@jbrowse/plugin-data-management 2.3.3 → 2.4.0

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedDialog.d.ts

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+import { HierarchicalTrackSelectorModel } from '../../model';
+declare function FacetedDlg(props: {
+    handleClose: () => void;
+    model: HierarchicalTrackSelectorModel;
+}): JSX.Element;
+declare const _default: typeof FacetedDlg;
+export default _default;

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedDialog.js

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+import React from 'react';
+import { DialogContent } from '@mui/material';
+import { Dialog } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
+import FacetedSelector from './FacetedSelector';
+function FacetedDlg(props) {
+    const { handleClose } = props;
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, maxWidth: "xl", title: "Faceted track selector" },
+        React.createElement(DialogContent, null,
+            React.createElement(FacetedSelector, { ...props }))));
+}
+export default observer(FacetedDlg);
+//# sourceMappingURL=FacetedDialog.js.map

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedDialog.js.map

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package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedHeader.d.ts

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+/// <reference types="react" />
+import { HierarchicalTrackSelectorModel } from '../../model';
+export default function FacetedHeader({ setFilterText, setUseShoppingCart, setHideSparse, hideSparse, useShoppingCart, filterText, model, }: {
+    setFilterText: (arg: string) => void;
+    setUseShoppingCart: (arg: boolean) => void;
+    setHideSparse: (arg: boolean) => void;
+    filterText: string;
+    useShoppingCart: boolean;
+    hideSparse: boolean;
+    model: HierarchicalTrackSelectorModel;
+}): JSX.Element;

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedHeader.js

@@ -0,0 +1,42 @@
+import React, { useState } from 'react';
+import { Grid, IconButton, InputAdornment, TextField } from '@mui/material';
+import { Menu } from '@jbrowse/core/ui';
+// icons
+import ClearIcon from '@mui/icons-material/Clear';
+import MoreVert from '@mui/icons-material/MoreVert';
+// locals
+import ShoppingCart from '../ShoppingCart';
+export default function FacetedHeader({ setFilterText, setUseShoppingCart, setHideSparse, hideSparse, useShoppingCart, filterText, model, }) {
+    const [anchorEl, setAnchorEl] = useState(null);
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Grid, { container: true, spacing: 4, alignItems: "center" },
+            React.createElement(Grid, { item: true },
+                React.createElement(TextField, { label: "Search...", value: filterText, onChange: event => setFilterText(event.target.value), InputProps: {
+                        endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                            React.createElement(IconButton, { onClick: () => setFilterText('') },
+                                React.createElement(ClearIcon, null)))),
+                    } })),
+            React.createElement(Grid, { item: true },
+                React.createElement(IconButton, { onClick: event => setAnchorEl(event.currentTarget) },
+                    React.createElement(MoreVert, null))),
+            React.createElement(Grid, { item: true },
+                React.createElement(ShoppingCart, { model: model }))),
+        React.createElement(Menu, { anchorEl: anchorEl, open: !!anchorEl, onClose: () => setAnchorEl(null), onMenuItemClick: (_event, callback) => {
+                callback();
+                setAnchorEl(null);
+            }, menuItems: [
+                {
+                    label: 'Add tracks to selection instead of turning them on/off',
+                    onClick: () => setUseShoppingCart(!useShoppingCart),
+                    type: 'checkbox',
+                    checked: useShoppingCart,
+                },
+                {
+                    label: 'Hide sparse metadata columns',
+                    onClick: () => setHideSparse(!hideSparse),
+                    checked: hideSparse,
+                    type: 'checkbox',
+                },
+            ] })));
+}
+//# sourceMappingURL=FacetedHeader.js.map

