@jbrowse/plugin-linear-genome-view 2.10.3 → 2.11.0

package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js

@@ -102,7 +102,6 @@ const blockState = mobx_state_tree_1.types
             renderInProgress = undefined;
         },
         setError(error) {
-            console.error(error);
             if (renderInProgress && !renderInProgress.signal.aborted) {
                 renderInProgress.abort();
             }

package/dist/LaunchLinearGenomeView/index.js

@@ -25,11 +25,19 @@ exports.default = (pluginManager) => {
                 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);
-                }
+                highlight.forEach(async (h) => {
+                    if (h) {
+                        const parsedLocString = (0, util_1.parseLocString)(h, refName => isValidRefName(refName, assembly));
+                        const location = {
+                            ...parsedLocString,
+                            assemblyName: assembly,
+                        };
+                        if ((location === null || location === void 0 ? void 0 : location.start) !== undefined &&
+                            (location === null || location === void 0 ? void 0 : location.end) !== undefined) {
+                            view.addToHighlights(location);
+                        }
+                    }
+                });
             }
             await (0, searchUtils_1.handleSelectedRegion)({ input: loc, model: view, assembly: asm });
             const idsNotFound = [];
@@ -39,7 +47,7 @@ exports.default = (pluginManager) => {
             }
         }
         catch (e) {
-            session.notify(`${e}`, 'error');
+            session.notifyError(`${e}`, e);
             throw e;
         }
     });

package/dist/LinearBasicDisplay/components/SetMaxHeight.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
 declare const SetMaxHeightDialog: ({ model, handleClose, }: {
     model: {
-        maxHeight?: number | undefined;
+        maxHeight?: number;
         setMaxHeight: (arg?: number) => void;
     };
     handleClose: () => void;

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

@@ -4,131 +4,7 @@ import { ContentBlock } from '@jbrowse/core/util/blockTypes';
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
 declare const Cytobands: ({ overview, block, assembly, }: {
     overview: Base1DViewModel;
-    assembly?: ({
-        configuration: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: unknown;
-        loaded: boolean;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string | undefined;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-        readonly refNameColors: string[];
-    } & {
-        readonly refNames: string[] | undefined;
-    } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-    } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string | undefined;
-        }, lcAliases: {
-            [x: string]: string | undefined;
-        }): void;
-        setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        setLoadingP(p?: Promise<void> | undefined): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
-        }>;
-    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    }, {
-        error: unknown;
-        loaded: boolean;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string | undefined;
-        } | undefined;
-        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string | undefined;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
-        readonly refNameColors: string[];
-    } & {
-        readonly refNames: string[] | undefined;
-    } & {
-        getCanonicalRefName(refName: string): string | undefined;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-    } & {
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string | undefined;
-        }, lcAliases: {
-            [x: string]: string | undefined;
-        }): void;
-        setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        setLoadingP(p?: Promise<void> | undefined): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string | undefined;
-        }>;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+    assembly?: Assembly;
     block: ContentBlock;
 }) => React.JSX.Element;
 export default Cytobands;

package/dist/LinearGenomeView/components/ExportSvgDialog.js

@@ -35,6 +35,10 @@ function LoadingMessage() {
 function useSvgLocal(key, val) {
     return (0, util_1.useLocalStorage)('svg-' + key, val);
 }
+function TextField2({ children, ...rest }) {
+    return (react_1.default.createElement("div", null,
+        react_1.default.createElement(material_1.TextField, { ...rest }, children)));
+}
 function ExportSvgDialog({ model, handleClose, }) {
     const session = (0, util_1.getSession)(model);
     const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
@@ -47,15 +51,13 @@ function ExportSvgDialog({ model, handleClose, }) {
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         react_1.default.createElement(material_1.DialogContent, null,
             error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(LoadingMessage, null)) : null,
-            react_1.default.createElement(material_1.TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
-            react_1.default.createElement("br", null),
-            react_1.default.createElement(material_1.TextField, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
+            react_1.default.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
+            react_1.default.createElement(TextField2, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
                 react_1.default.createElement(material_1.MenuItem, { value: "offset" }, "Offset"),
                 react_1.default.createElement(material_1.MenuItem, { value: "overlay" }, "Overlay"),
                 react_1.default.createElement(material_1.MenuItem, { value: "left" }, "Left"),
                 react_1.default.createElement(material_1.MenuItem, { value: "none" }, "None")),
-            react_1.default.createElement("br", null),
-            session.allThemes ? (react_1.default.createElement(material_1.TextField, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
+            session.allThemes ? (react_1.default.createElement(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
             // @ts-expect-error
             val.name || '(Unknown name)'))))) : null,
             offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
@@ -76,6 +78,8 @@ function ExportSvgDialog({ model, handleClose, }) {
                     catch (e) {
                         console.error(e);
                         setError(e);
+                    }
+                    finally {
                         setLoading(false);
                     }
                 } }, "Submit"))));

