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

package/dist/index.d.ts

@@ -38,8 +38,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     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;
@@ -83,8 +90,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     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;
@@ -292,8 +306,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     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;
@@ -497,8 +518,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                     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;
@@ -587,8 +615,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 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;
@@ -792,8 +827,15 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 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;
@@ -904,6 +946,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
+                highlight: (Required<import("@jbrowse/core/util").ParsedLocString> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>>) | undefined;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -968,6 +1011,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -1223,6 +1267,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 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<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
             }, {
                 width: number;
             } & {
@@ -1287,6 +1332,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -1552,6 +1598,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
+                highlight: (Required<import("@jbrowse/core/util").ParsedLocString> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>>) | undefined;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -1616,6 +1663,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -1871,6 +1919,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 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<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
             }, {
                 width: number;
             } & {
@@ -1935,6 +1984,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -2200,6 +2250,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 showCytobandsSetting: boolean;
                 trackLabels: string;
                 showGridlines: boolean;
+                highlight: (Required<import("@jbrowse/core/util").ParsedLocString> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IMaybe<import("mobx-state-tree").IType<Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>>) | undefined;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
                 width: number;
             } & {
@@ -2264,6 +2315,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;
@@ -2519,6 +2571,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 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<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>, Required<import("@jbrowse/core/util").ParsedLocString>>>;
             }, {
                 width: number;
             } & {
@@ -2583,6 +2636,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setHideHeaderOverview(b: boolean): void;
                 setHideNoTracksActive(b: boolean): void;
                 setShowGridlines(b: boolean): void;
+                setHighlight(highlight: Required<import("@jbrowse/core/util").ParsedLocString> | undefined): void;
                 scrollTo(offsetPx: number): number;
                 zoomTo(bpPerPx: number, offset?: number, centerAtOffset?: boolean): number;
                 setOffsets(left?: import("./LinearGenomeView").BpOffset | undefined, right?: import("./LinearGenomeView").BpOffset | undefined): void;

package/esm/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/esm/BaseLinearDisplay/components/BlockMsg.js

@@ -1,5 +1,5 @@
 import React from 'react';
-import { Tooltip, Button, Alert } from '@mui/material';
+import { Tooltip, Alert } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     ellipses: {
@@ -7,10 +7,9 @@ const useStyles = makeStyles()({
         overflow: 'hidden',
     },
 });
-export default function BlockMsg({ message, severity, buttonText, icon, action, }) {
+export default function BlockMsg({ message, severity, action, }) {
     const { classes } = useStyles();
-    const button = action ? (React.createElement(Button, { "data-testid": "reload_button", onClick: action, startIcon: icon }, buttonText)) : null;
-    return (React.createElement(Alert, { severity: severity, action: button, classes: { message: classes.ellipses } },
+    return (React.createElement(Alert, { severity: severity, action: action, classes: { message: classes.ellipses } },
         React.createElement(Tooltip, { title: message },
             React.createElement("div", null, message))));
 }

package/esm/BaseLinearDisplay/components/LinearBlocks.js

@@ -32,8 +32,8 @@ const RenderedBlocks = observer(function ({ model, }) {
         if (block instanceof ContentBlock) {
             const state = blockState.get(block.key);
             return (React.createElement(ContentBlockComponent, { block: block, key: `${model.id}-${block.key}` },
-                state && state.ReactComponent ? (React.createElement(state.ReactComponent, { model: state })) : null,
-                state && state.maxHeightReached ? (React.createElement("div", { className: classes.heightOverflowed, style: {
+                (state === null || state === void 0 ? void 0 : state.ReactComponent) ? (React.createElement(state.ReactComponent, { model: state })) : null,
+                (state === null || state === void 0 ? void 0 : state.maxHeightReached) ? (React.createElement("div", { className: classes.heightOverflowed, style: {
                         top: state.layout.getTotalHeight() - 16,
                         pointerEvents: 'none',
                         height: 16,

package/esm/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/esm/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js

