@jbrowse/plugin-data-management 1.7.11 → 2.1.0

package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js

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+import React from 'react';
+import { Button, Dialog, DialogTitle, DialogContent, DialogActions, IconButton, Tooltip, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import CloseIcon from '@mui/icons-material/Close';
+import { observer } from 'mobx-react';
+import { readConfObject, } from '@jbrowse/core/configuration';
+const useStyles = makeStyles()(theme => ({
+    closeButton: {
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
+    },
+    connectionContainer: {
+        margin: theme.spacing(4),
+        width: 500,
+    },
+}));
+function ManageConnectionsDlg({ session, handleClose, breakConnection, }) {
+    const { classes } = useStyles();
+    const { adminMode, connections, sessionConnections } = session;
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, maxWidth: "lg" },
+        React.createElement(DialogTitle, null,
+            "Delete connections",
+            React.createElement(IconButton, { className: classes.closeButton, onClick: () => handleClose() },
+                React.createElement(CloseIcon, null))),
+        React.createElement(DialogContent, null,
+            React.createElement(Typography, null, "Click the X icon to delete the connection from your config completely"),
+            React.createElement("div", { className: classes.connectionContainer },
+                connections.map(conf => {
+                    const name = readConfObject(conf, 'name');
+                    return (React.createElement("div", { key: `conn-${name}` },
+                        React.createElement(Typography, null,
+                            adminMode || (sessionConnections === null || sessionConnections === void 0 ? void 0 : sessionConnections.includes(conf)) ? (React.createElement(IconButton, { onClick: () => breakConnection(conf, true) },
+                                React.createElement(CloseIcon, { color: "error" }))) : (React.createElement(Tooltip, { title: "Unable to delete connection in config file as non-admin user" },
+                                React.createElement(IconButton, null,
+                                    React.createElement(CloseIcon, { color: "disabled" })))),
+                            name)));
+                }),
+                !connections.length ? (React.createElement(Typography, null, "No connections found")) : null)),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { onClick: () => handleClose(), variant: "contained", color: "primary" }, "Close"))));
+}
+export default observer(ManageConnectionsDlg);
+//# sourceMappingURL=ManageConnectionsDialog.js.map

package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js.map

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package/esm/HierarchicalTrackSelectorWidget/components/Node.d.ts

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+/// <reference types="react" />
+import { HierarchicalTrackSelectorModel, TreeNode } from '../model';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export interface InfoArgs {
+    target: HTMLElement;
+    id: string;
+    conf: AnyConfigurationModel;
+}
+export default function Node(props: {
+    data: {
+        nestingLevel: number;
+        checked: boolean;
+        conf: AnyConfigurationModel;
+        drawerPosition: unknown;
+        id: string;
+        isLeaf: boolean;
+        name: string;
+        onChange: Function;
+        toggleCollapse: (arg: string) => void;
+        tree: TreeNode;
+        selected: boolean;
+        model: HierarchicalTrackSelectorModel;
+    };
+    isOpen: boolean;
+    style?: {
+        height: number;
+    };
+    setOpen: (arg: boolean) => void;
+}): JSX.Element;

