react-msaview 9.0.0 → 9.1.1

package/dist/components/rowpanels/RowPanelBlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"RowPanelBlock.js","sourceRoot":"","sources":["../../../src/components/rowpanels/RowPanelBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpD,OAAO,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAA;AAClE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAA;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AAKpD,4EAA4E;AAC5E,sEAAsE;AACtE,SAAS,UAAU,CAAC,EAClB,KAAK,EACL,KAAK,EACL,IAAI,EACJ,CAAC,GAMF;IACC,IAAI,KAAK,CAAC,IAAI,KAAK,OAAO,EAAE,CAAC;QAC3B,OAAO;YACL,GAAG,KAAK,CAAC,MAAM,KAAK,KAAK,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,QAAQ,EAAE;SACvE,CAAA;IACH,CAAC;IACD,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK;SACrB,GAAG,CAAC,IAAI,CAAC;QACV,EAAE,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,IAAI,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAA;IAC/C,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,EAAE,CAAA;IACX,CAAC;IACD,MAAM,EAAE,UAAU,EAAE,GAAG,IAAI,CAAA;IAC3B,MAAM,MAAM,GACV,UAAU,CAAC,MAAM,KAAK,SAAS;QAC7B,CAAC,CAAC,EAAE;QACJ,CAAC,CAAC,UAAU,CAAC,MAAM,GAAG,CAAC;YACrB,CAAC,CAAC,MAAM;YACR,CAAC,CAAC,MAAM,CAAA;IACd,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,YAAY,CAAC,UAAU,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAC7E,OAAO;QACL,WAAW,CAAC,UAAU,CAAC,IAAI,UAAU,CAAC,SAAS;QAC/C,GAAG,UAAU,CAAC,KAAK,IAAI,UAAU,CAAC,GAAG,GAAG,MAAM,EAAE;QAChD,GAAG,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,KAAK,KAAK,KAAK,EAAE,CAAC,CAAC;KAC7D,CAAA;AACH,CAAC;AAED,MAAM,aAAa,GAAG,QAAQ,CAAC,UAAU,EACvC,KAAK,EACL,KAAK,EACL,OAAO,GAKR;IACC,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,cAAc,EAGnD,CAAA;IACJ,MAAM,KAAK,GAAG,cAAc,EAAE,CAAA;IAC9B,MAAM,EAAE,SAAS,EAAE,kBAAkB,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC1D,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAA;IACzB,MAAM,MAAM,GAAG,SAAS,CAAA;IACxB,MAAM,WAAW,GAAG,KAAK,GAAG,kBAAkB,CAAA;IAC9C,MAAM,YAAY,GAAG,MAAM,GAAG,kBAAkB,CAAA;IAEhD,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,cAAc,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,CAAA;QAC7D,CAAC;QACD,KAAK,EAAE,WAAW;QAClB,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,OAAO,CAAC;KACrC,CAAC,CAAA;IAEF,OAAO,CACL;QACE,gCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,YAAY,EACpB,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE,GAAG,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,EACrE,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,mEAAmE;gBACnE,oEAAoE;gBACpE,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,KAAK,CAAC,aAAa,CAAC,qBAAqB,EAAE,CAAA;gBACjE,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,OAAO,GAAG,GAAG,GAAG,OAAO,CAAC,GAAG,SAAS,CAAC,CAAA;gBACnE,MAAM,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,IAAI,CAAC,IAAI,CAAA;gBACzC,MAAM,KAAK,GACT,IAAI,KAAK,SAAS;oBAChB,CAAC,CAAC,EAAE;oBACJ,CAAC,CAAC,UAAU,CAAC;wBACT,KAAK;wBACL,KAAK;wBACL,IAAI;wBACJ,CAAC,EAAE,KAAK,CAAC,OAAO,GAAG,IAAI;qBACxB,CAAC,CAAA;gBACR,OAAO,CACL,KAAK,EACL,IAAI,KAAK,SAAS,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC;oBACtC,CAAC,CAAC,SAAS;oBACX,CAAC,CAAC,EAAE,IAAI,EAAE,KAAK,EAAE,CACpB,CAAA;gBACD,KAAK,CAAC,WAAW,CAAC,SAAS,EAAE,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YACpE,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,WAAW,EAAE,CAAA;gBACb,KAAK,CAAC,WAAW,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;YACzC,CAAC,GACD;QACD,MAAM,CAAC,CAAC,CAAC,CACR,oBAAC,WAAW,IAAC,WAAW,EAAE,MAAM,CAAC,WAAW;YAC1C,iCAAM,MAAM,CAAC,KAAK,CAAC,IAAI,CAAO;YAC7B,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAC9B,6BAAK,GAAG,EAAE,IAAI,IAAG,IAAI,CAAO,CAC7B,CAAC,CACU,CACf,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,aAAa,CAAA"}

