@jbrowse/plugin-data-management 1.7.11 → 2.0.0

package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js

@@ -0,0 +1,326 @@
+import React, { Suspense, lazy, useCallback, useMemo, useState, useRef, useEffect, } from 'react';
+import { Checkbox, Fab, FormControlLabel, IconButton, InputAdornment, Menu, MenuItem, TextField, Tooltip, Typography, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+// icons
+import ClearIcon from '@mui/icons-material/Clear';
+import AddIcon from '@mui/icons-material/Add';
+import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
+import ArrowRightIcon from '@mui/icons-material/ArrowRight';
+import MenuIcon from '@mui/icons-material/Menu';
+import MoreIcon from '@mui/icons-material/MoreHoriz';
+import { Cable } from '@jbrowse/core/ui/Icons';
+// other
+import AutoSizer from 'react-virtualized-auto-sizer';
+import JBrowseMenu from '@jbrowse/core/ui/Menu';
+import { getSession, isSessionModelWithWidgets, isSessionModelWithConnections, isSessionWithAddTracks, } from '@jbrowse/core/util';
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { observer } from 'mobx-react';
+import { VariableSizeTree } from 'react-vtree';
+// lazy components
+const CloseConnectionDialog = lazy(() => import('./CloseConnectionDialog'));
+const DeleteConnectionDialog = lazy(() => import('./DeleteConnectionDialog'));
+const ManageConnectionsDialog = lazy(() => import('./ManageConnectionsDialog'));
+const ToggleConnectionsDialog = lazy(() => import('./ToggleConnectionsDialog'));
+const useStyles = makeStyles()(theme => {
+    var _a, _b;
+    return ({
+        searchBox: {
+            margin: theme.spacing(2),
+        },
+        menuIcon: {
+            marginRight: theme.spacing(1),
+            marginBottom: 0,
+        },
+        fab: {
+            position: 'absolute',
+            bottom: theme.spacing(6),
+            right: theme.spacing(6),
+        },
+        compactCheckbox: {
+            padding: 0,
+        },
+        checkboxLabel: {
+            marginRight: 0,
+            '&:hover': {
+                backgroundColor: '#eee',
+            },
+        },
+        // 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',
+        },
+    });
+});
+// An individual node in the track selector. Note: manually sets cursor:
+// pointer improves usability for what can be clicked
+function Node(props) {
+    const { data, isOpen, style, setOpen } = props;
+    const { isLeaf, nestingLevel, checked, id, name, onChange, toggleCollapse, conf, onMoreInfo, drawerPosition, } = data;
+    const { classes } = useStyles();
+    const width = 10;
+    const marginLeft = nestingLevel * width + (isLeaf ? width : 0);
+    const unsupported = (name === null || name === void 0 ? void 0 : name.endsWith('(Unsupported)')) || (name === null || name === void 0 ? void 0 : name.endsWith('(Unknown)'));
+    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-${idx}`, style: { left: idx * width + 4, height: style === null || style === void 0 ? void 0 : style.height }, className: classes.nestingLevelMarker }))),
+        React.createElement("div", { className: !isLeaf ? classes.accordionCard : undefined, onClick: () => {
+                toggleCollapse(id);
+                setOpen(!isOpen);
+            }, style: {
+                marginLeft,
+                whiteSpace: 'nowrap',
+                width: '100%',
+            } },
+            React.createElement("div", { className: !isLeaf ? classes.accordionColor : undefined }, !isLeaf ? (React.createElement("div", { className: classes.accordionText },
+                React.createElement(Typography, null,
+                    isOpen ? React.createElement(ArrowDropDownIcon, null) : React.createElement(ArrowRightIcon, null),
+                    name))) : (React.createElement(React.Fragment, null,
+                React.createElement(Tooltip, { title: description, placement: drawerPosition === 'left' ? 'right' : 'left' },
+                    React.createElement(FormControlLabel, { className: classes.checkboxLabel, control: React.createElement(Checkbox, { className: classes.compactCheckbox, checked: checked, onChange: () => onChange(id), color: "primary", disabled: unsupported, inputProps: {
+                                // @ts-ignore
+                                'data-testid': `htsTrackEntry-${id}`,
+                            } }), label: name })),