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedHeader.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"FacetedHeader.js","sourceRoot":"","sources":["../../../../src/HierarchicalTrackSelectorWidget/components/faceted/FacetedHeader.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,cAAc,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAC3E,OAAO,EAAE,IAAI,EAAE,MAAM,kBAAkB,CAAA;AAEvC,QAAQ;AACR,OAAO,SAAS,MAAM,2BAA2B,CAAA;AACjD,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AAEnD,SAAS;AACT,OAAO,YAAY,MAAM,iBAAiB,CAAA;AAG1C,MAAM,CAAC,OAAO,UAAU,aAAa,CAAC,EACpC,aAAa,EACb,kBAAkB,EAClB,aAAa,EACb,UAAU,EACV,eAAe,EACf,UAAU,EACV,KAAK,GASN;IACC,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAqB,IAAI,CAAC,CAAA;IAElE,OAAO,CACL;QACE,oBAAC,IAAI,IAAC,SAAS,QAAC,OAAO,EAAE,CAAC,EAAE,UAAU,EAAC,QAAQ;YAC7C,oBAAC,IAAI,IAAC,IAAI;gBACR,oBAAC,SAAS,IACR,KAAK,EAAC,WAAW,EACjB,KAAK,EAAE,UAAU,EACjB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,aAAa,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EACpD,UAAU,EAAE;wBACV,YAAY,EAAE,CACZ,oBAAC,cAAc,IAAC,QAAQ,EAAC,KAAK;4BAC5B,oBAAC,UAAU,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,EAAE,CAAC;gCAC1C,oBAAC,SAAS,OAAG,CACF,CACE,CAClB;qBACF,GACD,CACG;YAEP,oBAAC,IAAI,IAAC,IAAI;gBACR,oBAAC,UAAU,IAAC,OAAO,EAAE,KAAK,CAAC,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,aAAa,CAAC;oBAC5D,oBAAC,QAAQ,OAAG,CACD,CACR;YACP,oBAAC,IAAI,IAAC,IAAI;gBACR,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CACzB,CACF;QACP,oBAAC,IAAI,IACH,QAAQ,EAAE,QAAQ,EAClB,IAAI,EAAE,CAAC,CAAC,QAAQ,EAChB,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,CAAC,IAAI,CAAC,EAChC,eAAe,EAAE,CAAC,MAAM,EAAE,QAAQ,EAAE,EAAE;gBACpC,QAAQ,EAAE,CAAA;gBACV,WAAW,CAAC,IAAI,CAAC,CAAA;YACnB,CAAC,EACD,SAAS,EAAE;gBACT;oBACE,KAAK,EAAE,wDAAwD;oBAC/D,OAAO,EAAE,GAAG,EAAE,CAAC,kBAAkB,CAAC,CAAC,eAAe,CAAC;oBACnD,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,eAAe;iBACzB;gBACD;oBACE,KAAK,EAAE,8BAA8B;oBACrC,OAAO,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,CAAC,UAAU,CAAC;oBACzC,OAAO,EAAE,UAAU;oBACnB,IAAI,EAAE,UAAU;iBACjB;aACF,GACD,CACD,CACJ,CAAA;AACH,CAAC"}

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.d.ts

@@ -0,0 +1,12 @@
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { HierarchicalTrackSelectorModel } from '../../model';
+export interface InfoArgs {
+    target: HTMLElement;
+    id: string;
+    conf: AnyConfigurationModel;
+}
+declare const _default: ({ model, }: {
+    model: HierarchicalTrackSelectorModel;
+}) => JSX.Element;
+export default _default;