@@ -1,12 +1,16 @@
-import React from 'react';
+import React, { lazy } from 'react';
+import { Tooltip, IconButton } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
 import { getParent } from 'mobx-state-tree';
 import { LoadingEllipses } from '@jbrowse/core/ui';
+import { getSession } from '@jbrowse/core/util';
 // icons
 import RefreshIcon from '@mui/icons-material/Refresh';
+import ReportIcon from '@mui/icons-material/Report';
 // locals
 import BlockMsg from './BlockMsg';
+const ErrorMessageStackTraceDialog = lazy(() => import('@jbrowse/core/ui/ErrorMessageStackTraceDialog'));
 const useStyles = makeStyles()(theme => {
     const bg = theme.palette.action.disabledBackground;
     return {
@@ -18,11 +22,9 @@ const useStyles = makeStyles()(theme => {
         },
     };
 });
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 const LoadingMessage = observer(({ model }) => {
     const { classes } = useStyles();
     const { status: blockStatus } = model;
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const { message: displayStatus } = getParent(model, 2);
     const status = displayStatus || blockStatus;
     return (React.createElement("div", { className: classes.loading },
@@ -30,7 +32,18 @@ const LoadingMessage = observer(({ model }) => {
 });
 const ServerSideRenderedBlockContent = observer(function ({ model, }) {
     if (model.error) {
-        return (React.createElement(BlockMsg, { message: `${model.error}`, severity: "error", buttonText: "reload", icon: React.createElement(RefreshIcon, null), action: model.reload }));
+        return (React.createElement(BlockMsg, { message: `${model.error}`, severity: "error", action: React.createElement(React.Fragment, null,
+                React.createElement(Tooltip, { title: "Reload track" },
+                    React.createElement(IconButton, { "data-testid": "reload_button", onClick: () => model.reload() },
+                        React.createElement(RefreshIcon, null))),
+                React.createElement(Tooltip, { title: "Show stack trace" },
+                    React.createElement(IconButton, { onClick: () => {
+                            getSession(model).queueDialog(onClose => [
+                                ErrorMessageStackTraceDialog,
+                                { onClose, error: model.error },
+                            ]);
+                        } },
+                        React.createElement(ReportIcon, null)))) }));
     }
     else if (model.message) {
         // the message can be a fully rendered react component, e.g. the region too large message

package/esm/BaseLinearDisplay/components/TooLargeMessage.js

@@ -1,12 +1,13 @@
 import React from 'react';
 // locals
 import BlockMsg from '../components/BlockMsg';
+import { Button } from '@mui/material';
 function TooLargeMessage({ model, }) {
     const { regionTooLargeReason } = model;
-    return (React.createElement(BlockMsg, { severity: "warning", action: () => {
-            model.setFeatureDensityStatsLimit(model.featureDensityStats);
-            model.reload();
-        }, buttonText: "Force load", message: [
+    return (React.createElement(BlockMsg, { severity: "warning", action: React.createElement(Button, { onClick: () => {
+                model.setFeatureDensityStatsLimit(model.featureDensityStats);
+                model.reload();
+            } }, "Force load"), message: [
             regionTooLargeReason,
             'Zoom in to see features or force load (may be slow)',
         ]

package/esm/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/esm/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/esm/LaunchLinearGenomeView/index.js

@@ -1,11 +1,12 @@
-import { when } from '@jbrowse/core/util';
+import { when, parseLocString, } from '@jbrowse/core/util';
 import { handleSelectedRegion } from '../searchUtils';
 export 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 when(() => !!view.volatileWidth);
             if (!assembly) {
@@ -15,18 +16,25 @@ export default (pluginManager) => {
             if (!asm) {
                 throw new Error(`Assembly "${assembly}" not found when launching linear genome view`);
             }
-            await 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 = 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 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/esm/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/esm/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/esm/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/esm/LinearGenomeView/components/Highlight.js

@@ -0,0 +1,94 @@
+import React, { useRef, useState } from 'react';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import { colord } from '@jbrowse/core/util/colord';
+import { getSession, } from '@jbrowse/core/util';
+import { Menu } from '@jbrowse/core/ui';
+import { IconButton, Tooltip, useTheme } from '@mui/material';
+// icons
+import LinkIcon from '@mui/icons-material/Link';
+import CloseIcon from '@mui/icons-material/Close';
+import BookmarkIcon from '@mui/icons-material/Bookmark';
+const useStyles = makeStyles()(theme => {
+    var _a, _b, _c, _d, _e, _f;
+    return ({
+        highlight: {
+            height: '100%',
+            position: 'absolute',
+            background: `${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 = observer(function Highlight({ model }) {
+    var _a, _b;
+    const { classes } = useStyles();
+    const [open, setOpen] = useState(false);
+    const anchorEl = useRef(null);
+    const color = (_b = (_a = useTheme().palette.quaternary) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod';
+    const session = getSession(model);
+    const dismissHighlight = () => {
+        model.setHighlight(undefined);
+    };
+    const menuItems = [
+        {
+            label: 'Dismiss highlight',
+            icon: CloseIcon,
+            onClick: () => dismissHighlight(),
+        },
+        {
+            label: 'Bookmark highlighted region',
+            icon: BookmarkIcon,
+            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.createElement(React.Fragment, null, h ? (React.createElement("div", { className: classes.highlight, style: {
+            left: h.left,
+            width: h.width,
+        } },
+        React.createElement(Tooltip, { title: 'Highlighted from URL parameter', arrow: true },
+            React.createElement(IconButton, { ref: anchorEl, onClick: () => setOpen(true) },
+                React.createElement(LinkIcon, { fontSize: "small", sx: {
+                        color: `${colord(color).darken(0.2).toRgbString()}`,
+                    } }))),
+        React.createElement(Menu, { anchorEl: anchorEl.current, onMenuItemClick: (_event, callback) => {
+                callback(session);
+                handleClose();
+            }, open: open, onClose: handleClose, menuItems: menuItems }))) : null));
+});
+export default Highlight;

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

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+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;