@jbrowse/core 2.4.2 → 2.6.0

package/ui/Tooltip.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { Feature } from '../util';
 declare const _default: ({ offsetX, offsetY, configuration, feature, timeout, }: {
     offsetX: number;
@@ -10,5 +10,5 @@ declare const _default: ({ offsetX, offsetY, configuration, feature, timeout, }:
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>;
     feature?: Feature | undefined;
     timeout?: number | undefined;
-}) => JSX.Element | null;
+}) => React.JSX.Element | null;
 export default _default;

package/ui/index.d.ts

@@ -1,6 +1,5 @@
 export * from './theme';
 export { LogoFull, Logomark } from './Logo';
-export { default as App } from './App';
 export { default as AssemblySelector } from './AssemblySelector';
 export { default as CascadingMenu } from './CascadingMenu';
 export { default as Dialog } from './Dialog';

package/ui/index.js

@@ -17,13 +17,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SanitizedHTML = exports.ResizeHandle = exports.ReturnToImportFormDialog = exports.Tooltip = exports.PrerenderedCanvas = exports.Menu = exports.LoadingEllipses = exports.FileSelector = exports.FatalErrorDialog = exports.FactoryResetDialog = exports.ErrorMessage = exports.EditableTypography = exports.Dialog = exports.CascadingMenu = exports.AssemblySelector = exports.App = exports.Logomark = exports.LogoFull = void 0;
+exports.SanitizedHTML = exports.ResizeHandle = exports.ReturnToImportFormDialog = exports.Tooltip = exports.PrerenderedCanvas = exports.Menu = exports.LoadingEllipses = exports.FileSelector = exports.FatalErrorDialog = exports.FactoryResetDialog = exports.ErrorMessage = exports.EditableTypography = exports.Dialog = exports.CascadingMenu = exports.AssemblySelector = exports.Logomark = exports.LogoFull = void 0;
 __exportStar(require("./theme"), exports);
 var Logo_1 = require("./Logo");
 Object.defineProperty(exports, "LogoFull", { enumerable: true, get: function () { return Logo_1.LogoFull; } });
 Object.defineProperty(exports, "Logomark", { enumerable: true, get: function () { return Logo_1.Logomark; } });
-var App_1 = require("./App");
-Object.defineProperty(exports, "App", { enumerable: true, get: function () { return __importDefault(App_1).default; } });
 var AssemblySelector_1 = require("./AssemblySelector");
 Object.defineProperty(exports, "AssemblySelector", { enumerable: true, get: function () { return __importDefault(AssemblySelector_1).default; } });
 var CascadingMenu_1 = require("./CascadingMenu");

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/Base1DUtils.js

@@ -109,7 +109,8 @@ function pxToBp(self, px) {
         }
     }
     if (bp >= bpSoFar && displayedRegions.length > 0) {
-        const r = displayedRegions[displayedRegions.length - 1];
+        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+        const r = displayedRegions.at(-1);
         const len = r.end - r.start;
         const offset = bp - bpSoFar + len;
         const snap = (0, mobx_state_tree_1.getSnapshot)(r);

package/util/QuickLRU.d.ts

@@ -27,6 +27,6 @@ export default class QuickLRU extends Map<any, any> {
     entriesDescending(): Generator<any[], void, unknown>;
     entriesAscending(): Generator<any[], void, unknown>;
     entries(): Generator<any[], void, unknown>;
-    forEach(callbackFunction: any, thisArgument?: QuickLRU): void;
+    forEach(callbackFunction: any, thisArgument?: this): void;
     [Symbol.iterator](): Generator<any[], void, unknown>;
 }

package/util/blockTypes.js

@@ -7,7 +7,7 @@ class BlockSet {
     }
     push(block) {
         if (block instanceof ElidedBlock && this.blocks.length > 0) {
-            const lastBlock = this.blocks[this.blocks.length - 1];
+            const lastBlock = this.blocks.at(-1);
             if (lastBlock instanceof ElidedBlock) {
                 lastBlock.push(block);
                 return;

package/util/formatFastaStrings.js

@@ -9,7 +9,7 @@ exports.formatSeqFasta = exports.formatFastaLines = void 0;
  * @returns formatted sequence string
  */
 function formatFastaLines(seqString) {
-    return seqString.replace(/(.{1,80})/g, '$1\n').trimEnd();
+    return seqString.replaceAll(/(.{1,80})/g, '$1\n').trimEnd();
 }
 exports.formatFastaLines = formatFastaLines;
 /**