package/esm/HierarchicalTrackSelectorWidget/components/Node.js

@@ -0,0 +1,149 @@
+import React, { useState } from 'react';
+import { Checkbox, FormControlLabel, IconButton, Tooltip, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+// icons
+import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
+import ArrowRightIcon from '@mui/icons-material/ArrowRight';
+import MoreHorizIcon from '@mui/icons-material/MoreHoriz';
+import JBrowseMenu from '@jbrowse/core/ui/Menu';
+import { getSession } from '@jbrowse/core/util';
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { getAllChildren } from './util';
+const useStyles = makeStyles()(theme => {
+    var _a, _b;
+    return ({
+        compactCheckbox: {
+            padding: 0,
+        },
+        checkboxLabel: {
+            marginRight: 0,
+            '&:hover': {
+                backgroundColor: '#eee',
+            },
+        },
+        contrastColor: {
+            color: theme.palette.secondary.contrastText,
+        },
+        // this accordionBase element's small padding is used to give a margin to
+        // accordionColor it a "margin" because the virtualized elements can't really
+        // use margin in a conventional way (it doesn't affect layout)
+        accordionBase: {
+            display: 'flex',
+        },
+        accordionCard: {
+            padding: 3,
+            cursor: 'pointer',
+            display: 'flex',
+        },
+        nestingLevelMarker: {
+            position: 'absolute',
+            borderLeft: '1.5px solid #555',
+        },
+        // accordionColor set's display:flex so that the child accordionText use
+        // vertically centered text
+        accordionColor: {
+            // @ts-ignore
+            background: (_a = theme.palette.tertiary) === null || _a === void 0 ? void 0 : _a.main,
+            // @ts-ignore
+            color: (_b = theme.palette.tertiary) === null || _b === void 0 ? void 0 : _b.contrastText,
+            width: '100%',
+            display: 'flex',
+            paddingLeft: 5,
+        },
+        // margin:auto 0 to center text vertically
+        accordionText: {
+            margin: 'auto 0',
+        },
+    });
+});
+function treeToMap(tree, map = new Map()) {
+    if (tree.id && tree.children.length) {
+        map.set(tree.id, tree);
+    }
+    for (let i = 0; i < tree.children.length; i++) {
+        const node = tree.children[i];
+        treeToMap(node, map);
+    }
+    return map;
+}
+function isUnsupported(name = '') {
+    return name.endsWith('(Unsupported)') || name.endsWith('(Unknown)');
+}
+// An individual node in the track selector. Note: manually sets cursor:
+// pointer improves usability for what can be clicked
+export default function Node(props) {
+    var _a, _b;
+    const { data, isOpen, style, setOpen } = props;
+    const { checked, conf, drawerPosition, id, isLeaf, model, name, nestingLevel, onChange, selected, toggleCollapse, tree, } = data;
+    const { classes } = useStyles();
+    const width = 10;
+    const [menuEl, setMenuEl] = useState(null);
+    const [info, setInfo] = useState();
+    const marginLeft = nestingLevel * width + (isLeaf ? width : 0);
+    const description = (conf && readConfObject(conf, ['description'])) || '';
+    return (React.createElement("div", { style: style, className: !isLeaf ? classes.accordionBase : undefined },
+        new Array(nestingLevel).fill(0).map((_, idx) => (React.createElement("div", { key: `mark-${idx}`, style: { left: idx * width + 4, height: style === null || style === void 0 ? void 0 : style.height }, className: classes.nestingLevelMarker }))),
+        React.createElement("div", { className: !isLeaf ? classes.accordionCard : undefined, onClick: () => {
+                if (!menuEl) {
+                    toggleCollapse(id);
+                    setOpen(!isOpen);
+                }
+            }, style: {
+                marginLeft,
+                whiteSpace: 'nowrap',
+                width: '100%',
+            } },
+            React.createElement("div", { className: !isLeaf ? classes.accordionColor : undefined },
+                !isLeaf ? (React.createElement("div", { className: classes.accordionText },
+                    React.createElement(Typography, null,
+                        isOpen ? React.createElement(ArrowDropDownIcon, null) : React.createElement(ArrowRightIcon, null),
+                        name,
+                        React.createElement(IconButton, { onClick: event => {
+                                setMenuEl(event.currentTarget);
+                                event.stopPropagation();
+                            }, className: classes.contrastColor },
+                            React.createElement(MoreHorizIcon, null))))) : (React.createElement(React.Fragment, null,
+                    React.createElement(Tooltip, { title: description + (selected ? ' (in selection)' : ''), placement: drawerPosition === 'left' ? 'right' : 'left' },
+                        React.createElement(FormControlLabel, { className: classes.checkboxLabel, control: React.createElement(Checkbox, { className: classes.compactCheckbox, checked: checked, onChange: () => onChange(id), disabled: isUnsupported(name), inputProps: {
+                                    // @ts-ignore
+                                    'data-testid': `htsTrackEntry-${id}`,
+                                } }), label: React.createElement("div", { style: {
+                                    background: selected ? '#cccc' : undefined,
+                                    padding: 1,
+                                } }, name) })),
+                    React.createElement(IconButton, { onClick: e => setInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, color: "secondary", "data-testid": `htsTrackEntryMenu-${id}` },
+                        React.createElement(MoreHorizIcon, null)))),
+                menuEl ? (React.createElement(JBrowseMenu, { anchorEl: menuEl, menuItems: [
+                        {
+                            label: 'Add to selection',
+                            onClick: () => model.addToSelection(getAllChildren(treeToMap(tree).get(id))),
+                        },
+                        {
+                            label: 'Remove from selection',
+                            onClick: () => model.removeFromSelection(getAllChildren(treeToMap(tree).get(id))),
+                        },
+                    ], onMenuItemClick: (_event, callback) => {
+                        callback();
+                        setMenuEl(null);
+                    }, open: Boolean(menuEl), onClose: () => setMenuEl(null) })) : null,
+                info ? (React.createElement(JBrowseMenu, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: [
+                        ...(((_b = (_a = getSession(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, info.conf)) ||
+                            []),
+                        {
+                            label: 'Add to selection',
+                            onClick: () => model.addToSelection([info.conf]),
+                        },
+                        ...(selected
+                            ? [
+                                {
+                                    label: 'Remove from selection',
+                                    onClick: () => model.removeFromSelection([info.conf]),
+                                },
+                            ]
+                            : []),
+                    ], onMenuItemClick: (_event, callback) => {
+                        callback();
+                        setInfo(undefined);
+                    }, open: Boolean(info), onClose: () => setInfo(undefined) })) : null))));
+}
+//# sourceMappingURL=Node.js.map

