@apollo-annotation/jbrowse-plugin-apollo 0.3.10 → 0.3.12

package/dist/makeDisplayComponent.d.ts

@@ -0,0 +1,9 @@
+import type { LinearApolloDisplay as LinearApolloDisplayI } from './LinearApolloDisplay/stateModel';
+import type { LinearApolloSixFrameDisplay as LinearApolloSixFrameDisplayI } from './LinearApolloSixFrameDisplay/stateModel';
+export declare const LinearApolloDisplayComponent: ({ model, ...other }: {
+    model: LinearApolloDisplayI;
+}) => import("react/jsx-runtime").JSX.Element;
+export declare const LinearApolloSixFrameDisplayComponent: ({ model, ...other }: {
+    model: LinearApolloSixFrameDisplayI;
+}) => import("react/jsx-runtime").JSX.Element;
+//# sourceMappingURL=makeDisplayComponent.d.ts.map

package/dist/makeDisplayComponent.d.ts.map

@@ -0,0 +1 @@
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package/dist/menus/index.d.ts

@@ -0,0 +1,2 @@
+export { addTopLevelMenus } from './topLevelMenu';
+//# sourceMappingURL=index.d.ts.map

package/dist/menus/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/menus/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAA"}

package/dist/menus/topLevelMenu.d.ts

@@ -0,0 +1,3 @@
+import type { AbstractMenuManager } from '@jbrowse/core/util';
+export declare function addTopLevelMenus(rootModel: AbstractMenuManager): void;
+//# sourceMappingURL=topLevelMenu.d.ts.map

package/dist/menus/topLevelMenu.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"topLevelMenu.d.ts","sourceRoot":"","sources":["../../src/menus/topLevelMenu.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,mBAAmB,EAEpB,MAAM,oBAAoB,CAAA;AAkB3B,wBAAgB,gBAAgB,CAAC,SAAS,EAAE,mBAAmB,QAsH9D"}

package/dist/menus/topLevelMenuAdmin.d.ts

@@ -0,0 +1,3 @@
+import type { AbstractMenuManager } from '@jbrowse/core/util';
+export declare function addTopLevelAdminMenus(rootModel: AbstractMenuManager): void;
+//# sourceMappingURL=topLevelMenuAdmin.d.ts.map

package/dist/menus/topLevelMenuAdmin.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"topLevelMenuAdmin.d.ts","sourceRoot":"","sources":["../../src/menus/topLevelMenuAdmin.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,mBAAmB,EAEpB,MAAM,oBAAoB,CAAA;AAmB3B,wBAAgB,qBAAqB,CAAC,SAAS,EAAE,mBAAmB,QAmInE"}

package/dist/session/index.d.ts

@@ -0,0 +1,2 @@
+export * from './session';
+//# sourceMappingURL=index.d.ts.map

package/dist/session/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/session/index.ts"],"names":[],"mappings":"AAAA,cAAc,WAAW,CAAA"}

package/dist/types.d.ts

@@ -0,0 +1,10 @@
+import type { BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes';
+import type { AppRootModel } from '@jbrowse/core/util';
+import type { ApolloInternetAccountModel } from './ApolloInternetAccount/model';
+import type { ApolloSessionModel } from './session';
+export interface ApolloRootModel extends Omit<AppRootModel, 'session'> {
+    session: ApolloSessionModel;
+    internetAccounts: (BaseInternetAccountModel | ApolloInternetAccountModel)[];
+}
+export declare function isApolloInternetAccount(internetAccount: BaseInternetAccountModel | ApolloInternetAccountModel): internetAccount is ApolloInternetAccountModel;
+//# sourceMappingURL=types.d.ts.map

