching, false);
+                    } }, "Hide all")))) : null,
+        groups.map(({ title, entries }) => (React.createElement(Box, { key: title },
+            groups.length > 1 ? (React.createElement(Typography, { variant: "caption", color: "text.secondary" }, title)) : null,
+            entries.map(({ id, label }) => (React.createElement(FormControlLabel, { key: id, sx: { display: 'flex' }, control: React.createElement(Checkbox, { size: "small", checked: shown.has(id), onChange: () => {
+                        model.toggleTrack(id);
+                    }, sx: { py: 0.25 } }), label: label, slotProps: { typography: { variant: 'body2' } } })))))),
+        groups.length === 0 ? (React.createElement(Typography, { variant: "body2" }, "No track matches")) : null));
+});
+export default TrackList;
+//# sourceMappingURL=TrackList.js.map

package/dist/components/settings/TrackList.js.map

@@ -0,0 +1 @@
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package/dist/components/tracks/TrackBlocks.js

@@ -1,13 +1,13 @@
 import React from 'react';
-import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { useCanvasTheme } from '../../darkReader.js';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import { TrackResizeHandle } from '../ResizeHandles.js';
 import { drawTrackBlock } from './drawTracks.js';
 const TrackBlock = observer(function ({ model, track, offsetX, }) {
     const { blockSize, highResScaleFactor } = model;
     const { height } = track.model;
-    const theme = useTheme();
+    const theme = useCanvasTheme();
     const canvasWidth = blockSize * highResScaleFactor;
     const canvasHeight = height * highResScaleFactor;
     const ref = useCanvasAutorun({

package/dist/components/tracks/TrackBlocks.js.map

@@ -1 +1 @@
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package/dist/components/tracks/TrackTooltipContent.js

@@ -93,7 +93,8 @@ const TrackTooltipContent = observer(function ({ model, track, col, }) {
         case 'logo': {
             return React.createElement(LogoTooltip, { model: model, col: col });
         }
-        case 'text': {
+        case 'text':
+        case 'reference': {
             return React.createElement(TextTooltip, { model: model, track: track, col: col });
         }
         case 'arc': {

