@jbrowse/plugin-data-management 2.4.2 → 2.6.1

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

@@ -3,10 +3,11 @@ 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';
+import { DataGrid, GridToolbar } from '@mui/x-data-grid';
 // jbrowse
 import { getTrackName } from '@jbrowse/core/util/tracks';
-import { ResizeHandle, SanitizedHTML } from '@jbrowse/core/ui';
+import { ResizeHandle } from '@jbrowse/core/ui';
+import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
 import JBrowseMenu from '@jbrowse/core/ui/Menu';
 import ResizeBar, { useResizeBar } from '@jbrowse/core/ui/ResizeBar';
 import { getEnv, getSession, measureGridWidth, useDebounce, } from '@jbrowse/core/util';
@@ -21,26 +22,26 @@ 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;
+    var _a, _b;
+    const { view, selection } = model;
     const { pluginManager } = getEnv(model);
     const { ref, scrollLeft } = useResizeBar();
     const [filterText, setFilterText] = useState('');
+    const [showOptions, setShowOptions] = useState(false);
     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 tracks = view.tracks;
     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)
+        return model.trackConfigurations
             .filter(conf => matches(filterDebounced, conf, session))
             .map(track => {
             var _a, _b;
@@ -56,14 +57,12 @@ export default observer(function FacetedSelector({ model, }) {
                 ...metadata,
             };
         });
-    }, [assemblyName, model, filterDebounced, session]);
+    }, [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.flatMap(row => getRootKeys(row.metadata)))].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 fields = useMemo(() => ['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 => [
@@ -115,35 +114,39 @@ export default observer(function FacetedSelector({ model, }) {
                         }) },
                         React.createElement(MoreHoriz, null))));
             },
-            width: widthsDebounced.name || 100, // can be undefined before useEffect update
+            width: (_a = widthsDebounced.name) !== null && _a !== void 0 ? _a : 100,
         },
-        ...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 }) : '';
-            },
-        })),
+        ...filteredNonMetadataKeys.map(e => {
+            var _a;
+            return ({
+                field: e,
+                width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 100,
+                renderCell: (params) => {
+                    const { value } = params;
+                    return value ? React.createElement(SanitizedHTML, { html: value }) : '';
+                },
+            });
+        }),
+        ...filteredMetadataKeys.map(e => {
+            var _a;
+            return ({
+                field: e,
+                width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 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 shownTrackIds = tracks.map(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) => {
+        info ? (React.createElement(JBrowseMenu, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: ((_b = session.getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.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(FacetedHeader, { setHideSparse: setHideSparse, setShowOptions: setShowOptions, setFilterText: setFilterText, setUseShoppingCart: setUseShoppingCart, hideSparse: hideSparse, showOptions: showOptions, filterText: filterText, useShoppingCart: useShoppingCart, model: model }),
         React.createElement("div", { ref: ref, style: {
                 display: 'flex',
                 overflow: 'hidden',
@@ -154,11 +157,11 @@ export default observer(function FacetedSelector({ model, }) {
                     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) => [
+                React.createElement(ResizeBar, { checkbox: true, widths: Object.values(widths).map(f => f !== null && f !== void 0 ? f : 100), 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 => {
+                React.createElement(DataGrid, { rows: rows.filter(row => arrFilters.every(([key, val]) => val.includes(row[key]))), columnVisibilityModel: visible, onColumnVisibilityModelChange: newModel => setVisible(newModel), columnHeaderHeight: 35, checkboxSelection: true, disableRowSelectionOnClick: true, keepNonExistentRowsSelected: true, onRowSelectionModelChange: userSelectedIds => {
                         if (!useShoppingCart) {
                             const a1 = shownTrackIds;
                             const a2 = userSelectedIds;
@@ -175,7 +178,9 @@ export default observer(function FacetedSelector({ model, }) {
                             const tracks = userSelectedIds.map(id => resolveIdentifier(schema, root, id));
                             model.setSelection(tracks);
                         }
-                    }, selectionModel: useShoppingCart ? selection.map(s => s.trackId) : shownTrackIds, columns: columns, rowHeight: 25 })),
+                    }, rowSelectionModel: useShoppingCart ? selection.map(s => s.trackId) : shownTrackIds, slots: { toolbar: showOptions ? GridToolbar : null }, slotProps: {
+                        toolbar: { printOptions: { disableToolbarButton: true } },
+                    }, 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 })))));

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

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

@@ -1,7 +1,6 @@
-/// <reference types="react" />
+import React from 'react';
 import { HierarchicalTrackSelectorModel } from '../../model';
-declare const _default: ({ model, setAssemblyIdx, }: {
+declare const _default: ({ model, }: {
     model: HierarchicalTrackSelectorModel;
-    setAssemblyIdx: Function;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