package/dist/types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,qCAAqC,CAAA;AACnF,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AAEtD,OAAO,KAAK,EAAE,0BAA0B,EAAE,MAAM,+BAA+B,CAAA;AAC/E,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAEnD,MAAM,WAAW,eAAgB,SAAQ,IAAI,CAAC,YAAY,EAAE,SAAS,CAAC;IACpE,OAAO,EAAE,kBAAkB,CAAA;IAC3B,gBAAgB,EAAE,CAAC,wBAAwB,GAAG,0BAA0B,CAAC,EAAE,CAAA;CAC5E;AAED,wBAAgB,uBAAuB,CACrC,eAAe,EAAE,wBAAwB,GAAG,0BAA0B,GACrE,eAAe,IAAI,0BAA0B,CAE/C"}

package/dist/util/annotationFeatureUtils.d.ts

@@ -0,0 +1,7 @@
+import type { AnnotationFeature } from '@apollo-annotation/mst';
+export declare function getFeatureName(feature: AnnotationFeature): string;
+export declare function getFeatureId(feature: AnnotationFeature): string;
+export declare function getFeatureNameOrId(feature: AnnotationFeature): string;
+export declare function getStrand(strand: number | undefined): "" | "Forward" | "Reverse";
+export declare function getRelatedFeatures(feature: AnnotationFeature, bp: number, includeSiblings?: boolean): AnnotationFeature[];
+//# sourceMappingURL=annotationFeatureUtils.d.ts.map

package/dist/util/annotationFeatureUtils.d.ts.map

@@ -0,0 +1 @@
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package/dist/util/copyToClipboard.d.ts

@@ -0,0 +1,2 @@
+export declare function copyToClipboard(element: HTMLElement): Promise<void>;
+//# sourceMappingURL=copyToClipboard.d.ts.map

package/dist/util/copyToClipboard.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"copyToClipboard.d.ts","sourceRoot":"","sources":["../../src/util/copyToClipboard.ts"],"names":[],"mappings":"AAAA,wBAAsB,eAAe,CAAC,OAAO,EAAE,WAAW,iBAoBzD"}

package/dist/util/glyphUtils.d.ts

@@ -0,0 +1,31 @@
+import type { AnnotationFeature, TranscriptPartCoding } from '@apollo-annotation/mst';
+import type { MenuItem } from '@jbrowse/core/ui';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { LinearApolloDisplayMouseEvents } from '../LinearApolloDisplay/stateModel/mouseEvents';
+import type { LinearApolloSixFrameDisplayMouseEvents } from '../LinearApolloSixFrameDisplay/stateModel/mouseEvents';
+import type { ApolloSessionModel } from '../session';
+import type { MousePositionWithFeature } from '.';
+type NavLocation = Parameters<LinearGenomeViewModel['navTo']>[0];
+export declare function selectFeatureAndOpenWidget(stateModel: LinearApolloDisplayMouseEvents | LinearApolloSixFrameDisplayMouseEvents, feature: AnnotationFeature): void;
+export declare function isTranscriptFeature(feature: AnnotationFeature, session: ApolloSessionModel): boolean;
+export declare function isExonFeature(feature: AnnotationFeature, session: ApolloSessionModel): boolean;
+export declare function isCDSFeature(feature: AnnotationFeature, session: ApolloSessionModel): boolean;
+export interface AdjacentExons {
+    upstream: AnnotationFeature | undefined;
+    downstream: AnnotationFeature | undefined;
+}
+export declare function getAdjacentExons(currentExon: AnnotationFeature, display: LinearApolloDisplayMouseEvents | LinearApolloSixFrameDisplayMouseEvents, mousePosition: MousePositionWithFeature, session: ApolloSessionModel): AdjacentExons;
+export declare function getStreamIcon(strand: 1 | -1 | undefined, isUpstream: boolean, isFlipped: boolean | undefined): import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+    muiName: string;
+};
+export declare function getMinAndMaxPx(feature: AnnotationFeature | TranscriptPartCoding, refName: string, regionNumber: number, lgv: LinearGenomeViewModel): [number, number] | undefined;
+export declare function getOverlappingEdge(feature: AnnotationFeature, x: number, minMax: [number, number]): {
+    feature: AnnotationFeature;
+    edge: 'min' | 'max';
+} | undefined;
+export declare function isSelectedFeature(feature: AnnotationFeature, selectedFeature: AnnotationFeature | undefined): boolean;
+export declare function containsSelectedFeature(feature: AnnotationFeature, selectedFeature: AnnotationFeature | undefined): boolean;
+export declare function getContextMenuItemsForFeature(display: LinearApolloSixFrameDisplayMouseEvents | LinearApolloDisplayMouseEvents, sourceFeature: AnnotationFeature): MenuItem[];
+export declare function navToFeatureCenter(feature: AnnotationFeature, paddingPct: number, refSeqLength: number): NavLocation;
+export {};
+//# sourceMappingURL=glyphUtils.d.ts.map

