@jbrowse/plugin-linear-genome-view 2.10.3 → 2.11.1

package/esm/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/esm/LinearGenomeView/components/Cytobands.js

@@ -3,6 +3,7 @@ import { observer } from 'mobx-react';
 // locals
 import { HEADER_OVERVIEW_HEIGHT } from '..';
 import { getCytobands } from './util';
+import { getFillProps } from '@jbrowse/core/util';
 // rounded rect from https://stackoverflow.com/a/45889603/2129219
 // prettier-ignore
 function rightRoundedRect(x, y, width, height, radius) {
@@ -63,28 +64,26 @@ const Cytobands = observer(function ({ overview, block, assembly, }) {
         const e = overview.bpToPx({ refName, coord: end }) || 0;
         const l = Math.min(s, e);
         const w = Math.abs(e - s);
-        const c = colorMap[type];
+        const c = colorMap[type] || 'black';
         if (type === 'acen' && !centromereSeen) {
             centromereSeen = true; // the next acen entry is drawn with different right triangle
-            const tri = reversed
-                ? rightTriangle(s - w, 0, w, h)
-                : leftTriangle(s, 0, w, h);
-            return React.createElement("polygon", { key: k, points: tri, fill: c });
+            return (React.createElement("polygon", { key: k, points: reversed
+                    ? rightTriangle(s - w, 0, w, h)
+                    : leftTriangle(s, 0, w, h), ...getFillProps(c) }));
         }
         else if (type === 'acen' && centromereSeen) {
-            const tri = reversed
-                ? leftTriangle(s - w, 0, w, h)
-                : rightTriangle(s, 0, w, h);
-            return React.createElement("polygon", { key: k, points: tri, fill: c });
+            return (React.createElement("polygon", { key: k, points: reversed
+                    ? leftTriangle(s - w, 0, w, h)
+                    : rightTriangle(s, 0, w, h), ...getFillProps(c) }));
         }
         else if (lcap === index) {
-            return React.createElement("path", { key: k, d: leftRoundedRect(l, 0, w, h, 8), fill: c });
+            return (React.createElement("path", { key: k, d: leftRoundedRect(l, 0, w, h, 8), ...getFillProps(c) }));
         }
         else if (rcap === index) {
-            return React.createElement("path", { key: k, d: rightRoundedRect(l, 0, w, h, 8), fill: c });
+            return (React.createElement("path", { key: k, d: rightRoundedRect(l, 0, w, h, 8), ...getFillProps(c) }));
         }
         else {
-            return React.createElement("rect", { key: k, x: l, y: 0, width: w, height: h, fill: c });
+            return (React.createElement("rect", { key: k, x: l, y: 0, width: w, height: h, ...getFillProps(c) }));
         }
     })));
 });

package/esm/LinearGenomeView/components/ExportSvgDialog.js

@@ -10,6 +10,10 @@ function LoadingMessage() {
 function useSvgLocal(key, val) {
     return useLocalStorage('svg-' + key, val);
 }
+function TextField2({ children, ...rest }) {
+    return (React.createElement("div", null,
+        React.createElement(TextField, { ...rest }, children)));
+}
 export default function ExportSvgDialog({ model, handleClose, }) {
     const session = getSession(model);
     const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
@@ -22,15 +26,13 @@ export default function ExportSvgDialog({ model, handleClose, }) {
     return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         React.createElement(DialogContent, null,
             error ? (React.createElement(ErrorMessage, { error: error })) : loading ? (React.createElement(LoadingMessage, null)) : null,
-            React.createElement(TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
-            React.createElement("br", null),
-            React.createElement(TextField, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
+            React.createElement(TextField2, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
+            React.createElement(TextField2, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
                 React.createElement(MenuItem, { value: "offset" }, "Offset"),
                 React.createElement(MenuItem, { value: "overlay" }, "Overlay"),
                 React.createElement(MenuItem, { value: "left" }, "Left"),
                 React.createElement(MenuItem, { value: "none" }, "None")),
-            React.createElement("br", null),
-            session.allThemes ? (React.createElement(TextField, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key }, 
+            session.allThemes ? (React.createElement(TextField2, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key }, 
             // @ts-expect-error
             val.name || '(Unknown name)'))))) : null,
             offscreenCanvas ? (React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (React.createElement(Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
@@ -51,6 +53,8 @@ export default function ExportSvgDialog({ model, handleClose, }) {
                     catch (e) {
                         console.error(e);
                         setError(e);
+                    }
+                    finally {
                         setLoading(false);
                     }
                 } }, "Submit"))));

package/esm/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/esm/LinearGenomeView/components/Highlight.js

