@jbrowse/plugin-linear-genome-view 2.10.1 → 2.10.3

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/RefNameAutocomplete/EndAdornment.js

@@ -38,7 +38,7 @@ function HelpAdornment() {
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(material_1.IconButton, { onClick: () => setHelpDialogDisplayed(true), size: "small" },
             react_1.default.createElement(Help_1.default, { fontSize: "small" })),
-        isHelpDialogDisplayed ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+        isHelpDialogDisplayed ? (react_1.default.createElement(react_1.Suspense, { fallback: null },
             react_1.default.createElement(HelpDialog, { handleClose: () => setHelpDialogDisplayed(false) }))) : null));
 }
 function EndAdornment({ showHelp, endAdornment, }) {

package/dist/LinearGenomeView/components/RefNameAutocomplete/index.js

@@ -34,7 +34,6 @@ const material_1 = require("@mui/material");
 const util_2 = require("./util");
 const AutocompleteTextField_1 = __importDefault(require("./AutocompleteTextField"));
 const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp = true, minWidth = 200, maxWidth = 550, TextFieldProps = {}, }) {
-    var _a;
     const session = (0, util_1.getSession)(model);
     const { assemblyManager } = session;
     const [open, setOpen] = (0, react_1.useState)(false);
@@ -73,6 +72,14 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
     const inputBoxVal = coarseVisibleLocStrings || value || '';
     // heuristic, text width + 60 accommodates help icon and search icon
     const width = Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 14) + 100, minWidth), maxWidth);
+    const regions = assembly === null || assembly === void 0 ? void 0 : assembly.regions;
+    const regionOptions = (0, react_1.useMemo)(() => (regions === null || regions === void 0 ? void 0 : regions.map(option => ({
+        result: new BaseResults_1.RefSequenceResult({
+            refName: option.refName,
+            label: option.refName,
+            matchedAttribute: 'refName',
+        }),
+    }))) || [], [regions]);
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked
     return (react_1.default.createElement(react_1.default.Fragment, null,
@@ -98,14 +105,6 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
                     onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
                 }
                 setInputValue(inputBoxVal);
-            }, options: !(searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length)
-                ? ((_a = assembly === null || assembly === void 0 ? void 0 : assembly.regions) === null || _a === void 0 ? void 0 : _a.map(option => ({
-                    result: new BaseResults_1.RefSequenceResult({
-                        refName: option.refName,
-                        label: option.refName,
-                        matchedAttribute: 'refName',
-                    }),
-                }))) || []
-                : searchOptions, getOptionDisabled: option => option.group === 'limitOption', filterOptions: (opts, { inputValue }) => (0, util_2.getFiltered)(opts, inputValue), renderInput: params => (react_1.default.createElement(AutocompleteTextField_1.default, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() })));
+            }, options: (searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? searchOptions : regionOptions, getOptionDisabled: option => option.group === 'limitOption', filterOptions: (opts, { inputValue }) => (0, util_2.getFiltered)(opts, inputValue), renderInput: params => (react_1.default.createElement(AutocompleteTextField_1.default, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() })));
 });
 exports.default = RefNameAutocomplete;