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js

@@ -0,0 +1,183 @@
+import React, { useMemo, useState, useEffect, useReducer } from 'react';
+import { IconButton } from '@mui/material';
+import { transaction } from 'mobx';
+import { observer } from 'mobx-react';
+import { getRoot, resolveIdentifier } from 'mobx-state-tree';
+import { DataGrid } from '@mui/x-data-grid';
+// jbrowse
+import { getTrackName } from '@jbrowse/core/util/tracks';
+import { ResizeHandle, SanitizedHTML } from '@jbrowse/core/ui';
+import JBrowseMenu from '@jbrowse/core/ui/Menu';
+import ResizeBar, { useResizeBar } from '@jbrowse/core/ui/ResizeBar';
+import { getEnv, getSession, measureGridWidth, useDebounce, } from '@jbrowse/core/util';
+import { readConfObject, } from '@jbrowse/core/configuration';
+// icons
+import MoreHoriz from '@mui/icons-material/MoreHoriz';
+// locals
+import { matches } from '../../model';
+import FacetedHeader from './FacetedHeader';
+import FacetFilters from './FacetFilters';
+import { getRootKeys } from './util';
+const nonMetadataKeys = ['category', 'adapter', 'description'];
+const frac = 0.75;
+export default observer(function FacetedSelector({ model, }) {
+    var _a;
+    const { assemblyNames, view, selection } = model;
+    const { pluginManager } = getEnv(model);
+    const { ref, scrollLeft } = useResizeBar();
+    const [filterText, setFilterText] = useState('');
+    const [info, setInfo] = useState();
+    const [useShoppingCart, setUseShoppingCart] = useState(false);
+    const [hideSparse, setHideSparse] = useState(true);
+    const [panelWidth, setPanelWidth] = useState(400);
+    const assemblyName = assemblyNames[0];
+    const session = getSession(model);
+    const filterDebounced = useDebounce(filterText, 400);
+    const [filters, dispatch] = useReducer((state, update) => {
+        return { ...state, [update.key]: update.val };
+    }, {});
+    const rows = useMemo(() => {
+        // metadata is spread onto the object for easier access and sorting
+        // by the mui data grid (it's unable to sort by nested objects)
+        return model
+            .trackConfigurations(assemblyName)
+            .filter(conf => matches(filterDebounced, conf, session))
+            .map(track => {
+            var _a, _b;
+            const metadata = readConfObject(track, 'metadata');
+            return {
+                id: track.trackId,
+                conf: track,
+                name: getTrackName(track, session),
+                category: (_a = readConfObject(track, 'category')) === null || _a === void 0 ? void 0 : _a.join(', '),
+                adapter: (_b = readConfObject(track, 'adapter')) === null || _b === void 0 ? void 0 : _b.type,
+                description: readConfObject(track, 'description'),
+                metadata,
+                ...metadata,
+            };
+        });
+    }, [assemblyName, model, filterDebounced, session]);
+    const filteredNonMetadataKeys = useMemo(() => nonMetadataKeys.filter(f => !hideSparse ? true : rows.map(r => r[f]).filter(f => !!f).length > 5), [hideSparse, rows]);
+    const filteredMetadataKeys = useMemo(() => [...new Set(rows.map(row => getRootKeys(row.metadata)).flat())].filter(f => !hideSparse
+        ? true
+        : rows.map(r => r.metadata[f]).filter(f => !!f).length > 5), [hideSparse, rows]);
+    const fields = useMemo(() => {
+        return ['name', ...filteredNonMetadataKeys, ...filteredMetadataKeys];
+    }, [filteredNonMetadataKeys, filteredMetadataKeys]);
+    const [widths, setWidths] = useState({
+        name: measureGridWidth(rows.map(r => r.name), { maxWidth: 500, stripHTML: true }) + 15,
+        ...Object.fromEntries(filteredNonMetadataKeys.map(e => [
+            e,
+            measureGridWidth(rows.map(r => r[e]), { maxWidth: 400, stripHTML: true }),
+        ])),
+        ...Object.fromEntries(filteredMetadataKeys.map(e => [
+            e,
+            measureGridWidth(rows.map(r => r.metadata[e]), { maxWidth: 400, stripHTML: true }),
+        ])),
+    });
+    const [visible, setVisible] = useState(Object.fromEntries(fields.map(c => [c, true])));
+    useEffect(() => {
+        setVisible(visible => ({
+            ...Object.fromEntries(fields.map(c => [c, true])),
+            ...visible,
+        }));
+    }, [fields]);
+    useEffect(() => {
+        setWidths(widths => ({
+            name: widths.name,
+            ...Object.fromEntries(filteredNonMetadataKeys
+                .filter(f => visible[f])
+                .map(e => [
+                e,
+                measureGridWidth(rows.map(r => r[e]), { stripHTML: true, maxWidth: 400 }),
+            ])),
+            ...Object.fromEntries(filteredMetadataKeys
+                .filter(f => visible[f])
+                .map(e => [
+                e,
+                measureGridWidth(rows.map(r => r.metadata[e]), { stripHTML: true, maxWidth: 400 }),
+            ])),
+        }));
+    }, [filteredMetadataKeys, visible, filteredNonMetadataKeys, hideSparse, rows]);
+    const widthsDebounced = useDebounce(widths, 400);
