@jbrowse/core 2.13.1 → 2.14.0

package/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js

@@ -33,12 +33,12 @@ function ArrayValue({ name, value, description, prefix = [], }) {
             react_1.default.createElement(BasicValue_1.default, { value: value[0] })));
     }
     else if (value.every(val => (0, is_object_1.default)(val))) {
-        return (react_1.default.createElement(react_1.default.Fragment, null, value.map((val, i) => (react_1.default.createElement(Attributes_1.default, { key: JSON.stringify(val) + '-' + i, attributes: val, prefix: [...prefix, name + '-' + i] })))));
+        return (react_1.default.createElement(react_1.default.Fragment, null, value.map((val, i) => (react_1.default.createElement(Attributes_1.default, { key: `${JSON.stringify(val)}-${i}`, attributes: val, prefix: [...prefix, `${name}-${i}`] })))));
     }
     else {
         return (react_1.default.createElement("div", { className: classes.field },
             react_1.default.createElement(FieldName_1.default, { prefix: prefix, description: description, name: name }),
-            value.map((val, i) => (react_1.default.createElement("div", { key: JSON.stringify(val) + '-' + i, className: classes.fieldSubvalue },
+            value.map((val, i) => (react_1.default.createElement("div", { key: `${JSON.stringify(val)}-${i}`, className: classes.fieldSubvalue },
                 react_1.default.createElement(BasicValue_1.default, { value: val }))))));
     }
 }

package/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js

@@ -21,6 +21,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
 }));
 function BasicValue({ value }) {
     const { classes } = useStyles();
-    const isLink = `${value}`.match(/^https?:\/\//);
+    const isLink = /^https?:\/\//.exec(`${value}`);
     return (react_1.default.createElement("div", { className: classes.fieldValue }, react_1.default.isValidElement(value) ? (value) : isLink ? (react_1.default.createElement(material_1.Link, { href: `${value}` }, `${value}`)) : (react_1.default.createElement(ui_1.SanitizedHTML, { html: (0, is_object_1.default)(value) ? JSON.stringify(value) : String(value) }))));
 }

package/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js

@@ -78,7 +78,9 @@ function DataGridDetails({ value, prefix, name, }) {
     if (unionKeys.size < keys.length + 5) {
         return (react_1.default.createElement("div", { className: classes.margin },
             react_1.default.createElement(FieldName_1.default, { prefix: prefix, name: name }),
-            react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: checked, onChange: event => setChecked(event.target.checked) }), label: react_1.default.createElement(material_1.Typography, { variant: "body2" }, "Show options") }),
+            react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: checked, onChange: event => {
+                        setChecked(event.target.checked);
+                    } }), label: react_1.default.createElement(material_1.Typography, { variant: "body2" }, "Show options") }),
             react_1.default.createElement(x_data_grid_1.DataGrid, { autoHeight: true, disableRowSelectionOnClick: true, rows: rows, rowHeight: 20, columnHeaderHeight: 35, hideFooter: rows.length < 25, slots: {
                     toolbar: checked ? x_data_grid_1.GridToolbar : null,
                 }, slotProps: {