@@ -10,28 +10,28 @@ 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;
+    var _a, _b;
     return ({
         highlight: {
             height: '100%',
             position: 'absolute',
-            background: `${colord((_b = (_a = theme.palette.quaternary) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod')
+            overflow: 'hidden',
+            background: `${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 = observer(function Highlight({ model }) {
-    var _a, _b;
+const Highlight = observer(function Highlight({ model, highlight, }) {
+    var _a, _b, _c;
     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 color = (_b = (_a = useTheme().palette.highlight) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod';
     const session = getSession(model);
+    const { assemblyManager } = session;
     const dismissHighlight = () => {
-        model.setHighlight(undefined);
+        model.removeHighlight(highlight);
     };
     const menuItems = [
         {
@@ -48,7 +48,7 @@ const Highlight = observer(function Highlight({ model }) {
                     bookmarkWidget = session.addWidget('GridBookmarkWidget', 'GridBookmark');
                 }
                 // @ts-ignore
-                bookmarkWidget.addBookmark(model.highlight);
+                bookmarkWidget.addBookmark(highlight);
                 dismissHighlight();
             },
         },
@@ -56,9 +56,6 @@ const Highlight = observer(function Highlight({ model }) {
     function handleClose() {
         setOpen(false);
     }
-    if (!model.highlight) {
-        return null;
-    }
     // coords
     const mapCoords = (r) => {
         const s = model.bpToPx({
@@ -76,19 +73,26 @@ const Highlight = observer(function Highlight({ model }) {
             }
             : undefined;
     };
-    const h = mapCoords(model.highlight);
-    return (React.createElement(React.Fragment, null, h ? (React.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.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(IconButton, { ref: anchorEl, onClick: () => setOpen(true), style: { zIndex: 3 } },
                 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));
+            }, open: open, onClose: handleClose, menuItems: menuItems }))) : null;
+});
+const HighlightGroup = observer(function HighlightGroup({ model, }) {
+    return model.highlight.map((highlight, idx) => (React.createElement(Highlight, { key: JSON.stringify(highlight) + '-' + idx, model: model, highlight: highlight })));
 });
-export default Highlight;
+export default HighlightGroup;

