@jbrowse/core 2.6.2 → 2.7.0

package/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.d.ts

@@ -1,13 +1,4 @@
 import React from 'react';
-export declare const useStyles: (params: void, styleOverrides?: {
-    props: any;
-    ownerState?: Record<string, unknown> | undefined;
-} | undefined) => {
-    classes: Record<"field" | "fieldSubvalue", string>;
-    theme: import("@mui/material").Theme;
-    css: import("tss-react").Css;
-    cx: import("tss-react").Cx;
-};
 export default function ArrayValue({ name, value, description, prefix, }: {
     description?: React.ReactNode;
     name: string;

package/BaseFeatureWidget/BaseFeatureDetail/ArrayValue.js

@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.useStyles = void 0;
 const react_1 = __importDefault(require("react"));
 const is_object_1 = __importDefault(require("is-object"));
 const mui_1 = require("tss-react/mui");
@@ -11,7 +10,7 @@ const mui_1 = require("tss-react/mui");
 const Attributes_1 = __importDefault(require("./Attributes"));
 const FieldName_1 = __importDefault(require("./FieldName"));
 const BasicValue_1 = __importDefault(require("./BasicValue"));
-exports.useStyles = (0, mui_1.makeStyles)()(theme => ({
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     field: {
         display: 'flex',
         flexWrap: 'wrap',
@@ -26,7 +25,7 @@ exports.useStyles = (0, mui_1.makeStyles)()(theme => ({
     },
 }));
 function ArrayValue({ name, value, description, prefix = [], }) {
-    const { classes } = (0, exports.useStyles)();
+    const { classes } = useStyles();
     if (value.length === 1) {
         return (0, is_object_1.default)(value[0]) ? (react_1.default.createElement(Attributes_1.default, { attributes: value[0], prefix: [...prefix, name] })) : (react_1.default.createElement("div", { className: classes.field },
             react_1.default.createElement(FieldName_1.default, { prefix: prefix, description: description, name: name }),

package/BaseFeatureWidget/BaseFeatureDetail/Attributes.d.ts

@@ -2,9 +2,7 @@ import React from 'react';
 export default function Attributes(props: {
     attributes: {
         [key: string]: unknown;
-        __jbrowsefmt?: {
-            [key: string]: unknown;
-        };
+        __jbrowsefmt?: Record<string, unknown>;
     };
     omit?: string[];
     omitSingleLevel?: string[];

package/BaseFeatureWidget/BaseFeatureDetail/BasicValue.d.ts

@@ -1,13 +1,4 @@
 import React from 'react';
-export declare const useStyles: (params: void, styleOverrides?: {
-    props: any;
-    ownerState?: Record<string, unknown> | undefined;
-} | undefined) => {
-    classes: Record<"fieldValue", string>;
-    theme: import("@mui/material").Theme;
-    css: import("tss-react").Css;
-    cx: import("tss-react").Cx;
-};
 export default function BasicValue({ value }: {
     value: unknown;
 }): React.JSX.Element;

package/BaseFeatureWidget/BaseFeatureDetail/BasicValue.js

@@ -3,14 +3,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.useStyles = void 0;
 const react_1 = __importDefault(require("react"));
 const mui_1 = require("tss-react/mui");
 const is_object_1 = __importDefault(require("is-object"));
 const material_1 = require("@mui/material");
 // locals
 const ui_1 = require("../../ui");
-exports.useStyles = (0, mui_1.makeStyles)()(theme => ({
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     fieldValue: {
         wordBreak: 'break-word',
         maxHeight: 300,
@@ -20,7 +19,7 @@ exports.useStyles = (0, mui_1.makeStyles)()(theme => ({
     },
 }));
 function BasicValue({ value }) {
-    const { classes } = (0, exports.useStyles)();
+    const { classes } = useStyles();
     const isLink = `${value}`.match(/^https?:\/\//);
     return (react_1.default.createElement("div", { className: classes.fieldValue }, react_1.default.isValidElement(value) ? (value) : isLink ? (react_1.default.createElement(material_1.Link, { href: `${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.d.ts

