@jbrowse/plugin-linear-genome-view 2.10.2 → 2.10.3

package/dist/BaseLinearDisplay/components/BlockMsg.d.ts

@@ -1,9 +1,7 @@
 import React from 'react';
 import { AlertColor } from '@mui/material';
-export default function BlockMsg({ message, severity, buttonText, icon, action, }: {
+export default function BlockMsg({ message, severity, action, }: {
     message: string;
     severity?: AlertColor;
-    buttonText?: string;
-    icon?: React.ReactNode;
-    action?: () => void;
+    action?: React.ReactNode;
 }): React.JSX.Element;

package/dist/BaseLinearDisplay/components/BlockMsg.js

@@ -12,10 +12,9 @@ const useStyles = (0, mui_1.makeStyles)()({
         overflow: 'hidden',
     },
 });
-function BlockMsg({ message, severity, buttonText, icon, action, }) {
+function BlockMsg({ message, severity, action, }) {
     const { classes } = useStyles();
-    const button = action ? (react_1.default.createElement(material_1.Button, { "data-testid": "reload_button", onClick: action, startIcon: icon }, buttonText)) : null;
-    return (react_1.default.createElement(material_1.Alert, { severity: severity, action: button, classes: { message: classes.ellipses } },
+    return (react_1.default.createElement(material_1.Alert, { severity: severity, action: action, classes: { message: classes.ellipses } },
         react_1.default.createElement(material_1.Tooltip, { title: message },
             react_1.default.createElement("div", null, message))));
 }

package/dist/BaseLinearDisplay/components/LinearBlocks.js

@@ -38,8 +38,8 @@ const RenderedBlocks = (0, mobx_react_1.observer)(function ({ model, }) {
         if (block instanceof blockTypes_1.ContentBlock) {
             const state = blockState.get(block.key);
             return (react_1.default.createElement(Block_1.ContentBlock, { block: block, key: `${model.id}-${block.key}` },
-                state && state.ReactComponent ? (react_1.default.createElement(state.ReactComponent, { model: state })) : null,
-                state && state.maxHeightReached ? (react_1.default.createElement("div", { className: classes.heightOverflowed, style: {
+                (state === null || state === void 0 ? void 0 : state.ReactComponent) ? (react_1.default.createElement(state.ReactComponent, { model: state })) : null,
+                (state === null || state === void 0 ? void 0 : state.maxHeightReached) ? (react_1.default.createElement("div", { className: classes.heightOverflowed, style: {
                         top: state.layout.getTotalHeight() - 16,
                         pointerEvents: 'none',
                         height: 16,

package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.d.ts

@@ -1,4 +1,12 @@
+import React from 'react';
 declare const ServerSideRenderedBlockContent: ({ model, }: {
-    model: any;
-}) => any;
+    model: {
+        error?: unknown;
+        reload: () => void;
+        message: React.ReactNode;
+        filled?: boolean;
+        status?: string;
+        reactElement?: React.ReactElement;
+    };
+}) => React.JSX.Element | undefined;
 export default ServerSideRenderedBlockContent;