package/dist/util/glyphUtils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"glyphUtils.d.ts","sourceRoot":"","sources":["../../src/util/glyphUtils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,iBAAiB,EACjB,oBAAoB,EACrB,MAAM,wBAAwB,CAAA;AAE/B,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAA;AAMhD,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,oCAAoC,CAAA;AAI/E,OAAO,KAAK,EAAE,8BAA8B,EAAE,MAAM,+CAA+C,CAAA;AACnG,OAAO,KAAK,EAAE,sCAAsC,EAAE,MAAM,uDAAuD,CAAA;AAEnH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAEpD,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,GAAG,CAAA;AAEjD,KAAK,WAAW,GAAG,UAAU,CAAC,qBAAqB,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAEhE,wBAAgB,0BAA0B,CACxC,UAAU,EACN,8BAA8B,GAC9B,sCAAsC,EAC1C,OAAO,EAAE,iBAAiB,QAmC3B;AAED,wBAAgB,mBAAmB,CACjC,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAST;AAED,wBAAgB,aAAa,CAC3B,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAMT;AAED,wBAAgB,YAAY,CAC1B,OAAO,EAAE,iBAAiB,EAC1B,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAMT;AAED,MAAM,WAAW,aAAa;IAC5B,QAAQ,EAAE,iBAAiB,GAAG,SAAS,CAAA;IACvC,UAAU,EAAE,iBAAiB,GAAG,SAAS,CAAA;CAC1C;AAED,wBAAgB,gBAAgB,CAC9B,WAAW,EAAE,iBAAiB,EAC9B,OAAO,EACH,8BAA8B,GAC9B,sCAAsC,EAC1C,aAAa,EAAE,wBAAwB,EACvC,OAAO,EAAE,kBAAkB,GAC1B,aAAa,CAkDf;AAED,wBAAgB,aAAa,CAC3B,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,GAAG,SAAS,EAC1B,UAAU,EAAE,OAAO,EACnB,SAAS,EAAE,OAAO,GAAG,SAAS;;EAsB/B;AAED,wBAAgB,cAAc,CAC5B,OAAO,EAAE,iBAAiB,GAAG,oBAAoB,EACjD,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,MAAM,EACpB,GAAG,EAAE,qBAAqB,GACzB,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,SAAS,CAkB9B;AAED,wBAAgB,kBAAkB,CAChC,OAAO,EAAE,iBAAiB,EAC1B,CAAC,EAAE,MAAM,EACT,MAAM,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,GACvB;IAAE,OAAO,EAAE,iBAAiB,CAAC;IAAC,IAAI,EAAE,KAAK,GAAG,KAAK,CAAA;CAAE,GAAG,SAAS,CAajE;AAED,wBAAgB,iBAAiB,CAC/B,OAAO,EAAE,iBAAiB,EAC1B,eAAe,EAAE,iBAAiB,GAAG,SAAS,WAG/C;AAED,wBAAgB,uBAAuB,CACrC,OAAO,EAAE,iBAAiB,EAC1B,eAAe,EAAE,iBAAiB,GAAG,SAAS,GAC7C,OAAO,CAQT;AAqBD,wBAAgB,6BAA6B,CAC3C,OAAO,EACH,sCAAsC,GACtC,8BAA8B,EAClC,aAAa,EAAE,iBAAiB,GAC/B,QAAQ,EAAE,CAwGZ;AAED,wBAAgB,kBAAkB,CAChC,OAAO,EAAE,iBAAiB,EAC1B,UAAU,EAAE,MAAM,EAClB,YAAY,EAAE,MAAM,GACnB,WAAW,CAKb"}