package/esm/LinearGenomeView/components/MiniControls.js

@@ -1,13 +1,13 @@
 import React from 'react';
 import { observer } from 'mobx-react';
-import { IconButton, Paper } from '@mui/material';
+import { IconButton, Paper, alpha } from '@mui/material';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import { makeStyles } from 'tss-react/mui';
+import { getSession } from '@jbrowse/core/util';
 // icons
 import ZoomIn from '@mui/icons-material/ZoomIn';
 import ZoomOut from '@mui/icons-material/ZoomOut';
 import ArrowDown from '@mui/icons-material/KeyboardArrowDown';
-import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-import { makeStyles } from 'tss-react/mui';
-import { getSession } from '@jbrowse/core/util';
 const useStyles = makeStyles()(theme => ({
     background: {
         position: 'absolute',
@@ -16,22 +16,20 @@ const useStyles = makeStyles()(theme => ({
         background: theme.palette.background.paper,
     },
     focusedBackground: {
-        background: theme.palette.secondary.light,
-        svg: {
-            fill: theme.palette.secondary.contrastText,
-        },
+        background: alpha(theme.palette.secondary.light, 0.2),
     },
 }));
 const MiniControls = observer(function ({ model, }) {
-    const { classes, cx } = useStyles();
+    const { classes } = useStyles();
     const { id, bpPerPx, maxBpPerPx, minBpPerPx, scaleFactor, hideHeader } = model;
     const { focusedViewId } = getSession(model);
-    return hideHeader ? (React.createElement(Paper, { className: cx(classes.background, focusedViewId === id ? classes.focusedBackground : undefined) },
-        React.createElement(CascadingMenuButton, { menuItems: model.menuItems() },
-            React.createElement(ArrowDown, { fontSize: "small" })),
-        React.createElement(IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1 },
-            React.createElement(ZoomOut, { fontSize: "small" })),
-        React.createElement(IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1 },
-            React.createElement(ZoomIn, { fontSize: "small" })))) : null;
+    return hideHeader ? (React.createElement(Paper, { className: classes.background },
+        React.createElement(Paper, { className: focusedViewId === id ? classes.focusedBackground : undefined },
+            React.createElement(CascadingMenuButton, { menuItems: model.menuItems() },
+                React.createElement(ArrowDown, { fontSize: "small" })),
+            React.createElement(IconButton, { "data-testid": "zoom_out", onClick: () => model.zoom(bpPerPx * 2), disabled: bpPerPx >= maxBpPerPx - 0.0001 || scaleFactor !== 1 },
+                React.createElement(ZoomOut, { fontSize: "small" })),
+            React.createElement(IconButton, { "data-testid": "zoom_in", onClick: () => model.zoom(bpPerPx / 2), disabled: bpPerPx <= minBpPerPx + 0.0001 || scaleFactor !== 1 },
+                React.createElement(ZoomIn, { fontSize: "small" }))))) : null;
 });
 export default MiniControls;

package/esm/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/esm/LinearGenomeView/components/OverviewHighlight.js

@@ -2,23 +2,26 @@ import React from 'react';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import { colord } from '@jbrowse/core/util/colord';
+import { getSession, notEmpty, } from '@jbrowse/core/util';
 const useStyles = makeStyles()(theme => {
     var _a, _b, _c, _d, _e, _f;
     return ({
         highlight: {
             height: '100%',
             position: 'absolute',
-            background: `${colord((_b = (_a = theme.palette.quaternary) === null || _a === void 0 ? void 0 : _a.main) !== null && _b !== void 0 ? _b : 'goldenrod')
+            background: `${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 ${(_f = (_e = theme.palette.highlight) === null || _e === void 0 ? void 0 : _e.main) !== null && _f !== void 0 ? _f : 'goldenrod'}`,
         },
     });
 });
 const OverviewHighlight = observer(function OverviewHighlight({ model, overview, }) {
     const { classes } = useStyles();
     const { cytobandOffset } = model;
+    const session = getSession(model);
+    const { assemblyManager } = session;
     // coords
     const mapCoords = (r) => {
         const s = overview.bpToPx({
@@ -36,13 +39,19 @@ const OverviewHighlight = observer(function OverviewHighlight({ model, overview,
             }
             : undefined;
     };
-    if (!model.highlight) {
-        return null;
-    }
-    const h = mapCoords(model.highlight);
-    return (React.createElement(React.Fragment, null, h ? (React.createElement("div", { className: classes.highlight, style: {
-            width: h.width,
-            left: h.left,
-        } })) : null));
+    return model.highlight
+        .map(h => {
+        var _a;
+        const asm = assemblyManager.get(h === null || h === void 0 ? void 0 : h.assemblyName);
+        return mapCoords({
+            ...h,
+            refName: (_a = asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(h.refName)) !== null && _a !== void 0 ? _a : h.refName,
+        });
+    })
+        .filter(notEmpty)
+        .map(({ left, width }, idx) => (React.createElement("div", { key: `${left}_${width}_${idx}`, className: classes.highlight, style: {
+            width: width,
+            left: left,
+        } })));
 });
 export default OverviewHighlight;

package/esm/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/esm/LinearGenomeView/components/OverviewScalebar.js