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

@@ -3,7 +3,7 @@ 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 { getSession, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
 import { readConfObject, } from '@jbrowse/core/configuration';
 // icons
 import MenuIcon from '@mui/icons-material/Menu';
@@ -18,7 +18,7 @@ const useStyles = makeStyles()(theme => ({
         marginBottom: 0,
     },
 }));
-export default observer(function HamburgerMenu({ model, setAssemblyIdx, }) {
+export default observer(function HamburgerMenu({ model, }) {
     const session = getSession(model);
     const [menuEl, setMenuEl] = useState();
     const [modalInfo, setModalInfo] = useState();
@@ -26,7 +26,6 @@ export default observer(function HamburgerMenu({ model, setAssemblyIdx, }) {
     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');
         const result = session.prepareToBreakConnection(connectionConf);
@@ -48,26 +47,6 @@ export default observer(function HamburgerMenu({ model, setAssemblyIdx, }) {
             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)),
@@ -75,31 +54,47 @@ export default observer(function HamburgerMenu({ model, setAssemblyIdx, }) {
                 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
+                ...(isSessionWithAddTracks(session)
                     ? [
                         {
-                            label: 'Select assembly...',
-                            subMenu: assemblyNames.map((name, idx) => ({
-                                label: name,
-                                onClick: () => setAssemblyIdx(idx),
-                            })),
+                            label: 'Add track...',
+                            onClick: () => {
+                                if (isSessionModelWithWidgets(session)) {
+                                    session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                                        view: model.view.id,
+                                    }));
+                                }
+                            },
+                        },
+                    ]
+                    : []),
+                ...(isSessionModelWithConnections(session)
+                    ? [
+                        {
+                            label: 'Turn on/off connections...',
+                            onClick: () => setConnectionToggleOpen(true),
+                        },
+                    ]
+                    : []),
+                ...(isSessionModelWithConnectionEditing(session)
+                    ? [
+                        {
+                            label: 'Add connection...',
+                            onClick: () => {
+                                if (isSessionModelWithWidgets(session)) {
+                                    session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
+                                }
+                            },
+                        },
+                        {
+                            label: 'Delete connections...',
+                            onClick: () => setConnectionManagerOpen(true),
                         },
                     ]
                     : []),
             ] }),
-        React.createElement(Suspense, { fallback: React.createElement("div", null) },
-            modalInfo ? (React.createElement(CloseConnectionDlg, { modalInfo: modalInfo, setModalInfo: setModalInfo })) : null,
+        React.createElement(Suspense, { fallback: React.createElement(React.Fragment, null) },
+            modalInfo ? (React.createElement(CloseConnectionDlg, { modalInfo: modalInfo, onClose: () => setModalInfo(undefined) })) : 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)));

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

@@ -1 +1 @@
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+{"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,mCAAmC,EACnC,6BAA6B,EAC7B,yBAAyB,EACzB,sBAAsB,GACvB,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,GAGN;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;IAE/B,SAAS,eAAe,CACtB,cAAqC,EACrC,kBAA4B;QAE5B,MAAM,IAAI,GAAG,cAAc,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;QACnD,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,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,GAAG,CAAC,sBAAsB,CAAC,OAAO,CAAC;oBACjC,CAAC,CAAC;wBACE;4BACE,KAAK,EAAE,cAAc;4BACrB,OAAO,EAAE,GAAG,EAAE;gCACZ,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE;oCACtC,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,gBAAgB,EAAE,gBAAgB,EAAE;wCACpD,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,EAAE;qCACpB,CAAC,CACH,CAAA;iCACF;4BACH,CAAC;yBACF;qBACF;oBACH,CAAC,CAAC,EAAE,CAAC;gBACP,GAAG,CAAC,6BAA6B,CAAC,OAAO,CAAC;oBACxC,CAAC,CAAC;wBACE;4BACE,KAAK,EAAE,4BAA4B;4BACnC,OAAO,EAAE,GAAG,EAAE,CAAC,uBAAuB,CAAC,IAAI,CAAC;yBAC7C;qBACF;oBACH,CAAC,CAAC,EAAE,CAAC;gBACP,GAAG,CAAC,mCAAmC,CAAC,OAAO,CAAC;oBAC9C,CAAC,CAAC;wBACE;4BACE,KAAK,EAAE,mBAAmB;4BAC1B,OAAO,EAAE,GAAG,EAAE;gCACZ,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE;oCACtC,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CACf,qBAAqB,EACrB,qBAAqB,CACtB,CACF,CAAA;iCACF;4BACH,CAAC;yBACF;wBACD;4BACE,KAAK,EAAE,uBAAuB;4BAC9B,OAAO,EAAE,GAAG,EAAE,CAAC,wBAAwB,CAAC,IAAI,CAAC;yBAC9C;qBACF;oBACH,CAAC,CAAC,EAAE,CAAC;aACR,GACD;QACF,oBAAC,QAAQ,IAAC,QAAQ,EAAE,oBAAC,KAAK,CAAC,QAAQ,OAAG;YACnC,SAAS,CAAC,CAAC,CAAC,CACX,oBAAC,kBAAkB,IACjB,SAAS,EAAE,SAAS,EACpB,OAAO,EAAE,GAAG,EAAE,CAAC,YAAY,CAAC,SAAS,CAAC,GACtC,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/tree/HierarchicalHeader.d.ts