package/dist/components/tracks/TrackTooltipContent.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TrackTooltipContent.js","sourceRoot":"","sources":["../../../src/components/tracks/TrackTooltipContent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAA;AACvD,OAAO,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAA;AAKhD,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAA;AAEpD,MAAM,YAAY,GAAG,CAAC,CAAA;AAEtB,SAAS,WAAW,CAAC,EAAE,KAAK,EAAE,GAAG,EAAwC;IACvE,MAAM,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IAC5B,MAAM,GAAG,GAAG,UAAU;QACpB,CAAC,CAAC,KAAK,CAAC,0BAA0B,CAAC,UAAU,EAAE,GAAG,CAAC;QACnD,CAAC,CAAC,SAAS,CAAA;IACb,OAAO,CACL;;QACU,GAAG,GAAG,CAAC;QACd,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,UAAU,IAAI,GAAG,GAAG,CACnD,CACL,CAAA;AACH,CAAC;AAED,SAAS,UAAU,CAAC,EAClB,KAAK,EACL,KAAK,EACL,GAAG,GAKJ;IACC,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,KAAK,CAAC,KAAK,CAAA;IAChC,MAAM,KAAK,GAAG,cAAc,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAA;IAC5C,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAClC;QACE,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAI;QACvC,+BAAM;QACL,IAAI;;QAAI,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CACrB,CACP,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,EAAE,KAAK,EAAE,GAAG,EAAwC;IACvE,MAAM,KAAK,GAAG,KAAK,CAAC,aAAa,CAAC,GAAG,CAAC,CAAA;IACtC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO,IAAI,CAAA;IACb,CAAC;IACD,MAAM,EAAE,KAAK,EAAE,eAAe,EAAE,iBAAiB,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACxE,MAAM,KAAK,GAAG,eAAe,CAAC,KAAK,CAAC,QAAQ,EAAE,GAAG,EAAE,KAAK,CAAC,eAAe,CAAC,CAAA;IACzE,MAAM,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;IAClD,OAAO,CACL;QACE,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAI;;QAAG,KAAK;;QAC/C,+BAAM;;QACQ,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC;;QAC7B,+BAAM;;QACM,eAAe,IAAI,GAAG;;QAAI,GAAG,CAAC,iBAAiB,CAAC;;QAC5D,+BAAM;;QACC,GAAG,CAAC,WAAW,CAAC;QACvB,+BAAM;QACL,KAAK,CAAC,YAAY,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CACvD,8BAAM,GAAG,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE,WAAW,EAAE,CAAC,EAAE;YACzC,MAAM;;YAAG,GAAG,CAAC,KAAK,GAAG,KAAK,CAAC,CACvB,CACR,CAAC,CACE,CACP,CAAA;AACH,CAAC;AAED,SAAS,WAAW,CAAC,EACnB,KAAK,EACL,KAAK,EACL,GAAG,GAKJ;IACC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,KAAK,CAAC,KAAK,CAAA;IAClC,MAAM,MAAM,GAAG,IAAI,EAAE,CAAC,GAAG,CAAC,CAAA;IAC1B,OAAO,MAAM,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACnC;QACE,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAI;QACvC,+BAAM;QACL,IAAI;;QAAI,MAAM,KAAK,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CACtC,CACP,CAAA;AACH,CAAC;AAED,SAAS,UAAU,CAAC,EAClB,KAAK,EACL,KAAK,EACL,GAAG,GAKJ;IACC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,KAAK,CAAC,KAAK,CAAA;IAClC,MAAM,QAAQ,GAAG,CAAC,IAAI,IAAI,EAAE,CAAC;SAC1B,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,KAAK,KAAK,GAAG,IAAI,GAAG,CAAC,GAAG,KAAK,GAAG,CAAC;SACnD,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAA;IAC5D,OAAO,QAAQ,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACpC;QACE,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAI;QACvC,+BAAM;QACL,IAAI;;QAAe,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,YAAY,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;QAC7D,QAAQ,CAAC,MAAM,GAAG,YAAY,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAC1C,CACP,CAAA;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,mBAAmB,GAAG,QAAQ,CAAC,UAAU,EAC7C,KAAK,EACL,KAAK,EACL,GAAG,GAKJ;IACC,QAAQ,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC;QACzB,KAAK,KAAK,EAAE,CAAC;YACX,OAAO,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAI,CAAA;QAC7D,CAAC;QACD,KAAK,MAAM,EAAE,CAAC;YACZ,OAAO,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAI,CAAA;QAChD,CAAC;QACD,KAAK,MAAM,CAAC;QACZ,KAAK,WAAW,EAAE,CAAC;YACjB,OAAO,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAI,CAAA;QAC9D,CAAC;QACD,KAAK,KAAK,EAAE,CAAC;YACX,OAAO,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAI,CAAA;QAC7D,CAAC;QACD,KAAK,OAAO,EAAE,CAAC;YACb,OAAO,CACL;gBACE,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,GAAI,CACnC,CACP,CAAA;QACH,CAAC;IACH,CAAC;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,mBAAmB,CAAA"}

