@jbrowse/plugin-linear-genome-view 2.13.0 → 2.14.0

package/dist/BaseLinearDisplay/components/LinearBlocks.js

@@ -45,10 +45,10 @@ const RenderedBlocks = (0, mobx_react_1.observer)(function ({ model, }) {
                         height: 16,
                     } }, "Max height reached")) : null));
         }
-        else if (block.type === 'ElidedBlock') {
+        if (block.type === 'ElidedBlock') {
             return react_1.default.createElement(Block_1.ElidedBlock, { key: key, width: block.widthPx });
         }
-        else if (block.type === 'InterRegionPaddingBlock') {
+        if (block.type === 'InterRegionPaddingBlock') {
             return (react_1.default.createElement(Block_1.InterRegionPaddingBlock, { key: key, width: block.widthPx, style: { background: 'none' }, boundary: block.variant === 'boundary' }));
         }
         throw new Error(`invalid block type ${JSON.stringify(block)}`);

package/dist/BaseLinearDisplay/components/ServerSideRenderedBlockContent.js

@@ -62,7 +62,9 @@ const ServerSideRenderedBlockContent = (0, mobx_react_1.observer)(function ({ mo
     if (model.error) {
         return (react_1.default.createElement(BlockMsg_1.default, { message: `${model.error}`, severity: "error", action: react_1.default.createElement(react_1.default.Fragment, null,
                 react_1.default.createElement(material_1.Tooltip, { title: "Reload track" },
-                    react_1.default.createElement(material_1.IconButton, { "data-testid": "reload_button", onClick: () => model.reload() },
+                    react_1.default.createElement(material_1.IconButton, { "data-testid": "reload_button", onClick: () => {
+                            model.reload();
+                        } },
                         react_1.default.createElement(Refresh_1.default, null))),
                 react_1.default.createElement(material_1.Tooltip, { title: "Show stack trace" },
                     react_1.default.createElement(material_1.IconButton, { onClick: () => {

package/dist/BaseLinearDisplay/components/Tooltip.js

@@ -47,7 +47,7 @@ const Tooltip = (0, mobx_react_1.observer)(function ({ model, clientMouseCoord,
     const contents = featureUnderMouse
         ? (0, configuration_1.getConf)(model, 'mouseover', { feature: featureUnderMouse })
         : undefined;
-    const popperTheme = (_a = theme === null || theme === void 0 ? void 0 : theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
+    const popperTheme = (_a = theme.components) === null || _a === void 0 ? void 0 : _a.MuiPopper;
     return featureUnderMouse && contents ? (react_1.default.createElement(material_1.Portal, { container: (_b = popperTheme === null || popperTheme === void 0 ? void 0 : popperTheme.defaultProps) === null || _b === void 0 ? void 0 : _b.container },
         react_1.default.createElement("div", { className: classes.tooltip, ref: refs.setFloating, style: {
                 ...floatingStyles,

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts

@@ -139,7 +139,7 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: React.FC<{

package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js

@@ -137,7 +137,7 @@ function stateModelFactory() {
         get features() {
             const featureMaps = [];
             for (const block of self.blockState.values()) {
-                if (block === null || block === void 0 ? void 0 : block.features) {
+                if (block.features) {
                     featureMaps.push(block.features);
                 }
             }
@@ -171,7 +171,7 @@ function stateModelFactory() {
             let ret;
             self.blockState.forEach(block => {
                 var _a;
-                const val = (_a = block === null || block === void 0 ? void 0 : block.layout) === null || _a === void 0 ? void 0 : _a.getByID(id);
+                const val = (_a = block.layout) === null || _a === void 0 ? void 0 : _a.getByID(id);
                 if (val) {
                     ret = val;
                 }
@@ -252,7 +252,9 @@ function stateModelFactory() {
                 self.setError();
                 self.setCurrStatsBpPerPx(0);
                 self.clearFeatureDensityStats();
-                [...self.blockState.values()].map(val => val.doReload());
+                [...self.blockState.values()].forEach(val => {
+                    val.doReload();
+                });
                 superReload();
             },
         };
@@ -374,6 +376,7 @@ function stateModelFactory() {
         },
     }))
         .preProcessSnapshot(snap => {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!snap) {
             return snap;
         }
@@ -383,9 +386,9 @@ function stateModelFactory() {
         const { height, ...rest } = snap;
         return { heightPreConfig: height, ...rest };
     })
-        .postProcessSnapshot(self => {
+        .postProcessSnapshot(snap => {
         // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
-        const r = self;
+        const r = snap;
         const { blockState, ...rest } = r;
         return rest;
     });