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

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

package/dist/LinearGenomeView/components/Highlight.js

@@ -38,28 +38,28 @@ 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;
+    var _a, _b;
     return ({
         highlight: {
             height: '100%',
             position: 'absolute',
-            background: `${(0, colord_1.colord)((_b = (_a = theme.palette.quaternary) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod')
+            overflow: 'hidden',
+            background: `${(0, colord_1.colord)((_b = (_a = theme.palette.highlight) === 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 Highlight = (0, mobx_react_1.observer)(function Highlight({ model, highlight, }) {
+    var _a, _b, _c;
     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 color = (_b = (_a = (0, material_1.useTheme)().palette.highlight) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod';
     const session = (0, util_1.getSession)(model);
+    const { assemblyManager } = session;
     const dismissHighlight = () => {
-        model.setHighlight(undefined);
+        model.removeHighlight(highlight);
     };
     const menuItems = [
         {
@@ -76,7 +76,7 @@ const Highlight = (0, mobx_react_1.observer)(function Highlight({ model }) {
                     bookmarkWidget = session.addWidget('GridBookmarkWidget', 'GridBookmark');
                 }
                 // @ts-ignore
-                bookmarkWidget.addBookmark(model.highlight);
+                bookmarkWidget.addBookmark(highlight);
                 dismissHighlight();
             },
         },
@@ -84,9 +84,6 @@ const Highlight = (0, mobx_react_1.observer)(function Highlight({ model }) {
     function handleClose() {
         setOpen(false);
     }
-    if (!model.highlight) {
-        return null;
-    }
     // coords
     const mapCoords = (r) => {
         const s = model.bpToPx({
@@ -104,19 +101,26 @@ const Highlight = (0, mobx_react_1.observer)(function Highlight({ model }) {
             }
             : 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: {
+    const asm = assemblyManager.get(highlight === null || highlight === void 0 ? void 0 : highlight.assemblyName);
+    const h = mapCoords({
+        ...highlight,
+        refName: (_c = asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(highlight.refName)) !== null && _c !== void 0 ? _c : highlight.refName,
+    });
+    return 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(material_1.IconButton, { ref: anchorEl, onClick: () => setOpen(true), style: { zIndex: 3 } },
                 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));
+            }, open: open, onClose: handleClose, menuItems: menuItems }))) : null;
+});
+const HighlightGroup = (0, mobx_react_1.observer)(function HighlightGroup({ model, }) {
+    return model.highlight.map((highlight, idx) => (react_1.default.createElement(Highlight, { key: JSON.stringify(highlight) + '-' + idx, model: model, highlight: highlight })));
 });
-exports.default = Highlight;
+exports.default = HighlightGroup;

