@jbrowse/plugin-data-management 2.6.1 → 2.6.3

package/dist/AddConnectionWidget/components/AddConnectionWidget.js

@@ -84,4 +84,3 @@ exports.default = (0, mobx_react_1.observer)(function AddConnectionWidget({ mode
                             }
                         }, className: classes.button, "data-testid": "addConnectionNext" }, activeStep === steps.length - 1 ? 'Connect' : 'Next')))))))));
 });
-//# sourceMappingURL=AddConnectionWidget.js.map

package/dist/AddConnectionWidget/components/ConfigureConnection.js

@@ -32,4 +32,3 @@ exports.default = (0, mobx_react_1.observer)(function ({ connectionType, model,
     return (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },
         react_1.default.createElement(ConfigEditorComponent, { model: { target: model }, session: session })));
 });
-//# sourceMappingURL=ConfigureConnection.js.map

package/dist/AddConnectionWidget/components/ConnectionTypeSelect.js

@@ -42,4 +42,3 @@ exports.default = (0, mobx_react_1.observer)(function ConnectionTypeSelect({ con
             connectionType.url ? (react_1.default.createElement(material_1.IconButton, { href: connectionType.url, rel: "noopener noreferrer", target: "_blank" },
                 react_1.default.createElement(OpenInNew_1.default, null))) : null)) : null, select: true, fullWidth: true, onChange: event => setConnectionType(connectionTypeChoices.find(c => c.name === event.target.value)), variant: "outlined" }, connectionTypeChoices.map(c => (react_1.default.createElement(material_1.MenuItem, { key: c.name, value: c.name }, c.displayName || c.name))))) : null));
 });
-//# sourceMappingURL=ConnectionTypeSelect.js.map

package/dist/AddConnectionWidget/index.js

@@ -42,4 +42,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/AddConnectionWidget/model.js

@@ -6,4 +6,3 @@ exports.default = mobx_state_tree_1.types.model('AddConnectionModel', {
     id: mst_1.ElementId,
     type: mobx_state_tree_1.types.literal('AddConnectionWidget'),
 });
-//# sourceMappingURL=model.js.map

package/dist/AddTrackWidget/components/AddTrackWidget.js

@@ -52,4 +52,3 @@ function AddTrackSelector({ model }) {
         react_1.default.createElement(Component, { model: model })));
 }
 exports.default = (0, mobx_react_1.observer)(AddTrackSelector);
-//# sourceMappingURL=AddTrackWidget.js.map

package/dist/AddTrackWidget/components/ConfirmTrack.js

@@ -123,4 +123,3 @@ exports.default = (0, mobx_react_1.observer)(function ConfirmTrack({ model, }) {
                     } }) }))),
         util_1.isElectron && check && supportedForIndexing ? (react_1.default.createElement(TextIndexingConfig_1.default, { model: model })) : null));
 });
-//# sourceMappingURL=ConfirmTrack.js.map

package/dist/AddTrackWidget/components/DefaultAddTrackWorkflow.js

@@ -155,4 +155,3 @@ function AddTrackWorkflow({ model }) {
                     react_1.default.createElement(material_1.Alert, { severity: "error" }, trackErrorMessage))) : null)))))));
 }
 exports.default = (0, mobx_react_1.observer)(AddTrackWorkflow);
-//# sourceMappingURL=DefaultAddTrackWorkflow.js.map

package/dist/AddTrackWidget/components/PasteConfigWorkflow.js

@@ -64,4 +64,3 @@ function AddTrackWorkflow({ model }) {
             } }, "Submit")));
 }
 exports.default = (0, mobx_react_1.observer)(AddTrackWorkflow);
-//# sourceMappingURL=PasteConfigWorkflow.js.map

package/dist/AddTrackWidget/components/TextIndexingConfig.js

@@ -100,4 +100,3 @@ const TextIndexingConfig = (0, mobx_react_1.observer)(function ({ model, }) {
                             } })))))))));
 });
 exports.default = TextIndexingConfig;
-//# sourceMappingURL=TextIndexingConfig.js.map

