@jbrowse/core 2.4.2 → 2.5.0

package/ui/AboutDialog.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationModel } from '../configuration';
 export declare function FileInfoPanel({ config }: {
     config: AnyConfigurationModel;

package/ui/AppLogo.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AnyConfigurationModel } from '../configuration';
 declare const Logo: ({ session, }: {
     session: {

package/ui/AssemblySelector.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { InputProps as IIP, TextFieldProps as TFP } from '@mui/material';
 import { AbstractSessionModel } from '../util';
 declare const AssemblySelector: ({ session, onChange, selected, InputProps, TextFieldProps, localStorageKey, helperText, }: {

package/ui/CascadingMenu.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { MenuItem as JBMenuItem } from './Menu';
 import { PopupState } from 'material-ui-popup-state/hooks';
 declare function CascadingMenuChildren(props: {

package/ui/ColorPicker.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 export declare const PopoverPicker: ({ color, onChange, }: {
     color: string;
     onChange: (color: string) => void;

package/ui/Dialog.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { DialogProps } from '@mui/material';
 declare function JBrowseDialog(props: DialogProps & {
     title: string;

package/ui/Dialog.js

@@ -27,6 +27,7 @@ function DialogError({ error }) {
 function JBrowseDialog(props) {
     const { classes } = useStyles();
     const { title, children, onClose } = props;
+    const theme = (0, material_1.useTheme)();
     return (react_1.default.createElement(material_1.Dialog, { ...props },
         react_1.default.createElement(material_1.ScopedCssBaseline, null,
             react_1.default.createElement(material_1.DialogTitle, null,
@@ -37,6 +38,18 @@ function JBrowseDialog(props) {
                     } },
                     react_1.default.createElement(Close_1.default, null))) : null),
             react_1.default.createElement(material_1.Divider, null),
-            react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { FallbackComponent: DialogError }, children))));
+            react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { FallbackComponent: DialogError },
+                react_1.default.createElement(material_1.ThemeProvider, { theme: (0, material_1.createTheme)(theme, {
+                        components: {
+                            MuiInputBase: {
+                                styleOverrides: {
+                                    input: {
+                                        // xref https://github.com/GMOD/jbrowse-components/pull/3666
+                                        boxSizing: 'content-box!important',
+                                    },
+                                },
+                            },
+                        },
+                    }) }, children)))));
 }
 exports.default = (0, mobx_react_1.observer)(JBrowseDialog);

package/ui/DrawerWidget.d.ts

@@ -1,6 +1,5 @@
-/// <reference types="react" />
 import { SessionWithDrawerWidgets } from '../util/types';
-declare const DrawerWidget: ({ session }: {
+declare const DrawerWidget: ({ session, }: {
     session: SessionWithDrawerWidgets;
 }) => JSX.Element;
 export default DrawerWidget;

package/ui/DrawerWidget.js

@@ -59,7 +59,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         background: theme.palette.secondary.main,
     },
 }));
-const DrawerHeader = (0, mobx_react_1.observer)(({ session, setToolbarHeight, }) => {
+const DrawerHeader = (0, mobx_react_1.observer)(function ({ session, setToolbarHeight, }) {
     const { pluginManager } = (0, util_1.getEnv)(session);
     const { visibleWidget, activeWidgets, drawerPosition } = session;
     const { classes } = useStyles();
@@ -109,7 +109,7 @@ const DrawerHeader = (0, mobx_react_1.observer)(({ session, setToolbarHeight, })
                 setAnchorEl(null);
             } }, option))))));
 });
-const DrawerWidget = (0, mobx_react_1.observer)(({ session }) => {
+const DrawerWidget = (0, mobx_react_1.observer)(function ({ session, }) {
     const { visibleWidget } = session;
     const { pluginManager } = (0, util_1.getEnv)(session);
     const DrawerComponent = visibleWidget
@@ -125,6 +125,8 @@ const DrawerWidget = (0, mobx_react_1.observer)(({ session }) => {
     return (react_1.default.createElement(Drawer_1.default, { session: session },
         react_1.default.createElement(DrawerHeader, { session: session, setToolbarHeight: setToolbarHeight }),
         react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(LoadingEllipses_1.default, null) },
-            react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { FallbackComponent: ({ error }) => react_1.default.createElement(ErrorMessage_1.default, { error: error }) }, DrawerComponent ? (react_1.default.createElement(DrawerComponent, { model: visibleWidget, session: session, toolbarHeight: toolbarHeight })) : null))));
+            react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { FallbackComponent: ({ error }) => react_1.default.createElement(ErrorMessage_1.default, { error: error }) }, DrawerComponent ? (react_1.default.createElement(react_1.default.Fragment, null,
+                react_1.default.createElement(DrawerComponent, { model: visibleWidget, session: session, toolbarHeight: toolbarHeight }),
+                react_1.default.createElement("div", { style: { height: 300 } }))) : null))));
 });
 exports.default = DrawerWidget;