+    const columns = [
+        {
+            field: 'name',
+            hideable: false,
+            renderCell: (params) => {
+                const { value, id, row } = params;
+                return (React.createElement(React.Fragment, null,
+                    React.createElement(SanitizedHTML, { html: value }),
+                    React.createElement(IconButton, { onClick: e => setInfo({
+                            target: e.currentTarget,
+                            id: id,
+                            conf: row.conf,
+                        }) },
+                        React.createElement(MoreHoriz, null))));
+            },
+            width: widthsDebounced.name || 100, // can be undefined before useEffect update
+        },
+        ...filteredNonMetadataKeys.map(e => ({
+            field: e,
+            width: widthsDebounced[e] || 100,
+            renderCell: (params) => {
+                const { value } = params;
+                return value ? React.createElement(SanitizedHTML, { html: value }) : '';
+            },
+        })),
+        ...filteredMetadataKeys.map(e => ({
+            field: e,
+            width: widthsDebounced[e] || 100,
+            renderCell: (params) => {
+                const { value } = params;
+                return value ? React.createElement(SanitizedHTML, { html: value }) : '';
+            },
+        })),
+    ];
+    const shownTrackIds = view.tracks.map(
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    (t) => t.configuration.trackId);
+    const arrFilters = Object.entries(filters).filter(f => f[1].length > 0);
+    return (React.createElement(React.Fragment, null,
+        info ? (React.createElement(JBrowseMenu, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: ((_a = session.getTrackActionMenuItems) === null || _a === void 0 ? void 0 : _a.call(session, info.conf)) || [], onMenuItemClick: (_event, callback) => {
+                callback();
+                setInfo(undefined);
+            }, open: !!info, onClose: () => setInfo(undefined) })) : null,
+        React.createElement(FacetedHeader, { setHideSparse: setHideSparse, setFilterText: setFilterText, setUseShoppingCart: setUseShoppingCart, hideSparse: hideSparse, filterText: filterText, useShoppingCart: useShoppingCart, model: model }),
+        React.createElement("div", { ref: ref, style: {
+                display: 'flex',
+                overflow: 'hidden',
+                height: window.innerHeight * frac,
+                width: window.innerWidth * frac,
+            } },
+            React.createElement("div", { style: {
+                    height: window.innerHeight * frac,
+                    width: window.innerWidth * frac - panelWidth,
+                } },
+                React.createElement(ResizeBar, { checkbox: true, widths: Object.values(widths), setWidths: newWidths => setWidths(Object.fromEntries(Object.entries(widths).map((entry, idx) => [
+                        entry[0],
+                        newWidths[idx],
+                    ]))), scrollLeft: scrollLeft }),
+                React.createElement(DataGrid, { rows: rows.filter(row => arrFilters.every(([key, val]) => val.includes(row[key]))), columnVisibilityModel: visible, onColumnVisibilityModelChange: newModel => setVisible(newModel), headerHeight: 35, checkboxSelection: true, disableSelectionOnClick: true, keepNonExistentRowsSelected: true, onSelectionModelChange: userSelectedIds => {
+                        if (!useShoppingCart) {
+                            const a1 = shownTrackIds;
+                            const a2 = userSelectedIds;
+                            // synchronize the user selection with the view
+                            // see share https://stackoverflow.com/a/33034768/2129219
+                            transaction(() => {
+                                a1.filter(x => !a2.includes(x)).map(t => view.hideTrack(t));
+                                a2.filter(x => !a1.includes(x)).map(t => view.showTrack(t));
+                            });
+                        }
+                        else {
+                            const root = getRoot(model);
+                            const schema = pluginManager.pluggableConfigSchemaType('track');
+                            const tracks = userSelectedIds.map(id => resolveIdentifier(schema, root, id));
+                            model.setSelection(tracks);
+                        }
+                    }, selectionModel: useShoppingCart ? selection.map(s => s.trackId) : shownTrackIds, columns: columns, rowHeight: 25 })),
+            React.createElement(ResizeHandle, { vertical: true, onDrag: dist => setPanelWidth(panelWidth - dist), style: { background: 'grey', width: 5 } }),
+            React.createElement("div", { style: { width: panelWidth, overflowY: 'auto', overflowX: 'hidden' } },
+                React.createElement(FacetFilters, { width: panelWidth - 10, rows: rows, columns: columns, dispatch: dispatch, filters: filters })))));
+});
+//# sourceMappingURL=FacetedSelector.js.map