package/dist/BaseLinearDisplay/models/FeatureDensityMixin.js

@@ -4,7 +4,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = FeatureDensityMixin;
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = __importDefault(require("react"));
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
@@ -103,9 +102,9 @@ function FeatureDensityMixin() {
         /**
          * #action
          */
-        async getFeatureDensityStats() {
+        getFeatureDensityStats() {
             if (!self.featureDensityStatsP) {
-                self.featureDensityStatsP = (0, util_2.getFeatureDensityStatsPre)(self).catch(e => {
+                self.featureDensityStatsP = (0, util_2.getFeatureDensityStatsPre)(self).catch((e) => {
                     if ((0, mobx_state_tree_1.isAlive)(self)) {
                         this.setFeatureDensityStatsP(undefined);
                     }

package/dist/BaseLinearDisplay/models/renderSvg.d.ts

@@ -4,5 +4,5 @@ import { ExportSvgOptions } from '../../LinearGenomeView';
 import { BaseLinearDisplayModel } from './BaseLinearDisplayModel';
 export declare function renderBaseLinearDisplaySvg(self: BaseLinearDisplayModel, opts: ExportSvgOptions & {
     overrideHeight: number;
-    theme: ThemeOptions;
+    theme?: ThemeOptions;
 }): Promise<React.JSX.Element>;

package/dist/BaseLinearDisplay/models/renderSvg.js

@@ -71,7 +71,9 @@ async function renderBaseLinearDisplaySvg(self, opts) {
         const { offsetPx, widthPx } = block;
         const offset = offsetPx - viewOffsetPx;
         const clipid = (0, util_2.getId)(id, index);
-        return (react_1.default.createElement(react_1.default.Fragment, { key: `frag-${index}` },
+        return (
+        /* biome-ignore lint/suspicious/noArrayIndexKey: */
+        react_1.default.createElement(react_1.default.Fragment, { key: `frag-${index}` },
             react_1.default.createElement("defs", null,
                 react_1.default.createElement("clipPath", { id: clipid },
                     react_1.default.createElement("rect", { x: 0, y: 0, width: widthPx, height: overrideHeight || height }))),

package/dist/BaseLinearDisplay/models/util.d.ts

@@ -7,7 +7,7 @@ export interface RenderProps {
     renderProps: Record<string, any>;
     displayError: unknown;
     rpcManager: {
-        call: Function;
+        call: (...args: unknown[]) => void;
     };
     cannotBeRenderedReason: string;
 }

package/dist/BaseLinearDisplay/models/util.js

@@ -7,17 +7,15 @@ const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const mobx_state_tree_1 = require("mobx-state-tree");
 function getDisplayStr(totalBytes) {
-    let displayBp;
     if (Math.floor(totalBytes / 1000000) > 0) {
-        displayBp = `${Number.parseFloat((totalBytes / 1000000).toPrecision(3))} Mb`;
+        return `${Number.parseFloat((totalBytes / 1000000).toPrecision(3))} Mb`;
     }
     else if (Math.floor(totalBytes / 1000) > 0) {
-        displayBp = `${Number.parseFloat((totalBytes / 1000).toPrecision(3))} Kb`;
+        return `${Number.parseFloat((totalBytes / 1000).toPrecision(3))} Kb`;
     }
     else {
-        displayBp = `${Math.floor(totalBytes)} bytes`;
+        return `${Math.floor(totalBytes)} bytes`;
     }
-    return displayBp;
 }
 // stabilize clipid under test for snapshot
 function getId(id, index) {