@@ -1,13 +1,4 @@
 import React from 'react';
-export declare const useStyles: (params: void, styleOverrides?: {
-    props: any;
-    ownerState?: Record<string, unknown> | undefined;
-} | undefined) => {
-    classes: Record<"margin", string>;
-    theme: import("@mui/material").Theme;
-    css: import("tss-react").Css;
-    cx: import("tss-react").Cx;
-};
 export default function DataGridDetails({ value, prefix, name, }: {
     name: string;
     prefix?: string[];

package/BaseFeatureWidget/BaseFeatureDetail/DataGridDetails.js

@@ -26,25 +26,30 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.useStyles = void 0;
 const react_1 = __importStar(require("react"));
 const mui_1 = require("tss-react/mui");
 const x_data_grid_1 = require("@mui/x-data-grid");
 const material_1 = require("@mui/material");
 // locals
 const util_1 = require("../../util");
-const ResizeBar_1 = __importStar(require("../../ui/ResizeBar"));
+const ResizeBar_1 = __importDefault(require("../../ui/ResizeBar"));
 const FieldName_1 = __importDefault(require("./FieldName"));
 const UriLink_1 = __importDefault(require("./UriLink"));
-exports.useStyles = (0, mui_1.makeStyles)()(theme => ({
+const useResizeBar_1 = require("../../ui/useResizeBar");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     margin: {
         margin: theme.spacing(1),
         width: '100%',
     },
+    cell: {
+        whiteSpace: 'nowrap',
+        overflow: 'hidden',
+        textOverflow: 'ellipsis',
+    },
 }));
 function DataGridDetails({ value, prefix, name, }) {
-    const { classes } = (0, exports.useStyles)();
-    const { ref, scrollLeft } = (0, ResizeBar_1.useResizeBar)();
+    const { classes } = useStyles();
+    const { ref, scrollLeft } = (0, useResizeBar_1.useResizeBar)();
     const [checked, setChecked] = (0, react_1.useState)(false);
     const keys = Object.keys(value[0]).sort();
     const unionKeys = new Set(keys);
@@ -88,7 +93,7 @@ function DataGridDetails({ value, prefix, name, }) {
                         field: val,
                         renderCell: params => {
                             const value = params.value;
-                            return (0, util_1.isUriLocation)(value) ? (react_1.default.createElement(UriLink_1.default, { value: value })) : (react_1.default.createElement(react_1.default.Fragment, null, (0, util_1.getStr)(value)));
+                            return (react_1.default.createElement("div", { className: classes.cell }, (0, util_1.isUriLocation)(value) ? (react_1.default.createElement(UriLink_1.default, { value: value })) : (react_1.default.createElement(react_1.default.Fragment, null, (0, util_1.getStr)(value)))));
                         },
                         width: widths[index],
                     })) }))));

package/BaseFeatureWidget/BaseFeatureDetail/FieldName.d.ts

@@ -1,13 +1,4 @@
 import React from 'react';
-export declare const useStyles: (params: void, styleOverrides?: {
-    props: any;
-    ownerState?: Record<string, unknown> | undefined;
-} | undefined) => {
-    classes: Record<"fieldDescription" | "fieldName", string>;
-    theme: import("@mui/material").Theme;
-    css: import("tss-react").Css;
-    cx: import("tss-react").Cx;
-};
 export default function FieldName({ description, name, width, prefix, }: {
     description?: React.ReactNode;
     name: string;

package/BaseFeatureWidget/BaseFeatureDetail/FieldName.js

@@ -3,11 +3,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.useStyles = void 0;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
-exports.useStyles = (0, mui_1.makeStyles)()(theme => ({
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     fieldDescription: {
         '&:hover': {
             background: theme.palette.mode === 'dark' ? '#e65100' : 'yellow',
@@ -24,7 +23,7 @@ exports.useStyles = (0, mui_1.makeStyles)()(theme => ({
     },
 }));
 function FieldName({ description, name, width, prefix = [], }) {
-    const { classes, cx } = (0, exports.useStyles)();
+    const { classes, cx } = useStyles();
     const val = [...prefix, name].join('.');
     return description ? (react_1.default.createElement(material_1.Tooltip, { title: description, placement: "left" },
         react_1.default.createElement("div", { className: cx(classes.fieldDescription, classes.fieldName) }, val))) : (react_1.default.createElement("div", { className: classes.fieldName, style: { width: width } }, val));