package/dist/AddTrackWidget/components/TrackAdapterSelector.js

@@ -47,4 +47,3 @@ const TrackAdapterSelector = (0, mobx_react_1.observer)(({ model }) => {
     })));
 });
 exports.default = TrackAdapterSelector;
-//# sourceMappingURL=TrackAdapterSelector.js.map

package/dist/AddTrackWidget/components/TrackSourceSelect.js

@@ -26,4 +26,3 @@ function TrackSourceSelect({ model }) {
         react_1.default.createElement(ui_1.FileSelector, { name: "Index file", description: "(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.", location: model.indexTrackData, setLocation: model.setIndexTrackData, setName: model.setTrackName, rootModel: rootModel })));
 }
 exports.default = (0, mobx_react_1.observer)(TrackSourceSelect);
-//# sourceMappingURL=TrackSourceSelect.js.map

package/dist/AddTrackWidget/components/TrackTypeSelector.js

@@ -24,4 +24,3 @@ const TrackTypeSelector = (0, mobx_react_1.observer)(({ model }) => {
         } }, trackTypes.map(({ name, displayName }) => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, displayName)))));
 });
 exports.default = TrackTypeSelector;
-//# sourceMappingURL=TrackTypeSelector.js.map

package/dist/AddTrackWidget/index.js

@@ -42,4 +42,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/AddTrackWidget/model.js

@@ -154,4 +154,3 @@ function f(pluginManager) {
     }));
 }
 exports.default = f;
-//# sourceMappingURL=model.js.map

package/dist/AssemblyManager/AssemblyAddForm.js

@@ -130,4 +130,3 @@ const AssemblyAddForm = (0, mobx_react_1.observer)(function ({ rootModel, setFor
         react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", startIcon: react_1.default.createElement(Add_1.default, null), onClick: createAssembly }, "Create new assembly")));
 });
 exports.default = AssemblyAddForm;
-//# sourceMappingURL=AssemblyAddForm.js.map

package/dist/AssemblyManager/AssemblyEditor.js

@@ -11,4 +11,3 @@ const AssemblyEditor = (0, mobx_react_1.observer)(({ assembly, }) => {
         react_1.default.createElement(plugin_config_1.ConfigurationEditor, { model: { target: assembly } })));
 });
 exports.default = AssemblyEditor;
-//# sourceMappingURL=AssemblyEditor.js.map

package/dist/AssemblyManager/AssemblyManager.js

@@ -54,4 +54,3 @@ const AssemblyManager = (0, mobx_react_1.observer)(function ({ rootModel, onClos
                 react_1.default.createElement(material_1.Button, { variant: "contained", startIcon: react_1.default.createElement(Add_1.default, null), onClick: () => setFormOpen(true) }, "Add new assembly"))) : null)));
 });
 exports.default = AssemblyManager;
-//# sourceMappingURL=AssemblyManager.js.map

package/dist/AssemblyManager/AssemblyTable.js

@@ -41,4 +41,3 @@ const AssemblyTable = (0, mobx_react_1.observer)(function ({ rootModel, setIsAss
             })))));
 });
 exports.default = AssemblyTable;
-//# sourceMappingURL=AssemblyTable.js.map

package/dist/AssemblyManager/index.js

@@ -6,4 +6,3 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = void 0;
 var AssemblyManager_1 = require("./AssemblyManager");
 Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(AssemblyManager_1).default; } });
-//# sourceMappingURL=index.js.map

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalFab.js

@@ -68,4 +68,3 @@ exports.default = (0, mobx_react_1.observer)(function HierarchicalFab({ model, }
                     }
                 } }, "Add track")) : null))) : null));
 });
-//# sourceMappingURL=HierarchicalFab.js.map