package/dist/LinearGenomeView/components/MiniControls.js

@@ -6,13 +6,13 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
+const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
+const mui_1 = require("tss-react/mui");
+const util_1 = require("@jbrowse/core/util");
 // icons
 const ZoomIn_1 = __importDefault(require("@mui/icons-material/ZoomIn"));
 const ZoomOut_1 = __importDefault(require("@mui/icons-material/ZoomOut"));
 const KeyboardArrowDown_1 = __importDefault(require("@mui/icons-material/KeyboardArrowDown"));
-const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
-const mui_1 = require("tss-react/mui");
-const util_1 = require("@jbrowse/core/util");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     background: {
         position: 'absolute',
@@ -21,22 +21,20 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         background: theme.palette.background.paper,
     },
     focusedBackground: {
-        background: theme.palette.secondary.light,
-        svg: {
-            fill: theme.palette.secondary.contrastText,
-        },
+        background: (0, material_1.alpha)(theme.palette.secondary.light, 0.2),
     },
 }));
 const MiniControls = (0, mobx_react_1.observer)(function ({ model, }) {
-    const { classes, cx } = useStyles();
+    const { classes } = useStyles();
     const { id, bpPerPx, maxBpPerPx, minBpPerPx, scaleFactor, hideHeader } = model;
     const { focusedViewId } = (0, util_1.getSession)(model);
-    return hideHeader ? (react_1.default.createElement(material_1.Paper, { className: cx(classes.background, focusedViewId === id ? classes.focusedBackground : undefined) },
-        react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: model.menuItems() },
-            react_1.default.createElement(KeyboardArrowDown_1.default, { fontSize: "small" })),
-        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1 },
-            react_1.default.createElement(ZoomOut_1.default, { fontSize: "small" })),
-        react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1 },
-            react_1.default.createElement(ZoomIn_1.default, { fontSize: "small" })))) : null;
+    return hideHeader ? (react_1.default.createElement(material_1.Paper, { className: classes.background },
+        react_1.default.createElement(material_1.Paper, { className: focusedViewId === id ? classes.focusedBackground : undefined },
+            react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: model.menuItems() },
+                react_1.default.createElement(KeyboardArrowDown_1.default, { fontSize: "small" })),
+            react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1 },
+                react_1.default.createElement(ZoomOut_1.default, { fontSize: "small" })),
+            react_1.default.createElement(material_1.IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1 },
+                react_1.default.createElement(ZoomIn_1.default, { fontSize: "small" }))))) : null;
 });
 exports.default = MiniControls;

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

@@ -5,5 +5,5 @@ type LGV = LinearGenomeViewModel;
 declare const OverviewHighlight: ({ model, overview, }: {
     model: LGV;
     overview: Base1DViewModel;
-}) => React.JSX.Element | null;
+}) => React.JSX.Element[];
 export default OverviewHighlight;

package/dist/LinearGenomeView/components/OverviewHighlight.js

@@ -7,23 +7,26 @@ 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 util_1 = require("@jbrowse/core/util");
 const useStyles = (0, mui_1.makeStyles)()(theme => {
     var _a, _b, _c, _d, _e, _f;
     return ({
         highlight: {
             height: '100%',
             position: 'absolute',
-            background: `${(0, colord_1.colord)((_b = (_a = theme.palette.quaternary) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod')
+            background: `${(0, colord_1.colord)((_b = (_a = theme.palette.highlight) === 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'}`,
+            borderLeft: `1px solid ${(_d = (_c = theme.palette.highlight) === null || _c === void 0 ? void 0 : _c.main) !== null && _d !== void 0 ? _d : 'goldenrod'}`,
+            borderRight: `1px solid ${(_f = (_e = theme.palette.highlight) === null || _e === void 0 ? void 0 : _e.main) !== null && _f !== void 0 ? _f : 'goldenrod'}`,
         },
     });
 });
 const OverviewHighlight = (0, mobx_react_1.observer)(function OverviewHighlight({ model, overview, }) {
     const { classes } = useStyles();
     const { cytobandOffset } = model;
+    const session = (0, util_1.getSession)(model);
+    const { assemblyManager } = session;
     // coords
     const mapCoords = (r) => {
         const s = overview.bpToPx({
@@ -41,13 +44,19 @@ const OverviewHighlight = (0, mobx_react_1.observer)(function OverviewHighlight(
             }
             : undefined;
     };
-    if (!model.highlight) {
-        return null;
-    }
-    const h = mapCoords(model.highlight);
-    return (react_1.default.createElement(react_1.default.Fragment, null, h ? (react_1.default.createElement("div", { className: classes.highlight, style: {
-            width: h.width,
-            left: h.left,
-        } })) : null));
+    return model.highlight
+        .map(h => {
+        var _a;
+        const asm = assemblyManager.get(h === null || h === void 0 ? void 0 : h.assemblyName);
+        return mapCoords({
+            ...h,
+            refName: (_a = asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(h.refName)) !== null && _a !== void 0 ? _a : h.refName,
+        });
+    })
+        .filter(util_1.notEmpty)
+        .map(({ left, width }, idx) => (react_1.default.createElement("div", { key: `${left}_${width}_${idx}`, className: classes.highlight, style: {
+            width: width,
+            left: left,
+        } })));
 });
 exports.default = OverviewHighlight;