+                React.createElement(IconButton, { onClick: e => onMoreInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, color: "secondary", "data-testid": `htsTrackEntryMenu-${id}` },
+                    React.createElement(MoreIcon, null))))))));
+}
+function getNodeData(node, nestingLevel, extra) {
+    const isLeaf = !!node.conf;
+    return {
+        data: {
+            defaultHeight: isLeaf ? 22 : 40,
+            isLeaf,
+            isOpenByDefault: true,
+            nestingLevel,
+            ...node,
+            ...extra,
+        },
+        nestingLevel,
+        node,
+    };
+}
+// this is the main tree component for the hierarchical track selector in note:
+// in jbrowse-web the toolbar is position="sticky" which means the autosizer
+// includes the height of the toolbar, so we subtract the given offsets
+const HierarchicalTree = observer(({ height, tree, model, }) => {
+    var _a;
+    const { filterText, view } = model;
+    const treeRef = useRef(null);
+    const [info, setMoreInfo] = useState();
+    const session = getSession(model);
+    const { drawerPosition } = session;
+    const extra = useMemo(() => ({
+        onChange: (trackId) => view.toggleTrack(trackId),
+        toggleCollapse: (pathName) => model.toggleCategory(pathName),
+        onMoreInfo: setMoreInfo,
+        drawerPosition,
+    }), [view, model, drawerPosition]);
+    const treeWalker = useCallback(function* treeWalker() {
+        for (let i = 0; i < tree.children.length; i++) {
+            const r = tree.children[i];
+            yield getNodeData(r, 0, extra);
+        }
+        while (true) {
+            // @ts-ignore
+            const parentMeta = yield;
+            for (let i = 0; i < parentMeta.node.children.length; i++) {
+                const curr = parentMeta.node.children[i];
+                yield getNodeData(curr, parentMeta.nestingLevel + 1, extra);
+            }
+        }
+    }, [tree, extra]);
+    const conf = info === null || info === void 0 ? void 0 : info.conf;
+    const menuItems = (conf && ((_a = session.getTrackActionMenuItems) === null || _a === void 0 ? void 0 : _a.call(session, conf))) || [];
+    useEffect(() => {
+        // @ts-ignore
+        treeRef.current.recomputeTree({
+            refreshNodes: true,
+            useDefaultHeight: true,
+        });
+    }, [tree, filterText]);
+    return (React.createElement(React.Fragment, null,
+        React.createElement(VariableSizeTree, { ref: treeRef, treeWalker: treeWalker, height: height }, Node),
+        React.createElement(JBrowseMenu, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: menuItems, onMenuItemClick: (_event, callback) => {
+                callback();
+                setMoreInfo(undefined);
+            }, open: Boolean(info), onClose: () => setMoreInfo(undefined) })));
+});
+// Don't use autosizer in jest and instead hardcode a height, otherwise fails
+// jest tests
+const AutoSizedHierarchicalTree = ({ tree, model, offset, }) => {
+    return typeof jest === 'undefined' ? (React.createElement(AutoSizer, { disableWidth: true }, ({ height }) => {
+        return (React.createElement(HierarchicalTree, { height: height - offset, model: model, tree: tree }));
+    })) : (React.createElement(HierarchicalTree, { height: 9000, model: model, tree: tree }));
+};
+const Wrapper = ({ overrideDimensions, children, }) => {
+    return overrideDimensions ? (React.createElement("div", { style: { ...overrideDimensions } }, children)) : (React.createElement(React.Fragment, null, children));
+};
+const HierarchicalTrackSelectorContainer = observer(({ model, toolbarHeight, overrideDimensions, }) => {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    const [anchorEl, setAnchorEl] = useState(null);
+    function handleFabClose() {
+        setAnchorEl(null);
+    }
+    const hasConnections = isSessionModelWithConnections(session);
+    const hasAddTrack = isSessionWithAddTracks(session);
+    return (React.createElement(Wrapper, { overrideDimensions: overrideDimensions },
+        React.createElement(HierarchicalTrackSelector, { model: model, toolbarHeight: toolbarHeight }),
+        hasAddTrack || hasConnections ? (React.createElement(React.Fragment, null,
+            React.createElement(Fab, { color: "secondary", className: classes.fab, onClick: event => setAnchorEl(event.currentTarget) },