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js

@@ -52,4 +52,3 @@ const HierarchicalTrackSelector = (0, mobx_react_1.observer)(function ({ model,
         react_1.default.createElement(AutoSizedHierarchicalTree, { tree: model.hierarchy, model: model, offset: toolbarHeight + headerHeight })));
 });
 exports.default = HierarchicalTrackSelectorContainer;
-//# sourceMappingURL=HierarchicalTrackSelector.js.map

package/dist/HierarchicalTrackSelectorWidget/components/ShoppingCart.js

@@ -67,4 +67,3 @@ exports.default = (0, mobx_react_1.observer)(function ShoppingCart({ model, }) {
                 })),
             ] })));
 });
-//# sourceMappingURL=ShoppingCart.js.map

package/dist/HierarchicalTrackSelectorWidget/components/dialogs/CloseConnectionDialog.js

@@ -24,4 +24,3 @@ exports.default = (0, mobx_react_1.observer)(function CloseConnectionDialog({ mo
                     }
                     : () => { }, color: "primary" }, "OK"))));
 });
-//# sourceMappingURL=CloseConnectionDialog.js.map

package/dist/HierarchicalTrackSelectorWidget/components/dialogs/DeleteConnectionDialog.js

@@ -26,4 +26,3 @@ function DeleteConnectionDialog({ deleteDialogDetails, session, handleClose, })
                 } }, "OK"))));
 }
 exports.default = (0, mobx_react_1.observer)(DeleteConnectionDialog);
-//# sourceMappingURL=DeleteConnectionDialog.js.map

package/dist/HierarchicalTrackSelectorWidget/components/dialogs/ManageConnectionsDialog.js

@@ -38,4 +38,3 @@ function ManageConnectionsDlg({ session, handleClose, breakConnection, }) {
             react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), variant: "contained", color: "primary" }, "Close"))));
 }
 exports.default = (0, mobx_react_1.observer)(ManageConnectionsDlg);
-//# sourceMappingURL=ManageConnectionsDialog.js.map

package/dist/HierarchicalTrackSelectorWidget/components/dialogs/ToggleConnectionsDialog.js

@@ -53,4 +53,3 @@ exports.default = (0, mobx_react_1.observer)(function ToggleConnectionDialog({ s
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), variant: "contained", color: "primary" }, "Close"))));
 });
-//# sourceMappingURL=ToggleConnectionsDialog.js.map

package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetFilters.js

@@ -96,4 +96,3 @@ function FacetFilters({ rows, columns, dispatch, filters, width, }) {
     return (react_1.default.createElement("div", null, facets.map((column, index) => (react_1.default.createElement(FacetFilter, { key: column.field, vals: [...uniqs[index]], column: column, width: width, dispatch: dispatch, filters: filters })))));
 }
 exports.default = FacetFilters;
-//# sourceMappingURL=FacetFilters.js.map

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

@@ -15,4 +15,3 @@ function FacetedDlg(props) {
             react_1.default.createElement(FacetedSelector_1.default, { ...props }))));
 }
 exports.default = (0, mobx_react_1.observer)(FacetedDlg);
-//# sourceMappingURL=FacetedDialog.js.map

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

@@ -74,4 +74,3 @@ function FacetedHeader({ setFilterText, setUseShoppingCart, setHideSparse, setSh
             ] })));
 }
 exports.default = FacetedHeader;
-//# sourceMappingURL=FacetedHeader.js.map