package/BaseFeatureWidget/BaseFeatureDetail/index.js

@@ -29,7 +29,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.Attributes = exports.BaseAttributes = exports.BaseCoreDetails = void 0;
 exports.BaseCard = BaseCard;
 exports.FeatureDetails = FeatureDetails;
-/* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = __importStar(require("react"));
 const react_error_boundary_1 = require("react-error-boundary");
 const material_1 = require("@mui/material");
@@ -54,22 +53,26 @@ const coreDetails = [
     'description',
     'type',
 ];
-const useStyles = (0, mui_1.makeStyles)()(theme => {
-    var _a;
-    return ({
-        expansionPanelDetails: {
-            display: 'block',
-            padding: theme.spacing(1),
-        },
-        expandIcon: {
-            color: ((_a = theme.palette.tertiary) === null || _a === void 0 ? void 0 : _a.contrastText) || '#fff',
-        },
-    });
-});
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    expansionPanelDetails: {
+        display: 'block',
+        padding: theme.spacing(1),
+    },
+    expandIcon: {
+        color: theme.palette.tertiary.contrastText || '#fff',
+    },
+}));
 function BaseCard({ children, title, defaultExpanded = true, }) {
     const { classes } = useStyles();
     const [expanded, setExpanded] = (0, react_1.useState)(defaultExpanded);
-    return (react_1.default.createElement(material_1.Accordion, { expanded: expanded, onChange: () => setExpanded(s => !s), TransitionProps: { unmountOnExit: true, timeout: 150 } },
+    return (react_1.default.createElement(material_1.Accordion, { expanded: expanded, onChange: () => {
+            setExpanded(s => !s);
+        }, slotProps: {
+            transition: {
+                unmountOnExit: true,
+                timeout: 150,
+            },
+        } },
         react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.expandIcon }) },
             react_1.default.createElement(material_1.Typography, { variant: "button" }, title)),
         react_1.default.createElement(material_1.AccordionDetails, { className: classes.expansionPanelDetails }, children)));
@@ -89,7 +92,6 @@ function Position(props) {
 function CoreDetails(props) {
     const { feature } = props;
     const obj = feature;
-    // eslint-disable-next-line no-underscore-dangle
     const formattedFeat = { ...obj, ...obj.__jbrowsefmt };
     const { start, end } = formattedFeat;
     const displayedDetails = {
@@ -132,21 +134,19 @@ function FeatureDetails(props) {
         feature,
         model,
     });
+    const m = mate;
     return (react_1.default.createElement(BaseCard, { title: (0, util_2.generateTitle)(name, id, type) },
         react_1.default.createElement(material_1.Typography, null, "Core details"),
         react_1.default.createElement(CoreDetails, { ...props }),
-        mate ? (react_1.default.createElement(react_1.default.Fragment, null,
+        m ? (react_1.default.createElement(react_1.default.Fragment, null,
             react_1.default.createElement(material_1.Divider, null),
             react_1.default.createElement(material_1.Typography, null, "Mate details"),
             react_1.default.createElement(CoreDetails, { ...props, feature: {
-                    ...mate,
-                    // @ts-expect-error
-                    start: mate.start,
-                    // @ts-expect-error
-                    end: mate.end,
-                    // @ts-expect-error
-                    refName: mate.refName,
-                    uniqueId: uniqueId + '-mate',
+                    ...m,
+                    start: m.start,
+                    end: m.end,
+                    refName: m.refName,
+                    uniqueId: `${uniqueId}-mate`,
                 } }))) : null,
         react_1.default.createElement(material_1.Divider, null),
         react_1.default.createElement(material_1.Typography, null, "Attributes"),
@@ -157,7 +157,10 @@ function FeatureDetails(props) {
             react_1.default.createElement(material_1.Divider, null),
             react_1.default.createElement(BaseCard, { title: ExtraPanel.name },
                 react_1.default.createElement(ExtraPanel.Component, { ...props })))) : null,
-        depth < maxDepth && (subfeatures === null || subfeatures === void 0 ? void 0 : subfeatures.length) ? (react_1.default.createElement(BaseCard, { title: "Subfeatures", defaultExpanded: depth < 1 }, subfeatures.map((sub, idx) => (react_1.default.createElement(FeatureDetails, { key: JSON.stringify(sub), feature: { ...sub, uniqueId: `${uniqueId}_${idx}` }, model: model, depth: depth + 1 }))))) : null));
+        depth < maxDepth && (subfeatures === null || subfeatures === void 0 ? void 0 : subfeatures.length) ? (react_1.default.createElement(BaseCard, { title: "Subfeatures", defaultExpanded: depth < 1 }, subfeatures.map((sub, idx) => (react_1.default.createElement(FeatureDetails, { key: JSON.stringify(sub), feature: {
+                ...sub,
+                uniqueId: `${uniqueId}_${idx}`,
+            }, model: model, depth: depth + 1 }))))) : null));
 }
 const BaseFeatureDetail = (0, mobx_react_1.observer)(function ({ model }) {
     const { error, featureData } = model;

package/BaseFeatureWidget/BaseFeatureDetail/util.js

@@ -35,7 +35,7 @@ function accessNested(arr, obj = {}) {
     });
     return typeof obj2 === 'string'
         ? obj2
-        : (0, is_object_1.default)(obj2) && typeof (obj2 === null || obj2 === void 0 ? void 0 : obj2.Description) === 'string'
+        : (0, is_object_1.default)(obj2) && typeof obj2.Description === 'string'
             ? obj2.Description
             : undefined;
 }