package/ui/DropDownMenu.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { MenuItem } from './Menu';
 declare function DropDownMenu({ menuTitle, session, menuItems, }: {
     menuTitle: string;

package/ui/ErrorMessage.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare const ErrorMessage: ({ error }: {
     error: unknown;
 }) => JSX.Element;

package/ui/FactoryResetDialog.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare const _default: ({ onClose, open, onFactoryReset, }: {
     onClose: Function;
     open: boolean;

package/ui/FatalErrorDialog.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare const FatalErrorDialog: ({ componentStack, error, onFactoryReset, resetButtonText, }: {
     componentStack?: string | undefined;
     error?: unknown;

package/ui/FileSelector/FileSelector.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { FileLocation, AbstractRootModel } from '../../util/types';
 declare const _default: (props: {
     location?: FileLocation | undefined;

package/ui/FileSelector/LocalFileChooser.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { FileLocation } from '../../util/types';
 declare function LocalFileChooser(props: {
     location?: FileLocation;

package/ui/FileSelector/UrlChooser.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { FileLocation } from '../../util/types';
 declare function UrlChooser(props: {
     location?: FileLocation;

package/ui/Icons.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { SvgIconProps } from '@mui/material/SvgIcon';
 export declare function ContentCopy(props: SvgIconProps): JSX.Element;
 export declare function Indexing(props: SvgIconProps): JSX.Element;

package/ui/LoadingEllipses.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { TypographyProps } from '@mui/material';
 interface Props extends TypographyProps {
     message?: string;

package/ui/Logo.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 type LogoVariant = 'color' | 'black' | 'white';
 interface LogoProps {
     variant?: LogoVariant;

package/ui/PrerenderedCanvas.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function PrerenderedCanvas(props: {
     width: number;
     height: number;

package/ui/ResizeBar.js

@@ -42,7 +42,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         position: 'absolute',
         height: '100%',
         pointerEvents: 'none',
-        background: theme.palette.divider,
+        background: theme.palette.action.disabled,
         width: 1,
     },
     hiddenTick: {

package/ui/ResizeHandle.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function ResizeHandle({ onDrag, vertical, flexbox, className: originalClassName, ...props }: {
     onDrag: (arg: number) => number | void;
     vertical?: boolean;

package/ui/ReturnToImportFormDialog.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function ReturnToImportFormDialog({ model, handleClose, }: {
     model: {
         clearView: Function;

package/ui/SanitizedHTML.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 export declare function isHTML(str: string): boolean;
 export default function SanitizedHTML({ html }: {
     html: string;

package/ui/SanitizedHTML.js

@@ -53,6 +53,12 @@ function isHTML(str) {
     return full.test(str);
 }
 exports.isHTML = isHTML;
+// note this is mocked during testing, see
+// packages/__mocks__/@jbrowse/core/ui/SanitizedHTML something about dompurify
+// behavior causes errors during tests, was seen in
+// products/jbrowse-web/src/tests/Connection.test.tsx test (can delete mock to
+// see)
+//
 function SanitizedHTML({ html }) {
     const value = isHTML(html) ? html : (0, escape_html_1.default)(html);
     if (!added) {

package/ui/Snackbar.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { AbstractSessionModel, NotificationLevel, SnackAction } from '../util';
 type SnackbarMessage = [string, NotificationLevel, SnackAction];

package/ui/Tooltip.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Feature } from '../util';
 declare const _default: ({ offsetX, offsetY, configuration, feature, timeout, }: {
     offsetX: number;

package/ui/ViewContainerTitle.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { IBaseViewModel } from '../pluggableElementTypes';
 declare const _default: ({ view, }: {
     view: IBaseViewModel;

package/ui/ViewLauncher.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { NotificationLevel, SnackAction, SessionWithDrawerWidgets } from '../util';
 import { MenuItem as JBMenuItem } from './Menu';
 type SnackbarMessage = [string, NotificationLevel, SnackAction];