package/esm/HierarchicalTrackSelectorWidget/components/Node.js.map

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

@@ -0,0 +1,11 @@
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { AbstractSessionModel } from '@jbrowse/core/util';
+declare function ToggleConnectionDialog({ session, handleClose, assemblyName, breakConnection, }: {
+    handleClose: () => void;
+    session: AbstractSessionModel;
+    assemblyName: string;
+    breakConnection: (arg: AnyConfigurationModel) => void;
+}): JSX.Element;
+declare const _default: typeof ToggleConnectionDialog;
+export default _default;

package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js

@@ -0,0 +1,57 @@
+import React from 'react';
+import { Button, Checkbox, Dialog, DialogTitle, DialogContent, DialogActions, FormControlLabel, IconButton, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import CloseIcon from '@mui/icons-material/Close';
+import { observer } from 'mobx-react';
+import { readConfObject, } from '@jbrowse/core/configuration';
+const useStyles = makeStyles()(theme => ({
+    closeButton: {
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
+    },
+    connectionContainer: {
+        width: 500,
+        margin: theme.spacing(4),
+    },
+}));
+function ToggleConnectionDialog({ session, handleClose, assemblyName, breakConnection, }) {
+    const { classes } = useStyles();
+    const { connections, connectionInstances: instances = [] } = session;
+    const assemblySpecificConnections = connections.filter(c => {
+        const configAssemblyNames = readConfObject(c, 'assemblyNames');
+        if (configAssemblyNames.length === 0) {
+            return true;
+        }
+        return configAssemblyNames.includes(assemblyName);
+    });
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, maxWidth: "lg" },
+        React.createElement(DialogTitle, null,
+            "Turn on/off connections",
+            React.createElement(IconButton, { className: classes.closeButton, onClick: () => handleClose() },
+                React.createElement(CloseIcon, null))),
+        React.createElement(DialogContent, null,
+            React.createElement(Typography, null, "Use the checkbox to turn on/off connections"),
+            React.createElement("div", { className: classes.connectionContainer },
+                assemblySpecificConnections.map(conf => {
+                    const name = readConfObject(conf, 'name');
+                    const found = instances.find(conn => name === conn.name);
+                    return (React.createElement(FormControlLabel, { key: conf.connectionId, control: React.createElement(Checkbox, { checked: !!found, onChange: () => {
+                                var _a;
+                                if (found) {
+                                    breakConnection(conf);
+                                }
+                                else {
+                                    (_a = session.makeConnection) === null || _a === void 0 ? void 0 : _a.call(session, conf);
+                                }
+                            }, color: "primary" }), label: name }));
+                }),
+                !assemblySpecificConnections.length ? (React.createElement(Typography, null,
+                    "No connections found for ",
+                    assemblyName)) : null)),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { onClick: () => handleClose(), variant: "contained", color: "primary" }, "Close"))));
+}
+export default observer(ToggleConnectionDialog);
+//# sourceMappingURL=ToggleConnectionsDialog.js.map