package/dist/LaunchLinearGenomeView/index.js

@@ -27,22 +27,23 @@ function LaunchLinearGenomeViewF(pluginManager) {
             }
             if (highlight !== undefined) {
                 highlight.forEach(async (h) => {
-                    if (h) {
-                        const parsedLocString = (0, util_1.parseLocString)(h, refName => isValidRefName(refName, assembly));
-                        const location = {
-                            ...parsedLocString,
+                    const p = (0, util_1.parseLocString)(h, refName => isValidRefName(refName, assembly));
+                    const { start, end } = p;
+                    if (start !== undefined && end !== undefined) {
+                        view.addToHighlights({
+                            ...p,
+                            start,
+                            end,
                             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 = [];
-            tracks.forEach(track => tryTrack(view, track, idsNotFound));
+            tracks.forEach(track => {
+                tryTrack(view, track, idsNotFound);
+            });
             if (idsNotFound.length) {
                 throw new Error(`Could not resolve identifiers: ${idsNotFound.join(',')}`);
             }
@@ -58,7 +59,7 @@ function tryTrack(model, trackId, idsNotFound) {
         model.showTrack(trackId);
     }
     catch (e) {
-        if (`${e}`.match('Could not resolve identifier')) {
+        if (/Could not resolve identifier/.exec(`${e}`)) {
             idsNotFound.push(trackId);
         }
         else {

package/dist/LinearBareDisplay/model.d.ts

@@ -128,7 +128,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
     readonly DisplayBlurb: import("react").FC<{

package/dist/LinearBasicDisplay/components/AddFiltersDialog.js

@@ -55,7 +55,9 @@ const AddFiltersDialog = (0, mobx_react_1.observer)(function ({ model, handleClo
                 .split('\n')
                 .map(line => line.trim())
                 .filter(line => !!line)
-                .map(line => checkJexl(line.trim()));
+                .map(line => {
+                checkJexl(line.trim());
+            });
             setError(undefined);
         }
         catch (e) {
@@ -79,7 +81,9 @@ const AddFiltersDialog = (0, mobx_react_1.observer)(function ({ model, handleClo
                         react_1.default.createElement("code", null, "jexl:get(feature,'score') > 400"),
                         " - show only features that have a score greater than 400"))),
             error ? react_1.default.createElement("p", { className: classes.error }, `${error}`) : null,
-            react_1.default.createElement(material_1.TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => setData(event.target.value), InputProps: {
+            react_1.default.createElement(material_1.TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => {
+                    setData(event.target.value);
+                }, InputProps: {
                     classes: {
                         input: classes.textAreaFont,
                     },
@@ -89,6 +93,8 @@ const AddFiltersDialog = (0, mobx_react_1.observer)(function ({ model, handleClo
                     model.setJexlFilters(data.split('\n'));
                     handleClose();
                 } }, "Submit"),
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
 });
 exports.default = AddFiltersDialog;

package/dist/LinearBasicDisplay/components/SetMaxHeightDialog.js

@@ -40,12 +40,16 @@ const SetMaxHeightDialog = (0, mobx_react_1.observer)(function ({ model, handleC
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set max height" },
         react_1.default.createElement(material_1.DialogContent, { className: classes.root },
             react_1.default.createElement(material_1.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
-            react_1.default.createElement(material_1.TextField, { value: max, onChange: event => setMax(event.target.value), placeholder: "Enter max score" })),
+            react_1.default.createElement(material_1.TextField, { value: max, onChange: event => {
+                    setMax(event.target.value);
+                }, placeholder: "Enter max score" })),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
                     model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
                     handleClose();
                 } }, "Submit"),
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"))));
 });
 exports.default = SetMaxHeightDialog;

package/dist/LinearBasicDisplay/model.d.ts

@@ -156,7 +156,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-        onHorizontalScroll?: Function;
+        onHorizontalScroll?: () => void;
         blockState? /**
          * #getter
          */: Record<string, any>;
@@ -294,9 +294,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
             [x: string]: any;
-        } & import("mobx-state-tree/dist/internal" /**
-         * #property
-         */).NonEmptyObject & {
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
                 [x: string]: any;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);