+                React.createElement(AddIcon, null)),
+            React.createElement(Menu, { anchorEl: anchorEl, open: Boolean(anchorEl), onClose: () => setAnchorEl(null) },
+                hasConnections ? (React.createElement(MenuItem, { onClick: () => {
+                        handleFabClose();
+                        if (isSessionModelWithWidgets(session)) {
+                            session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
+                        }
+                    } }, "Add connection")) : null,
+                hasAddTrack ? (React.createElement(MenuItem, { onClick: () => {
+                        handleFabClose();
+                        if (isSessionModelWithWidgets(session)) {
+                            session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                                view: model.view.id,
+                            }));
+                        }
+                    } }, "Add track")) : null))) : null));
+});
+const HierarchicalTrackSelectorHeader = observer(({ model, setHeaderHeight, setAssemblyIdx, assemblyIdx, }) => {
+    const { classes } = useStyles();
+    const session = getSession(model);
+    const [connectionAnchorEl, setConnectionAnchorEl] = useState();
+    const [menuAnchorEl, setMenuAnchorEl] = useState();
+    const [modalInfo, setModalInfo] = useState();
+    const [deleteDialogDetails, setDeleteDialogDetails] = useState();
+    const [connectionManagerOpen, setConnectionManagerOpen] = useState(false);
+    const [connectionToggleOpen, setConnectionToggleOpen] = useState(false);
+    const { assemblyNames } = model;
+    const assemblyName = assemblyNames[assemblyIdx];
+    function breakConnection(connectionConf, deletingConnection) {
+        const name = readConfObject(connectionConf, 'name');
+        // @ts-ignore
+        const result = session.prepareToBreakConnection(connectionConf);
+        if (result) {
+            const [safelyBreakConnection, dereferenceTypeCount] = result;
+            if (Object.keys(dereferenceTypeCount).length > 0) {
+                setModalInfo({
+                    connectionConf,
+                    safelyBreakConnection,
+                    dereferenceTypeCount,
+                    name,
+                });
+            }
+            else {
+                safelyBreakConnection();
+            }
+        }
+        if (deletingConnection) {
+            setDeleteDialogDetails({ name, connectionConf });
+        }
+    }
+    const connectionMenuItems = [
+        {
+            label: 'Turn on/off connections...',
+            onClick: () => setConnectionToggleOpen(true),
+        },
+    ];
+    if (isSessionModelWithConnections(session)) {
+        connectionMenuItems.unshift({
+            label: 'Add connection',
+            onClick: () => {
+                if (isSessionModelWithWidgets(session)) {
+                    const widget = session.addWidget('AddConnectionWidget', 'addConnectionWidget');
+                    session.showWidget(widget);
+                }
+            },
+        });
+        connectionMenuItems.push({
+            label: 'Delete connections...',
+            onClick: () => setConnectionManagerOpen(true),
+        });
+    }
+    const assemblyMenuItems = assemblyNames.length > 1
+        ? [
+            {
+                label: 'Select assembly...',
+                subMenu: assemblyNames.map((name, idx) => ({
+                    label: name,
+                    onClick: () => setAssemblyIdx(idx),
+                })),
+            },
+        ]
+        : [];
+    const menuItems = [
+        {
+            label: 'Add track...',
+            onClick: () => {
+                if (isSessionModelWithWidgets(session)) {
+                    const widget = session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                        view: model.view.id,
+                    });
+                    session.showWidget(widget);
+                }
+            },
+        },
+        ...assemblyMenuItems,
+    ];
+    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' } },
+            isSessionWithAddTracks(session) && (React.createElement(IconButton, { className: classes.menuIcon, onClick: event => setMenuAnchorEl(event.currentTarget) },
+                React.createElement(MenuIcon, null))),