package/esm/HierarchicalTrackSelectorWidget/components/ToggleConnectionsDialog.js.map

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

@@ -0,0 +1,3 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { TreeNode } from '../model';
+export declare function getAllChildren(subtree?: TreeNode): AnyConfigurationModel[];

package/esm/HierarchicalTrackSelectorWidget/components/util.js

@@ -0,0 +1,5 @@
+export function getAllChildren(subtree) {
+    // @ts-ignore
+    return ((subtree === null || subtree === void 0 ? void 0 : subtree.children.map(t => t.children.length ? getAllChildren(t) : t.conf)) || []).flat(Infinity);
+}
+//# sourceMappingURL=util.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/HierarchicalTrackSelectorWidget/components/util.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,cAAc,CAAC,OAAkB;IAC/C,aAAa;IACb,OAAO,CACL,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CACxB,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,IAA8B,CAC1E,KAAI,EAAE,CACR,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;AAClB,CAAC"}

package/esm/HierarchicalTrackSelectorWidget/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/esm/HierarchicalTrackSelectorWidget/configSchema.js

@@ -0,0 +1,4 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+const configSchema = ConfigurationSchema('HierarchicalTrackSelectorWidget', {});
+export default configSchema;
+//# sourceMappingURL=configSchema.js.map

package/esm/HierarchicalTrackSelectorWidget/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/HierarchicalTrackSelectorWidget/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,MAAM,YAAY,GAAG,mBAAmB,CAAC,iCAAiC,EAAE,EAAE,CAAC,CAAA;AAC/E,eAAe,YAAY,CAAA"}

package/esm/HierarchicalTrackSelectorWidget/index.d.ts

@@ -0,0 +1,4 @@
+import stateModelFactory, { HierarchicalTrackSelectorModel } from './model';
+import configSchema from './configSchema';
+export { stateModelFactory, configSchema };
+export type { HierarchicalTrackSelectorModel };

package/esm/HierarchicalTrackSelectorWidget/index.js

@@ -0,0 +1,4 @@
+import stateModelFactory from './model';
+import configSchema from './configSchema';
+export { stateModelFactory, configSchema };
+//# sourceMappingURL=index.js.map

package/esm/HierarchicalTrackSelectorWidget/index.js.map

@@ -0,0 +1 @@
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package/esm/HierarchicalTrackSelectorWidget/model.d.ts