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

@@ -42,11 +42,10 @@ const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
 // icons
 const MoreHoriz_1 = __importDefault(require("@mui/icons-material/MoreHoriz"));
-// locals
-const model_1 = require("../../model");
+const util_2 = require("../../util");
 const FacetedHeader_1 = __importDefault(require("./FacetedHeader"));
 const FacetFilters_1 = __importDefault(require("./FacetFilters"));
-const util_2 = require("./util");
+const util_3 = require("./util");
 const nonMetadataKeys = ['category', 'adapter', 'description'];
 const frac = 0.75;
 exports.default = (0, mobx_react_1.observer)(function FacetedSelector({ model, }) {
@@ -70,7 +69,7 @@ exports.default = (0, mobx_react_1.observer)(function FacetedSelector({ model, }
         // 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
-            .filter(conf => (0, model_1.matches)(filterDebounced, conf, session))
+            .filter(conf => (0, util_2.matches)(filterDebounced, conf, session))
             .map(track => {
             var _a, _b;
             const metadata = (0, configuration_1.readConfObject)(track, 'metadata');
@@ -87,7 +86,7 @@ exports.default = (0, mobx_react_1.observer)(function FacetedSelector({ model, }
         });
     }, [model, filterDebounced, session]);
     const filteredNonMetadataKeys = (0, react_1.useMemo)(() => nonMetadataKeys.filter(f => !hideSparse ? true : rows.map(r => r[f]).filter(f => !!f).length > 5), [hideSparse, rows]);
-    const filteredMetadataKeys = (0, react_1.useMemo)(() => [...new Set(rows.flatMap(row => (0, util_2.getRootKeys)(row.metadata)))].filter(f => !hideSparse
+    const filteredMetadataKeys = (0, react_1.useMemo)(() => [...new Set(rows.flatMap(row => (0, util_3.getRootKeys)(row.metadata)))].filter(f => !hideSparse
         ? true
         : rows.map(r => r.metadata[f]).filter(f => !!f).length > 5), [hideSparse, rows]);
     const fields = (0, react_1.useMemo)(() => ['name', ...filteredNonMetadataKeys, ...filteredMetadataKeys], [filteredNonMetadataKeys, filteredMetadataKeys]);
@@ -213,4 +212,3 @@ exports.default = (0, mobx_react_1.observer)(function FacetedSelector({ model, }
             react_1.default.createElement("div", { style: { width: panelWidth, overflowY: 'auto', overflowX: 'hidden' } },
                 react_1.default.createElement(FacetFilters_1.default, { width: panelWidth - 10, rows: rows, columns: columns, dispatch: dispatch, filters: filters })))));
 });
-//# sourceMappingURL=FacetedSelector.js.map

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

@@ -7,4 +7,3 @@ function getRootKeys(obj) {
         .filter(f => !!f);
 }
 exports.getRootKeys = getRootKeys;
-//# sourceMappingURL=util.js.map