+            session.makeConnection && (React.createElement(IconButton, { className: classes.menuIcon, onClick: event => setConnectionAnchorEl(event.currentTarget) },
+                React.createElement(Cable, null))),
+            React.createElement(TextField, { className: classes.searchBox, label: "Filter tracks", value: model.filterText, onChange: event => model.setFilterText(event.target.value), fullWidth: true, InputProps: {
+                    endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                        React.createElement(IconButton, { color: "secondary", onClick: model.clearFilterText },
+                            React.createElement(ClearIcon, null)))),
+                } })),
+        React.createElement(JBrowseMenu, { anchorEl: connectionAnchorEl, open: Boolean(connectionAnchorEl), onMenuItemClick: (_, callback) => {
+                callback();
+                setConnectionAnchorEl(undefined);
+            }, onClose: () => setConnectionAnchorEl(undefined), menuItems: connectionMenuItems }),
+        React.createElement(JBrowseMenu, { anchorEl: menuAnchorEl, open: Boolean(menuAnchorEl), onMenuItemClick: (_, callback) => {
+                callback();
+                setMenuAnchorEl(undefined);
+            }, onClose: () => setMenuAnchorEl(undefined), menuItems: menuItems }),
+        React.createElement(Suspense, { fallback: React.createElement("div", null) },
+            modalInfo ? (React.createElement(CloseConnectionDialog, { modalInfo: modalInfo, setModalInfo: setModalInfo })) : deleteDialogDetails ? (React.createElement(DeleteConnectionDialog, { handleClose: () => setDeleteDialogDetails(undefined), deleteDialogDetails: deleteDialogDetails, session: session })) : null,
+            connectionManagerOpen ? (React.createElement(ManageConnectionsDialog, { handleClose: () => setConnectionManagerOpen(false), breakConnection: breakConnection, session: session })) : null,
+            connectionToggleOpen ? (React.createElement(ToggleConnectionsDialog, { handleClose: () => setConnectionToggleOpen(false), session: session, breakConnection: breakConnection, assemblyName: assemblyName })) : null)));
+});
+const HierarchicalTrackSelector = observer(({ model, toolbarHeight = 0, }) => {
+    const [assemblyIdx, setAssemblyIdx] = useState(0);
+    const [headerHeight, setHeaderHeight] = useState(0);
+    const { assemblyNames } = model;
+    const assemblyName = assemblyNames[assemblyIdx];
+    return assemblyName ? (React.createElement(React.Fragment, null,
+        React.createElement(HierarchicalTrackSelectorHeader, { model: model, setHeaderHeight: setHeaderHeight, setAssemblyIdx: setAssemblyIdx, assemblyIdx: assemblyIdx }),
+        React.createElement(AutoSizedHierarchicalTree, { tree: model.hierarchy(assemblyName), model: model, offset: toolbarHeight + headerHeight }))) : null;
+});
+export default HierarchicalTrackSelectorContainer;
+//# sourceMappingURL=HierarchicalTrackSelector.js.map

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

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

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { AbstractSessionModel } from '@jbrowse/core/util';
+declare function ManageConnectionsDlg({ session, handleClose, breakConnection, }: {
+    handleClose: () => void;
+    session: AbstractSessionModel;
+    breakConnection: (conf: AnyConfigurationModel, arg: boolean) => void;
+}): JSX.Element;
+declare const _default: typeof ManageConnectionsDlg;
+export default _default;

package/esm/HierarchicalTrackSelectorWidget/components/ManageConnectionsDialog.js

@@ -0,0 +1,45 @@
+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

@@ -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/index.d.ts

@@ -0,0 +1,2 @@
+export { default as stateModelFactory } from './model';
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/HierarchicalTrackSelectorWidget/index.js

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

package/esm/HierarchicalTrackSelectorWidget/index.js.map

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

@@ -0,0 +1,61 @@
+import { Instance } from 'mobx-state-tree';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { AbstractView } from 'react';
+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>>;
+}, {
+    setView(view: AbstractView): 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>;