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 {
@@ -354,4 +356,18 @@ export declare function max(arr: number[], init?: number): number;
 export declare function min(arr: number[], init?: number): number;
 export declare function sum(arr: number[]): number;
 export declare function avg(arr: number[]): number;
+export declare function groupBy<T>(array: T[], predicate: (v: T) => string): {
+    [key: string]: T[];
+};
+export declare function notEmpty<T>(value: T | null | undefined): value is T;
+export declare function mergeIntervals<T extends {
+    start: number;
+    end: number;
+}>(intervals: T[], w?: number): T[];
+interface BasicFeature {
+    end: number;
+    start: number;
+    refName: string;
+}
+export declare function gatherOverlaps(regions: BasicFeature[]): BasicFeature[];
 export { default as SimpleFeature, type Feature, type SimpleFeatureSerialized, isFeature, } from './simpleFeature';

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.gatherOverlaps = exports.mergeIntervals = exports.notEmpty = exports.groupBy = 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"));
@@ -316,8 +316,8 @@ function parseLocStringOneBased(locString, isValidRefName) {
                     return {
                         assemblyName,
                         refName: prefix,
-                        start: +start.replace(/,/g, ''),
-                        end: +end.replace(/,/g, ''),
+                        start: +start.replaceAll(',', ''),
+                        end: +end.replaceAll(',', ''),
                         reversed,
                     };
                 }
@@ -330,15 +330,15 @@ function parseLocStringOneBased(locString, isValidRefName) {
                         return {
                             assemblyName,
                             refName: prefix,
-                            start: +start.replace(/,/g, ''),
+                            start: +start.replaceAll(',', ''),
                             reversed,
                         };
                     }
                     return {
                         assemblyName,
                         refName: prefix,
-                        start: +start.replace(/,/g, ''),
-                        end: +start.replace(/,/g, ''),
+                        start: +start.replaceAll(',', ''),
+                        end: +start.replaceAll(',', ''),
                         reversed,
                     };
                 }
@@ -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];
@@ -716,7 +725,7 @@ exports.complement = (() => {
         G: 'C',
     };
     return (seqString) => {
-        return seqString.replace(complementRegex, m => complementTable[m] || '');
+        return seqString.replaceAll(complementRegex, m => complementTable[m] || '');
     };
 })();
 function blobToDataURL(blob) {
@@ -995,7 +1004,7 @@ function getStr(obj) {
 exports.getStr = getStr;
 // tries to measure grid width without HTML tags included
 function coarseStripHTML(s) {
-    return s.replace(/(<([^>]+)>)/gi, '');
+    return s.replaceAll(/(<([^>]+)>)/gi, '');
 }
 // heuristic measurement for a column of a @mui/x-data-grid, pass in values from a column
 function measureGridWidth(elements, args) {
@@ -1051,6 +1060,63 @@ function avg(arr) {
     return sum(arr) / arr.length;
 }
 exports.avg = avg;
+function groupBy(array, predicate) {
+    var _a;
+    const result = {};
+    for (const value of array) {
+        const entry = (result[_a = predicate(value)] || (result[_a] = []));
+        entry.push(value);
+    }
+    return result;
+}
+exports.groupBy = groupBy;
+function notEmpty(value) {
+    return value !== null && value !== undefined;
+}
+exports.notEmpty = notEmpty;
+function mergeIntervals(intervals, w = 5000) {
+    // test if there are at least 2 intervals
+    if (intervals.length <= 1) {
+        return intervals;
+    }
+    const stack = [];
+    let top = null;
+    // sort the intervals based on their start values
+    intervals = intervals.sort((a, b) => a.start - b.start);
+    // push the 1st interval into the stack
+    stack.push(intervals[0]);
+    // start from the next interval and merge if needed
+    for (let i = 1; i < intervals.length; i++) {
+        // get the top element
+        // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+        top = stack.at(-1);
+        // if the current interval doesn't overlap with the
+        // stack top element, push it to the stack
+        if (top.end + w < intervals[i].start - w) {
+            stack.push(intervals[i]);
+        }
+        // otherwise update the end value of the top element
+        // if end of current interval is higher
+        else if (top.end < intervals[i].end) {
+            top.end = Math.max(top.end, intervals[i].end);
+            stack.pop();
+            stack.push(top);
+        }
+    }
+    return stack;
+}
+exports.mergeIntervals = mergeIntervals;
+function gatherOverlaps(regions) {
+    const memo = {};
+    for (const x of regions) {
+        if (!memo[x.refName]) {
+            memo[x.refName] = [];
+        }
+        memo[x.refName].push(x);
+    }
+    return Object.values(memo).flatMap(group => mergeIntervals(group.sort((a, b) => a.start - b.start)));
+}
+exports.gatherOverlaps = gatherOverlaps;
 var simpleFeature_1 = require("./simpleFeature");
 Object.defineProperty(exports, "SimpleFeature", { enumerable: true, get: function () { return __importDefault(simpleFeature_1).default; } });
 Object.defineProperty(exports, "isFeature", { enumerable: true, get: function () { return simpleFeature_1.isFeature; } });