package/BaseFeatureWidget/BaseFeatureDetail/SimpleField.d.ts

@@ -1,13 +1,4 @@
 import React from 'react';
-export declare const useStyles: (params: void, styleOverrides?: {
-    props: any;
-    ownerState?: Record<string, unknown> | undefined;
-} | undefined) => {
-    classes: Record<"field", string>;
-    theme: import("@mui/material").Theme;
-    css: import("tss-react").Css;
-    cx: import("tss-react").Cx;
-};
 export default function SimpleField({ name, value, description, prefix, width, }: {
     description?: React.ReactNode;
     name: string;

package/BaseFeatureWidget/BaseFeatureDetail/SimpleField.js

@@ -3,19 +3,18 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.useStyles = void 0;
 const react_1 = __importDefault(require("react"));
 const mui_1 = require("tss-react/mui");
 const FieldName_1 = __importDefault(require("./FieldName"));
 const BasicValue_1 = __importDefault(require("./BasicValue"));
-exports.useStyles = (0, mui_1.makeStyles)()({
+const useStyles = (0, mui_1.makeStyles)()({
     field: {
         display: 'flex',
         flexWrap: 'wrap',
     },
 });
 function SimpleField({ name, value, description, prefix, width, }) {
-    const { classes } = (0, exports.useStyles)();
+    const { classes } = useStyles();
     return value !== null && value !== undefined ? (react_1.default.createElement("div", { className: classes.field },
         react_1.default.createElement(FieldName_1.default, { prefix: prefix, description: description, name: name, width: width }),
         react_1.default.createElement(BasicValue_1.default, { value: value }))) : null;

package/BaseFeatureWidget/BaseFeatureDetail/UriField.d.ts

@@ -1,13 +1,4 @@
 import React from 'react';
-export declare const useStyles: (params: void, styleOverrides?: {
-    props: any;
-    ownerState?: Record<string, unknown> | undefined;
-} | undefined) => {
-    classes: Record<"field", string>;
-    theme: import("@mui/material").Theme;
-    css: import("tss-react").Css;
-    cx: import("tss-react").Cx;
-};
 export default function UriField({ value, prefix, name, }: {
     value: {
         uri: string;

package/BaseFeatureWidget/BaseFeatureDetail/UriField.js

@@ -3,19 +3,18 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.useStyles = void 0;
 const react_1 = __importDefault(require("react"));
 const FieldName_1 = __importDefault(require("./FieldName"));
 const mui_1 = require("tss-react/mui");
 const BasicValue_1 = __importDefault(require("./BasicValue"));
-exports.useStyles = (0, mui_1.makeStyles)()({
+const useStyles = (0, mui_1.makeStyles)()({
     field: {
         display: 'flex',
         flexWrap: 'wrap',
     },
 });
 function UriField({ value, prefix, name, }) {
-    const { classes } = (0, exports.useStyles)();
+    const { classes } = useStyles();
     const { uri, baseUri = '' } = value;
     let href;
     try {