package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js

@@ -1,17 +1,44 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+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 mobx_state_tree_1 = require("mobx-state-tree");
 const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
 // icons
 const Refresh_1 = __importDefault(require("@mui/icons-material/Refresh"));
+const Report_1 = __importDefault(require("@mui/icons-material/Report"));
 // locals
 const BlockMsg_1 = __importDefault(require("./BlockMsg"));
+const ErrorMessageStackTraceDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@jbrowse/core/ui/ErrorMessageStackTraceDialog'))));
 const useStyles = (0, mui_1.makeStyles)()(theme => {
     const bg = theme.palette.action.disabledBackground;
     return {
@@ -23,11 +50,9 @@ const useStyles = (0, mui_1.makeStyles)()(theme => {
         },
     };
 });
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 const LoadingMessage = (0, mobx_react_1.observer)(({ model }) => {
     const { classes } = useStyles();
     const { status: blockStatus } = model;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { message: displayStatus } = (0, mobx_state_tree_1.getParent)(model, 2);
     const status = displayStatus || blockStatus;
     return (react_1.default.createElement("div", { className: classes.loading },
@@ -35,7 +60,18 @@ const LoadingMessage = (0, mobx_react_1.observer)(({ model }) => {
 });
 const ServerSideRenderedBlockContent = (0, mobx_react_1.observer)(function ({ model, }) {
     if (model.error) {
-        return (react_1.default.createElement(BlockMsg_1.default, { message: `${model.error}`, severity: "error", buttonText: "reload", icon: react_1.default.createElement(Refresh_1.default, null), action: model.reload }));
+        return (react_1.default.createElement(BlockMsg_1.default, { message: `${model.error}`, severity: "error", action: react_1.default.createElement(react_1.default.Fragment, null,
+                react_1.default.createElement(material_1.Tooltip, { title: "Reload track" },
+                    react_1.default.createElement(material_1.IconButton, { "data-testid": "reload_button", onClick: () => model.reload() },
+                        react_1.default.createElement(Refresh_1.default, null))),
+                react_1.default.createElement(material_1.Tooltip, { title: "Show stack trace" },
+                    react_1.default.createElement(material_1.IconButton, { onClick: () => {
+                            (0, util_1.getSession)(model).queueDialog(onClose => [
+                                ErrorMessageStackTraceDialog,
+                                { onClose, error: model.error },
+                            ]);
+                        } },
+                        react_1.default.createElement(Report_1.default, null)))) }));
     }
     else if (model.message) {
         // the message can be a fully rendered react component, e.g. the region too large message

package/dist/BaseLinearDisplay/components/TooLargeMessage.js

@@ -6,12 +6,13 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 // locals
 const BlockMsg_1 = __importDefault(require("../components/BlockMsg"));
+const material_1 = require("@mui/material");
 function TooLargeMessage({ model, }) {
     const { regionTooLargeReason } = model;
-    return (react_1.default.createElement(BlockMsg_1.default, { severity: "warning", action: () => {
-            model.setFeatureDensityStatsLimit(model.featureDensityStats);
-            model.reload();
-        }, buttonText: "Force load", message: [
+    return (react_1.default.createElement(BlockMsg_1.default, { severity: "warning", action: react_1.default.createElement(material_1.Button, { onClick: () => {
+                model.setFeatureDensityStatsLimit(model.featureDensityStats);
+                model.reload();
+            } }, "Force load"), message: [
             regionTooLargeReason,
             'Zoom in to see features or force load (may be slow)',
         ]

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -58,8 +58,15 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: React.ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+            };
+        }) => React.JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -342,8 +349,15 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: React.ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+            };
+        }) => React.JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.d.ts

@@ -28,8 +28,15 @@ declare const blockState: import("mobx-state-tree").IModelType<{
     message: string | undefined;
     maxHeightReached: boolean;
     ReactComponent: ({ model, }: {
-        model: any;
-    }) => any;
+        model: {
+            error?: unknown;
+            reload: () => void;
+            message: React.ReactNode;
+            filled?: boolean | undefined;
+            status?: string | undefined;
+            reactElement?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+        };
+    }) => React.JSX.Element | undefined;
     renderProps: any;
 } & {
     doReload(): void;