package/dist/LinearBasicDisplay/model.js

@@ -198,14 +198,18 @@ function stateModelFactory(configSchema) {
                         icon: Visibility_1.default,
                         type: 'checkbox',
                         checked: self.showLabels,
-                        onClick: () => self.toggleShowLabels(),
+                        onClick: () => {
+                            self.toggleShowLabels();
+                        },
                     },
                     {
                         label: 'Show descriptions',
                         icon: Visibility_1.default,
                         type: 'checkbox',
                         checked: self.showDescriptions,
-                        onClick: () => self.toggleShowDescriptions(),
+                        onClick: () => {
+                            self.toggleShowDescriptions();
+                        },
                     },
                     {
                         label: 'Display mode',
@@ -217,7 +221,9 @@ function stateModelFactory(configSchema) {
                             'collapse',
                         ].map(val => ({
                             label: val,
-                            onClick: () => self.setDisplayMode(val),
+                            onClick: () => {
+                                self.setDisplayMode(val);
+                            },
                         })),
                     },
                     {

package/dist/LinearGenomeView/components/Cytobands.js

@@ -10,26 +10,11 @@ const __1 = require("..");
 const util_1 = require("./util");
 const util_2 = require("@jbrowse/core/util");
 // rounded rect from https://stackoverflow.com/a/45889603/2129219
-// prettier-ignore
 function rightRoundedRect(x, y, width, height, radius) {
-    return "M" + x + "," + y
-        + "h" + (width - radius)
-        + "a" + radius + "," + radius + " 0 0 1 " + radius + "," + radius
-        + "v" + (height - 2 * radius)
-        + "a" + radius + "," + radius + " 0 0 1 " + -radius + "," + radius
-        + "h" + (radius - width)
-        + "z";
+    return `M${x},${y}h${width - radius}a${radius},${radius} 0 0 1 ${radius},${radius}v${height - 2 * radius}a${radius},${radius} 0 0 1 ${-radius},${radius}h${radius - width}z`;
 }
-// prettier-ignore
 function leftRoundedRect(x, y, width, height, radius) {
-    return "M" + (x + radius) + "," + y
-        + "h" + (width - radius)
-        + "v" + height
-        + "h" + (radius - width)
-        + "a" + radius + "," + radius + " 0 0 1 " + (-radius) + "," + (-radius)
-        + "v" + (2 * radius - height)
-        + "a" + radius + "," + radius + " 0 0 1 " + radius + "," + (-radius)
-        + "z";
+    return `M${x + radius},${y}h${width - radius}v${height}h${radius - width}a${radius},${radius} 0 0 1 ${-radius},${-radius}v${2 * radius - height}a${radius},${radius} 0 0 1 ${radius},${-radius}z`;
 }
 function leftTriangle(x, y, width, height) {
     return [
@@ -76,20 +61,18 @@ const Cytobands = (0, mobx_react_1.observer)(function ({ overview, block, assemb
                     ? rightTriangle(s - w, 0, w, h)
                     : leftTriangle(s, 0, w, h), ...(0, util_2.getFillProps)(c) }));
         }
-        else if (type === 'acen' && centromereSeen) {
+        if (type === 'acen' && centromereSeen) {
             return (react_1.default.createElement("polygon", { key: k, points: reversed
                     ? leftTriangle(s - w, 0, w, h)
                     : rightTriangle(s, 0, w, h), ...(0, util_2.getFillProps)(c) }));
         }
-        else if (lcap === index) {
+        if (lcap === index) {
             return (react_1.default.createElement("path", { key: k, d: leftRoundedRect(l, 0, w, h, 8), ...(0, util_2.getFillProps)(c) }));
         }
-        else if (rcap === index) {
+        if (rcap === index) {
             return (react_1.default.createElement("path", { key: k, d: rightRoundedRect(l, 0, w, h, 8), ...(0, util_2.getFillProps)(c) }));
         }
-        else {
-            return (react_1.default.createElement("rect", { key: k, x: l, y: 0, width: w, height: h, ...(0, util_2.getFillProps)(c) }));
-        }
+        return (react_1.default.createElement("rect", { key: k, x: l, y: 0, width: w, height: h, ...(0, util_2.getFillProps)(c) }));
     })));
 });
 exports.default = Cytobands;