package/dist/util/index.d.ts

@@ -0,0 +1,10 @@
+import type { ApolloInternetAccountModel } from '../ApolloInternetAccount/model';
+import type { ApolloSessionModel } from '../session';
+export declare function createFetchErrorMessage(response: Response, additionalText?: string): Promise<string>;
+/** given a session, get our ApolloInternetAccount */
+export declare function getApolloInternetAccount(session: ApolloSessionModel): ApolloInternetAccountModel | undefined;
+export * from './loadAssemblyIntoClient';
+export * from './annotationFeatureUtils';
+export * from './glyphUtils';
+export * from './mouseEventsUtils';
+//# sourceMappingURL=index.d.ts.map

package/dist/util/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/util/index.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,0BAA0B,EAAE,MAAM,gCAAgC,CAAA;AAChF,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAA;AAGpD,wBAAsB,uBAAuB,CAC3C,QAAQ,EAAE,QAAQ,EAClB,cAAc,CAAC,EAAE,MAAM,GACtB,OAAO,CAAC,MAAM,CAAC,CAWjB;AAED,qDAAqD;AACrD,wBAAgB,wBAAwB,CAAC,OAAO,EAAE,kBAAkB,GAG9D,0BAA0B,GAC1B,SAAS,CACd;AAED,cAAc,0BAA0B,CAAA;AACxC,cAAc,0BAA0B,CAAA;AACxC,cAAc,cAAc,CAAA;AAC5B,cAAc,oBAAoB,CAAA"}

package/dist/util/loadAssemblyIntoClient.d.ts

@@ -0,0 +1,5 @@
+import { type ClientDataStore } from '@apollo-annotation/common';
+import type { ApolloAssemblyI, CheckResultSnapshot } from '@apollo-annotation/mst';
+export declare function loadAssemblyIntoClient(assemblyId: string, gff3FileText: string, apolloDataStore: ClientDataStore): Promise<ApolloAssemblyI>;
+export declare function checkFeatures(assembly: ApolloAssemblyI): Promise<CheckResultSnapshot[]>;
+//# sourceMappingURL=loadAssemblyIntoClient.d.ts.map

package/dist/util/loadAssemblyIntoClient.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"loadAssemblyIntoClient.d.ts","sourceRoot":"","sources":["../../src/util/loadAssemblyIntoClient.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,eAAe,EAAiB,MAAM,2BAA2B,CAAA;AAC/E,OAAO,KAAK,EACV,eAAe,EACf,mBAAmB,EACpB,MAAM,wBAAwB,CAAA;AAU/B,wBAAsB,sBAAsB,CAC1C,UAAU,EAAE,MAAM,EAClB,YAAY,EAAE,MAAM,EACpB,eAAe,EAAE,eAAe,4BAyDjC;AAED,wBAAsB,aAAa,CACjC,QAAQ,EAAE,eAAe,GACxB,OAAO,CAAC,mBAAmB,EAAE,CAAC,CAehC"}