package/dist/LaunchLinearGenomeView/index.js

@@ -5,9 +5,10 @@ const searchUtils_1 = require("../searchUtils");
 exports.default = (pluginManager) => {
     pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', 
     // @ts-expect-error
-    async ({ session, assembly, loc, tracks = [], tracklist, nav, }) => {
+    async ({ session, assembly, loc, tracks = [], tracklist, nav, highlight, }) => {
         try {
             const { assemblyManager } = session;
+            const { isValidRefName } = assemblyManager;
             const view = session.addView('LinearGenomeView', {});
             await (0, util_1.when)(() => !!view.volatileWidth);
             if (!assembly) {
@@ -17,18 +18,25 @@ exports.default = (pluginManager) => {
             if (!asm) {
                 throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
             }
-            await (0, searchUtils_1.handleSelectedRegion)({ input: loc, model: view, assembly: asm });
-            const idsNotFound = [];
-            tracks.forEach(track => tryTrack(view, track, idsNotFound));
-            if (idsNotFound.length) {
-                throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
-            }
             if (tracklist) {
                 view.activateTrackSelector();
             }
             if (nav !== undefined) {
                 view.setHideHeader(!nav);
             }
+            if (highlight !== undefined) {
+                const location = (0, util_1.parseLocString)(highlight, refName => isValidRefName(refName, assembly));
+                if ((location === null || location === void 0 ? void 0 : location.start) !== undefined && (location === null || location === void 0 ? void 0 : location.end) !== undefined) {
+                    location.assemblyName = assembly;
+                    view.setHighlight(location);
+                }
+            }
+            await (0, searchUtils_1.handleSelectedRegion)({ input: loc, model: view, assembly: asm });
+            const idsNotFound = [];
+            tracks.forEach(track => tryTrack(view, track, idsNotFound));
+            if (idsNotFound.length) {
+                throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
+            }
         }
         catch (e) {
             session.notify(`${e}`, 'error');

package/dist/LinearBareDisplay/model.d.ts

@@ -42,8 +42,15 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -267,8 +274,15 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/dist/LinearBasicDisplay/model.d.ts

@@ -47,8 +47,17 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined; /**
+                 * #getter
+                 */
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -343,8 +352,17 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined; /**
+                 * #getter
+                 */
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/dist/LinearGenomeView/components/Highlight.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { LinearGenomeViewModel } from '../model';
+type LGV = LinearGenomeViewModel;
+declare const Highlight: ({ model }: {
+    model: LGV;
+}) => React.JSX.Element | null;
+export default Highlight;

package/dist/LinearGenomeView/components/Highlight.js

@@ -0,0 +1,122 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const colord_1 = require("@jbrowse/core/util/colord");
+const util_1 = require("@jbrowse/core/util");
+const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+// icons
+const Link_1 = __importDefault(require("@mui/icons-material/Link"));
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const Bookmark_1 = __importDefault(require("@mui/icons-material/Bookmark"));
+const useStyles = (0, mui_1.makeStyles)()(theme => {
+    var _a, _b, _c, _d, _e, _f;
+    return ({
+        highlight: {
+            height: '100%',
+            position: 'absolute',
+            background: `${(0, colord_1.colord)((_b = (_a = theme.palette.quaternary) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod')
+                .alpha(0.35)
+                .toRgbString()}`,
+            borderLeft: `1px solid ${(_d = (_c = theme.palette.quaternary) === null || _c === void 0 ? void 0 : _c.main) !== null && _d !== void 0 ? _d : 'goldenrod'}`,
+            borderRight: `1px solid ${(_f = (_e = theme.palette.quaternary) === null || _e === void 0 ? void 0 : _e.main) !== null && _f !== void 0 ? _f : 'goldenrod'}`,
+        },
+    });
+});
+const Highlight = (0, mobx_react_1.observer)(function Highlight({ model }) {
+    var _a, _b;
+    const { classes } = useStyles();
+    const [open, setOpen] = (0, react_1.useState)(false);
+    const anchorEl = (0, react_1.useRef)(null);
+    const color = (_b = (_a = (0, material_1.useTheme)().palette.quaternary) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod';
+    const session = (0, util_1.getSession)(model);
+    const dismissHighlight = () => {
+        model.setHighlight(undefined);
+    };
+    const menuItems = [
+        {
+            label: 'Dismiss highlight',
+            icon: Close_1.default,
+            onClick: () => dismissHighlight(),
+        },
+        {
+            label: 'Bookmark highlighted region',
+            icon: Bookmark_1.default,
+            onClick: () => {
+                let bookmarkWidget = session.widgets.get('GridBookmark');
+                if (!bookmarkWidget) {
+                    bookmarkWidget = session.addWidget('GridBookmarkWidget', 'GridBookmark');
+                }
+                // @ts-ignore
+                bookmarkWidget.addBookmark(model.highlight);
+                dismissHighlight();
+            },
+        },
+    ];
+    function handleClose() {
+        setOpen(false);
+    }
+    if (!model.highlight) {
+        return null;
+    }
+    // coords
+    const mapCoords = (r) => {
+        const s = model.bpToPx({
+            refName: r.refName,
+            coord: r.start,
+        });
+        const e = model.bpToPx({
+            refName: r.refName,
+            coord: r.end,
+        });
+        return s && e
+            ? {
+                width: Math.max(Math.abs(e.offsetPx - s.offsetPx), 3),
+                left: Math.min(s.offsetPx, e.offsetPx) - model.offsetPx,
+            }
+            : undefined;
+    };
+    const h = mapCoords(model.highlight);
+    return (react_1.default.createElement(react_1.default.Fragment, null, h ? (react_1.default.createElement("div", { className: classes.highlight, style: {
+            left: h.left,
+            width: h.width,
+        } },
+        react_1.default.createElement(material_1.Tooltip, { title: 'Highlighted from URL parameter', arrow: true },
+            react_1.default.createElement(material_1.IconButton, { ref: anchorEl, onClick: () => setOpen(true) },
+                react_1.default.createElement(Link_1.default, { fontSize: "small", sx: {
+                        color: `${(0, colord_1.colord)(color).darken(0.2).toRgbString()}`,
+                    } }))),
+        react_1.default.createElement(ui_1.Menu, { anchorEl: anchorEl.current, onMenuItemClick: (_event, callback) => {
+                callback(session);
+                handleClose();
+            }, open: open, onClose: handleClose, menuItems: menuItems }))) : null));
+});
+exports.default = Highlight;