@@ -1,9 +1,8 @@
-/// <reference types="react" />
+import React from 'react';
 import { HierarchicalTrackSelectorModel } from '../../model';
-declare function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, setAssemblyIdx, }: {
+declare function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, }: {
     model: HierarchicalTrackSelectorModel;
     setHeaderHeight: (n: number) => void;
-    setAssemblyIdx: (n: number) => void;
-}): JSX.Element;
+}): React.JSX.Element;
 declare const _default: typeof HierarchicalTrackSelectorHeader;
 export default _default;

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

@@ -17,13 +17,13 @@ const useStyles = makeStyles()(theme => ({
         marginBottom: 0,
     },
 }));
-function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, setAssemblyIdx, }) {
+function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, }) {
     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(HamburgerMenu, { model: model }),
             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" },

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

@@ -1 +1 @@
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package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.d.ts

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

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

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

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

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { NodeData } from '../util';
 export interface InfoArgs {
@@ -8,4 +8,4 @@ export interface InfoArgs {
 }
 export default function TrackLabel({ data }: {
     data: NodeData;
-}): JSX.Element;
+}): React.JSX.Element;

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

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { NodeData } from '../util';
 export default function Node({ data, isOpen, style, setOpen, }: {
     data: NodeData;
@@ -7,4 +7,4 @@ export default function Node({ data, isOpen, style, setOpen, }: {
         height: number;
     };
     setOpen: (arg: boolean) => void;
-}): JSX.Element;
+}): React.JSX.Element;

package/esm/HierarchicalTrackSelectorWidget/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/HierarchicalTrackSelectorWidget/model.d.ts

@@ -14,10 +14,25 @@ export type TreeNode = {
 export declare function generateHierarchy(model: HierarchicalTrackSelectorModel, trackConfigurations: AnyConfigurationModel[], collapsed: {
     get: (arg: string) => boolean | undefined;
 }, extra?: string): TreeNode[];
+/**
+ * #stateModel HierarchicalTrackSelectorWidget
+ */
 export default function stateTreeFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     */
     type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
+    /**
+     * #property
+     */
     collapsed: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+    /**
+     * #property
+     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
     selection: ({
@@ -27,28 +42,74 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
     filterText: string;
 } & {
+    /**
+     * #action
+     */
     setSelection(elt: AnyConfigurationModel[]): void;
+    /**
+     * #action
+     */
     addToSelection(elt: AnyConfigurationModel[]): void;
+    /**
+     * #action
+     */
     removeFromSelection(elt: AnyConfigurationModel[]): void;
+    /**
+     * #action
+     */
     clearSelection(): void;
+    /**
+     * #action
+     */
     setView(view: unknown): void;
+    /**
+     * #action
+     */
     toggleCategory(pathName: string): void;
+    /**
+     * #action
+     */
     clearFilterText(): void;
+    /**
+     * #action
+     */
     setFilterText(newText: string): void;
 } & {
-    getRefSeqTrackConf(assemblyName: string): any;
+    /**
+     * #method
+     */
+    getRefSeqTrackConf(assemblyName: string): AnyConfigurationModel | undefined;
 } & {
-    trackConfigurations(assemblyName: string): any[];
+    /**
+     * #getter
+     */
     readonly assemblyNames: string[];
-    connectionTrackConfigurations(assemblyName: string, connection: {
+} & {
+    /**
+     * #method
+     * filter out tracks that don't match the current display types
+     */
+    connectionTrackConfigurations(connection: {
         tracks: AnyConfigurationModel[];
     }): ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+    /**
+     * #getter
+     * filter out tracks that don't match the current assembly/display types
+     */
+    readonly trackConfigurations: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: unknown): any;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
 } & {
-    hierarchy(assemblyName: string): {
+    /**
+     * #getter
+     */
+    readonly hierarchy: {
         name: string;
         id: string;
         children: ({
@@ -64,7 +125,10 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             children: TreeNode[];
         })[];
     };
-    connectionHierarchy(assemblyName: string, connection: {
+    /**
+     * #method
+     */
+    connectionHierarchy(connection: {
         name: string;
         tracks: AnyConfigurationModel[];
     }): TreeNode[];