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

@@ -27,33 +27,23 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
-const Menu_1 = __importDefault(require("@jbrowse/core/ui/Menu"));
 const util_1 = require("@jbrowse/core/util");
 const configuration_1 = require("@jbrowse/core/configuration");
+const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
 // icons
-const Menu_2 = __importDefault(require("@mui/icons-material/Menu"));
+const Menu_1 = __importDefault(require("@mui/icons-material/Menu"));
 // lazy components
 const CloseConnectionDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../dialogs/CloseConnectionDialog'))));
 const DeleteConnectionDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../dialogs/DeleteConnectionDialog'))));
 const ManageConnectionsDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../dialogs/ManageConnectionsDialog'))));
 const ToggleConnectionsDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../dialogs/ToggleConnectionsDialog'))));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    menuIcon: {
-        marginRight: theme.spacing(1),
-        marginBottom: 0,
-    },
-}));
 exports.default = (0, mobx_react_1.observer)(function HamburgerMenu({ model, }) {
     const session = (0, util_1.getSession)(model);
-    const [menuEl, setMenuEl] = (0, react_1.useState)();
     const [modalInfo, setModalInfo] = (0, react_1.useState)();
     const [deleteDlgDetails, setDeleteDlgDetails] = (0, react_1.useState)();
     const [connectionToggleOpen, setConnectionToggleOpen] = (0, react_1.useState)(false);
     const [connectionManagerOpen, setConnectionManagerOpen] = (0, react_1.useState)(false);
-    const { classes } = useStyles();
     function breakConnection(connectionConf, deletingConnection) {
         const name = (0, configuration_1.readConfObject)(connectionConf, 'name');
         const result = session.prepareToBreakConnection(connectionConf);
@@ -76,12 +66,7 @@ exports.default = (0, mobx_react_1.observer)(function HamburgerMenu({ model, })
         }
     }
     return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.IconButton, { className: classes.menuIcon, onClick: event => setMenuEl(event.currentTarget) },
-            react_1.default.createElement(Menu_2.default, null)),
-        react_1.default.createElement(Menu_1.default, { anchorEl: menuEl, open: Boolean(menuEl), onMenuItemClick: (_, callback) => {
-                callback();
-                setMenuEl(undefined);
-            }, onClose: () => setMenuEl(undefined), menuItems: [
+        react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: [
                 ...((0, util_1.isSessionWithAddTracks)(session)
                     ? [
                         {
@@ -120,11 +105,41 @@ exports.default = (0, mobx_react_1.observer)(function HamburgerMenu({ model, })
                         },
                     ]
                     : []),
-            ] }),
+                { type: 'divider' },
+                {
+                    label: 'Sort tracks by name',
+                    type: 'checkbox',
+                    checked: model.activeSortTrackNames,
+                    onClick: () => model.setSortTrackNames(!model.activeSortTrackNames),
+                },
+                {
+                    label: 'Sort categories by name',
+                    type: 'checkbox',
+                    checked: model.activeSortCategories,
+                    onClick: () => model.setSortCategories(!model.activeSortCategories),
+                },
+                { type: 'divider' },
+                ...(model.hasAnySubcategories
+                    ? [
+                        {
+                            label: 'Collapse subcategories',
+                            onClick: () => model.collapseSubCategories(),
+                        },
+                    ]
+                    : []),
+                {
+                    label: 'Collapse top-level categories',
+                    onClick: () => model.collapseTopLevelCategories(),
+                },
+                {
+                    label: 'Expand all categories',
+                    onClick: () => model.expandAllCategories(),
+                },
+            ] },
+            react_1.default.createElement(Menu_1.default, null)),
         react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(react_1.default.Fragment, null) },
             modalInfo ? (react_1.default.createElement(CloseConnectionDlg, { modalInfo: modalInfo, onClose: () => setModalInfo(undefined) })) : null,
             deleteDlgDetails ? (react_1.default.createElement(DeleteConnectionDlg, { handleClose: () => setDeleteDlgDetails(undefined), deleteDialogDetails: deleteDlgDetails, session: session })) : null,
             connectionManagerOpen ? (react_1.default.createElement(ManageConnectionsDlg, { handleClose: () => setConnectionManagerOpen(false), breakConnection: breakConnection, session: session })) : null,
             connectionToggleOpen ? (react_1.default.createElement(ToggleConnectionsDlg, { handleClose: () => setConnectionToggleOpen(false), session: session, breakConnection: breakConnection })) : null)));
 });
-//# sourceMappingURL=HamburgerMenu.js.map

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

@@ -45,21 +45,24 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         marginBottom: 0,
     },
 }));
+const SearchTracksTextField = (0, mobx_react_1.observer)(function ({ model, }) {
+    const { filterText } = model;
+    const { classes } = useStyles();
+    return (react_1.default.createElement(material_1.TextField, { className: classes.searchBox, label: "Filter tracks", value: filterText, onChange: event => model.setFilterText(event.target.value), fullWidth: true, InputProps: {
+            endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
+                react_1.default.createElement(material_1.IconButton, { onClick: () => model.clearFilterText() },
+                    react_1.default.createElement(Clear_1.default, null)))),
+        } }));
+});
 function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, }) {
     const { classes } = useStyles();
     const [facetedOpen, setFacetedOpen] = (0, react_1.useState)(false);
-    const { filterText } = model;
     return (react_1.default.createElement("div", { ref: ref => setHeaderHeight((ref === null || ref === void 0 ? void 0 : ref.getBoundingClientRect().height) || 0), "data-testid": "hierarchical_track_selector" },
         react_1.default.createElement("div", { style: { display: 'flex' } },
             react_1.default.createElement(HamburgerMenu_1.default, { model: model }),
             react_1.default.createElement(ShoppingCart_1.default, { model: model }),
-            react_1.default.createElement(material_1.TextField, { className: classes.searchBox, label: "Filter tracks", value: filterText, onChange: event => model.setFilterText(event.target.value), fullWidth: true, InputProps: {
-                    endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
-                        react_1.default.createElement(material_1.IconButton, { onClick: () => model.clearFilterText() },
-                            react_1.default.createElement(Clear_1.default, null)))),
-                } }),
+            react_1.default.createElement(SearchTracksTextField, { model: model }),
             react_1.default.createElement(material_1.Button, { className: classes.menuIcon, onClick: () => setFacetedOpen(true) }, "Open faceted selector")),
         react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) }, facetedOpen ? (react_1.default.createElement(FacetedDialog, { handleClose: () => setFacetedOpen(false), model: model })) : null)));
 }
 exports.default = (0, mobx_react_1.observer)(HierarchicalTrackSelectorHeader);
-//# sourceMappingURL=HierarchicalHeader.js.map