package/BaseFeatureWidget/BaseFeatureDetail/index.d.ts

@@ -2,15 +2,6 @@ import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { BaseCardProps, BaseProps } from '../types';
 import { SimpleFeatureSerialized } from '../../util';
-export declare const useStyles: (params: void, styleOverrides?: {
-    props: any;
-    ownerState?: Record<string, unknown> | undefined;
-} | undefined) => {
-    classes: Record<"expandIcon" | "expansionPanelDetails", string>;
-    theme: import("@mui/material").Theme;
-    css: import("tss-react").Css;
-    cx: import("tss-react").Cx;
-};
 export declare function BaseCard({ children, title, defaultExpanded, }: BaseCardProps): React.JSX.Element;
 export declare const BaseCoreDetails: (props: BaseProps) => React.JSX.Element;
 export declare const BaseAttributes: (props: BaseProps) => React.JSX.Element;
@@ -28,6 +19,6 @@ export declare function FeatureDetails(props: {
     descriptions?: Record<string, React.ReactNode>;
     formatter?: (val: unknown, key: string) => React.ReactNode;
 }): React.JSX.Element;
-declare const _default: ({ model }: BaseInputProps) => React.JSX.Element | null;
-export default _default;
+declare const BaseFeatureDetail: ({ model }: BaseInputProps) => React.JSX.Element | null;
+export default BaseFeatureDetail;
 export { default as Attributes } from './Attributes';

package/BaseFeatureWidget/BaseFeatureDetail/index.js

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Attributes = exports.FeatureDetails = exports.BaseAttributes = exports.BaseCoreDetails = exports.BaseCard = exports.useStyles = void 0;
+exports.Attributes = exports.FeatureDetails = exports.BaseAttributes = exports.BaseCoreDetails = exports.BaseCard = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = __importStar(require("react"));
 const react_error_boundary_1 = require("react-error-boundary");
@@ -52,7 +52,7 @@ const coreDetails = [
     'description',
     'type',
 ];
-exports.useStyles = (0, mui_1.makeStyles)()(theme => {
+const useStyles = (0, mui_1.makeStyles)()(theme => {
     var _a;
     return ({
         expansionPanelDetails: {
@@ -65,7 +65,7 @@ exports.useStyles = (0, mui_1.makeStyles)()(theme => {
     });
 });
 function BaseCard({ children, title, defaultExpanded = true, }) {
-    const { classes } = (0, exports.useStyles)();
+    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 } },
         react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.expandIcon }) },
@@ -151,7 +151,7 @@ function FeatureDetails(props) {
         (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));
 }
 exports.FeatureDetails = FeatureDetails;
-exports.default = (0, mobx_react_1.observer)(function ({ model }) {
+const BaseFeatureDetail = (0, mobx_react_1.observer)(function ({ model }) {
     const { error, featureData } = model;
     if (error) {
         return react_1.default.createElement(ui_1.ErrorMessage, { error: error });
@@ -166,5 +166,6 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
     const g = JSON.parse(JSON.stringify(featureData, (_, v) => (v === undefined ? null : v)));
     return (0, util_2.isEmpty)(g) ? null : react_1.default.createElement(FeatureDetails, { model: model, feature: g });
 });
+exports.default = BaseFeatureDetail;
 var Attributes_2 = require("./Attributes");
 Object.defineProperty(exports, "Attributes", { enumerable: true, get: function () { return __importDefault(Attributes_2).default; } });

package/BaseFeatureWidget/SequenceFeatureDetails/ProteinSequence.d.ts

@@ -3,7 +3,5 @@ import { Feat } from '../util';
 export default function ProteinSequence({ cds, sequence, codonTable, }: {
     cds: Feat[];
     sequence: string;
-    codonTable: {
-        [key: string]: string;
-    };
+    codonTable: Record<string, string>;
 }): React.JSX.Element;

package/BaseFeatureWidget/SequenceFeatureDetails/SequencePanel.js

@@ -10,7 +10,7 @@ const CDNASequence_1 = __importDefault(require("./CDNASequence"));
 const ProteinSequence_1 = __importDefault(require("./ProteinSequence"));
 const GenomicSequence_1 = __importDefault(require("./GenomicSequence"));
 const CDSSequence_1 = __importDefault(require("./CDSSequence"));
-const SeqPanel = react_1.default.forwardRef(function (props, ref) {
+const SeqPanel = react_1.default.forwardRef(function SeqPanel2(props, ref) {
     const { feature, mode, intronBp = 10 } = props;
     let { sequence: { seq, upstream = '', downstream = '' }, } = props;
     const { subfeatures = [] } = feature;