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+import { Instance } from 'mobx-state-tree';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare type TreeNode = {
+    name: string;
+    id: string;
+    conf?: AnyConfigurationModel;
+    checked?: boolean;
+    isOpenByDefault?: boolean;
+    children: TreeNode[];
+};
+export declare function generateHierarchy(model: HierarchicalTrackSelectorModel, trackConfigurations: AnyConfigurationModel[], collapsed: {
+    get: (arg: string) => boolean | undefined;
+}): TreeNode[];
+export default function stateTreeFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
+    collapsed: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+    filterText: import("mobx-state-tree").IType<string | undefined, string, string>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+}, {
+    selection: ({
+        [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>)[];
+} & {
+    addToSelection(elt: AnyConfigurationModel[]): void;
+    removeFromSelection(elt: AnyConfigurationModel[]): void;
+    clearSelection(): void;
+    setView(view: unknown): void;
+    toggleCategory(pathName: string): void;
+    clearFilterText(): void;
+    setFilterText(newText: string): void;
+} & {
+    getRefSeqTrackConf(assemblyName: string): any;
+} & {
+    trackConfigurations(assemblyName: string): any[];
+    readonly assemblyNames: string[];
+    connectionTrackConfigurations(assemblyName: string, 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>)[];
+} & {
+    hierarchy(assemblyName: string): {
+        name: string;
+        id: string;
+        children: ({
+            id: any;
+            name: any;
+            children: TreeNode[];
+            state: {
+                expanded: boolean;
+            };
+        } | {
+            name: string;
+            id: string;
+            children: TreeNode[];
+        })[];
+    };
+    connectionHierarchy(assemblyName: string, connection: {
+        tracks: AnyConfigurationModel[];
+    }): TreeNode[];
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export declare type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
+export declare type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;