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js.map

@@ -0,0 +1 @@
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package/esm/HierarchicalTrackSelectorWidget/components/faceted/util.d.ts

@@ -0,0 +1 @@
+export declare function getRootKeys(obj: Record<string, unknown>): string[];

package/esm/HierarchicalTrackSelectorWidget/components/faceted/util.js

@@ -0,0 +1,6 @@
+export function getRootKeys(obj) {
+    return Object.entries(obj)
+        .map(([key, val]) => (typeof val === 'string' ? key : ''))
+        .filter(f => !!f);
+}
+//# sourceMappingURL=util.js.map

package/esm/HierarchicalTrackSelectorWidget/components/faceted/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../../src/HierarchicalTrackSelectorWidget/components/faceted/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,WAAW,CAAC,GAA4B;IACtD,OAAO,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC;SACvB,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,OAAO,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;SACzD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrB,CAAC"}

package/esm/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { HierarchicalTrackSelectorModel } from '../../model';
+declare const _default: ({ model, setAssemblyIdx, }: {
+    model: HierarchicalTrackSelectorModel;
+    setAssemblyIdx: Function;
+}) => JSX.Element;
+export default _default;

package/esm/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.js

@@ -0,0 +1,108 @@
+import React, { Suspense, lazy, useState } from 'react';
+import { IconButton } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import JBrowseMenu from '@jbrowse/core/ui/Menu';
+import { getSession, isSessionModelWithWidgets, isSessionModelWithConnections, } from '@jbrowse/core/util';
+import { readConfObject, } from '@jbrowse/core/configuration';
+// icons
+import MenuIcon from '@mui/icons-material/Menu';
+// lazy components
+const CloseConnectionDlg = lazy(() => import('../dialogs/CloseConnectionDialog'));
+const DeleteConnectionDlg = lazy(() => import('../dialogs/DeleteConnectionDialog'));
+const ManageConnectionsDlg = lazy(() => import('../dialogs/ManageConnectionsDialog'));
+const ToggleConnectionsDlg = lazy(() => import('../dialogs/ToggleConnectionsDialog'));
+const useStyles = makeStyles()(theme => ({
+    menuIcon: {
+        marginRight: theme.spacing(1),
+        marginBottom: 0,
+    },
+}));
+export default observer(function HamburgerMenu({ model, setAssemblyIdx, }) {
+    const session = getSession(model);
+    const [menuEl, setMenuEl] = useState();
+    const [modalInfo, setModalInfo] = useState();
+    const [deleteDlgDetails, setDeleteDlgDetails] = useState();
+    const [connectionToggleOpen, setConnectionToggleOpen] = useState(false);
+    const [connectionManagerOpen, setConnectionManagerOpen] = useState(false);
+    const { classes } = useStyles();
+    const { assemblyNames } = model;
+    function breakConnection(connectionConf, deletingConnection) {
+        const name = readConfObject(connectionConf, 'name');
+        // @ts-ignore
+        const result = session.prepareToBreakConnection(connectionConf);
+        if (result) {
+            const [safelyBreakConnection, dereferenceTypeCount] = result;
+            if (Object.keys(dereferenceTypeCount).length > 0) {
+                setModalInfo({
+                    connectionConf,
+                    safelyBreakConnection,
+                    dereferenceTypeCount,
+                    name,
+                });
+            }
+            else {
+                safelyBreakConnection();
+            }
+        }
+        if (deletingConnection) {
+            setDeleteDlgDetails({ name, connectionConf });
+        }
+    }
+    const connectionMenuItems = [
+        {
+            label: 'Turn on/off connections...',
+            onClick: () => setConnectionToggleOpen(true),
+        },
+    ];
+    if (isSessionModelWithConnections(session)) {
+        connectionMenuItems.unshift({
+            label: 'Add connection...',
+            onClick: () => {
+                if (isSessionModelWithWidgets(session)) {
+                    session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
+                }
+            },
+        });
+        connectionMenuItems.push({
+            label: 'Delete connections...',
+            onClick: () => setConnectionManagerOpen(true),
+        });
+    }
+    return (React.createElement(React.Fragment, null,
+        React.createElement(IconButton, { className: classes.menuIcon, onClick: event => setMenuEl(event.currentTarget) },
+            React.createElement(MenuIcon, null)),
+        React.createElement(JBrowseMenu, { anchorEl: menuEl, open: Boolean(menuEl), onMenuItemClick: (_, callback) => {
+                callback();
+                setMenuEl(undefined);
+            }, onClose: () => setMenuEl(undefined), menuItems: [
+                {
+                    label: 'Add track...',
+                    onClick: () => {
+                        if (isSessionModelWithWidgets(session)) {
+                            session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                                view: model.view.id,
+                            }));
+                        }
+                    },
+                },
+                ...(session.makeConnection ? connectionMenuItems : []),
+                ...(assemblyNames.length > 1
+                    ? [
+                        {
+                            label: 'Select assembly...',
+                            subMenu: assemblyNames.map((name, idx) => ({
+                                label: name,
+                                onClick: () => setAssemblyIdx(idx),
+                            })),
+                        },
+                    ]
+                    : []),
+            ] }),
+        React.createElement(Suspense, { fallback: React.createElement("div", null) },
+            modalInfo ? (React.createElement(CloseConnectionDlg, { modalInfo: modalInfo, setModalInfo: setModalInfo })) : null,
+            deleteDlgDetails ? (React.createElement(DeleteConnectionDlg, { handleClose: () => setDeleteDlgDetails(undefined), deleteDialogDetails: deleteDlgDetails, session: session })) : null,
+            connectionManagerOpen ? (React.createElement(ManageConnectionsDlg, { handleClose: () => setConnectionManagerOpen(false), breakConnection: breakConnection, session: session })) : null,
+            connectionToggleOpen ? (React.createElement(ToggleConnectionsDlg, { handleClose: () => setConnectionToggleOpen(false), session: session, breakConnection: breakConnection })) : null)));
+});
+//# sourceMappingURL=HamburgerMenu.js.map