package/BaseFeatureWidget/util.js

@@ -29,9 +29,7 @@ function calculateUTRs(cds, exons) {
     if (!cds.length) {
         return [];
     }
-    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
     const firstCds = cds.at(0);
-    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
     const lastCds = cds.at(-1);
     const firstCdsIdx = exons.findIndex(exon => exon.end >= firstCds.start && exon.start <= firstCds.start);
     const lastCdsIdx = exons.findIndex(exon => exon.end >= lastCds.end && exon.start <= lastCds.end);
@@ -53,9 +51,7 @@ function calculateUTRs2(cds, parentFeat) {
     if (!cds.length) {
         return [];
     }
-    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
     const firstCds = cds.at(0);
-    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
     const lastCds = cds.at(-1);
     const fiveUTRs = [{ start: parentFeat.start, end: firstCds.start }].map(elt => ({ ...elt, type: 'five_prime_UTR' }));
     const threeUTRs = [{ start: lastCds.end, end: parentFeat.end }].map(elt => ({

package/PluginManager.d.ts

@@ -30,17 +30,11 @@ type PluggableElementTypeGroup = 'renderer' | 'adapter' | 'display' | 'track' |
 /** internal class that holds the info for a certain element type */
 declare class TypeRecord<ElementClass extends PluggableElementBase> {
     typeName: string;
-    baseClass: {
-        new (...args: any[]): ElementClass;
-    } | (Function & {
+    baseClass: (new (...args: unknown[]) => ElementClass) | (Function & {
         prototype: ElementClass;
     });
-    registeredTypes: {
-        [name: string]: ElementClass;
-    };
-    constructor(typeName: string, baseClass: {
-        new (...args: any[]): ElementClass;
-    } | (Function & {
+    registeredTypes: Record<string, ElementClass>;
+    constructor(typeName: string, baseClass: (new (...args: unknown[]) => ElementClass) | (Function & {
         prototype: ElementClass;
     }));
     add(name: string, t: ElementClass): void;
@@ -85,9 +79,7 @@ export default class PluginManager {
     rootModel?: AbstractRootModel;
     extensionPoints: Map<string, Function[]>;
     constructor(initialPlugins?: (Plugin | PluginLoadRecord)[]);
-    pluginConfigurationSchemas(): {
-        [key: string]: unknown;
-    };
+    pluginConfigurationSchemas(): Record<string, unknown>;
     addPlugin(load: Plugin | PluginLoadRecord | RuntimePluginLoadRecord): this;
     getPlugin(name: string): Plugin | undefined;
     hasPlugin(name: string): boolean;
@@ -207,9 +199,9 @@ export default class PluginManager {
         '@jbrowse/core/util/mst-reflection': typeof import("./util/mst-reflection");
         '@jbrowse/core/util/rxjs': typeof import("./util/rxjs");
         '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail': {
-            Attributes: (props: any) => import("react").JSX.Element;
-            FeatureDetails: (props: any) => import("react").JSX.Element;
-            BaseCard: (props: any) => import("react").JSX.Element;
+            Attributes: import("react").ForwardRefExoticComponent<Omit<any, "ref"> & import("react").RefAttributes<unknown>>;
+            FeatureDetails: import("react").ForwardRefExoticComponent<Omit<any, "ref"> & import("react").RefAttributes<unknown>>;
+            BaseCard: import("react").ForwardRefExoticComponent<Omit<any, "ref"> & import("react").RefAttributes<unknown>>;
         };
         '@jbrowse/core/data_adapters/BaseAdapter': typeof import("./data_adapters/BaseAdapter");
         mobx: typeof import("mobx");
@@ -229,8 +221,8 @@ export default class PluginManager {
             makeStyles: <Params = void, RuleNameSubsetReferencableInNestedSelectors extends string = never>(params?: {
                 name?: string | Record<string, unknown> | undefined;
                 uniqId?: string | undefined;
-            } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: import("@mui/material").Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, styleOverrides?: {
-                props: any;
+            } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: import("@mui/material").Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, muiStyleOverridesParams?: {
+                props: Record<string, unknown>;
                 ownerState?: Record<string, unknown> | undefined;
             } | undefined) => {
                 classes: Record<RuleName, string>;