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

@@ -5,6 +5,6 @@ type LGV = LinearGenomeViewModel;
 declare const OverviewRubberband: ({ model, overview, ControlComponent, }: {
     model: LGV;
     overview: Base1DViewModel;
-    ControlComponent?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+    ControlComponent?: React.ReactElement;
 }) => React.JSX.Element;
 export default OverviewRubberband;

package/dist/LinearGenomeView/components/OverviewScalebar.js

@@ -146,6 +146,7 @@ const Scalebar = (0, mobx_react_1.observer)(function ({ model, scale, overview,
     const { classes } = useStyles();
     const theme = (0, material_1.useTheme)();
     const { dynamicBlocks, showCytobands, cytobandOffset } = model;
+    const { pluginManager } = (0, util_1.getEnv)(model);
     const visibleRegions = dynamicBlocks.contentBlocks;
     const overviewVisibleRegions = overview.dynamicBlocks;
     const { tertiary, primary } = theme.palette;
@@ -166,6 +167,7 @@ const Scalebar = (0, mobx_react_1.observer)(function ({ model, scale, overview,
     }) || 0;
     const color = showCytobands ? '#f00' : scalebarColor;
     const transparency = showCytobands ? 0.1 : 0.3;
+    const additional = pluginManager.evaluateExtensionPoint('LinearGenomeView-OverviewScalebarComponent', undefined, { model, overview });
     return (react_1.default.createElement("div", { className: classes.scalebar },
         react_1.default.createElement("div", { className: classes.scalebarVisibleRegion, style: {
                 width: lastOverviewPx - firstOverviewPx,
@@ -181,7 +183,8 @@ const Scalebar = (0, mobx_react_1.observer)(function ({ model, scale, overview,
                     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 })));
+        react_1.default.createElement(OverviewHighlight_1.default, { model: model, overview: overview }),
+        additional));
 });
 const OverviewScalebar = (0, mobx_react_1.observer)(function ({ model, children, }) {
     const { classes } = useStyles();

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

@@ -4,6 +4,6 @@ import { LinearGenomeViewModel } from '..';
 declare const OverviewScalebarPolygon: ({ model, overview, useOffset, }: {
     model: LinearGenomeViewModel;
     overview: Base1DViewModel;
-    useOffset?: boolean | undefined;
+    useOffset?: boolean;
 }) => React.JSX.Element | null;
 export default OverviewScalebarPolygon;

package/dist/LinearGenomeView/components/RefNameAutocomplete/index.d.ts

@@ -4,15 +4,15 @@ import { TextFieldProps as TFP } from '@mui/material';
 import { LinearGenomeViewModel } from '../../model';
 declare const RefNameAutocomplete: ({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp, minWidth, maxWidth, TextFieldProps, }: {
     model: LinearGenomeViewModel;
-    onSelect?: ((region: BaseResult) => void) | undefined;
-    onChange?: ((val: string) => void) | undefined;
-    assemblyName?: string | undefined;
-    value?: string | undefined;
+    onSelect?: (region: BaseResult) => void;
+    onChange?: (val: string) => void;
+    assemblyName?: string;
+    value?: string;
     fetchResults: (query: string) => Promise<BaseResult[]>;
-    style?: React.CSSProperties | undefined;
-    minWidth?: number | undefined;
-    maxWidth?: number | undefined;
-    showHelp?: boolean | undefined;
-    TextFieldProps?: TFP | undefined;
+    style?: React.CSSProperties;
+    minWidth?: number;
+    maxWidth?: number;
+    showHelp?: boolean;
+    TextFieldProps?: TFP;
 }) => React.JSX.Element;
 export default RefNameAutocomplete;