package/dist/LinearGenomeView/components/OverviewHighlight.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
+import { LinearGenomeViewModel } from '../model';
+type LGV = LinearGenomeViewModel;
+declare const OverviewHighlight: ({ model, overview, }: {
+    model: LGV;
+    overview: Base1DViewModel;
+}) => React.JSX.Element | null;
+export default OverviewHighlight;

package/dist/LinearGenomeView/components/OverviewHighlight.js

@@ -0,0 +1,53 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const colord_1 = require("@jbrowse/core/util/colord");
+const useStyles = (0, mui_1.makeStyles)()(theme => {
+    var _a, _b, _c, _d, _e, _f;
+    return ({
+        highlight: {
+            height: '100%',
+            position: 'absolute',
+            background: `${(0, colord_1.colord)((_b = (_a = theme.palette.quaternary) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod')
+                .alpha(0.35)
+                .toRgbString()}`,
+            borderLeft: `1px solid ${(_d = (_c = theme.palette.quaternary) === null || _c === void 0 ? void 0 : _c.main) !== null && _d !== void 0 ? _d : 'goldenrod'}`,
+            borderRight: `1px solid ${(_f = (_e = theme.palette.quaternary) === null || _e === void 0 ? void 0 : _e.main) !== null && _f !== void 0 ? _f : 'goldenrod'}`,
+        },
+    });
+});
+const OverviewHighlight = (0, mobx_react_1.observer)(function OverviewHighlight({ model, overview, }) {
+    const { classes } = useStyles();
+    const { cytobandOffset } = model;
+    // coords
+    const mapCoords = (r) => {
+        const s = overview.bpToPx({
+            ...r,
+            coord: r.reversed ? r.end : r.start,
+        });
+        const e = overview.bpToPx({
+            ...r,
+            coord: r.reversed ? r.start : r.end,
+        });
+        return s !== undefined && e != undefined
+            ? {
+                width: Math.abs(e - s),
+                left: s + cytobandOffset,
+            }
+            : undefined;
+    };
+    if (!model.highlight) {
+        return null;
+    }
+    const h = mapCoords(model.highlight);
+    return (react_1.default.createElement(react_1.default.Fragment, null, h ? (react_1.default.createElement("div", { className: classes.highlight, style: {
+            width: h.width,
+            left: h.left,
+        } })) : null));
+});
+exports.default = OverviewHighlight;