package/ui/ViewMenu.d.ts

@@ -1,9 +1,8 @@
-/// <reference types="react" />
 import { SvgIconProps, IconButtonProps as IconButtonPropsType } from '@mui/material';
 import { IBaseViewModel } from '../pluggableElementTypes/models';
 declare const ViewMenu: ({ model, IconButtonProps, IconProps, }: {
     model: IBaseViewModel;
-    IconButtonProps?: IconButtonPropsType<"button", {}> | undefined;
+    IconButtonProps?: IconButtonPropsType | undefined;
     IconProps: SvgIconProps;
 }) => JSX.Element;
 export default ViewMenu;

package/ui/ViewPanel.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { AbstractViewModel, NotificationLevel, SessionWithDrawerWidgets, SnackAction } from '../util';
 import { MenuItem as JBMenuItem } from './Menu';
 type SnackbarMessage = [string, NotificationLevel, SnackAction];

package/ui/react-colorful.d.ts

@@ -13,5 +13,5 @@ declare function Ce(r: any): e.FunctionComponentElement<any>;
 declare function me(r: any): e.FunctionComponentElement<any>;
 declare function pe(r: any): e.FunctionComponentElement<any>;
 declare function X(e: any): void;
-import e from "react";
+import e from 'react';
 export { Ne as HexColorInput, J as HexColorPicker, oe as HslColorPicker, le as HslStringColorPicker, Z as HslaColorPicker, re as HslaStringColorPicker, de as HsvColorPicker, he as HsvStringColorPicker, se as HsvaColorPicker, ue as HsvaStringColorPicker, _e as RgbColorPicker, Ce as RgbStringColorPicker, me as RgbaColorPicker, pe as RgbaStringColorPicker, X as setNonce };

package/ui/theme.js

@@ -246,11 +246,6 @@ function createDefaultProps(theme) {
                     transitionDuration: 0,
                 },
             },
-            MuiMenuList: {
-                defaultProps: {
-                    dense: true,
-                },
-            },
             MuiMenuItem: {
                 defaultProps: {
                     dense: true,
@@ -266,8 +261,6 @@ function createDefaultProps(theme) {
                 styleOverrides: {
                     // the default link color uses theme.palette.primary.main which is
                     // very bad with dark mode+midnight primary
-                    //
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
                     root: ({ theme }) => ({
                         color: theme.palette.text.secondary,
                     }),
@@ -282,10 +275,7 @@ function createDefaultProps(theme) {
                     // keeps the forest-green checkbox by default but for darkmode, uses
                     // a text-like coloring to ensure contrast
                     // xref https://stackoverflow.com/a/72546130/2129219
-                    //
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                    root: (props) => {
-                        const { theme } = props;
+                    root: ({ theme }) => {
                         return theme.palette.mode === 'dark'
                             ? {
                                 color: theme.palette.text.secondary,
@@ -306,10 +296,7 @@ function createDefaultProps(theme) {
                     // keeps the forest-green checkbox by default but for darkmode, uses
                     // a text-like coloring to ensure contrast
                     // xref https://stackoverflow.com/a/72546130/2129219
-                    //
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                    root: (props) => {
-                        const { theme } = props;
+                    root: ({ theme }) => {
                         return theme.palette.mode === 'dark'
                             ? {
                                 color: theme.palette.text.secondary,
@@ -331,9 +318,7 @@ function createDefaultProps(theme) {
                     // a text-like coloring to ensure contrast
                     // xref https://stackoverflow.com/a/72546130/2129219
                     //
-                    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                    root: (props) => {
-                        const { theme } = props;
+                    root: ({ theme }) => {
                         return theme.palette.mode === 'dark'
                             ? {
                                 color: theme.palette.text.secondary,