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeatureDetails.js

@@ -59,18 +59,24 @@ const SequenceFeatureDetails = (0, mobx_react_1.observer)(function ({ model, fea
                         onClick: () => {
                             // this is given a setTimeout because it allows the menu to
                             // close before dialog opens
-                            setTimeout(() => setOpenInDialog(true), 1);
+                            setTimeout(() => {
+                                setOpenInDialog(true);
+                            }, 1);
                         },
                     },
                 ] })),
         openInDialog ? (react_1.default.createElement("div", null,
             "Open in dialog...",
             react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },
-                react_1.default.createElement(SequenceDialog, { model: model, feature: feature, handleClose: () => setOpenInDialog(false) })))) : (react_1.default.createElement("div", null,
+                react_1.default.createElement(SequenceDialog, { model: model, feature: feature, handleClose: () => {
+                        setOpenInDialog(false);
+                    } })))) : (react_1.default.createElement("div", null,
             feature.type === 'gene' ? (react_1.default.createElement(material_1.Typography, null, "Note: inspect subfeature sequences for protein/CDS computations")) : null,
-            error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : !sequence ? (react_1.default.createElement(ui_1.LoadingEllipses, null)) : sequence ? ('error' in sequence ? (react_1.default.createElement(react_1.default.Fragment, null,
+            error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : !sequence ? (react_1.default.createElement(ui_1.LoadingEllipses, null)) : 'error' in sequence ? (react_1.default.createElement(react_1.default.Fragment, null,
                 react_1.default.createElement(material_1.Typography, { color: "error" }, sequence.error),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "inherit", onClick: () => setForce(true) }, "Force load"))) : (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },
-                react_1.default.createElement(SequencePanel, { ref: seqPanelRef, feature: feature, sequence: sequence, model: sequenceFeatureDetails })))) : (react_1.default.createElement(material_1.Typography, null, "No sequence found"))))));
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "inherit", onClick: () => {
+                        setForce(true);
+                    } }, "Force load"))) : (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },
+                react_1.default.createElement(SequencePanel, { ref: seqPanelRef, feature: feature, sequence: sequence, model: sequenceFeatureDetails })))))));
 });
 exports.default = SequenceFeatureDetails;

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.d.ts

@@ -4,5 +4,5 @@ import { SimpleFeatureSerialized } from '../../util';
 declare const SequenceFeaturePanel: ({ model, feature, }: {
     model: BaseFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-}) => React.JSX.Element | null;
+}) => React.JSX.Element;
 export default SequenceFeaturePanel;

package/BaseFeatureWidget/SequenceFeatureDetails/SequenceFeaturePanel.js

@@ -53,15 +53,19 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
 const SequenceFeaturePanel = (0, mobx_react_1.observer)(function ({ model, feature, }) {
     const { classes } = useStyles();
     const [shown, setShown] = (0, react_1.useState)(false);
-    return model ? (react_1.default.createElement("div", { className: classes.container },
+    return (react_1.default.createElement("div", { className: classes.container },
         react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
-            react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => setShown(!shown) }, shown ? 'Hide feature sequence' : 'Show feature sequence')),
-        react_1.default.createElement(material_1.IconButton, { onClick: () => (0, util_1.getSession)(model).queueDialog(handleClose => [
-                HelpDialog,
-                { handleClose },
-            ]) },
+            react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
+                    setShown(!shown);
+                } }, shown ? 'Hide feature sequence' : 'Show feature sequence')),
+        react_1.default.createElement(material_1.IconButton, { onClick: () => {
+                (0, util_1.getSession)(model).queueDialog(handleClose => [
+                    HelpDialog,
+                    { handleClose },
+                ]);
+            } },
             react_1.default.createElement(Help_1.default, null)),
         shown ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },
-            react_1.default.createElement(SequenceFeatureDetails, { key: feature.uniqueId, model: model, feature: feature }))) : null)) : null;
+            react_1.default.createElement(SequenceFeatureDetails, { key: feature.uniqueId, model: model, feature: feature }))) : null));
 });
 exports.default = SequenceFeaturePanel;

package/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js

@@ -95,7 +95,7 @@ const SequencePanel = (0, mobx_react_1.observer)(react_1.default.forwardRef(func
     return (react_1.default.createElement("div", { "data-testid": "sequence_panel", ref: ref, style: { maxHeight: 300, overflow: 'auto' } },
         react_1.default.createElement(Container, null,
             react_1.default.createElement("div", { style: { background: 'white' } }, `>${[
-                (feature.name || feature.id) + '-' + mode,
+                `${feature.name || feature.id}-${mode}`,
                 `${feature.refName}:${(0, util_1.toLocale)(feature.start + 1)}-${(0, util_1.toLocale)(feature.end)}${getStrand(feature.strand)}`,
                 mode.endsWith('updownstream')
                     ? `+/- ${(0, util_1.toLocale)(model.upDownBp)} up/downstream bp`