package/dist/components/tracks/drawTracks.js

@@ -1,6 +1,7 @@
 import { columnLogoStack } from '../../sequenceLogo.js';
 import { setFontSize } from '../../setFontSize.js';
 import { contrastTextFn } from '../../util.js';
+import { tileColorFn } from '../msa/tileColor.js';
 import { visibleColRange } from '../msa/visibleColRange.js';
 function drawConservationBars({ ctx, values, color, colWidth, trackHeight, offsetX, blockSize, }) {
     const { xStart, xEnd } = visibleColRange({
@@ -60,7 +61,7 @@ function drawArcs({ ctx, arcs, color, colWidth, trackHeight, offsetX, blockSize,
         ctx.stroke();
     }
 }
-function drawTextTrackContent({ ctx, data, colorScheme, contrastText, bgColor, drawLetters, colWidth, rowHeight, offsetX, blockSize, }) {
+function drawTextTrackContent({ ctx, data, colorAt, contrastText, bgColor, drawLetters, colWidth, rowHeight, offsetX, blockSize, }) {
     const { xStart, xEnd } = visibleColRange({
         offsetX,
         blockWidth: blockSize,
@@ -69,9 +70,9 @@ function drawTextTrackContent({ ctx, data, colorScheme, contrastText, bgColor, d
     const str = data?.slice(xStart, xEnd);
     for (let i = 0; str && i < str.length; i++) {
         const letter = str[i];
-        const upper = letter.toUpperCase();
-        const fill = bgColor ? colorScheme[upper] : undefined;
-        const x = (xStart + i) * colWidth;
+        const col = xStart + i;
+        const fill = bgColor ? colorAt(col, letter) : undefined;
+        const x = col * colWidth;
         if (fill) {
             ctx.fillStyle = fill;
             ctx.fillRect(x, 0, colWidth, rowHeight);
@@ -259,15 +260,21 @@ export function drawTrackBlock({ model, ctx, track, offsetX, offsetY = 0, theme,
             });
             break;
         }
-        case 'text': {
+        case 'text':
+        case 'reference': {
             const { bgColor, fontSize, rowHeight, showMsaLetters } = model;
+            const scheme = customColorScheme ?? model.colorScheme;
             ctx.textAlign = 'center';
             ctx.textBaseline = 'middle';
             setFontSize(ctx, fontSize);
             drawTextTrackContent({
                 ctx,
                 data,
-                colorScheme: customColorScheme ?? model.colorScheme,
+                // the reference row takes its colors from the alignment's own
+                // scheme, per column under a dynamic one
+                colorAt: kind === 'reference'
+                    ? tileColorFn(model)
+                    : (_col, letter) => scheme[letter.toUpperCase()],
                 contrastText: contrastTextFn(theme),
                 bgColor,
                 drawLetters: showMsaLetters,

package/dist/components/tracks/drawTracks.js.map

@@ -1 +1 @@
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package/dist/components/tree/TreeCanvasBlock.js

@@ -1,8 +1,8 @@
 import React, { useState } from 'react';
 import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
-import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { useCanvasTheme } from '../../darkReader.js';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import TreeMenu from './TreeMenu.js';
 import { renderTreeCanvas } from './renderTreeCanvas.js';
@@ -17,7 +17,7 @@ const useStyles = makeStyles()(theme => ({
 }));
 const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const { classes } = useStyles();
-    const theme = useTheme();
+    const theme = useCanvasTheme();
     const [menu, setMenu] = useState();
     const { clickMap, anchor, hitTest, onMouseMove, onMouseLeave } = useTreeHover({ model, offsetY });
     const hovered = anchor?.value;