package/util/index.d.ts

@@ -1,9 +1,10 @@
 /// <reference types="react" />
 import PluginManager from '../PluginManager';
-import { IAnyStateTreeNode, IStateTreeNode } from 'mobx-state-tree';
+import { IAnyStateTreeNode, IStateTreeNode, Instance } from 'mobx-state-tree';
 import { IReactionPublic, IReactionOptions } from 'mobx';
 import { Feature } from './simpleFeature';
 import { AssemblyManager, Region, TypeTestedByPredicate } from './types';
+import { Region as MUIRegion } from './types/mst';
 import { BaseBlock } from './blockTypes';
 export * from './types';
 export * from './aborting';
@@ -165,6 +166,7 @@ export declare function iterMap<T, U>(iter: Iterable<T>, func: (arg: T) => U, si
  * Otherwise, findLastIndex returns -1.
  */
 export declare function findLastIndex<T>(array: Array<T>, predicate: (value: T, index: number, obj: T[]) => boolean): number;
+export declare function findLast<T>(array: Array<T>, predicate: (value: T, index: number, obj: T[]) => boolean): T | undefined;
 /**
  * makes a mobx reaction with the given functions, that calls actions on the
  * model for each stage of execution, and to abort the reaction function when
@@ -183,7 +185,7 @@ export declare function findLastIndex<T>(array: Array<T>, predicate: (value: T,
  * @param errorFunction -
  */
 export declare function makeAbortableReaction<T, U, V>(self: T, dataFunction: (arg: T) => U, asyncReactionFunction: (arg: U | undefined, signal: AbortSignal, model: T, handle: IReactionPublic) => Promise<V>, reactionOptions: IReactionOptions, startedFunction: (aborter: AbortController) => void, successFunction: (arg: V) => void, errorFunction: (err: unknown) => void): void;
-export declare function renameRegionIfNeeded(refNameMap: Record<string, string>, region: Region): Region & {
+export declare function renameRegionIfNeeded(refNameMap: Record<string, string>, region: Region | Instance<typeof MUIRegion>): Region & {
     originalRefName?: string;
 };
 export declare function renameRegionsIfNeeded<ARGTYPE extends {

package/util/index.js

@@ -17,8 +17,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.supportedIndexingAdapters = exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.blobToDataURL = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.shorten = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLastIndex = exports.iterMap = exports.bpSpanPx = exports.featureSpanPx = exports.cartesianToPolar = exports.polarToCartesian = exports.degToRad = exports.radToDeg = exports.bpToPx = exports.clamp = exports.compareLocStrings = exports.compareLocs = exports.parseLocString = exports.parseLocStringOneBased = exports.assembleLocStringFast = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useWidthSetter = exports.useDebounce = exports.inProduction = exports.inDevelopment = void 0;
-exports.isFeature = exports.SimpleFeature = exports.avg = exports.sum = exports.min = exports.max = exports.localStorageSetItem = exports.localStorageGetItem = exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = void 0;
+exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.blobToDataURL = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.shorten = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLast = exports.findLastIndex = exports.iterMap = exports.bpSpanPx = exports.featureSpanPx = exports.cartesianToPolar = exports.polarToCartesian = exports.degToRad = exports.radToDeg = exports.bpToPx = exports.clamp = exports.compareLocStrings = exports.compareLocs = exports.parseLocString = exports.parseLocStringOneBased = exports.assembleLocStringFast = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useWidthSetter = exports.useDebounce = exports.inProduction = exports.inDevelopment = void 0;
+exports.isFeature = exports.SimpleFeature = exports.avg = exports.sum = exports.min = exports.max = exports.localStorageSetItem = exports.localStorageGetItem = exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = exports.supportedIndexingAdapters = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
@@ -534,6 +534,16 @@ function findLastIndex(array, predicate) {
     return -1;
 }
 exports.findLastIndex = findLastIndex;
+function findLast(array, predicate) {
+    let l = array.length;
+    while (l--) {
+        if (predicate(array[l], l, array)) {
+            return array[l];
+        }
+    }
+    return undefined;
+}
+exports.findLast = findLast;
 /**
  * makes a mobx reaction with the given functions, that calls actions on the
  * model for each stage of execution, and to abort the reaction function when
@@ -613,8 +623,7 @@ function renameRegionIfNeeded(refNameMap, region) {
     if (region && (refNameMap === null || refNameMap === void 0 ? void 0 : refNameMap[region.refName])) {
         // clone the region so we don't modify it
         region = (0, mobx_state_tree_1.isStateTreeNode)(region)
-            ? // @ts-expect-error
-                { ...(0, mobx_state_tree_1.getSnapshot)(region) }
+            ? { ...(0, mobx_state_tree_1.getSnapshot)(region) }
             : { ...region };
         // modify it directly in the container
         const newRef = refNameMap[region.refName];

package/util/layouts/PrecomputedMultiLayout.d.ts

@@ -1,4 +1,4 @@
 export default class PrecomputedMultiLayout extends MultiLayout<any, any> {
     constructor(json: any);
 }
-import MultiLayout from "./MultiLayout";
+import MultiLayout from './MultiLayout';