@@ -4,7 +4,7 @@ import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
 // core
 import Base1DView from '@jbrowse/core/util/Base1DViewModel';
-import { getSession, getTickDisplayStr } from '@jbrowse/core/util';
+import { getEnv, getSession, getTickDisplayStr } from '@jbrowse/core/util';
 import { ContentBlock } from '@jbrowse/core/util/blockTypes';
 // locals
 import { HEADER_BAR_HEIGHT, HEADER_OVERVIEW_HEIGHT, } from '..';
@@ -118,6 +118,7 @@ const Scalebar = observer(function ({ model, scale, overview, }) {
     const { classes } = useStyles();
     const theme = useTheme();
     const { dynamicBlocks, showCytobands, cytobandOffset } = model;
+    const { pluginManager } = getEnv(model);
     const visibleRegions = dynamicBlocks.contentBlocks;
     const overviewVisibleRegions = overview.dynamicBlocks;
     const { tertiary, primary } = theme.palette;
@@ -138,6 +139,7 @@ const Scalebar = 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.createElement("div", { className: classes.scalebar },
         React.createElement("div", { className: classes.scalebarVisibleRegion, style: {
                 width: lastOverviewPx - firstOverviewPx,
@@ -153,7 +155,8 @@ const Scalebar = 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.createElement(OverviewBox, { scale: scale, block: block, model: model, overview: overview, key: `${JSON.stringify(block)}-${idx}` }));
         }),
-        React.createElement(OverviewHighlight, { model: model, overview: overview })));
+        React.createElement(OverviewHighlight, { model: model, overview: overview }),
+        additional));
 });
 const OverviewScalebar = observer(function ({ model, children, }) {
     const { classes } = useStyles();

package/esm/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/esm/LinearGenomeView/components/OverviewScalebarPolygon.js

@@ -3,6 +3,7 @@ import { useTheme, alpha } from '@mui/material';
 import { observer } from 'mobx-react';
 // locals
 import { HEADER_BAR_HEIGHT } from '..';
+import { getFillProps, getStrokeProps } from '@jbrowse/core/util';
 const OverviewScalebarPolygon = observer(function ({ model, overview, useOffset = true, }) {
     const theme = useTheme();
     const multiplier = Number(useOffset);
@@ -36,6 +37,6 @@ const OverviewScalebarPolygon = observer(function ({ model, overview, useOffset
         [topRight, 0],
         [topLeft, 0],
     ];
-    return (React.createElement("polygon", { points: points.toString(), fill: alpha(polygonColor, 0.3), stroke: alpha(polygonColor, 0.8) }));
+    return (React.createElement("polygon", { points: points.toString(), ...getFillProps(alpha(polygonColor, 0.3)), ...getStrokeProps(alpha(polygonColor, 0.8)) }));
 });
 export default OverviewScalebarPolygon;

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

@@ -17,7 +17,8 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
     const assembly = assemblyName ? assemblyManager.get(assemblyName) : undefined;
     const { coarseVisibleLocStrings, hasDisplayedRegions } = model;
     useEffect(() => {
-        let active = true;
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
         (async () => {
             try {
                 if (debouncedSearch === '' || !assemblyName) {
@@ -25,21 +26,14 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
                 }
                 setLoaded(false);
                 const results = await fetchResults(debouncedSearch);
-                if (active) {
-                    setLoaded(true);
-                    setSearchOptions(getDeduplicatedResult(results));
-                }
+                setLoaded(true);
+                setSearchOptions(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
@@ -54,29 +48,28 @@ const RefNameAutocomplete = observer(function ({ model, onSelect, assemblyName,
     }))) || [], [regions]);
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked
-    return (React.createElement(React.Fragment, null,
-        React.createElement(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 BaseResult({ 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 }) => getFiltered(opts, inputValue), renderInput: params => (React.createElement(AutocompleteTextField, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() })));
+    return (React.createElement(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 BaseResult({ 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 }) => getFiltered(opts, inputValue), renderInput: params => (React.createElement(AutocompleteTextField, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() }));
 });
 export default RefNameAutocomplete;

package/esm/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;