package/dist/LinearGenomeView/components/ExportSvgDialog.js

@@ -34,7 +34,7 @@ function LoadingMessage() {
         react_1.default.createElement(material_1.Typography, { display: "inline" }, "Creating SVG")));
 }
 function useSvgLocal(key, val) {
-    return (0, util_1.useLocalStorage)('svg-' + key, val);
+    return (0, util_1.useLocalStorage)(`svg-${key}`, val);
 }
 function TextField2({ children, ...rest }) {
     return (react_1.default.createElement("div", null,
@@ -52,18 +52,28 @@ 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(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(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")),
-            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 }, 
+            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"))),
+            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"))),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                    handleClose();
+                } }, "Cancel"),
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
                     setLoading(true);
                     setError(undefined);

package/dist/LinearGenomeView/components/GetSequenceDialog.js

@@ -76,7 +76,6 @@ async function fetchSequence(model, regions, signal) {
 }
 const GetSequenceDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
     const { classes } = useStyles();
-    const session = (0, util_1.getSession)(model);
     const [error, setError] = (0, react_1.useState)();
     const [sequenceChunks, setSequenceChunks] = (0, react_1.useState)();
     const [rev, setReverse] = (0, react_1.useState)(false);
@@ -85,7 +84,6 @@ const GetSequenceDialog = (0, mobx_react_1.observer)(function ({ model, handleCl
     const { leftOffset, rightOffset } = model;
     const loading = Boolean(sequenceChunks === undefined);
     (0, react_1.useEffect)(() => {
-        let active = true;
         const controller = new AbortController();
         (async () => {
             try {
@@ -97,26 +95,19 @@ const GetSequenceDialog = (0, mobx_react_1.observer)(function ({ model, handleCl
                     throw new Error('Selected region is out of bounds');
                 }
                 const chunks = await fetchSequence(model, selection, controller.signal);
-                if (active) {
-                    setSequenceChunks(chunks);
-                }
+                setSequenceChunks(chunks);
             }
             catch (e) {
                 console.error(e);
-                if (active) {
-                    setError(e);
-                }
+                setError(e);
             }
         })();
         return () => {
             controller.abort();
-            active = false;
         };
-    }, [model, session, leftOffset, rightOffset]);
+    }, [model, leftOffset, rightOffset]);
     const sequence = sequenceChunks
-        ? (0, formatFastaStrings_1.formatSeqFasta)(sequenceChunks
-            .filter(f => !!f)
-            .map(chunk => {
+        ? (0, formatFastaStrings_1.formatSeqFasta)(sequenceChunks.map(chunk => {
             let chunkSeq = chunk.get('seq');
             const chunkRefName = chunk.get('refName');
             const chunkStart = chunk.get('start') + 1;
@@ -155,14 +146,20 @@ const GetSequenceDialog = (0, mobx_react_1.observer)(function ({ model, handleCl
                     },
                 } }),
             react_1.default.createElement(material_1.FormGroup, null,
-                react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { value: rev, onChange: event => setReverse(event.target.checked) }), label: "Reverse sequence" }),
-                react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { value: comp, onChange: event => setComplement(event.target.checked) }), label: "Complement sequence" })),
+                react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { value: rev, onChange: event => {
+                            setReverse(event.target.checked);
+                        } }), label: "Reverse sequence" }),
+                react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { value: comp, onChange: event => {
+                            setComplement(event.target.checked);
+                        } }), label: "Complement sequence" })),
             react_1.default.createElement(material_1.Typography, { style: { margin: 10 } }, "Note: Check both boxes for the \"reverse complement\"")),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { onClick: () => {
                     (0, copy_to_clipboard_1.default)(sequence);
                     setCopied(true);
-                    setTimeout(() => setCopied(false), 500);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 500);
                 }, disabled: loading || !!error || sequenceTooLarge, color: "primary", startIcon: react_1.default.createElement(Icons_1.ContentCopy, null) }, copied ? 'Copied' : 'Copy to clipboard'),
             react_1.default.createElement(material_1.Button, { onClick: () => {
                     (0, file_saver_1.saveAs)(new Blob([sequence || ''], {