package/ReExports/modules.d.ts

@@ -124,9 +124,9 @@ declare const libs: {
     '@jbrowse/core/util/mst-reflection': typeof coreMstReflection;
     '@jbrowse/core/util/rxjs': typeof rxjs;
     '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail': {
-        Attributes: (props: any) => React.JSX.Element;
-        FeatureDetails: (props: any) => React.JSX.Element;
-        BaseCard: (props: any) => React.JSX.Element;
+        Attributes: React.ForwardRefExoticComponent<Omit<any, "ref"> & React.RefAttributes<unknown>>;
+        FeatureDetails: React.ForwardRefExoticComponent<Omit<any, "ref"> & React.RefAttributes<unknown>>;
+        BaseCard: React.ForwardRefExoticComponent<Omit<any, "ref"> & React.RefAttributes<unknown>>;
     };
     '@jbrowse/core/data_adapters/BaseAdapter': typeof BaseAdapterExports;
     mobx: typeof mobx;
@@ -146,8 +146,8 @@ declare const libs: {
         makeStyles: <Params = void, RuleNameSubsetReferencableInNestedSelectors extends string = never>(params?: {
             name?: string | Record<string, unknown> | undefined;
             uniqId?: string | undefined;
-        } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: MUIStyles.Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, styleOverrides?: {
-            props: any;
+        } | undefined) => <RuleName extends string>(cssObjectByRuleNameOrGetCssObjectByRuleName: Record<RuleName, import("tss-react").CSSObject> | ((theme: MUIStyles.Theme, params: Params, classes: Record<RuleNameSubsetReferencableInNestedSelectors, string>) => Record<RuleNameSubsetReferencableInNestedSelectors | RuleName, import("tss-react").CSSObject>)) => (params: Params, muiStyleOverridesParams?: {
+            props: Record<string, unknown>;
             ownerState?: Record<string, unknown> | undefined;
         } | undefined) => {
             classes: Record<RuleName, string>;

package/ReExports/modules.js

@@ -26,6 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable react-refresh/only-export-components */
 // this is all the stuff that the pluginManager re-exports for plugins to use
 const react_1 = __importStar(require("react"));
 const ReactJSXRuntime = __importStar(require("react/jsx-runtime"));
@@ -177,12 +178,13 @@ const Entries = {
     Tooltip: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Tooltip')))),
     Typography: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/material/Typography')))),
 };
-const LazyMUICore = Object.fromEntries(Object.entries(Entries).map(([key, ReactComponent]) => [
-    key,
+const LazyMUICore = Object.fromEntries(Object.entries(Entries).map(([key, ReactComponent]) => {
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    (props) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-        react_1.default.createElement(ReactComponent, { ...props }))),
-]));
+    const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+        react_1.default.createElement(ReactComponent, { ...props, ref: ref }))));
+    Component.displayName = key;
+    return [key, Component];
+}));
 const MaterialPrefixMUI = Object.fromEntries(Object.entries(LazyMUICore).map(([key, value]) => [
     '@material-ui/core/' + key,
     value,
@@ -349,21 +351,25 @@ const DataGridEntries = {
         default: module.GridViewStreamIcon,
     }))),
 };
-const LazyDataGridComponents = Object.fromEntries(Object.entries(DataGridEntries).map(([key, ReactComponent]) => [
-    key,
+const LazyDataGridComponents = Object.fromEntries(Object.entries(DataGridEntries).map(([key, ReactComponent]) => {
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    (props) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-        react_1.default.createElement(ReactComponent, { ...props }))),
-]));
+    const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+        react_1.default.createElement(ReactComponent, { ...props, ref: ref }))));
+    Component.displayName = key;
+    return [key, Component];
+}));
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
-const LazyAttributes = (props) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-    react_1.default.createElement(Attributes, { ...props })));
+const LazyAttributes = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+    react_1.default.createElement(Attributes, { ...props, ref: ref }))));
+LazyAttributes.displayName = 'Attributes';
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
-const LazyFeatureDetails = (props) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-    react_1.default.createElement(FeatureDetails, { ...props })));
+const LazyFeatureDetails = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+    react_1.default.createElement(FeatureDetails, { ...props, ref: ref }))));
+LazyFeatureDetails.displayName = 'FeatureDetails';
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
-const LazyBaseCard = (props) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
-    react_1.default.createElement(BaseCard, { ...props })));
+const LazyBaseCard = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+    react_1.default.createElement(BaseCard, { ...props, ref: ref }))));
+LazyBaseCard.displayName = 'BaseCard';
 const libs = {
     mobx,
     'mobx-state-tree': mst,
@@ -450,10 +456,10 @@ const libsList = Object.keys(libs);
 // systems and such) are included here, and vice versa
 const inLibsOnly = libsList.filter(mod => !list_1.default.includes(mod));
 if (inLibsOnly.length > 0) {
-    throw new Error(`The following modules are in the re-exports list, but not the modules libs: ${inLibsOnly.join(', ')}`);
+    throw new Error(`The following modules are in the modules libs, but not the re-exports list: ${inLibsOnly.join(', ')}`);
 }
 const inReExportsOnly = list_1.default.filter(mod => !libsList.includes(mod));
 if (inReExportsOnly.length) {
-    throw new Error(`The following modules are in the modules libs, but not the re-exports list: ${inReExportsOnly.join(', ')}`);
+    throw new Error(`The following modules are in the re-exports list, but not the modules libs: ${inReExportsOnly.join(', ')}`);
 }
 exports.default = libs;