package/util/stats.d.ts

@@ -1,7 +1,7 @@
 import { Observable } from 'rxjs';
 import { NoAssemblyRegion } from './types';
 import { Feature } from './simpleFeature';
-export interface UnrectifiedFeatureStats {
+export interface UnrectifiedQuantitativeStats {
     scoreMin: number;
     scoreMax: number;
     scoreSum: number;
@@ -9,7 +9,7 @@ export interface UnrectifiedFeatureStats {
     featureCount: number;
     basesCovered: number;
 }
-export interface FeatureStats extends UnrectifiedFeatureStats {
+export interface QuantitativeStats extends UnrectifiedQuantitativeStats {
     featureDensity: number;
     scoreMean: number;
     scoreStdDev: number;
@@ -31,7 +31,7 @@ export declare function calcStdFromSums(sum: number, sumSquares: number, n: numb
  * @returns - a summary stats object with
  * scoreMean, scoreStdDev, and featureDensity added
  */
-export declare function rectifyStats(s: UnrectifiedFeatureStats): FeatureStats;
+export declare function rectifyStats(s: UnrectifiedQuantitativeStats): QuantitativeStats;
 /**
  * calculates per-base scores for variable width features over a region
  *
@@ -47,5 +47,5 @@ export declare function calcPerBaseStats(region: NoAssemblyRegion, features: Fea
  * @param features - array of features which are possibly summary features
  * @returns - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
  */
-export declare function scoresToStats(region: NoAssemblyRegion, feats: Observable<Feature>): Promise<FeatureStats>;
-export declare function blankStats(): FeatureStats;
+export declare function scoresToStats(region: NoAssemblyRegion, feats: Observable<Feature>): Promise<QuantitativeStats>;
+export declare function blankStats(): QuantitativeStats;

package/util/types/index.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { Instance, SnapshotIn, IAnyStateTreeNode, IStateTreeNode, IType } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '../../configuration/configurationSchema';
+import { AnyConfigurationModel } from '../../configuration';
 import assemblyManager from '../../assemblyManager';
 import TextSearchManager from '../../TextSearch/TextSearchManager';
 import { MenuItem } from '../../ui';
@@ -65,6 +65,7 @@ export interface AbstractSessionModel extends AbstractViewContainer {
         name: string;
         connectionId: string;
         tracks: AnyConfigurationModel[];
+        configuration: AnyConfigurationModel;
     }[];
     makeConnection?: Function;
     adminMode?: boolean;
@@ -144,6 +145,7 @@ export interface AbstractViewModel {
 export declare function isViewModel(thing: unknown): thing is AbstractViewModel;
 export interface AbstractTrackModel {
     displays: AbstractDisplayModel[];
+    configuration: AnyConfigurationModel;
 }
 export declare function isTrackModel(thing: unknown): thing is AbstractTrackModel;
 export interface AbstractDisplayModel {

package/util/types/mst.d.ts

@@ -99,7 +99,17 @@ export declare const FileLocation: import("mobx-state-tree").ISnapshotProcessor<
 }> | import("mobx-state-tree").ModelSnapshotType<{
     locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
     localPath: import("mobx-state-tree").ISimpleType<string>;
-}>, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+}>, import("mobx-state-tree").ModelInstanceType<{
+    locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+    name: import("mobx-state-tree").ISimpleType<string>;
+    blobId: import("mobx-state-tree").ISimpleType<string>;
+}, {}> | import("mobx-state-tree").ModelInstanceType<{
+    locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+    localPath: import("mobx-state-tree").ISimpleType<string>;
+}, {}> | ({
+    locationType: "UriLocation";
+    uri: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
     locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
     uri: import("mobx-state-tree").ISimpleType<string>;
     baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -108,11 +118,4 @@ export declare const FileLocation: import("mobx-state-tree").ISnapshotProcessor<
         internetAccountType: import("mobx-state-tree").ISimpleType<string>;
         authInfo: import("mobx-state-tree").IType<any, any, any>;
     }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}>> | import("mobx-state-tree").ModelInstanceType<{
-    locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-    name: import("mobx-state-tree").ISimpleType<string>;
-    blobId: import("mobx-state-tree").ISimpleType<string>;
-}, {}> | import("mobx-state-tree").ModelInstanceType<{
-    locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-    localPath: import("mobx-state-tree").ISimpleType<string>;
-}, {}>>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/BaseFeatureWidget/SequenceBox.d.ts