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/HelpDialog.js

@@ -10,7 +10,9 @@ const ui_1 = require("@jbrowse/core/ui");
 // icons
 const Settings_1 = __importDefault(require("@mui/icons-material/Settings"));
 function HelpDialog({ handleClose, }) {
-    return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => handleClose(), title: "Feature sequence panel help" },
+    return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
+            handleClose();
+        }, title: "Feature sequence panel help" },
         react_1.default.createElement(material_1.DialogContent, null,
             react_1.default.createElement(material_1.Typography, { paragraph: true }, "The \"Feature sequence\" panel shows the underlying genomic sequence for a given feature, fetched from the reference genome."),
             react_1.default.createElement(material_1.Typography, null, "For gene features, this panel does special calculations to e.g. stitch together the coding sequence, the options are:"),
@@ -28,5 +30,7 @@ function HelpDialog({ handleClose, }) {
                 " to edit the number of bp displayed up/downstream and in the intron region"),
             react_1.default.createElement(material_1.Typography, null, "Note 2: The 'Copy HTML' function retains the colors from the sequence panel but cannot be pasted into some programs like notepad that only expect plain text.")),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), autoFocus: true, variant: "contained" }, "Close"))));
+            react_1.default.createElement(material_1.Button, { onClick: () => {
+                    handleClose();
+                }, autoFocus: true, variant: "contained" }, "Close"))));
 }

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceDialog.js

@@ -52,18 +52,24 @@ const SequenceDialog = (0, mobx_react_1.observer)(function ({ handleClose, model
     const seqPanelRef = (0, react_1.useRef)(null);
     const [force, setForce] = (0, react_1.useState)(false);
     const { sequence, error } = (0, hooks_1.useFeatureSequence)(model, feature, upDownBp, force);
-    return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => handleClose(), title: "Sequence view" },
+    return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
+            handleClose();
+        }, title: "Sequence view" },
         react_1.default.createElement(material_1.DialogContent, { className: classes.dialogContent },
             react_1.default.createElement("div", null,
                 react_1.default.createElement(SequenceTypeSelector_1.default, { model: sequenceFeatureDetails }),
                 react_1.default.createElement(SequenceFeatureMenu_1.default, { ref: seqPanelRef, model: sequenceFeatureDetails })),
             react_1.default.createElement("div", null,
                 feature.type === 'gene' ? (react_1.default.createElement(material_1.Typography, null, "Note: inspect subfeature sequences for protein/CDS computations")) : null,
-                error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : !sequence ? (react_1.default.createElement(ui_1.LoadingEllipses, null)) : sequence ? ('error' in sequence ? (react_1.default.createElement(react_1.default.Fragment, null,
+                error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : !sequence ? (react_1.default.createElement(ui_1.LoadingEllipses, null)) : 'error' in sequence ? (react_1.default.createElement(react_1.default.Fragment, null,
                     react_1.default.createElement(material_1.Typography, { color: "error" }, sequence.error),
-                    react_1.default.createElement(material_1.Button, { variant: "contained", color: "inherit", onClick: () => setForce(true) }, "Force load"))) : (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },
-                    react_1.default.createElement(SequencePanel_1.default, { ref: seqPanelRef, feature: feature, sequence: sequence, model: sequenceFeatureDetails })))) : (react_1.default.createElement(material_1.Typography, null, "No sequence found")))),
+                    react_1.default.createElement(material_1.Button, { variant: "contained", color: "inherit", onClick: () => {
+                            setForce(true);
+                        } }, "Force load"))) : (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },
+                    react_1.default.createElement(SequencePanel_1.default, { ref: seqPanelRef, feature: feature, sequence: sequence, model: sequenceFeatureDetails }))))),
         react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), variant: "contained" }, "Close"))));
+            react_1.default.createElement(material_1.Button, { onClick: () => {
+                    handleClose();
+                }, variant: "contained" }, "Close"))));
 });
 exports.default = SequenceDialog;