package/dist/components/tree/TreeCanvasBlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,QAAQ,MAAM,eAAgB,CAAA;AACrC,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAA;AAKhD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,QAAQ,EAAE,UAAU;QACpB,aAAa,EAAE,MAAM;QACrB,MAAM,EAAE,GAAG;QACX,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;KACvC;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,KAAK,GAAG,cAAc,EAAE,CAAA;IAC9B,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,GAAG,QAAQ,EAAkB,CAAA;IAClD,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,GAAG,YAAY,CAC3E,EAAE,KAAK,EAAE,OAAO,EAAE,CACnB,CAAA;IACD,MAAM,OAAO,GAAG,MAAM,EAAE,KAAK,CAAA;IAE7B,MAAM,EAAE,sBAAsB,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACvE,8EAA8E;IAC9E,MAAM,KAAK,GAAG,sBAAsB,CAAA;IACpC,MAAM,MAAM,GAAG,SAAS,CAAA;IAExB,MAAM,WAAW,GAAG,KAAK,GAAG,kBAAkB,CAAA;IAC9C,MAAM,YAAY,GAAG,MAAM,GAAG,kBAAkB,CAAA;IAChD,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,WAAW,EAAE,YAAY,CAAC,CAAA;YAC9C,gBAAgB,CAAC;gBACf,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,QAAQ;gBACR,KAAK;aACN,CAAC,CAAA;QACJ,CAAC;QACD,KAAK,EAAE,WAAW;QAClB,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,CAAC,KAAK,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,CAAC;KACxC,CAAC,CAAA;IAEF,MAAM,KAAK,GAAG;QACZ,KAAK;QACL,MAAM;QACN,GAAG,EAAE,OAAO;QACZ,IAAI,EAAE,CAAC;QACP,QAAQ,EAAE,UAAU;KACZ,CAAA;IAEV,OAAO,CACL;QACG,IAAI,CAAC,CAAC,CAAC,CACN,oBAAC,QAAQ,IACP,IAAI,EAAE,IAAI,EACV,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,OAAO,CAAC,SAAS,CAAC,CAAA;YACpB,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAER,gCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,YAAY,EACpB,KAAK,EAAE,EAAE,GAAG,KAAK,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,EAC5D,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,WAAW,CAAC,KAAK,CAAC,CAAA;YACpB,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,YAAY,EAAE,CAAA;YAChB,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;gBAC5B,IAAI,KAAK,EAAE,CAAC;oBACV,OAAO,CAAC;wBACN,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,EAAE,EAAE,KAAK,CAAC,EAAE;wBACZ,IAAI,EAAE,KAAK,CAAC,IAAI;wBAChB,IAAI,EAAE,CAAC,KAAK,CAAC,MAAM;qBACpB,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC,GACD;QAGD,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAC5B,6BACE,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE;gBACL,IAAI,EAAE,OAAO,CAAC,IAAI;gBAClB,GAAG,EAAE,OAAO,CAAC,IAAI;gBACjB,KAAK,EAAE,OAAO,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI;gBAClC,MAAM,EAAE,OAAO,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI;aACpC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,MAAM,CAAC,CAAC,CAAC,CACR,oBAAC,WAAW,IAAC,WAAW,EAAE,MAAM,CAAC,WAAW,IACzC,MAAM,CAAC,KAAK,CAAC,KAAK,IAAI,MAAM,CAAC,KAAK,CAAC,IAAI,CAC5B,CACf,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/tree/TreeMenu.js

@@ -7,7 +7,7 @@ const TreeMenu = observer(function ({ node, model, onClose, }) {
     const { name, id, leaf } = node;
     const isCollapsed = collapsed.includes(id);
     const isRoot = id === model.tree.id;
-    const noun = leaf ? 'subtree' : 'this node';
+    const noun = leaf ? 'subtree' : 'clade';
     return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: { left: node.x, top: node.y }, transitionDuration: 0, open: true, onClose: onClose },
         React.createElement(MenuItem, { dense: true, disabled: true }, name),
         leaf ? (React.createElement(MenuItem, { dense: true, onClick: () => {
@@ -24,13 +24,11 @@ const TreeMenu = observer(function ({ node, model, onClose, }) {
         leaf ? null : (React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.setShowOnly(showOnly === id ? undefined : id);
                 onClose();
-            } }, showOnly === id
-            ? 'Disable show only this node'
-            : 'Show only this node')),
+            } }, showOnly === id ? 'Show all rows' : 'Show only this clade')),
         leaf || isCollapsed ? null : (React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.toggleRotated(id);
                 onClose();
-            } }, "Rotate this node")),
+            } }, "Rotate clade")),
         isRoot ? null : (React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.rerootAt(id);
                 onClose();
@@ -38,7 +36,7 @@ const TreeMenu = observer(function ({ node, model, onClose, }) {
         leaf ? (React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.drawRelativeTo(name);
                 onClose();
-            } }, "Indicate differences from this row")) : null,
+            } }, "Use as reference row")) : null,
         leaf && relativeTo ? (React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.drawRelativeTo(undefined);
                 onClose();