package/util/io/index.js

@@ -101,7 +101,7 @@ function getInternetAccount(location, pluginManager) {
             configuration: location.internetAccountPreAuthorization.authInfo.configuration,
         });
     }
-    return;
+    return undefined;
 }
 // This fetch throws a special error if the response is "401" and includes a
 // "WWW-Authenticate: Basic" header. This is so downstream code can retry if

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/mst-reflection.js

@@ -58,8 +58,7 @@ exports.getUnionSubTypes = getUnionSubTypes;
  * get the type of one of the properties of the given MST model type
  */
 function getPropertyType(type, propertyName) {
-    const propertyType = type.properties[propertyName];
-    return propertyType;
+    return type.properties[propertyName];
 }
 exports.getPropertyType = getPropertyType;
 /**

package/util/offscreenCanvasUtils.d.ts

@@ -10,7 +10,7 @@ export declare function renderToAbstractCanvas(width: number, height: number, op
 }, cb: (ctx: CanvasRenderingContext2D) => RendererRet): Promise<{
     canvasRecordedData: any;
 } | {
-    reactElement: JSX.Element;
+    reactElement: React.JSX.Element;
 } | {
     imageData: any;
 }>;
@@ -24,5 +24,5 @@ export declare function ReactRendering({ rendering, }: {
         reactElement?: React.ReactNode;
         html?: string;
     };
-}): JSX.Element;
+}): React.JSX.Element;
 export {};

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';
@@ -63,8 +63,8 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     sessionConnections?: AnyConfigurationModel[];
     connectionInstances?: {
         name: string;
-        connectionId: string;
         tracks: AnyConfigurationModel[];
+        configuration: AnyConfigurationModel;
     }[];
     makeConnection?: Function;
     adminMode?: boolean;
@@ -97,6 +97,7 @@ export interface SessionWithWidgets extends AbstractSessionModel {
     minimized: boolean;
     visibleWidget?: Widget;
     widgets: Map<string, Widget>;
+    hideAllWidgets: () => void;
     activeWidgets: Map<string, Widget>;
     addWidget(typeName: string, id: string, initialState?: Record<string, unknown>, configuration?: {
         type: string;
@@ -114,9 +115,13 @@ export interface SessionWithDrawerWidgets extends SessionWithWidgets {
 }
 export declare function isSessionModelWithWidgets(thing: unknown): thing is SessionWithWidgets;
 interface SessionWithConnections {
-    addConnectionConf: (arg: AnyConfigurationModel) => void;
+    makeConnection: (arg: AnyConfigurationModel) => void;
 }
 export declare function isSessionModelWithConnections(thing: unknown): thing is SessionWithConnections;
+interface SessionWithConnectionEditing {
+    addConnectionConf: (arg: AnyConfigurationModel) => void;
+}
+export declare function isSessionModelWithConnectionEditing(thing: unknown): thing is SessionWithConnectionEditing;
 export interface SessionWithSessionPlugins extends AbstractSessionModel {
     sessionPlugins: JBrowsePlugin[];
     addSessionPlugin: Function;
@@ -144,6 +149,7 @@ 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/index.js

@@ -14,7 +14,7 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isRetryException = exports.isAuthNeededException = exports.RetryError = exports.AuthNeededError = exports.isUriLocation = exports.isAbstractMenuManager = exports.isRootModelWithInternetAccounts = exports.isAppRootModel = exports.isTrackViewModel = exports.isDisplayModel = exports.isTrackModel = exports.isViewModel = exports.isSelectionContainer = exports.isSessionWithSessionPlugins = exports.isSessionModelWithConnections = exports.isSessionModelWithWidgets = exports.isSessionWithAddTracks = exports.isSessionModelWithConfigEditing = exports.isSessionModel = exports.isViewContainer = void 0;
+exports.isRetryException = exports.isAuthNeededException = exports.RetryError = exports.AuthNeededError = exports.isUriLocation = exports.isAbstractMenuManager = exports.isRootModelWithInternetAccounts = exports.isAppRootModel = exports.isTrackViewModel = exports.isDisplayModel = exports.isTrackModel = exports.isViewModel = exports.isSelectionContainer = exports.isSessionWithSessionPlugins = exports.isSessionModelWithConnectionEditing = exports.isSessionModelWithConnections = exports.isSessionModelWithWidgets = exports.isSessionWithAddTracks = exports.isSessionModelWithConfigEditing = exports.isSessionModel = exports.isViewContainer = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 __exportStar(require("./util"), exports);
 function isViewContainer(thing) {
@@ -46,9 +46,13 @@ function isSessionModelWithWidgets(thing) {
 }
 exports.isSessionModelWithWidgets = isSessionModelWithWidgets;
 function isSessionModelWithConnections(thing) {
-    return isSessionModel(thing) && 'addConnectionConf' in thing;
+    return isSessionModel(thing) && 'makeConnection' in thing;
 }
 exports.isSessionModelWithConnections = isSessionModelWithConnections;
+function isSessionModelWithConnectionEditing(thing) {
+    return isSessionModel(thing) && 'addConnectionConf' in thing;
+}
+exports.isSessionModelWithConnectionEditing = isSessionModelWithConnectionEditing;
 function isSessionWithSessionPlugins(thing) {
     return isSessionModel(thing) && 'sessionPlugins' in thing;
 }