package/dist/components/rowpanels/renderFeaturePanel.d.ts

@@ -1,5 +1,7 @@
+import type { HierarchyNode } from '../../hierarchy.ts';
 import type { MsaViewModel } from '../../model.ts';
-import type { ResolvedFeaturePanel } from '../../types.ts';
+import type { NodeWithIdsAndLength, ResolvedFeaturePanel, RowPanelSpan } from '../../types.ts';
+import type { SpanSource } from '../msa/drawFeatureSpans.ts';
 import type { RenderCtx } from '../renderCtx.ts';
 import type { Theme } from '@mui/material';
 /**
@@ -19,3 +21,5 @@ export declare function renderFeaturePanel({ ctx, model, theme, panel, x, offset
     blockSizeYOverride?: number;
     highResScaleFactorOverride?: number;
 }): void;
+/** a features panel's spans over `leaves`, in panel pixels, a lane apiece */
+export declare function featurePanelSource(model: MsaViewModel, panel: ResolvedFeaturePanel, leaves: HierarchyNode<NodeWithIdsAndLength>[]): SpanSource<RowPanelSpan>;

package/dist/components/rowpanels/renderFeaturePanel.js

@@ -20,7 +20,17 @@ export function renderFeaturePanel({ ctx, model, theme, panel, x, offsetY, block
     ctx.translate(x, rowHeight / 2 - offsetY);
     drawFeatureSpans({
         ctx,
-        rows: spanRows(getVisibleLeaves({ model, offsetY, blockSizeY: by }), panel.spans),
+        ...featurePanelSource(model, panel, getVisibleLeaves({ model, offsetY, blockSizeY: by })),
+        contrastText: contrastTextFn(theme),
+        xMin: 0,
+        xMax: panel.width,
+    });
+}
+/** a features panel's spans over `leaves`, in panel pixels, a lane apiece */
+export function featurePanelSource(model, panel, leaves) {
+    const { rowHeight } = model;
+    return {
+        rows: spanRows(leaves, panel.spans),
         layout: {
             height: laneCount => Math.max(1, rowHeight / laneCount - rowPadding),
             top: (y, lane, h) => y - rowHeight + lane * (h + rowPadding) + rowPadding / 2,
@@ -29,9 +39,6 @@ export function renderFeaturePanel({ ctx, model, theme, panel, x, offsetY, block
         xOf: span => [span.xStart, span.xEnd],
         colors: panel.colors,
         labelOf: span => panel.labels?.get(span.annotation),
-        contrastText: contrastTextFn(theme),
-        xMin: 0,
-        xMax: panel.width,
-    });
+    };
 }
 //# sourceMappingURL=renderFeaturePanel.js.map

package/dist/components/rowpanels/renderFeaturePanel.js.map

@@ -1 +1 @@
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package/dist/components/settings/MenuItemsForm.d.ts

@@ -0,0 +1,10 @@
+import React from 'react';
+import type { MenuItem } from '@jbrowse/core/ui/Menu';
+/**
+ * A submenu of radios may name a compact control to render as: `segmented`
+ * for a few short choices, `select` for a longer list
+ */
+export type ChoiceDisplay = 'segmented' | 'select';
+export default function MenuItemsForm({ items }: {
+    items: MenuItem[];
+}): React.JSX.Element;

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/ZoomMenu.d.ts → settings/TrackList.d.ts}