package/esm/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"HamburgerMenu.js","sourceRoot":"","sources":["../../../../src/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,WAAW,MAAM,uBAAuB,CAAA;AAC/C,OAAO,EACL,UAAU,EACV,yBAAyB,EACzB,6BAA6B,GAC9B,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAEL,cAAc,GACf,MAAM,6BAA6B,CAAA;AAEpC,QAAQ;AACR,OAAO,QAAQ,MAAM,0BAA0B,CAAA;AAK/C,kBAAkB;AAClB,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,kCAAkC,CAAC,CACjD,CAAA;AACD,MAAM,mBAAmB,GAAG,IAAI,CAC9B,GAAG,EAAE,CAAC,MAAM,CAAC,mCAAmC,CAAC,CAClD,CAAA;AACD,MAAM,oBAAoB,GAAG,IAAI,CAC/B,GAAG,EAAE,CAAC,MAAM,CAAC,oCAAoC,CAAC,CACnD,CAAA;AACD,MAAM,oBAAoB,GAAG,IAAI,CAC/B,GAAG,EAAE,CAAC,MAAM,CAAC,oCAAoC,CAAC,CACnD,CAAA;AAED,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,QAAQ,EAAE;QACR,WAAW,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAC7B,YAAY,EAAE,CAAC;KAChB;CACF,CAAC,CAAC,CAAA;AAcH,eAAe,QAAQ,CAAC,SAAS,aAAa,CAAC,EAC7C,KAAK,EACL,cAAc,GAIf;IACC,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,QAAQ,EAAqB,CAAA;IACzD,MAAM,CAAC,SAAS,EAAE,YAAY,CAAC,GAAG,QAAQ,EAAa,CAAA;IACvD,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC,GAAG,QAAQ,EAAiB,CAAA;IACzE,MAAM,CAAC,oBAAoB,EAAE,uBAAuB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACvE,MAAM,CAAC,qBAAqB,EAAE,wBAAwB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACzE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAE/B,SAAS,eAAe,CACtB,cAAqC,EACrC,kBAA4B;QAE5B,MAAM,IAAI,GAAG,cAAc,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;QAEnD,aAAa;QACb,MAAM,MAAM,GAAG,OAAO,CAAC,wBAAwB,CAAC,cAAc,CAAC,CAAA;QAC/D,IAAI,MAAM,EAAE;YACV,MAAM,CAAC,qBAAqB,EAAE,oBAAoB,CAAC,GAAG,MAAM,CAAA;YAC5D,IAAI,MAAM,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE;gBAChD,YAAY,CAAC;oBACX,cAAc;oBACd,qBAAqB;oBACrB,oBAAoB;oBACpB,IAAI;iBACL,CAAC,CAAA;aACH;iBAAM;gBACL,qBAAqB,EAAE,CAAA;aACxB;SACF;QACD,IAAI,kBAAkB,EAAE;YACtB,mBAAmB,CAAC,EAAE,IAAI,EAAE,cAAc,EAAE,CAAC,CAAA;SAC9C;IACH,CAAC;IAED,MAAM,mBAAmB,GAAG;QAC1B;YACE,KAAK,EAAE,4BAA4B;YACnC,OAAO,EAAE,GAAG,EAAE,CAAC,uBAAuB,CAAC,IAAI,CAAC;SAC7C;KACF,CAAA;IAED,IAAI,6BAA6B,CAAC,OAAO,CAAC,EAAE;QAC1C,mBAAmB,CAAC,OAAO,CAAC;YAC1B,KAAK,EAAE,mBAAmB;YAC1B,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE;oBACtC,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,qBAAqB,EAAE,qBAAqB,CAAC,CAChE,CAAA;iBACF;YACH,CAAC;SACF,CAAC,CAAA;QAEF,mBAAmB,CAAC,IAAI,CAAC;YACvB,KAAK,EAAE,uBAAuB;YAC9B,OAAO,EAAE,GAAG,EAAE,CAAC,wBAAwB,CAAC,IAAI,CAAC;SAC9C,CAAC,CAAA;KACH;IACD,OAAO,CACL;QACE,oBAAC,UAAU,IACT,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,OAAO,EAAE,KAAK,CAAC,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,aAAa,CAAC;YAEhD,oBAAC,QAAQ,OAAG,CACD;QAEb,oBAAC,WAAW,IACV,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,OAAO,CAAC,MAAM,CAAC,EACrB,eAAe,EAAE,CAAC,CAAC,EAAE,QAAQ,EAAE,EAAE;gBAC/B,QAAQ,EAAE,CAAA;gBACV,SAAS,CAAC,SAAS,CAAC,CAAA;YACtB,CAAC,EACD,OAAO,EAAE,GAAG,EAAE,CAAC,SAAS,CAAC,SAAS,CAAC,EACnC,SAAS,EAAE;gBACT;oBACE,KAAK,EAAE,cAAc;oBACrB,OAAO,EAAE,GAAG,EAAE;wBACZ,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE;4BACtC,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,gBAAgB,EAAE,gBAAgB,EAAE;gCACpD,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,EAAE;6BACpB,CAAC,CACH,CAAA;yBACF;oBACH,CAAC;iBACF;gBACD,GAAG,CAAC,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,mBAAmB,CAAC,CAAC,CAAC,EAAE,CAAC;gBAEtD,GAAG,CAAC,aAAa,CAAC,MAAM,GAAG,CAAC;oBAC1B,CAAC,CAAC;wBACE;4BACE,KAAK,EAAE,oBAAoB;4BAC3B,OAAO,EAAE,aAAa,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,GAAG,EAAE,EAAE,CAAC,CAAC;gCACzC,KAAK,EAAE,IAAI;gCACX,OAAO,EAAE,GAAG,EAAE,CAAC,cAAc,CAAC,GAAG,CAAC;6BACnC,CAAC,CAAC;yBACJ;qBACF;oBACH,CAAC,CAAC,EAAE,CAAC;aACR,GACD;QACF,oBAAC,QAAQ,IAAC,QAAQ,EAAE,gCAAO;YACxB,SAAS,CAAC,CAAC,CAAC,CACX,oBAAC,kBAAkB,IACjB,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,YAAY,GAC1B,CACH,CAAC,CAAC,CAAC,IAAI;YACP,gBAAgB,CAAC,CAAC,CAAC,CAClB,oBAAC,mBAAmB,IAClB,WAAW,EAAE,GAAG,EAAE,CAAC,mBAAmB,CAAC,SAAS,CAAC,EACjD,mBAAmB,EAAE,gBAAgB,EACrC,OAAO,EAAE,OAAO,GAChB,CACH,CAAC,CAAC,CAAC,IAAI;YACP,qBAAqB,CAAC,CAAC,CAAC,CACvB,oBAAC,oBAAoB,IACnB,WAAW,EAAE,GAAG,EAAE,CAAC,wBAAwB,CAAC,KAAK,CAAC,EAClD,eAAe,EAAE,eAAe,EAChC,OAAO,EAAE,OAAO,GAChB,CACH,CAAC,CAAC,CAAC,IAAI;YACP,oBAAoB,CAAC,CAAC,CAAC,CACtB,oBAAC,oBAAoB,IACnB,WAAW,EAAE,GAAG,EAAE,CAAC,uBAAuB,CAAC,KAAK,CAAC,EACjD,OAAO,EAAE,OAAO,EAChB,eAAe,EAAE,eAAe,GAChC,CACH,CAAC,CAAC,CAAC,IAAI,CACC,CACV,CACJ,CAAA;AACH,CAAC,CAAC,CAAA"}