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/util/types/util.d.ts

@@ -1,5 +1,4 @@
 import React from 'react';
-import { IAnyModelType, Instance } from 'mobx-state-tree';
 import PluginManager from '../../PluginManager';
 /**
  * Obtain the return type of a constructor function type.
@@ -12,5 +11,3 @@ export type ClassReturnedBy<FACT extends (pm: PluginManager) => any> = InstanceT
 export type AnyReactComponentType = React.ComponentType<any>;
 /** get the type that a predicate asserts */
 export type TypeTestedByPredicate<PREDICATE extends (thing: any) => boolean> = PREDICATE extends (thing: any) => thing is infer TYPE ? TYPE : never;
-/** get the type for an instance of an MST model in a PM factory function */
-export type InstanceOfModelReturnedBy<FACTORY extends (pm: PluginManager) => IAnyModelType> = Instance<ReturnType<FACTORY>>;

package/BaseFeatureWidget/BaseFeatureDetail.d.ts

@@ -1,62 +0,0 @@
-import React from 'react';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { BaseCardProps, BaseProps } from './types';
-import { SimpleFeatureSerializedNoId } from '../util/simpleFeature';
-export declare const useStyles: (params: void, styleOverrides?: {
-    props: any;
-    ownerState?: Record<string, unknown> | undefined;
-} | undefined) => {
-    classes: Record<"expansionPanelDetails" | "expandIcon" | "field" | "fieldDescription" | "fieldName" | "fieldValue" | "fieldSubvalue", string>;
-    theme: import("@mui/material").Theme;
-    css: import("tss-react").Css;
-    cx: import("tss-react").Cx;
-};
-export declare function BaseCard({ children, title, defaultExpanded, }: BaseCardProps): JSX.Element;
-export declare const FieldName: ({ description, name, width, prefix, }: {
-    description?: React.ReactNode;
-    name: string;
-    prefix?: string[] | undefined;
-    width?: number | undefined;
-}) => JSX.Element;
-export declare const BasicValue: ({ value }: {
-    value: string | React.ReactNode;
-}) => JSX.Element;
-export declare function SimpleValue({ name, value, description, prefix, width, }: {
-    description?: React.ReactNode;
-    name: string;
-    value: any;
-    prefix?: string[];
-    width?: number;
-}): JSX.Element | null;
-export declare const BaseCoreDetails: (props: BaseProps) => JSX.Element;
-export declare function UriLink({ value, }: {
-    value: {
-        uri: string;
-        baseUri?: string;
-    };
-}): JSX.Element;
-export declare function Attributes(props: {
-    attributes: Record<string, any>;
-    omit?: string[];
-    omitSingleLevel?: string[];
-    formatter?: (val: unknown, key: string) => React.ReactNode;
-    descriptions?: Record<string, React.ReactNode>;
-    prefix?: string[];
-    hideUris?: boolean;
-}): JSX.Element;
-export declare const BaseAttributes: (props: BaseProps) => JSX.Element;
-export interface BaseInputProps extends BaseCardProps {
-    omit?: string[];
-    model: any;
-    descriptions?: Record<string, React.ReactNode>;
-    formatter?: (val: unknown, key: string) => React.ReactNode;
-}
-export declare function FeatureDetails(props: {
-    model: IAnyStateTreeNode;
-    feature: SimpleFeatureSerializedNoId;
-    depth?: number;
-    omit?: string[];
-    formatter?: (val: unknown, key: string) => React.ReactNode;
-}): JSX.Element;
-declare const _default: ({ model }: BaseInputProps) => JSX.Element | null;
-export default _default;