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceFeatureMenu.js

@@ -94,13 +94,17 @@ const SequenceFeatureMenu = (0, mobx_react_1.observer)(react_1.default.forwardRe
                             label: 'No coordinates',
                             type: 'radio',
                             checked: showCoordinatesSetting === 'none',
-                            onClick: () => model.setShowCoordinates('none'),
+                            onClick: () => {
+                                model.setShowCoordinates('none');
+                            },
                         },
                         {
                             label: 'Coordinates relative to feature start',
                             type: 'radio',
                             checked: showCoordinatesSetting === 'relative',
-                            onClick: () => model.setShowCoordinates('relative'),
+                            onClick: () => {
+                                model.setShowCoordinates('relative');
+                            },
                         },
                         ...(showGenomicCoordsOption
                             ? [
@@ -108,7 +112,9 @@ const SequenceFeatureMenu = (0, mobx_react_1.observer)(react_1.default.forwardRe
                                     label: 'Coordinates relative to genome (only available for continuous genome based sequence types)',
                                     type: 'radio',
                                     checked: showCoordinatesSetting === 'genomic',
-                                    onClick: () => model.setShowCoordinates('genomic'),
+                                    onClick: () => {
+                                        model.setShowCoordinates('genomic');
+                                    },
                                 },
                             ]
                             : []),
@@ -117,10 +123,14 @@ const SequenceFeatureMenu = (0, mobx_react_1.observer)(react_1.default.forwardRe
                 {
                     label: 'Settings',
                     icon: Settings_1.default,
-                    onClick: () => setShowSettings(true),
+                    onClick: () => {
+                        setShowSettings(true);
+                    },
                 },
             ] },
             react_1.default.createElement(MoreVert_1.default, null)),
-        showSettings ? (react_1.default.createElement(SequenceFeatureSettingsDialog, { model: model, handleClose: () => setShowSettings(false) })) : null));
+        showSettings ? (react_1.default.createElement(SequenceFeatureSettingsDialog, { model: model, handleClose: () => {
+                setShowSettings(false);
+            } })) : null));
 }));
 exports.default = SequenceFeatureMenu;

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SequenceTypeSelector.js

@@ -17,7 +17,9 @@ const SequenceTypeSelector = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
     const { intronBp, upDownBp, mode, hasCDS, hasExonOrCDS } = model;
     return (react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
-        react_1.default.createElement(material_1.Select, { size: "small", value: mode, onChange: event => model.setMode(event.target.value) }, Object.entries({
+        react_1.default.createElement(material_1.Select, { size: "small", value: mode, onChange: event => {
+                model.setMode(event.target.value);
+            } }, Object.entries({
             ...(hasCDS
                 ? {
                     cds: 'CDS',
@@ -35,7 +37,7 @@ const SequenceTypeSelector = (0, mobx_react_1.observer)(function ({ model, }) {
                 : {}),
             ...(hasExonOrCDS
                 ? {
-                    gene: `Genomic w/ full introns`,
+                    gene: 'Genomic w/ full introns',
                 }
                 : {}),
             ...(hasExonOrCDS

