@jbrowse/plugin-linear-genome-view 2.10.1 → 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/BaseLinearDisplay/models/util.js

@@ -20,8 +20,10 @@ function getDisplayStr(totalBytes) {
 exports.getDisplayStr = getDisplayStr;
 // stabilize clipid under test for snapshot
 function getId(id, index) {
-    const isJest = typeof jest === 'undefined';
-    return `clip-${isJest ? id : 'jest'}-${index}`;
+    const notJest = typeof jest === 'undefined';
+    return ['clip', notJest ? id : 'jest', index, notJest ? Math.random() : '']
+        .filter(f => !!f)
+        .join('-');
 }
 exports.getId = getId;
 async function getFeatureDensityStatsPre(self) {

package/dist/LaunchLinearGenomeView/index.js

@@ -1,13 +1,14 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const util_1 = require("@jbrowse/core/util");
-const searchUtils_1 = require("..//searchUtils");
+const searchUtils_1 = require("../searchUtils");
 exports.default = (pluginManager) => {
     pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', 
     // @ts-expect-error
-    async ({ session, assembly, loc, tracks = [], }) => {
+    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) {
@@ -17,6 +18,19 @@ exports.default = (pluginManager) => {
             if (!asm) {
                 throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
             }
+            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));

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

@@ -37,9 +37,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined; /**
-         * #property
-         */
+        renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -49,8 +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;
@@ -159,12 +166,11 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         }, {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
+            message: string | undefined; /**
+             * #action
+             */
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
-    /**
-     * #action
-     */
     readonly adapterConfig: any;
     readonly parentTrack: any;
     renderProps(): any;
@@ -193,9 +199,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly currentBytesRequested: number;
     readonly currentFeatureScreenDensity: number;
-    /**
-     * #getter
-     */
     readonly maxFeatureScreenDensity: any;
     readonly featureDensityStatsReady: boolean;
     readonly maxAllowableBytes: number;
@@ -205,7 +208,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setCurrStatsBpPerPx(n: number): void;
     setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
-    setFeatureDensityStatsP(arg: any): void;
+    setFeatureDensityStatsP(arg: any): void; /**
+     * #method
+     */
     setFeatureDensityStats(featureDensityStats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     clearFeatureDensityStats(): void;
 } & {
@@ -275,9 +280,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any; /**
-         * #property
-         */
+        setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     /**
@@ -304,9 +307,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         config: {
             [x: string]: any;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: unknown): any; /**
-             * #property
-             */
+            setSubschema(slotName: string, data: unknown): any;
         } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
     };
     /**
@@ -341,9 +342,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
-        renderInProgress: AbortController | undefined; /**
-         * #property
-         */
+        renderInProgress: AbortController | undefined;
         filled: boolean;
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
@@ -353,8 +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/LinearBasicDisplay/model.js

@@ -34,7 +34,7 @@ const mobx_state_tree_1 = require("mobx-state-tree");
 const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
 // locals
 const BaseLinearDisplay_1 = require("../BaseLinearDisplay");
-const SetMaxHeightDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeight'))));
+const SetMaxHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeight'))));
 /**
  * #stateModel LinearBasicDisplay
  * #category display
@@ -202,7 +202,7 @@ function stateModelFactory(configSchema) {
                         label: 'Set max height',
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                SetMaxHeightDlg,
+                                SetMaxHeightDialog,
                                 { model: self, handleClose },
                             ]);
                         },

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

@@ -1,6 +1,6 @@
 import React from 'react';
 import { ExportSvgOptions } from '..';
-export default function ExportSvgDlg({ model, handleClose, }: {
+export default function ExportSvgDialog({ model, handleClose, }: {
     model: {
         exportSvg(opts: ExportSvgOptions): Promise<void>;
     };

package/dist/LinearGenomeView/components/ExportSvgDialog.js

@@ -35,7 +35,7 @@ function LoadingMessage() {
 function useSvgLocal(key, val) {
     return (0, util_1.useLocalStorage)('svg-' + key, val);
 }
-function ExportSvgDlg({ model, handleClose, }) {
+function ExportSvgDialog({ model, handleClose, }) {
     const session = (0, util_1.getSession)(model);
     const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
     const [rasterizeLayers, setRasterizeLayers] = (0, react_1.useState)(offscreenCanvas);
@@ -80,4 +80,4 @@ function ExportSvgDlg({ model, handleClose, }) {
                     }
                 } }, "Submit"))));
 }
-exports.default = ExportSvgDlg;
+exports.default = ExportSvgDialog;

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;