package/esm/HierarchicalTrackSelectorWidget/components/{Header.d.ts → tree/HierarchicalHeader.d.ts}

@@ -1,10 +1,9 @@
 /// <reference types="react" />
-import { HierarchicalTrackSelectorModel } from '../model';
-declare function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, setAssemblyIdx, assemblyIdx, }: {
+import { HierarchicalTrackSelectorModel } from '../../model';
+declare function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, setAssemblyIdx, }: {
     model: HierarchicalTrackSelectorModel;
     setHeaderHeight: (n: number) => void;
     setAssemblyIdx: (n: number) => void;
-    assemblyIdx: number;
 }): JSX.Element;
 declare const _default: typeof HierarchicalTrackSelectorHeader;
 export default _default;

package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalHeader.js

@@ -0,0 +1,37 @@
+import React, { Suspense, lazy, useState } from 'react';
+import { Button, IconButton, InputAdornment, TextField } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+// icons
+import ClearIcon from '@mui/icons-material/Clear';
+import HamburgerMenu from './HamburgerMenu';
+import ShoppingCart from '../ShoppingCart';
+// lazies
+const FacetedDialog = lazy(() => import('../faceted/FacetedDialog'));
+const useStyles = makeStyles()(theme => ({
+    searchBox: {
+        margin: theme.spacing(2),
+    },
+    menuIcon: {
+        marginRight: theme.spacing(1),
+        marginBottom: 0,
+    },
+}));
+function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, setAssemblyIdx, }) {
+    const { classes } = useStyles();
+    const [facetedOpen, setFacetedOpen] = useState(false);
+    const { filterText } = model;
+    return (React.createElement("div", { ref: ref => setHeaderHeight((ref === null || ref === void 0 ? void 0 : ref.getBoundingClientRect().height) || 0), "data-testid": "hierarchical_track_selector" },
+        React.createElement("div", { style: { display: 'flex' } },
+            React.createElement(HamburgerMenu, { model: model, setAssemblyIdx: setAssemblyIdx }),
+            React.createElement(ShoppingCart, { model: model }),
+            React.createElement(TextField, { className: classes.searchBox, label: "Filter tracks", value: filterText, onChange: event => model.setFilterText(event.target.value), fullWidth: true, InputProps: {
+                    endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                        React.createElement(IconButton, { onClick: () => model.clearFilterText() },
+                            React.createElement(ClearIcon, null)))),
+                } }),
+            React.createElement(Button, { className: classes.menuIcon, onClick: () => setFacetedOpen(true) }, "Open faceted selector")),
+        React.createElement(Suspense, { fallback: React.createElement("div", null) }, facetedOpen ? (React.createElement(FacetedDialog, { handleClose: () => setFacetedOpen(false), model: model })) : null)));
+}
+export default observer(HierarchicalTrackSelectorHeader);
+//# sourceMappingURL=HierarchicalHeader.js.map