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

package/dist/components/settings/TrackList.js

@@ -0,0 +1,55 @@
+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 = [];
+    for (const { model: t } of model.tracks) {
+        ;
+        (computed.has(t.id) ? computedEntries : alignmentEntries).push({
+            id: t.id,
+            label: t.name,
+        });
+    }
+    return [
+        { title: 'Computed from the alignment', entries: computedEntries },
+        { title: 'Alignment annotations', entries: alignmentEntries },
+    ].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 @@
+{"version":3,"file":"TrackList.js","sourceRoot":"","sources":["../../../src/components/settings/TrackList.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EACL,GAAG,EACH,MAAM,EACN,QAAQ,EACR,gBAAgB,EAChB,SAAS,EACT,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AASrC,SAAS,WAAW,CAAC,KAAmB;IACtC,MAAM,QAAQ,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAA;IACxE,MAAM,eAAe,GAAY,EAAE,CAAA;IACnC,MAAM,gBAAgB,GAAY,EAAE,CAAA;IACpC,KAAK,MAAM,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;QACxC,CAAC;QAAA,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,IAAI,CAAC;YAC9D,EAAE,EAAE,CAAC,CAAC,EAAE;YACR,KAAK,EAAE,CAAC,CAAC,IAAI;SACd,CAAC,CAAA;IACJ,CAAC;IACD,OAAO;QACL,EAAE,KAAK,EAAE,6BAA6B,EAAE,OAAO,EAAE,eAAe,EAAE;QAClE,EAAE,KAAK,EAAE,uBAAuB,EAAE,OAAO,EAAE,gBAAgB,EAAE;KAC9D,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;AACrC,CAAC;AAED,8DAA8D;AAC9D,MAAM,UAAU,GAAG,EAAE,CAAA;AAErB,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,CAAC,EAAE,CAAC,CAAA;IACxC,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAA;IAChE,MAAM,GAAG,GAAG,WAAW,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,MAAM,GAAG,MAAM,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAA;IAC1C,MAAM,MAAM,GAAG,GAAG;SACf,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;QACT,GAAG,CAAC;QACJ,OAAO,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC;KACvE,CAAC,CAAC;SACF,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IACpC,MAAM,QAAQ,GAAG,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IAC9D,MAAM,IAAI,GAAG,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC,IAAI,UAAU,CAAA;IACxE,OAAO,CACL;QACG,IAAI,CAAC,CAAC,CAAC,CACN;YACE,oBAAC,SAAS,IACR,IAAI,EAAC,OAAO,EACZ,WAAW,EAAC,eAAe,EAC3B,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,KAAK,CAAC,EAAE;oBAChB,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;gBAC/B,CAAC,EACD,SAAS,SACT;YACF,oBAAC,GAAG,IAAC,EAAE,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;gBAC1B,oBAAC,MAAM,IACL,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC,QAAQ,EAAE,IAAI,CAAC,CAAA;oBACtC,CAAC,eAGM;gBACT,oBAAC,MAAM,IACL,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAA;oBACvC,CAAC,eAGM,CACL,CACL,CACJ,CAAC,CAAC,CAAC,IAAI;QACP,MAAM,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC,CAClC,oBAAC,GAAG,IAAC,GAAG,EAAE,KAAK;YACZ,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACnB,oBAAC,UAAU,IAAC,OAAO,EAAC,SAAS,EAAC,KAAK,EAAC,gBAAgB,IACjD,KAAK,CACK,CACd,CAAC,CAAC,CAAC,IAAI;YACP,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC,CAC9B,oBAAC,gBAAgB,IACf,GAAG,EAAE,EAAE,EACP,EAAE,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,EACvB,OAAO,EACL,oBAAC,QAAQ,IACP,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,EACtB,QAAQ,EAAE,GAAG,EAAE;wBACb,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;oBACvB,CAAC,EACD,EAAE,EAAE,EAAE,EAAE,EAAE,IAAI,EAAE,GAChB,EAEJ,KAAK,EAAE,KAAK,EACZ,SAAS,EAAE,EAAE,UAAU,EAAE,EAAE,OAAO,EAAE,OAAO,EAAE,EAAE,GAC/C,CACH,CAAC,CACE,CACP,CAAC;QACD,MAAM,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CACrB,oBAAC,UAAU,IAAC,OAAO,EAAC,OAAO,uBAA8B,CAC1D,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

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/drawTracks.d.ts

@@ -1,62 +1,10 @@
-import type { ColumnCounts } from '../../columnCounts.ts';
 import type { MsaViewModel } from '../../model.ts';
-import type { Arc, BasicTrack } from '../../types.ts';
+import type { BasicTrack } from '../../types.ts';
 import type { RenderCtx } from '../renderCtx.ts';
 import type { Theme } from '@mui/material';
-export declare function drawConservationBars({ ctx, values, color, colWidth, trackHeight, offsetX, blockSize, }: {
-    ctx: RenderCtx;
-    values: number[];
-    color: string;
-    colWidth: number;
-    trackHeight: number;
-    offsetX: number;
-    blockSize: number;
-}): void;
 export declare function barTrackValues(model: MsaViewModel, trackId: string): number[];
-export declare function drawArcs({ ctx, arcs, color, colWidth, trackHeight, offsetX, blockSize, }: {
-    ctx: RenderCtx;
-    arcs: Arc[] | undefined;
-    color: string;
-    colWidth: number;
-    trackHeight: number;
-    offsetX: number;
-    blockSize: number;
-}): void;
-export declare function drawTextTrackContent({ ctx, data, colorScheme, contrastText, bgColor, drawLetters, colWidth, rowHeight, offsetX, blockSize, }: {
-    ctx: RenderCtx;
-    data: string | undefined;
-    colorScheme: Record<string, string>;
-    contrastText: (color: string | undefined) => string;
-    bgColor: boolean;
-    drawLetters: boolean;
-    colWidth: number;
-    rowHeight: number;
-    offsetX: number;
-    blockSize: number;
-}): void;
 export declare function rulerStep(colWidth: number, minPixels?: number): number;
 export declare function rulerCols(xStart: number, end: number, colWidth: number): number[];
-export declare function drawColumnRuler({ ctx, numColumns, label, textColor, colWidth, trackHeight, offsetX, blockSize, }: {
-    ctx: RenderCtx;
-    numColumns: number;
-    label: (col: number) => string | undefined;
-    textColor: string;
-    colWidth: number;
-    trackHeight: number;
-    offsetX: number;
-    blockSize: number;
-}): void;
-export declare function drawSequenceLogo({ ctx, colStats, colorScheme, maxBits, textColor, colWidth, trackHeight, offsetX, blockSize, }: {
-    ctx: RenderCtx;
-    colStats: ColumnCounts;
-    colorScheme: Record<string, string>;
-    maxBits: number;
-    textColor: string;
-    colWidth: number;
-    trackHeight: number;
-    offsetX: number;
-    blockSize: number;
-}): void;
 /**
  * Draw one track's content into a block of the alignment's column space, at
  * `offsetY` within the ctx. Owns the transform, so the live canvas blocks and