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;
 } & {
@@ -238,19 +239,23 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    toggleHeader(): void;
+    setHideHeader(b: boolean): void;
     /**
      * #action
      */
-    toggleHeaderOverview(): void;
+    setHideHeaderOverview(b: boolean): void;
     /**
      * #action
      */
-    toggleNoTracksActive(): void;
+    setHideNoTracksActive(b: boolean): void;
     /**
      * #action
      */
-    toggleShowGridlines(): void;
+    setShowGridlines(b: boolean): void;
+    /**
+     * #action
+     */
+    setHighlight(highlight: Required<ParsedLocString> | undefined): void;
     /**
      * #action
      */
@@ -306,7 +311,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     /**
      * #action
      */
-    toggleCenterLine(): void;
+    setShowCenterLine(b: boolean): 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,
@@ -447,26 +452,32 @@ function stateModelFactory(pluginManager) {
         /**
          * #action
          */
-        toggleHeader() {
-            self.hideHeader = !self.hideHeader;
+        setHideHeader(b) {
+            self.hideHeader = b;
+        },
+        /**
+         * #action
+         */
+        setHideHeaderOverview(b) {
+            self.hideHeaderOverview = b;
         },
         /**
          * #action
          */
-        toggleHeaderOverview() {
-            self.hideHeaderOverview = !self.hideHeaderOverview;
+        setHideNoTracksActive(b) {
+            self.hideNoTracksActive = b;
         },
         /**
          * #action
          */
-        toggleNoTracksActive() {
-            self.hideNoTracksActive = !self.hideNoTracksActive;
+        setShowGridlines(b) {
+            self.showGridlines = b;
         },
         /**
          * #action
          */
-        toggleShowGridlines() {
-            self.showGridlines = !self.showGridlines;
+        setHighlight(highlight) {
+            self.highlight = highlight;
         },
         /**
          * #action
@@ -642,8 +653,8 @@ function stateModelFactory(pluginManager) {
         /**
          * #action
          */
-        toggleCenterLine() {
-            self.showCenterLine = !self.showCenterLine;
+        setShowCenterLine(b) {
+            self.showCenterLine = b;
         },
         /**
          * #action
@@ -920,32 +931,32 @@ function stateModelFactory(pluginManager) {
                             label: 'Show center line',
                             type: 'checkbox',
                             checked: self.showCenterLine,
-                            onClick: self.toggleCenterLine,
+                            onClick: () => self.setShowCenterLine(!self.showCenterLine),
                         },
                         {
                             label: 'Show header',
                             type: 'checkbox',
                             checked: !self.hideHeader,
-                            onClick: self.toggleHeader,
+                            onClick: () => self.setHideHeader(!self.hideHeader),
                         },
                         {
                             label: 'Show header overview',
                             type: 'checkbox',
                             checked: !self.hideHeaderOverview,
-                            onClick: self.toggleHeaderOverview,
+                            onClick: () => self.setHideHeaderOverview(!self.hideHeaderOverview),
                             disabled: self.hideHeader,
                         },
                         {
                             label: 'Show no tracks active button',
                             type: 'checkbox',
                             checked: !self.hideNoTracksActive,
-                            onClick: self.toggleNoTracksActive,
+                            onClick: () => self.setHideNoTracksActive(!self.hideNoTracksActive),
                         },
                         {
                             label: 'Show guidelines',
                             type: 'checkbox',
                             checked: self.showGridlines,
-                            onClick: self.toggleShowGridlines,
+                            onClick: () => self.setShowGridlines(!self.showGridlines),
                         },
                         ...(canShowCytobands
                             ? [

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;
 }[]>;
 /**

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;
             } & {
@@ -964,10 +1007,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                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;
@@ -981,7 +1025,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
@@ -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;
             } & {
@@ -1283,10 +1328,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                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;
@@ -1300,7 +1346,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
@@ -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;
             } & {
@@ -1612,10 +1659,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                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;
@@ -1629,7 +1677,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
@@ -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;
             } & {
@@ -1931,10 +1980,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                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;
@@ -1948,7 +1998,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
@@ -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;
             } & {
@@ -2260,10 +2311,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                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;
@@ -2277,7 +2329,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {
@@ -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;
             } & {
@@ -2579,10 +2632,11 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 setShowCytobands(flag: boolean): void;
                 setWidth(newWidth: number): void;
                 setError(error: unknown): void;
-                toggleHeader(): void;
-                toggleHeaderOverview(): void;
-                toggleNoTracksActive(): void;
-                toggleShowGridlines(): void;
+                setHideHeader(b: boolean): void;
+                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;
@@ -2596,7 +2650,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
                 closeView(): void;
                 toggleTrack(trackId: string): boolean;
                 setTrackLabels(setting: "offset" | "hidden" | "overlapping"): void;
-                toggleCenterLine(): void;
+                setShowCenterLine(b: boolean): void;
                 setDisplayedRegions(regions: import("@jbrowse/core/util").Region[]): void;
                 activateTrackSelector(): import("@jbrowse/core/util").Widget;
                 getSelectedRegions(leftOffset?: import("./LinearGenomeView").BpOffset | undefined, rightOffset?: import("./LinearGenomeView").BpOffset | undefined): {

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;