package/BaseFeatureWidget/SequenceFeatureDetails/dialogs/SettingsDialog.js

@@ -55,13 +55,21 @@ const SequenceFeatureSettingsDialog = (0, mobx_react_1.observer)(function ({ han
     const [upDownBp, setUpDownBp] = (0, react_1.useState)(`${model.upDownBp}`);
     const intronBpValid = !Number.isNaN(+intronBp);
     const upDownBpValid = !Number.isNaN(+upDownBp);
-    return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => handleClose(), title: "Feature sequence settings" },
+    return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
+            handleClose();
+        }, title: "Feature sequence settings" },
         react_1.default.createElement(material_1.DialogContent, { className: classes.dialogContent },
-            react_1.default.createElement(TextField2, { label: "Number of intronic bases around splice site to display", className: classes.formElt, value: intronBp, helperText: !intronBpValid ? 'Not a number' : '', error: !intronBpValid, onChange: event => setIntronBp(event.target.value) }),
-            react_1.default.createElement(TextField2, { label: "Number of bases up/down stream of feature to display", className: classes.formElt, value: upDownBp, helperText: !upDownBpValid ? 'Not a number' : '', error: !upDownBpValid, onChange: event => setUpDownBp(event.target.value) }),
+            react_1.default.createElement(TextField2, { label: "Number of intronic bases around splice site to display", className: classes.formElt, value: intronBp, helperText: !intronBpValid ? 'Not a number' : '', error: !intronBpValid, onChange: event => {
+                    setIntronBp(event.target.value);
+                } }),
+            react_1.default.createElement(TextField2, { label: "Number of bases up/down stream of feature to display", className: classes.formElt, value: upDownBp, helperText: !upDownBpValid ? 'Not a number' : '', error: !upDownBpValid, onChange: event => {
+                    setUpDownBp(event.target.value);
+                } }),
             react_1.default.createElement(FormControl2, null,
                 react_1.default.createElement(material_1.FormLabel, null, "Sequence capitalization"),
-                react_1.default.createElement(material_1.RadioGroup, { value: upperCaseCDS ? 'cds' : 'unchanged', onChange: e => model.setUpperCaseCDS(e.target.value === 'cds') },
+                react_1.default.createElement(material_1.RadioGroup, { value: upperCaseCDS ? 'cds' : 'unchanged', onChange: e => {
+                        model.setUpperCaseCDS(e.target.value === 'cds');
+                    } },
                     react_1.default.createElement(material_1.FormControlLabel, { value: "cds", control: react_1.default.createElement(material_1.Radio, { className: classes.root, size: "small" }), label: "Capitalize CDS and lower case everything else" }),
                     react_1.default.createElement(material_1.FormControlLabel, { value: "unchanged", control: react_1.default.createElement(material_1.Radio, { className: classes.root, size: "small" }), label: "Capitalization from reference genome sequence" })))),
         react_1.default.createElement(material_1.DialogActions, null,
@@ -70,6 +78,8 @@ const SequenceFeatureSettingsDialog = (0, mobx_react_1.observer)(function ({ han
                     model.setUpDownBp(+upDownBp);
                     handleClose();
                 }, disabled: !intronBpValid || !upDownBpValid, color: "primary", variant: "contained" }, "Submit"),
-            react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), color: "secondary", autoFocus: true, variant: "contained" }, "Cancel"))));
+            react_1.default.createElement(material_1.Button, { onClick: () => {
+                    handleClose();
+                }, color: "secondary", autoFocus: true, variant: "contained" }, "Cancel"))));
 });
 exports.default = SequenceFeatureSettingsDialog;

package/BaseFeatureWidget/SequenceFeatureDetails/hooks.js

@@ -9,12 +9,12 @@ function useFeatureSequence(model, feature, upDownBp, forceLoad) {
     const [sequence, setSequence] = (0, react_1.useState)();
     const [error, setError] = (0, react_1.useState)();
     (0, react_1.useEffect)(() => {
-        var _a;
+        var _a, _b;
         if (!model) {
             return;
         }
         const { assemblyManager, rpcManager } = (0, util_1.getSession)(model);
-        const [assemblyName] = ((_a = model.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
+        const assemblyName = ((_b = (_a = model.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) === null || _b === void 0 ? void 0 : _b[0]) || '';
         async function fetchSeq(start, end, refName) {
             const assembly = await assemblyManager.waitForAssembly(assemblyName);
             if (!assembly) {

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js

@@ -51,7 +51,7 @@ const CDNASequence = (0, mobx_react_1.observer)(function ({ utr, cds, exons, seq
             currRemainder,
             showCoordinates,
         });
-        middleChunks.push(react_1.default.createElement(SequenceDisplay_1.default, { key: JSON.stringify(chunk) + '-mid', model: model, color: chunk.type === 'CDS' ? util_1.cdsColor : util_1.utrColor, strand: mult, start: currStart, coordStart: coordStart, chunks: segments }));
+        middleChunks.push(react_1.default.createElement(SequenceDisplay_1.default, { key: `${JSON.stringify(chunk)}-mid`, model: model, color: chunk.type === 'CDS' ? util_1.cdsColor : util_1.utrColor, strand: mult, start: currStart, coordStart: coordStart, chunks: segments }));
         currRemainder = remainder;
         currStart = currStart + s.length * mult;
         coordStart = coordStart + s.length * mult;
@@ -66,7 +66,7 @@ const CDNASequence = (0, mobx_react_1.observer)(function ({ utr, cds, exons, seq
                 showCoordinates,
             });
             if (segments.length) {
-                middleChunks.push(react_1.default.createElement(SequenceDisplay_1.default, { key: JSON.stringify(chunk) + '-intron', model: model, strand: mult, coordStart: coordStart, start: currStart, chunks: segments }));
+                middleChunks.push(react_1.default.createElement(SequenceDisplay_1.default, { key: `${JSON.stringify(chunk)}-intron`, model: model, strand: mult, coordStart: coordStart, start: currStart, chunks: segments }));
                 currRemainder = remainder;
                 currStart = currStart + str.length * mult;
                 coordStart = coordStart + str.length * mult;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js