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

@@ -1,5 +1,6 @@
 import React from 'react';
-import { TreeNode, HierarchicalTrackSelectorModel } from '../../model';
+import { TreeNode } from '../../generateHierarchy';
+import { HierarchicalTrackSelectorModel } from '../../model';
 declare const _default: ({ height, tree, model, }: {
     height: number;
     tree: TreeNode;

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

@@ -88,4 +88,3 @@ exports.default = (0, mobx_react_1.observer)(function HierarchicalTree({ height,
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(react_vtree_1.VariableSizeTree, { ref: treeRef, treeWalker: treeWalker, height: height }, TrackListNode_1.default)));
 });
-//# sourceMappingURL=HierarchicalTree.js.map

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackCategory.js

@@ -80,10 +80,31 @@ function Category({ isOpen, setOpen, data, }) {
                         model.removeFromSelection((0, util_1.getAllChildren)(r));
                     },
                 },
+                {
+                    label: 'Show all tracks',
+                    onClick: () => {
+                        var _a;
+                        for (const entry of ((_a = (0, util_1.treeToMap)(tree).get(id)) === null || _a === void 0 ? void 0 : _a.children) || []) {
+                            if (!entry.children.length) {
+                                model.view.showTrack(entry.id);
+                            }
+                        }
+                    },
+                },
+                {
+                    label: 'Hide all tracks',
+                    onClick: () => {
+                        var _a;
+                        for (const entry of ((_a = (0, util_1.treeToMap)(tree).get(id)) === null || _a === void 0 ? void 0 : _a.children) || []) {
+                            if (!entry.children.length) {
+                                model.view.hideTrack(entry.id);
+                            }
+                        }
+                    },
+                },
             ], onMenuItemClick: (_event, callback) => {
                 callback();
                 setMenuEl(null);
             }, open: Boolean(menuEl), onClose: () => setMenuEl(null) })) : null));
 }
 exports.default = Category;
-//# sourceMappingURL=TrackCategory.js.map

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js

@@ -59,7 +59,7 @@ function TrackLabel({ data }) {
             react_1.default.createElement(material_1.FormControlLabel, { className: classes.checkboxLabel, control: react_1.default.createElement(material_1.Checkbox, { className: classes.compactCheckbox, checked: checked, onChange: () => onChange(id), disabled: (0, util_2.isUnsupported)(name), inputProps: {
                         // @ts-expect-error
                         'data-testid': `htsTrackEntry-${id}`,
-                    } }), label: react_1.default.createElement("div", { style: { background: selected ? '#cccc' : undefined } },
+                    } }), label: react_1.default.createElement("div", { "data-testid": `htsTrackLabel-${id}`, style: { background: selected ? '#cccc' : undefined } },
                     react_1.default.createElement(ui_1.SanitizedHTML, { html: name })) })),
         react_1.default.createElement(material_1.IconButton, { onClick: e => setInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, "data-testid": `htsTrackEntryMenu-${id}` },
             react_1.default.createElement(MoreHoriz_1.default, null)),
@@ -83,4 +83,3 @@ function TrackLabel({ data }) {
             }, open: Boolean(info), onClose: () => setInfo(undefined) })) : null));
 }
 exports.default = TrackLabel;
-//# sourceMappingURL=TrackLabel.js.map