package/dist/util/mouseEventsUtils.d.ts

@@ -0,0 +1,25 @@
+import type { AnnotationFeature } from '@apollo-annotation/mst';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+type MinEdge = 'min';
+type MaxEdge = 'max';
+export type Edge = MinEdge | MaxEdge;
+interface LocationChange {
+    featureId: string;
+    oldLocation: number;
+    newLocation: number;
+}
+export declare function getPropagatedLocationChanges(feature: AnnotationFeature, newLocation: number, edge: Edge, shrinkParent?: boolean): LocationChange[];
+/** extended information about the position of the mouse on the canvas, including the refName, bp, and displayedRegion number */
+export interface MousePosition {
+    x: number;
+    y: number;
+    refName: string;
+    bp: number;
+    regionNumber: number;
+    feature?: AnnotationFeature;
+}
+export type MousePositionWithFeature = Required<MousePosition>;
+export declare function isMousePositionWithFeature(mousePosition: MousePosition): mousePosition is MousePositionWithFeature;
+export declare function getMousePosition(event: React.MouseEvent, lgv: LinearGenomeViewModel): MousePosition;
+export {};
+//# sourceMappingURL=mouseEventsUtils.d.ts.map

package/dist/util/mouseEventsUtils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"mouseEventsUtils.d.ts","sourceRoot":"","sources":["../../src/util/mouseEventsUtils.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,wBAAwB,CAAA;AAC/D,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,oCAAoC,CAAA;AAE/E,KAAK,OAAO,GAAG,KAAK,CAAA;AACpB,KAAK,OAAO,GAAG,KAAK,CAAA;AACpB,MAAM,MAAM,IAAI,GAAG,OAAO,GAAG,OAAO,CAAA;AAEpC,UAAU,cAAc;IACtB,SAAS,EAAE,MAAM,CAAA;IACjB,WAAW,EAAE,MAAM,CAAA;IACnB,WAAW,EAAE,MAAM,CAAA;CACpB;AAiFD,wBAAgB,4BAA4B,CAC1C,OAAO,EAAE,iBAAiB,EAC1B,WAAW,EAAE,MAAM,EACnB,IAAI,EAAE,IAAI,EACV,YAAY,UAAQ,GACnB,cAAc,EAAE,CAgBlB;AAED,gIAAgI;AAChI,MAAM,WAAW,aAAa;IAC5B,CAAC,EAAE,MAAM,CAAA;IACT,CAAC,EAAE,MAAM,CAAA;IACT,OAAO,EAAE,MAAM,CAAA;IACf,EAAE,EAAE,MAAM,CAAA;IACV,YAAY,EAAE,MAAM,CAAA;IACpB,OAAO,CAAC,EAAE,iBAAiB,CAAA;CAC5B;AAED,MAAM,MAAM,wBAAwB,GAAG,QAAQ,CAAC,aAAa,CAAC,CAAA;AAE9D,wBAAgB,0BAA0B,CACxC,aAAa,EAAE,aAAa,GAC3B,aAAa,IAAI,wBAAwB,CAE3C;AAED,wBAAgB,gBAAgB,CAC9B,KAAK,EAAE,KAAK,CAAC,UAAU,EACvB,GAAG,EAAE,qBAAqB,GACzB,aAAa,CAQf"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/jbrowse-plugin-apollo",
-  "version": "0.3.10",
+  "version": "0.3.12",
   "description": "Apollo plugin for JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -13,9 +13,7 @@
   },
   "license": "Apache-2.0",
   "author": "JBrowse Team",
-  "main": "dist/index.js",
-  "module": "dist/index.esm.js",
-  "typings": "dist/index.d.ts",
+  "type": "module",
   "files": [
     "dist",
     "src"
@@ -24,12 +22,12 @@
     "setup": "rimraf .jbrowse && jbrowse create .jbrowse",
     "clean": "rimraf dist",
     "start": "yarn clean && npm-run-all --parallel start:watch start:server",
-    "start:watch": "JB_NPM=false NODE_ENV=development rollup --config --watch",
+    "start:watch": "JB_NPM=false NODE_ENV=development rollup --config rollup/rollup.config.mjs --watch",
     "start:server": "serve --no-request-logging --cors --listen 9000 --no-port-switching .",
-    "build": "yarn build:shared && yarn clean && rollup --config",