@@ -10,8 +10,8 @@ const SequenceDisplay = (0, mobx_react_1.observer)(function ({ chunks, start, co
     return chunks.map((chunk, idx) => {
         var _a;
         const f = coordStart - (start % charactersPerRow);
-        const prefix = (idx == 0 && start % charactersPerRow == 0) || idx > 0
-            ? `${f + idx * strand * charactersPerRow}`.padStart(4) + '   '
+        const prefix = (idx === 0 && start % charactersPerRow === 0) || idx > 0
+            ? `${`${f + idx * strand * charactersPerRow}`.padStart(4)}   `
             : '';
         const postfix = idx === chunks.length - 1 &&
             (((_a = chunks.at(-1)) === null || _a === void 0 ? void 0 : _a.replaceAll(' ', '').length) || 0) +
@@ -21,7 +21,9 @@ const SequenceDisplay = (0, mobx_react_1.observer)(function ({ chunks, start, co
             : showCoordinates
                 ? ' \n'
                 : '';
-        return (react_1.default.createElement(react_1.default.Fragment, { key: `${chunk}-${idx}` },
+        return (
+        /* biome-ignore lint/suspicious/noArrayIndexKey: */
+        react_1.default.createElement(react_1.default.Fragment, { key: `${chunk}-${idx}` },
             showCoordinates ? prefix : null,
             react_1.default.createElement("span", { style: { background: color } }, chunk),
             postfix));

package/BaseFeatureWidget/stateModelFactory.js

@@ -129,10 +129,8 @@ function stateModelFactory(pluginManager) {
                             ...(0, configuration_1.getConf)(track, ['formatDetails', arg2], { feature }),
                         });
                         if (track) {
-                            // eslint-disable-next-line no-underscore-dangle
                             feature.__jbrowsefmt = combine('feature', feature);
                             formatSubfeatures(feature, (0, configuration_1.getConf)(track, ['formatDetails', 'depth']), sub => {
-                                // eslint-disable-next-line no-underscore-dangle
                                 sub.__jbrowsefmt = combine('subfeatures', sub);
                             });
                         }

package/PluginLoader.d.ts

@@ -31,8 +31,7 @@ export interface CJSPluginDefinition {
     cjsUrl: string;
 }
 export declare function isCJSPluginDefinition(def: PluginDefinition): def is CJSPluginDefinition;
-export interface PluginDefinition extends Partial<UMDUrlPluginDefinition>, Partial<UMDLocPluginDefinition>, Partial<LegacyUMDPluginDefinition>, Partial<ESMLocPluginDefinition>, Partial<ESMUrlPluginDefinition>, Partial<CJSPluginDefinition> {
-}
+export type PluginDefinition = UMDUrlPluginDefinition | UMDLocPluginDefinition | LegacyUMDPluginDefinition | ESMLocPluginDefinition | ESMUrlPluginDefinition | CJSPluginDefinition;
 export interface PluginRecord {
     plugin: PluginConstructor;
     definition: PluginDefinition;