package/dist/LinearGenomeView/components/OverviewScalebar.js

@@ -41,6 +41,7 @@ const util_3 = require("./util");
 const OverviewRubberband_1 = __importDefault(require("./OverviewRubberband"));
 const Cytobands_1 = __importDefault(require("./Cytobands"));
 const OverviewScalebarPolygon_1 = __importDefault(require("./OverviewScalebarPolygon"));
+const OverviewHighlight_1 = __importDefault(require("./OverviewHighlight"));
 const wholeSeqSpacer = 2;
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     scalebar: {
@@ -179,7 +180,8 @@ const Scalebar = (0, mobx_react_1.observer)(function ({ model, scale, overview,
                     backgroundColor: '#999',
                     backgroundImage: 'repeating-linear-gradient(90deg, transparent, transparent 1px, rgba(255,255,255,.5) 1px, rgba(255,255,255,.5) 3px)',
                 } })) : (react_1.default.createElement(OverviewBox, { scale: scale, block: block, model: model, overview: overview, key: `${JSON.stringify(block)}-${idx}` }));
-        })));
+        }),
+        react_1.default.createElement(OverviewHighlight_1.default, { model: model, overview: overview })));
 });
 const OverviewScalebar = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { classes } = useStyles();

package/dist/LinearGenomeView/components/TracksContainer.js

@@ -41,6 +41,7 @@ const Gridlines_1 = __importDefault(require("./Gridlines"));
 const CenterLine_1 = __importDefault(require("./CenterLine"));
 const VerticalGuide_1 = __importDefault(require("./VerticalGuide"));
 const RubberbandSpan_1 = __importDefault(require("./RubberbandSpan"));
+const Highlight_1 = __importDefault(require("./Highlight"));
 const useStyles = (0, mui_1.makeStyles)()({
     tracksContainer: {
         position: 'relative',
@@ -67,6 +68,7 @@ const TracksContainer = (0, mobx_react_1.observer)(function TracksContainer({ ch
                 top: anchorPosition.clientY,
             }, onMenuItemClick: handleMenuItemClick, open: open, onClose: handleClose, menuItems: model.rubberBandMenuItems() })) : null,
         react_1.default.createElement(Rubberband_1.default, { model: model, ControlComponent: react_1.default.createElement(Scalebar_1.default, { model: model, style: { height: __1.SCALE_BAR_HEIGHT, boxSizing: 'border-box' } }) }),
+        react_1.default.createElement(Highlight_1.default, { model: model }),
         additional,
         children));
 });

package/dist/LinearGenomeView/model.d.ts

@@ -81,6 +81,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showCytobandsSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     trackLabels: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showGridlines: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    highlight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<ParsedLocString>, Required<ParsedLocString>, Required<ParsedLocString>>>;
 }, {
     width: number;
 } & {
@@ -251,6 +252,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setShowGridlines(b: boolean): void;
+    /**
+     * #action
+     */
+    setHighlight(highlight: Required<ParsedLocString> | undefined): void;
     /**
      * #action
      */

package/dist/LinearGenomeView/model.js

@@ -165,6 +165,11 @@ function stateModelFactory(pluginManager) {
          * show the "gridlines" in the track area
          */
         showGridlines: true,
+        /**
+         * #property
+         * highlights on the LGV from the URL parameters
+         */
+        highlight: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.frozen()),
     }))
         .volatile(() => ({
         volatileWidth: undefined,
@@ -468,6 +473,12 @@ function stateModelFactory(pluginManager) {
         setShowGridlines(b) {
             self.showGridlines = b;
         },
+        /**
+         * #action
+         */
+        setHighlight(highlight) {
+            self.highlight = highlight;
+        },
         /**
          * #action
          */

package/dist/LinearGenomeView/util.d.ts

@@ -24,8 +24,8 @@ export declare function generateLocations(regions: ParsedLocString[] | undefined
     assemblyName: string;
     parentRegion: import("@jbrowse/core/assemblyManager/assembly").BasicRegion;
     end?: number | undefined;
-    reversed?: boolean | undefined;
     start?: number | undefined;
+    reversed?: boolean | undefined;
     refName: string;
 }[]>;
 /**