package/TextSearch/TextSearchManager.d.ts

@@ -6,7 +6,7 @@ import { AnyConfigurationModel } from '../configuration';
 export interface SearchScope {
     includeAggregateIndexes: boolean;
     assemblyName: string;
-    tracks?: Array<string>;
+    tracks?: string[];
 }
 export default class TextSearchManager {
     pluginManager: PluginManager;

package/assemblyManager/assembly.d.ts

@@ -36,6 +36,8 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pm: Plugin
     refNameAliases: RefNameAliases | undefined;
     lowerCaseRefNameAliases: RefNameAliases | undefined;
     cytobands: Feature[] | undefined;
+} & {
+    getConf(arg: string): any;
 } & {
     /**
      * #getter

package/assemblyManager/assembly.js

@@ -108,6 +108,11 @@ function assemblyFactory(assemblyConfigType, pm) {
         refNameAliases: undefined,
         lowerCaseRefNameAliases: undefined,
         cytobands: undefined,
+    }))
+        .views(self => ({
+        getConf(arg) {
+            return self.configuration ? (0, configuration_1.getConf)(self, arg) : undefined;
+        },
     }))
         .views(self => ({
         /**
@@ -122,7 +127,7 @@ function assemblyFactory(assemblyConfigType, pm) {
          * #getter
          */
         get name() {
-            return (0, configuration_1.getConf)(self, 'name');
+            return self.getConf('name') || '';
         },
         /**
          * #getter
@@ -136,13 +141,13 @@ function assemblyFactory(assemblyConfigType, pm) {
          * #getter
          */
         get aliases() {
-            return (0, configuration_1.getConf)(self, 'aliases');
+            return self.getConf('aliases') || [];
         },
         /**
          * #getter
          */
         get displayName() {
-            return (0, configuration_1.getConf)(self, 'displayName');
+            return self.getConf('displayName');
         },
         /**
          * #getter
@@ -194,7 +199,7 @@ function assemblyFactory(assemblyConfigType, pm) {
          * #getter
          */
         get refNameColors() {
-            const colors = (0, configuration_1.getConf)(self, 'refNameColors');
+            const colors = self.getConf('refNameColors') || [];
             return colors.length === 0 ? refNameColors : colors;
         },
     }))