package/PluginLoader.js

@@ -13,13 +13,21 @@ const Plugin_1 = __importDefault(require("./Plugin"));
 const ReExports_1 = __importDefault(require("./ReExports"));
 const util_1 = require("./util");
 function isUMDPluginDefinition(def) {
-    return ((def.umdUrl !== undefined ||
+    return (
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    (def.umdUrl !== undefined ||
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         def.url !== undefined ||
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         def.umdLoc !== undefined) &&
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         def.name !== undefined);
 }
 function isESMPluginDefinition(def) {
-    return (def.esmUrl !== undefined ||
+    return (
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    def.esmUrl !== undefined ||
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         def.esmLoc !== undefined);
 }
 function promisifiedLoadScript(src) {
@@ -39,7 +47,7 @@ async function loadScript(scriptUrl) {
         return promisifiedLoadScript(scriptUrl);
     }
     // @ts-expect-error
-    if (globalThis === null || globalThis === void 0 ? void 0 : globalThis.importScripts) {
+    if (globalThis.importScripts) {
         // @ts-expect-error
         await globalThis.importScripts(scriptUrl);
         return;
@@ -47,16 +55,16 @@ async function loadScript(scriptUrl) {
     throw new Error('cannot figure out how to load external JS scripts in this environment');
 }
 function isCJSPluginDefinition(def) {
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     return def.cjsUrl !== undefined;
 }
 function pluginDescriptionString(pluginDefinition) {
-    var _a;
     if (isUMDPluginDefinition(pluginDefinition)) {
         return `UMD plugin ${pluginDefinition.name}`;
     }
     if (isESMPluginDefinition(pluginDefinition)) {
         return `ESM plugin ${pluginDefinition.esmUrl ||
-            ((_a = pluginDefinition.esmLoc) === null || _a === void 0 ? void 0 : _a.uri)}`;
+            pluginDefinition.esmLoc.uri}`;
     }
     if (isCJSPluginDefinition(pluginDefinition)) {
         return `CJS plugin ${pluginDefinition.cjsUrl}`;
@@ -91,9 +99,10 @@ class PluginLoader {
             throw new Error(`cannot load plugins using protocol "${parsedUrl.protocol}"`);
         }
         if (!this.fetchESM) {
-            throw new Error(`No ESM fetcher installed`);
+            throw new Error('No ESM fetcher installed');
         }
         const plugin = await this.fetchESM(parsedUrl.href);
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!plugin) {
             throw new Error(`Could not load ESM plugin: ${parsedUrl}`);
         }
@@ -141,6 +150,7 @@ class PluginLoader {
         else {
             throw new Error(`Could not determine plugin type: ${JSON.stringify(def)}`);
         }
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!plugin.default) {
             throw new Error(`${pluginDescriptionString(def)} does not have a default export, cannot load`);
         }

package/PluginManager.d.ts

@@ -36,7 +36,7 @@ declare class TypeRecord<ElementClass extends PluggableElementBase> {
     }));
     add(name: string, t: ElementClass): void;
     has(name: string): boolean;
-    get(name: string): ElementClass;
+    get(name: string): ElementClass | undefined;
     all(): ElementClass[];
 }
 type AnyFunction = (...args: any) => any;
@@ -104,7 +104,7 @@ export default class PluginManager {
     configure(): this;
     getElementTypeRecord(groupName: PluggableElementTypeGroup): TypeRecord<PluggableElementBase>;
     addElementType(groupName: PluggableElementTypeGroup, creationCallback: (pluginManager: PluginManager) => PluggableElementType): this;
-    getElementType(groupName: PluggableElementTypeGroup, typeName: string): PluggableElementBase;
+    getElementType(groupName: PluggableElementTypeGroup, typeName: string): PluggableElementBase | undefined;
     getElementTypesInGroup(groupName: PluggableElementTypeGroup): PluggableElementBase[];
     getTrackElements(): TrackType[];
     getConnectionElements(): ConnectionType[];
@@ -266,18 +266,18 @@ export default class PluginManager {
     jbrequire: (lib: keyof typeof ReExports | AnyFunction | {
         default: AnyFunction;
     }) => any;
-    getRendererType(typeName: string): RendererType;
+    getRendererType(typeName: string): RendererType | undefined;
     getRendererTypes(): RendererType[];
-    getAdapterType(typeName: string): AdapterType;
-    getTextSearchAdapterType(typeName: string): TextSearchAdapterType;
-    getTrackType(typeName: string): TrackType;
-    getDisplayType(typeName: string): DisplayType;
-    getViewType(typeName: string): ViewType;
-    getAddTrackWorkflow(typeName: string): AddTrackWorkflowType;
-    getWidgetType(typeName: string): WidgetType;
-    getConnectionType(typeName: string): ConnectionType;
-    getRpcMethodType(methodName: string): RpcMethodType;
-    getInternetAccountType(name: string): InternetAccountType;
+    getAdapterType(typeName: string): AdapterType | undefined;
+    getTextSearchAdapterType(typeName: string): TextSearchAdapterType | undefined;
+    getTrackType(typeName: string): TrackType | undefined;
+    getDisplayType(typeName: string): DisplayType | undefined;
+    getViewType(typeName: string): ViewType | undefined;
+    getAddTrackWorkflow(typeName: string): AddTrackWorkflowType | undefined;
+    getWidgetType(typeName: string): WidgetType | undefined;
+    getConnectionType(typeName: string): ConnectionType | undefined;
+    getRpcMethodType(methodName: string): RpcMethodType | undefined;
+    getInternetAccountType(name: string): InternetAccountType | undefined;
     addRendererType(cb: (pm: PluginManager) => RendererType): this;
     addAdapterType(cb: (pm: PluginManager) => AdapterType): this;
     addTextSearchAdapterType(cb: (pm: PluginManager) => TextSearchAdapterType): this;