package/dist/components/tracks/drawTracks.js

@@ -2,7 +2,7 @@ import { columnLogoStack } from '../../sequenceLogo.js';
 import { setFontSize } from '../../setFontSize.js';
 import { contrastTextFn } from '../../util.js';
 import { visibleColRange } from '../msa/visibleColRange.js';
-export function drawConservationBars({ ctx, values, color, colWidth, trackHeight, offsetX, blockSize, }) {
+function drawConservationBars({ ctx, values, color, colWidth, trackHeight, offsetX, blockSize, }) {
     const { xStart, xEnd } = visibleColRange({
         offsetX,
         blockWidth: blockSize,
@@ -29,7 +29,7 @@ export function barTrackValues(model, trackId) {
 }
 // An arc's apex scales with the square root of its span. Contact-map spans skew
 // short, and a linear scale flattens them along the baseline.
-export function drawArcs({ ctx, arcs, color, colWidth, trackHeight, offsetX, blockSize, }) {
+function drawArcs({ ctx, arcs, color, colWidth, trackHeight, offsetX, blockSize, }) {
     if (!arcs?.length) {
         return;
     }
@@ -60,7 +60,7 @@ export function drawArcs({ ctx, arcs, color, colWidth, trackHeight, offsetX, blo
         ctx.stroke();
     }
 }
-export function drawTextTrackContent({ ctx, data, colorScheme, contrastText, bgColor, drawLetters, colWidth, rowHeight, offsetX, blockSize, }) {
+function drawTextTrackContent({ ctx, data, colorScheme, contrastText, bgColor, drawLetters, colWidth, rowHeight, offsetX, blockSize, }) {
     const { xStart, xEnd } = visibleColRange({
         offsetX,
         blockWidth: blockSize,
@@ -106,7 +106,7 @@ export function rulerCols(xStart, end, colWidth) {
 }
 const RULER_FONT_SIZE = 10;
 const TICK_HEIGHT = 4;
-export function drawColumnRuler({ ctx, numColumns, label, textColor, colWidth, trackHeight, offsetX, blockSize, }) {
+function drawColumnRuler({ ctx, numColumns, label, textColor, colWidth, trackHeight, offsetX, blockSize, }) {
     const { xStart, xEnd } = visibleColRange({
         offsetX,
         blockWidth: blockSize,
@@ -138,7 +138,7 @@ export function drawColumnRuler({ ctx, numColumns, label, textColor, colWidth, t
 // the slices sum to the stack height.
 const CAP_HEIGHT_RATIO = 0.72;
 const MIN_LETTER_PX = 3;
-export function drawSequenceLogo({ ctx, colStats, colorScheme, maxBits, textColor, colWidth, trackHeight, offsetX, blockSize, }) {
+function drawSequenceLogo({ ctx, colStats, colorScheme, maxBits, textColor, colWidth, trackHeight, offsetX, blockSize, }) {
     const { xStart, xEnd } = visibleColRange({
         offsetX,
         blockWidth: blockSize,

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

@@ -1 +1 @@
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package/dist/components/tree/CladeLabels.d.ts

@@ -8,5 +8,5 @@ import type { MsaViewModel } from '../../model.ts';
  */
 declare const CladeLabels: ({ model }: {
     model: MsaViewModel;
-}) => React.JSX.Element | null;
+}) => React.JSX.Element;
 export default CladeLabels;