package/dist/components/tree/TreeMenu.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,iCAAkC,CAAC,CACjD,CAAA;AAUD,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,KAAK,EACL,OAAO,GAKR;IACC,MAAM,EAAE,SAAS,EAAE,QAAQ,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IACjD,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IAC/B,MAAM,WAAW,GAAG,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,MAAM,MAAM,GAAG,EAAE,KAAK,KAAK,CAAC,IAAI,CAAC,EAAE,CAAA;IACnC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,CAAA;IACvC,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,CAAC,EAAE,EAC7C,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CACI;QACV,IAAI,CAAC,CAAC,CAAC,CACN,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,kBAAkB;oBAClB,EAAE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,EAAE;iBACjE,CAAC,CAAA;gBACF,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ,CACZ,CAAC,CAAC,CAAC,IAAI;QACR,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,eAAe,CAAC,EAAE,CAAC,CAAA;gBACzB,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,WAAW,CAAC,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,CAC3C;QACV,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACb,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,QAAQ,KAAK,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;gBACnD,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,QAAQ,KAAK,EAAE,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,sBAAsB,CAClD,CACZ;QACA,IAAI,IAAI,WAAW,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAC5B,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,aAAa,CAAC,EAAE,CAAC,CAAA;gBACvB,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ,CACZ;QACA,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACf,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;gBAClB,OAAO,EAAE,CAAA;YACX,CAAC,kBAGQ,CACZ;QACA,IAAI,CAAC,CAAC,CAAC,CACN,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;gBAC1B,OAAO,EAAE,CAAA;YACX,CAAC,2BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI;QACP,IAAI,IAAI,UAAU,CAAC,CAAC,CAAC,CACpB,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,0BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI,CACH,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/tree/TreeOverview.js

@@ -1,6 +1,6 @@
 import React, { useState } from 'react';
-import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { useCanvasTheme } from '../../darkReader.js';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import { drawTreeOverview, drawTreeOverviewBox, treeOverviewImage, } from './renderTreeOverview.js';
 /**
@@ -13,7 +13,7 @@ import { drawTreeOverview, drawTreeOverviewBox, treeOverviewImage, } from './ren
  */
 const TreeOverview = observer(function ({ model }) {
     const { effectiveTreeAreaWidth, overviewHeight, highResScaleFactor } = model;
-    const theme = useTheme();
+    const theme = useCanvasTheme();
     const [hover, setHover] = useState();
     const width = Math.round(effectiveTreeAreaWidth * highResScaleFactor);
     const height = Math.round(overviewHeight * highResScaleFactor);