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackListNode.js

@@ -51,4 +51,3 @@ function Node({ data, isOpen, style, setOpen, }) {
             react_1.default.createElement("div", { className: !isLeaf ? classes.accordionColor : undefined }, !isLeaf ? (react_1.default.createElement(TrackCategory_1.default, { isOpen: isOpen, data: data, setOpen: setOpen })) : (react_1.default.createElement(TrackLabel_1.default, { data: data }))))));
 }
 exports.default = Node;
-//# sourceMappingURL=TrackListNode.js.map

package/dist/HierarchicalTrackSelectorWidget/components/util.d.ts

@@ -1,5 +1,6 @@
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { HierarchicalTrackSelectorModel, TreeNode } from '../model';
+import { HierarchicalTrackSelectorModel } from '../model';
+import { TreeNode } from '../generateHierarchy';
 export interface NodeData {
     nestingLevel: number;
     checked: boolean;

package/dist/HierarchicalTrackSelectorWidget/components/util.js

@@ -21,4 +21,3 @@ function isUnsupported(name = '') {
     return name.endsWith('(Unsupported)') || name.endsWith('(Unknown)');
 }
 exports.isUnsupported = isUnsupported;
-//# sourceMappingURL=util.js.map

package/dist/HierarchicalTrackSelectorWidget/configSchema.js

@@ -3,4 +3,3 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const configSchema = (0, configuration_1.ConfigurationSchema)('HierarchicalTrackSelectorWidget', {});
 exports.default = configSchema;
-//# sourceMappingURL=configSchema.js.map

package/dist/HierarchicalTrackSelectorWidget/filterTracks.d.ts

@@ -0,0 +1,12 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function filterTracks(tracks: AnyConfigurationModel[], self: {
+    view?: {
+        type: string;
+        trackSelectorAnyOverlap?: boolean;
+    };
+    assemblyNames: string[];
+}): ({
+    [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>)[];

package/dist/HierarchicalTrackSelectorWidget/filterTracks.js

@@ -0,0 +1,32 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.filterTracks = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("./util");
+function filterTracks(tracks, self) {
+    const { assemblyManager } = (0, util_1.getSession)(self);
+    const { pluginManager } = (0, util_1.getEnv)(self);
+    const { view } = self;
+    if (!view) {
+        return [];
+    }
+    const trackListAssemblies = self.assemblyNames
+        .map(a => assemblyManager.get(a))
+        .filter(util_1.notEmpty);
+    return tracks
+        .filter(c => {
+        const trackAssemblyNames = (0, configuration_1.readConfObject)(c, 'assemblyNames');
+        const trackAssemblies = trackAssemblyNames === null || trackAssemblyNames === void 0 ? void 0 : trackAssemblyNames.map(name => assemblyManager.get(name)).filter(util_1.notEmpty);
+        return view.trackSelectorAnyOverlap
+            ? (0, util_2.hasAnyOverlap)(trackAssemblies, trackListAssemblies)
+            : (0, util_2.hasAllOverlap)(trackAssemblies, trackListAssemblies);
+    })
+        .filter(c => {
+        const { displayTypes } = pluginManager.getViewType(view.type);
+        const compatDisplays = displayTypes.map(d => d.name);
+        const trackDisplays = c.displays.map((d) => d.type);
+        return (0, util_2.hasAnyOverlap)(compatDisplays, trackDisplays);
+    });
+}
+exports.filterTracks = filterTracks;

package/dist/HierarchicalTrackSelectorWidget/generateHierarchy.d.ts

@@ -0,0 +1,21 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export type TreeNode = {
+    name: string;
+    id: string;
+    conf?: AnyConfigurationModel;
+    checked?: boolean;
+    isOpenByDefault?: boolean;
+    children: TreeNode[];
+};
+export declare function generateHierarchy(model: {
+    filterText: string;
+    activeSortTrackNames: boolean;
+    activeSortCategories: boolean;
+    view?: {
+        tracks: {
+            configuration: AnyConfigurationModel;
+        }[];
+    };
+}, trackConfs: AnyConfigurationModel[], collapsed: {
+    get: (arg: string) => boolean | undefined;
+}, extra?: string): TreeNode[];