package/dist/LinearGenomeView/components/Header.js

@@ -55,9 +55,13 @@ const HeaderButtons = (0, mobx_react_1.observer)(({ model }) => {
 function PanControls({ model }) {
     const { classes } = useStyles();
     return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.Button, { variant: "outlined", className: classes.panButton, onClick: () => model.slide(-0.9) },
+        react_1.default.createElement(material_1.Button, { variant: "outlined", className: classes.panButton, onClick: () => {
+                model.slide(-0.9);
+            } },
             react_1.default.createElement(ArrowBack_1.default, null)),
-        react_1.default.createElement(material_1.Button, { variant: "outlined", className: classes.panButton, onClick: () => model.slide(0.9) },
+        react_1.default.createElement(material_1.Button, { variant: "outlined", className: classes.panButton, onClick: () => {
+                model.slide(0.9);
+            } },
             react_1.default.createElement(ArrowForward_1.default, null))));
 }
 const RegionWidth = (0, mobx_react_1.observer)(({ model }) => {

package/dist/LinearGenomeView/components/Highlight.js

@@ -37,25 +37,22 @@ const material_1 = require("@mui/material");
 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;
-    return ({
-        highlight: {
-            height: '100%',
-            position: 'absolute',
-            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()}`,
-        },
-    });
-});
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    highlight: {
+        height: '100%',
+        position: 'absolute',
+        overflow: 'hidden',
+        background: (0, colord_1.colord)(theme.palette.highlight.main).alpha(0.35).toRgbString(),
+    },
+    linkIcon: {
+        color: (0, colord_1.colord)(theme.palette.highlight.main).darken(0.2).toRgbString(),
+    },
+}));
 const Highlight = (0, mobx_react_1.observer)(function Highlight({ model, highlight, }) {
-    var _a, _b, _c;
+    var _a;
     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.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 = () => {
@@ -81,20 +78,20 @@ const Highlight = (0, mobx_react_1.observer)(function Highlight({ model, highlig
             }
             : undefined;
     };
-    const asm = assemblyManager.get(highlight === null || highlight === void 0 ? void 0 : highlight.assemblyName);
+    const asm = assemblyManager.get(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,
+        refName: (_a = asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(highlight.refName)) !== null && _a !== void 0 ? _a : 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), 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(material_1.Tooltip, { title: "Highlighted from URL parameter", arrow: 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", className: classes.linkIcon }))),
         react_1.default.createElement(ui_1.Menu, { anchorEl: anchorEl.current, onMenuItemClick: (_event, callback) => {
                 callback(session);
                 handleClose();
@@ -102,7 +99,9 @@ const Highlight = (0, mobx_react_1.observer)(function Highlight({ model, highlig
                 {
                     label: 'Dismiss highlight',
                     icon: Close_1.default,
-                    onClick: () => dismissHighlight(),
+                    onClick: () => {
+                        dismissHighlight();
+                    },
                 },
                 {
                     label: 'Bookmark highlighted region',
@@ -112,7 +111,7 @@ const Highlight = (0, mobx_react_1.observer)(function Highlight({ model, highlig
                         if (!bookmarkWidget) {
                             bookmarkWidget = session.addWidget('GridBookmarkWidget', 'GridBookmark');
                         }
-                        // @ts-ignore
+                        // @ts-expect-error
                         bookmarkWidget.addBookmark(highlight);
                         dismissHighlight();
                     },
@@ -120,6 +119,6 @@ const Highlight = (0, mobx_react_1.observer)(function Highlight({ model, highlig
             ] }))) : 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 })));
+    return model.highlight.map((highlight, idx) => (react_1.default.createElement(Highlight, { key: `${JSON.stringify(highlight)}-${idx}`, model: model, highlight: highlight })));
 });
 exports.default = HighlightGroup;