package/esm/HierarchicalTrackSelectorWidget/model.js

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+import { types, getParent, getEnv } from 'mobx-state-tree';
+import { getConf, readConfObject, } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+import { ElementId } from '@jbrowse/core/util/types/mst';
+function hasAnyOverlap(a1 = [], a2 = []) {
+    return !!a1.find(value => a2.includes(value));
+}
+function passesFilter(filter, config) {
+    const categories = readConfObject(config, 'category');
+    const filterLower = filter.toLowerCase();
+    return (getTrackName(config).toLowerCase().includes(filterLower) ||
+        !!(categories === null || categories === void 0 ? void 0 : categories.filter(c => c.toLowerCase().includes(filterLower)).length));
+}
+function getTrackName(config) {
+    if (!config.trackId) {
+        throw new Error('not a track');
+    }
+    return (readConfObject(config, 'name') ||
+        `Reference sequence (${readConfObject(getParent(config), 'name')})`);
+}
+function filterTracks(tracks, self, assemblyName) {
+    const { assemblyManager } = getSession(self);
+    const { pluginManager } = getEnv(self);
+    const assembly = assemblyManager.get(assemblyName);
+    if (!assembly) {
+        return [];
+    }
+    return tracks
+        .filter(c => {
+        const trackConfAssemblies = readConfObject(c, 'assemblyNames');
+        const { allAliases } = assembly;
+        return hasAnyOverlap(allAliases, trackConfAssemblies);
+    })
+        .filter(c => {
+        const { displayTypes } = pluginManager.getViewType(self.view.type);
+        const compatDisplays = displayTypes.map((d) => d.name);
+        const trackDisplays = c.displays.map((d) => d.type);
+        return hasAnyOverlap(compatDisplays, trackDisplays);
+    });
+}
+export function generateHierarchy(model, trackConfigurations, collapsed) {
+    const hierarchy = { children: [] };
+    const { filterText, view } = model;
+    trackConfigurations
+        .filter(conf => passesFilter(filterText, conf))
+        .forEach(conf => {
+        // copy the categories since this array can be mutated downstream
+        const categories = [...(readConfObject(conf, 'category') || [])];
+        // silly thing where if trackId ends with sessionTrack, then push it to
+        // a category that starts with a space to force sort to the top...
+        // double whammy hackyness
+        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 = categories.slice(0, i + 1).join(',');
+            if (!ret) {
+                const n = {
+                    children: [],
+                    name: category,
+                    id,
+                    isOpenByDefault: !collapsed.get(id),
+                };
+                currLevel.children.push(n);
+                currLevel = n;
+            }
+            else {
+                currLevel = ret;
+            }
+        }
+        const tracks = view.tracks;
+        // using splice here tries to group leaf nodes above hierarchical nodes
+        currLevel.children.splice(currLevel.children.findIndex(elt => elt.children.length), 0, {
+            id: conf.trackId,
+            name: getTrackName(conf),
+            conf,
+            checked: !!tracks.find(f => f.configuration === conf),
+            children: [],
+        });
+    });
+    return hierarchy.children;
+}
+export default function stateTreeFactory(pluginManager) {
+    return types
+        .model('HierarchicalTrackSelectorWidget', {
+        id: ElementId,
+        type: types.literal('HierarchicalTrackSelectorWidget'),
+        collapsed: types.map(types.boolean),
+        filterText: '',
+        view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
+    })
+        .volatile(() => ({
+        selection: [],
+    }))
+        .actions(self => ({
+        addToSelection(elt) {
+            self.selection = [...self.selection, ...elt];
+        },
+        removeFromSelection(elt) {
+            self.selection = self.selection.filter(f => !elt.includes(f));
+        },
+        clearSelection() {
+            self.selection = [];
+        },
+        setView(view) {
+            self.view = view;
+        },
+        toggleCategory(pathName) {
+            self.collapsed.set(pathName, !self.collapsed.get(pathName));
+        },
+        clearFilterText() {
+            self.filterText = '';
+        },
+        setFilterText(newText) {
+            self.filterText = newText;
+        },
+    }))
+        .views(self => ({
+        getRefSeqTrackConf(assemblyName) {
+            const { assemblyManager } = getSession(self);
+            const assembly = assemblyManager.get(assemblyName);
+            const trackConf = assembly === null || assembly === void 0 ? void 0 : assembly.configuration.sequence;
+            const viewType = pluginManager.getViewType(self.view.type);
+            if (!trackConf) {
+                return undefined;
+            }
+            for (const display of trackConf.displays) {
+                if (viewType.displayTypes.find(d => d.name === display.type)) {
+                    return trackConf;
+                }
+            }
+        },
+    }))
+        .views(self => ({
+        trackConfigurations(assemblyName) {
+            if (!self.view) {
+                return [];
+            }
+            const { tracks, assemblyManager } = getSession(self);
+            const assembly = assemblyManager.get(assemblyName);
+            if (!assembly) {
+                return [];
+            }
+            const refseq = self.getRefSeqTrackConf(assemblyName);
+            // filter out tracks that don't match the current assembly (check all
+            // assembly aliases) and display types
+            return (refseq ? [refseq] : []).concat([
+                ...filterTracks(tracks, self, assemblyName),
+            ]);
+        },
+        get assemblyNames() {
+            var _a;
+            return ((_a = self.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
+        },
+        connectionTrackConfigurations(assemblyName, connection) {
+            if (!self.view) {
+                return [];
+            }
+            // filter out tracks that don't match the current display types
+            return filterTracks(connection.tracks, self, assemblyName);
+        },
+    }))
+        .views(self => ({
+        hierarchy(assemblyName) {
+            const hier = generateHierarchy(
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            self, self.trackConfigurations(assemblyName), self.collapsed);
+            const session = getSession(self);
+            const { connections, connectionInstances } = session;
+            const conns = (connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.filter(c => {
+                const names = getConf(c, 'assemblyNames');
+                return names.length === 0 ? true : names.includes(assemblyName);
+            }).map((conn, index) => {
+                const c = connections[index];
+                return {
+                    id: c.connectionId,
+                    name: readConfObject(c, 'name'),
+                    children: this.connectionHierarchy(assemblyName, conn),
+                    state: {
+                        expanded: true,
+                    },
+                };
+            })) || [];
+            return {
+                name: 'Root',
+                id: 'Root',
+                children: [
+                    { name: 'Tracks', id: 'Tracks', children: hier },
+                    ...conns,
+                ],
+            };
+        },
+        connectionHierarchy(assemblyName, connection) {
+            return generateHierarchy(
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            self, self.connectionTrackConfigurations(assemblyName, connection), self.collapsed);
+        },
+    }));
+}
+//# sourceMappingURL=model.js.map