package/dist/HierarchicalTrackSelectorWidget/generateHierarchy.js

@@ -0,0 +1,98 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.generateHierarchy = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+// locals
+const util_2 = require("./util");
+function sortConfs(confs, sortNames, sortCategories) {
+    // uses readConfObject instead of getTrackName so that the undefined
+    // reference sequence track is sorted to the top
+    const ret = confs.map(c => {
+        var _a, _b, _c;
+        return [
+            c,
+            (0, configuration_1.readConfObject)(c, 'name'),
+            ((_a = (0, configuration_1.readConfObject)(c, 'category')) === null || _a === void 0 ? void 0 : _a[0]) || '',
+            ((_b = (0, configuration_1.readConfObject)(c, 'category')) === null || _b === void 0 ? void 0 : _b[1]) || '',
+            ((_c = (0, configuration_1.readConfObject)(c, 'category')) === null || _c === void 0 ? void 0 : _c[2]) || '',
+        ];
+    });
+    if (sortNames) {
+        ret.sort((a, b) => a[1].localeCompare(b[1]));
+    }
+    if (sortCategories) {
+        // sort up to three sub-category levels, harder to code it to go deeper
+        // than this and likely rarely used
+        ret.sort((a, b) => {
+            if (a[2] !== b[2]) {
+                return a[2].localeCompare(b[2]);
+            }
+            else if (a[3] !== b[3]) {
+                return a[3].localeCompare(b[3]);
+            }
+            else if (a[4] !== b[4]) {
+                return a[4].localeCompare(b[4]);
+            }
+            return 0;
+        });
+    }
+    return ret.map(a => a[0]);
+}
+function generateHierarchy(model, trackConfs, collapsed, extra) {
+    const hierarchy = { children: [] };
+    const { filterText, activeSortTrackNames, activeSortCategories, view } = model;
+    if (!view) {
+        return [];
+    }
+    const session = (0, util_1.getSession)(model);
+    const viewTracks = view.tracks;
+    const confs = trackConfs.filter(conf => (0, util_2.matches)(filterText, conf, session));
+    // uses getConf
+    for (const conf of sortConfs(confs, activeSortTrackNames, activeSortCategories)) {
+        // copy the categories since this array can be mutated downstream
+        const categories = [...((0, configuration_1.readConfObject)(conf, 'category') || [])];
+        // hack where if trackId ends with sessionTrack, then push it to a
+        // category that starts with a space to force sort to the top
+        if (conf.trackId.endsWith('sessionTrack')) {
+            categories.unshift(' Session tracks');
+        }
+        let currLevel = hierarchy;
+        // find existing category to put track into or create it
+        for (let i = 0; i < categories.length; i++) {
+            const category = categories[i];
+            const ret = currLevel.children.find(c => c.name === category);
+            const id = [extra, categories.slice(0, i + 1).join(',')]
+                .filter(f => !!f)
+                .join('-');
+            if (!ret) {
+                const n = {
+                    children: [],
+                    name: category,
+                    id,
+                    isOpenByDefault: !collapsed.get(id),
+                };
+                currLevel.children.push(n);
+                currLevel = n;
+            }
+            else {
+                currLevel = ret;
+            }
+        }
+        // uses splice to try to put all leaf nodes above "category nodes" if you
+        // change the splice to a simple push and open
+        // test_data/test_order/config.json you will see the weirdness
+        const r = currLevel.children.findIndex(elt => elt.children.length);
+        const idx = r === -1 ? currLevel.children.length : r;
+        currLevel.children.splice(idx, 0, {
+            id: conf.trackId,
+            name: (0, tracks_1.getTrackName)(conf, session),
+            conf,
+            checked: viewTracks.some(f => f.configuration === conf),
+            children: [],
+        });
+    }
+    return hierarchy.children;
+}
+exports.generateHierarchy = generateHierarchy;