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

@@ -45,7 +45,8 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
     const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
     const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
     (0, react_1.useEffect)(() => {
-        let active = true;
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
         (async () => {
             try {
                 if (debouncedSearch === '' || !assemblyName) {
@@ -53,21 +54,14 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
                 }
                 setLoaded(false);
                 const results = await fetchResults(debouncedSearch);
-                if (active) {
-                    setLoaded(true);
-                    setSearchOptions((0, util_2.getDeduplicatedResult)(results));
-                }
+                setLoaded(true);
+                setSearchOptions((0, util_2.getDeduplicatedResult)(results));
             }
             catch (e) {
                 console.error(e);
-                if (active) {
-                    session.notify(`${e}`, 'error');
-                }
+                session.notifyError(`${e}`, e);
             }
         })();
-        return () => {
-            active = false;
-        };
     }, [assemblyName, fetchResults, debouncedSearch, session, model]);
     const inputBoxVal = coarseVisibleLocStrings || value || '';
     // heuristic, text width + 60 accommodates help icon and search icon
@@ -82,29 +76,28 @@ const RefNameAutocomplete = (0, mobx_react_1.observer)(function ({ model, onSele
     }))) || [], [regions]);
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
-                setInputValue(newInputValue);
-                onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
-            }, loadingText: "loading results", open: open, onOpen: () => setOpen(true), onClose: () => {
-                setOpen(false);
-                setLoaded(true);
-                if (hasDisplayedRegions) {
-                    setCurrentSearch('');
-                    setSearchOptions(undefined);
-                }
-            }, onChange: (_event, selectedOption) => {
-                if (!selectedOption || !assemblyName) {
-                    return;
-                }
-                if (typeof selectedOption === 'string') {
-                    // handles string inputs on keyPress enter
-                    onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResults_1.default({ label: selectedOption }));
-                }
-                else {
-                    onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
-                }
-                setInputValue(inputBoxVal);
-            }, 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() })));
+    return (react_1.default.createElement(material_1.Autocomplete, { "data-testid": "autocomplete", disableListWrap: true, disableClearable: true, disabled: !assemblyName, freeSolo: true, includeInputInList: true, selectOnFocus: true, style: { ...style, width }, value: inputBoxVal, loading: !loaded, inputValue: inputValue, onInputChange: (_event, newInputValue) => {
+            setInputValue(newInputValue);
+            onChange === null || onChange === void 0 ? void 0 : onChange(newInputValue);
+        }, loadingText: "loading results", open: open, onOpen: () => setOpen(true), onClose: () => {
+            setOpen(false);
+            setLoaded(true);
+            if (hasDisplayedRegions) {
+                setCurrentSearch('');
+                setSearchOptions(undefined);
+            }
+        }, onChange: (_event, selectedOption) => {
+            if (!selectedOption || !assemblyName) {
+                return;
+            }
+            if (typeof selectedOption === 'string') {
+                // handles string inputs on keyPress enter
+                onSelect === null || onSelect === void 0 ? void 0 : onSelect(new BaseResults_1.default({ label: selectedOption }));
+            }
+            else {
+                onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
+            }
+            setInputValue(inputBoxVal);
+        }, 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/Rubberband.d.ts

@@ -3,6 +3,6 @@ import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare const Rubberband: ({ model, ControlComponent, }: {
     model: LGV;
-    ControlComponent?: React.ReactElement<any, string | React.JSXElementConstructor<any>> | undefined;
+    ControlComponent?: React.ReactElement;
 }) => React.JSX.Element;
 export default Rubberband;

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

@@ -1,7 +1,7 @@
 import React from 'react';
 import { LinearGenomeViewModel } from '..';
 declare const SearchBox: ({ model, showHelp, }: {
-    showHelp?: boolean | undefined;
+    showHelp?: boolean;
     model: LinearGenomeViewModel;
 }) => React.JSX.Element;
 export default SearchBox;