package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalHeader.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"HierarchicalHeader.js","sourceRoot":"","sources":["../../../../src/HierarchicalTrackSelectorWidget/components/tree/HierarchicalHeader.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvD,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,cAAc,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAC7E,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,QAAQ;AACR,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAIjD,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAC3C,OAAO,YAAY,MAAM,iBAAiB,CAAA;AAE1C,SAAS;AACT,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,0BAA0B,CAAC,CAAC,CAAA;AAEpE,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,SAAS,EAAE;QACT,MAAM,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KACzB;IACD,QAAQ,EAAE;QACR,WAAW,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAC7B,YAAY,EAAE,CAAC;KAChB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,+BAA+B,CAAC,EACvC,KAAK,EACL,eAAe,EACf,cAAc,GAKf;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,WAAW,EAAE,cAAc,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACrD,MAAM,EAAE,UAAU,EAAE,GAAG,KAAK,CAAA;IAE5B,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,CAAC,EAAE,CAAC,eAAe,CAAC,CAAA,GAAG,aAAH,GAAG,uBAAH,GAAG,CAAE,qBAAqB,GAAG,MAAM,KAAI,CAAC,CAAC,iBACzD,6BAA6B;QAEzC,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;YAC7B,oBAAC,aAAa,IAAC,KAAK,EAAE,KAAK,EAAE,cAAc,EAAE,cAAc,GAAI;YAC/D,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;YAE9B,oBAAC,SAAS,IACR,SAAS,EAAE,OAAO,CAAC,SAAS,EAC5B,KAAK,EAAC,eAAe,EACrB,KAAK,EAAE,UAAU,EACjB,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,aAAa,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC1D,SAAS,QACT,UAAU,EAAE;oBACV,YAAY,EAAE,CACZ,oBAAC,cAAc,IAAC,QAAQ,EAAC,KAAK;wBAC5B,oBAAC,UAAU,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,eAAe,EAAE;4BAChD,oBAAC,SAAS,OAAG,CACF,CACE,CAClB;iBACF,GACD;YACF,oBAAC,MAAM,IACL,SAAS,EAAE,OAAO,CAAC,QAAQ,EAC3B,OAAO,EAAE,GAAG,EAAE,CAAC,cAAc,CAAC,IAAI,CAAC,4BAG5B,CACL;QAEN,oBAAC,QAAQ,IAAC,QAAQ,EAAE,gCAAO,IACxB,WAAW,CAAC,CAAC,CAAC,CACb,oBAAC,aAAa,IACZ,WAAW,EAAE,GAAG,EAAE,CAAC,cAAc,CAAC,KAAK,CAAC,EACxC,KAAK,EAAE,KAAK,GACZ,CACH,CAAC,CAAC,CAAC,IAAI,CACC,CACP,CACP,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,+BAA+B,CAAC,CAAA"}

package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.d.ts

@@ -0,0 +1,8 @@
+/// <reference types="react" />
+import { TreeNode, HierarchicalTrackSelectorModel } from '../../model';
+declare const _default: ({ height, tree, model, }: {
+    height: number;
+    tree: TreeNode;
+    model: HierarchicalTrackSelectorModel;
+}) => JSX.Element;
+export default _default;

package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.js

@@ -0,0 +1,63 @@
+import React, { useCallback, useMemo, useRef, useEffect } from 'react';
+import { observer } from 'mobx-react';
+import { VariableSizeTree } from 'react-vtree';
+import { getSession } from '@jbrowse/core/util';
+import Node from './TrackListNode';
+function getNodeData(node, nestingLevel, extra, selection) {
+    const isLeaf = !!node.conf;
+    const selected = !!selection[node.id];
+    return {
+        data: {
+            defaultHeight: isLeaf ? 22 : 40,
+            isLeaf,
+            isOpenByDefault: true,
+            nestingLevel,
+            selected,
+            ...node,
+            ...extra,
+        },
+        nestingLevel,
+        node,
+    };
+}
+// this is the main tree component for the hierarchical track selector in note:
+// in jbrowse-web the toolbar is position="sticky" which means the autosizer
+// includes the height of the toolbar, so we subtract the given offsets
+export default observer(function HierarchicalTree({ height, tree, model, }) {
+    const { filterText, selection, view } = model;
+    const treeRef = useRef(null);
+    const session = getSession(model);
+    const { drawerPosition } = session;
+    const obj = useMemo(() => Object.fromEntries(selection.map(s => [s.trackId, s])), [selection]);
+    const extra = useMemo(() => ({
+        onChange: (trackId) => view.toggleTrack(trackId),
+        toggleCollapse: (pathName) => model.toggleCategory(pathName),
+        tree,
+        model,
+        drawerPosition,
+    }), [view, model, drawerPosition, tree]);
+    const treeWalker = useCallback(function* treeWalker() {
+        for (let i = 0; i < tree.children.length; i++) {
+            const r = tree.children[i];
+            yield getNodeData(r, 0, extra, obj);
+        }
+        while (true) {
+            // @ts-ignore
+            const parentMeta = yield;
+            for (let i = 0; i < parentMeta.node.children.length; i++) {
+                const curr = parentMeta.node.children[i];
+                yield getNodeData(curr, parentMeta.nestingLevel + 1, extra, obj);
+            }
+        }
+    }, [tree, extra, obj]);
+    useEffect(() => {
+        // @ts-ignore
+        treeRef.current.recomputeTree({
+            refreshNodes: true,
+            useDefaultHeight: true,
+        });
+    }, [tree, filterText]);
+    return (React.createElement(React.Fragment, null,
+        React.createElement(VariableSizeTree, { ref: treeRef, treeWalker: treeWalker, height: height }, Node)));
+});
+//# sourceMappingURL=HierarchicalTree.js.map

package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.js.map

@@ -0,0 +1 @@
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package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackCategory.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { NodeData } from '../util';
+export default function Category({ isOpen, setOpen, data, }: {
+    isOpen: boolean;
+    setOpen: (arg: boolean) => void;
+    data: NodeData;
+}): JSX.Element;