package/dist/components/tree/TreeOverview.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreeOverview.js","sourceRoot":"","sources":["../../../src/components/tree/TreeOverview.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,EACL,gBAAgB,EAChB,mBAAmB,EACnB,iBAAiB,GAClB,MAAM,yBAAyB,CAAA;AAIhC;;;;;;;GAOG;AACH,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACxE,MAAM,EAAE,sBAAsB,EAAE,cAAc,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAC5E,MAAM,KAAK,GAAG,cAAc,EAAE,CAAA;IAC9B,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,EAA0C,CAAA;IAC5E,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,sBAAsB,GAAG,kBAAkB,CAAC,CAAA;IACrE,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,kBAAkB,CAAC,CAAA;IAE9D,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;YAClC,MAAM,KAAK,GAAG,iBAAiB,CAAC;gBAC9B,KAAK;gBACL,KAAK;gBACL,KAAK,EAAE,sBAAsB;gBAC7B,MAAM,EAAE,cAAc;gBACtB,KAAK,EAAE,kBAAkB;aAC1B,CAAC,CAAA;YACF,GAAG,CAAC,KAAK,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAA;YACjD,MAAM,GAAG,GAAG;gBACV,KAAK;gBACL,GAAG;gBACH,KAAK,EAAE,sBAAsB;gBAC7B,MAAM,EAAE,cAAc;aACvB,CAAA;YACD,IAAI,KAAK,EAAE,CAAC;gBACV,GAAG,CAAC,SAAS,CACX,KAAK,EACL,CAAC,EACD,CAAC,EACD,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,MAAM,EACZ,CAAC,EACD,CAAC,EACD,GAAG,CAAC,KAAK,EACT,GAAG,CAAC,MAAM,CACX,CAAA;YACH,CAAC;iBAAM,CAAC;gBACN,gBAAgB,CAAC,EAAE,GAAG,GAAG,EAAE,KAAK,EAAE,CAAC,CAAA;YACrC,CAAC;YACD,IAAI,KAAK,EAAE,CAAC;gBACV,mBAAmB,CAAC;oBAClB,GAAG,GAAG;oBACN,IAAI,EAAE,KAAK,CAAC,IAAI;oBAChB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS;iBACpC,CAAC,CAAA;YACJ,CAAC;YACD,MAAM,KAAK,GAAG,KAAK,CAAC,qBAAqB,CAAA;YACzC,IAAI,KAAK,EAAE,CAAC;gBACV,mBAAmB,CAAC;oBAClB,GAAG,GAAG;oBACN,IAAI,EAAE,KAAK;oBACX,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO;iBAClC,CAAC,CAAA;YACJ,CAAC;QACH,CAAC;QACD,KAAK;QACL,MAAM;QACN,IAAI,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,CAAC;KAC5B,CAAC,CAAA;IAEF,OAAO,CACL,+CACc,eAAe,EAC3B,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;YACL,OAAO,EAAE,OAAO;YAChB,UAAU,EAAE,CAAC;YACb,MAAM,EAAE,SAAS;YACjB,KAAK,EAAE,sBAAsB;YAC7B,MAAM,EAAE,cAAc;SACvB,EACD,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,MAAM,GAAG,GAAG,KAAK,CAAC,eAAe,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC5D,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,IAAI,EAAE,EAAE,KAAK,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;QACvD,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;YACjB,QAAQ,CAAC,SAAS,CAAC,CAAA;QACrB,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;YACf,KAAK,CAAC,iBAAiB,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACpD,CAAC,GACD,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

package/dist/constants.d.ts

@@ -21,12 +21,14 @@ export type ScrollZoomAxis = (typeof scrollZoomAxes)[number];
 export declare const defaultScrollZoomAxis: ScrollZoomAxis;
 export declare const minLetterRowHeight = 8;
 export declare const minLetterColWidth = 5;
+export declare const zoomFrameMaxLetters = 2000;
 export declare const minFeatureLabelHeight = 9;
 export declare function fontSizeFor(rowHeight: number): number;
 export declare const labelFitFontSize: number;
 export declare const minColWidth = 0.2;
-export declare const minRowHeight = 1;
+export declare const minRowHeight = 0.2;
 export declare const maxCellSize = 80;
+export declare const settingsPanelWidth = 280;
 export declare const defaultBgColor = true;
 export declare const defaultColorSchemeName = "maeditor";
 export declare const defaultShowColumnStats = true;
@@ -43,6 +45,7 @@ export declare const defaultDrawTree = true;
 export declare const defaultDrawNodeBubbles = true;
 export declare const defaultDrawNodeLabels = false;
 export declare const defaultShowTreeOverview = false;
+export declare const defaultShowTreeScaleBar = false;
 export declare const defaultOverviewHeight = 120;
 export declare const maxNeighborJoiningRows = 500;
 export declare const rowTintAlpha = 0.25;