@@ -1,29 +0,0 @@
-/// <reference types="react" />
-import { Feat } from './util';
-export declare function GeneCDS({ cds, sequence }: {
-    cds: Feat[];
-    sequence: string;
-}): JSX.Element;
-export declare function GeneProtein({ cds, sequence, codonTable, }: {
-    cds: Feat[];
-    sequence: string;
-    codonTable: {
-        [key: string]: string;
-    };
-}): JSX.Element;
-export declare function GenecDNA({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, intronBp, }: {
-    utr: Feat[];
-    cds: Feat[];
-    exons: Feat[];
-    sequence: string;
-    upstream?: string;
-    downstream?: string;
-    includeIntrons?: boolean;
-    collapseIntron?: boolean;
-    intronBp: number;
-}): JSX.Element;
-export declare function Genomic({ sequence, upstream, downstream, }: {
-    sequence: string;
-    upstream?: string;
-    downstream?: string;
-}): JSX.Element;

package/BaseFeatureWidget/SequenceBox.js

@@ -1,63 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.Genomic = exports.GenecDNA = exports.GeneProtein = exports.GeneCDS = void 0;
-const react_1 = __importDefault(require("react"));
-const util_1 = require("./util");
-// note that these are currently put into the style section instead of being
-// defined in classes to aid copy and paste to an external document e.g. word
-const proteinColor = 'rgb(220,160,220)';
-const intronColor = undefined;
-const cdsColor = 'rgb(220,220,180)';
-const updownstreamColor = 'rgba(250,200,200)';
-const utrColor = 'rgb(200,240,240)';
-const genomeColor = 'rgb(200,280,200)';
-function GeneCDS({ cds, sequence }) {
-    return react_1.default.createElement("span", { style: { background: cdsColor } }, (0, util_1.stitch)(cds, sequence));
-}
-exports.GeneCDS = GeneCDS;
-function GeneProtein({ cds, sequence, codonTable, }) {
-    const str = (0, util_1.stitch)(cds, sequence);
-    let protein = '';
-    for (let i = 0; i < str.length; i += 3) {
-        // use & symbol for undefined codon, or partial slice
-        protein += codonTable[str.slice(i, i + 3)] || '&';
-    }
-    return react_1.default.createElement("span", { style: { background: proteinColor } }, protein);
-}
-exports.GeneProtein = GeneProtein;
-function GenecDNA({ utr, cds, exons, sequence, upstream, downstream, includeIntrons, collapseIntron, intronBp, }) {
-    const chunks = (cds.length ? [...cds, ...utr].sort((a, b) => a.start - b.start) : exons).filter(f => f.start !== f.end);
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        upstream ? (react_1.default.createElement("span", { style: {
-                background: updownstreamColor,
-            } }, upstream)) : null,
-        chunks.map((chunk, idx) => {
-            var _a;
-            const intron = sequence.slice(chunk.end, (_a = chunks[idx + 1]) === null || _a === void 0 ? void 0 : _a.start);
-            return (react_1.default.createElement(react_1.default.Fragment, { key: JSON.stringify(chunk) },
-                react_1.default.createElement("span", { style: {
-                        background: chunk.type === 'CDS' ? cdsColor : utrColor,
-                    } }, sequence.slice(chunk.start, chunk.end)),
-                includeIntrons && idx < chunks.length - 1 ? (react_1.default.createElement("span", { style: { background: intronColor } }, collapseIntron && intron.length > intronBp * 2
-                    ? `${intron.slice(0, intronBp)}...${intron.slice(-intronBp)}`
-                    : intron)) : null));
-        }),
-        downstream ? (react_1.default.createElement("span", { style: { background: updownstreamColor } }, downstream)) : null));
-}
-exports.GenecDNA = GenecDNA;
-function Genomic({ sequence, upstream, downstream, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        upstream ? (react_1.default.createElement("span", { style: {
-                background: updownstreamColor,
-            } }, upstream)) : null,
-        react_1.default.createElement("span", { style: {
-                background: genomeColor,
-            } }, sequence),
-        downstream ? (react_1.default.createElement("span", { style: {
-                background: updownstreamColor,
-            } }, downstream)) : null));
-}
-exports.Genomic = Genomic;

package/BaseFeatureWidget/SequenceFeatureDetails.d.ts

@@ -1,3 +0,0 @@
-/// <reference types="react" />
-import { BaseProps } from './types';
-export default function SequenceFeatureDetails({ model, feature }: BaseProps): JSX.Element | null;