+    "build": "yarn build:shared && yarn clean && rollup --config rollup/rollup.config.mjs",
     "browse": "serve --no-request-logging --listen 8999 --no-port-switching --symlinks .jbrowse",
-    "test": "jest",
-    "test:ci": "jest --coverage",
+    "test": "yarn node --experimental-vm-modules $(yarn bin jest)",
+    "test:ci": "yarn node --experimental-vm-modules $(yarn bin jest) --coverage",
     "start:collab-cypress": "yarn workspace @apollo-annotation/collaboration-server run cypress:start",
     "test:e2e": "yarn build && start-test \"npm-run-all --parallel start:server browse start:collab-cypress\" \"9000|8999|http://localhost:3999/health\" \"npm-run-all cypress:run\"",
     "test:e2e:debug": "yarn build && start-test \"npm-run-all --parallel start:server browse start:collab-cypress\" \"9000|8999|http://localhost:3999/health\" \"npm-run-all cypress:debug\"",
@@ -48,15 +46,15 @@
     }
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.10",
-    "@apollo-annotation/mst": "^0.3.10",
-    "@apollo-annotation/shared": "^0.3.10",
+    "@apollo-annotation/common": "^0.3.12",
+    "@apollo-annotation/mst": "^0.3.12",
+    "@apollo-annotation/shared": "^0.3.12",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
-    "@gmod/gff": "^2.0.0",
-    "@jbrowse/plugin-authentication": "^3.6.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.5",
-    "@mui/icons-material": "^6.5.0",
+    "@gmod/gff": "^2.1.0",
+    "@jbrowse/plugin-authentication": "^4.1.1",
+    "@jbrowse/plugin-linear-genome-view": "^4.1.1",
+    "@mui/icons-material": "^7.3.7",
     "@types/jsonpath": "^0.2.0",
     "autosuggest-highlight": "^3.3.4",
     "bson-objectid": "^2.0.4",
@@ -71,18 +69,38 @@
     "tslib": "^2.3.1"
   },
   "devDependencies": {
-    "@jbrowse/cli": "^3.6.5",
-    "@jbrowse/core": "^3.6.5",
+    "@babel/core": "^7.28.6",
+    "@babel/plugin-proposal-class-properties": "^7.18.6",
+    "@babel/preset-env": "^7.28.6",
+    "@jbrowse/cli": "^4.1.1",
+    "@jbrowse/core": "^4.1.1",
     "@jbrowse/development-tools": "^2.2.1",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
     "@jest/globals": "^29.0.3",
-    "@mui/material": "^7.0.0",
+    "@mui/material": "^7.3.7",
     "@mui/x-data-grid": "^8.0.0",
+    "@rollup/plugin-babel": "^6.1.0",
+    "@rollup/plugin-commonjs": "^29.0.0",
+    "@rollup/plugin-json": "^6.1.0",
+    "@rollup/plugin-node-resolve": "^16.0.3",
+    "@rollup/plugin-typescript": "^12.3.0",
     "@types/autosuggest-highlight": "^3",
+    "@types/babel-plugin-macros": "^3",
+    "@types/babel__core": "^7",
+    "@types/babel__preset-env": "^7",
     "@types/file-saver": "^2",
-    "@types/node": "^20.19.15",
+    "@types/lodash.merge": "^4",
+    "@types/node": "^24.10.9",
     "@types/prop-types": "^15",
     "@types/react": "^18.3.4",
     "@types/react-dom": "^18",
+    "babel-plugin-annotate-pure-calls": "^0.5.0",
+    "babel-plugin-dev-expression": "^0.2.3",
+    "babel-plugin-macros": "^3.1.0",
+    "babel-plugin-polyfill-regenerator": "^0.6.6",
+    "babel-plugin-transform-rename-import": "^2.3.0",
+    "builtin-modules": "^5.0.0",
+    "chalk": "^5.6.2",
     "cypress": "12.17.3",
     "cypress-image-diff-html-report": "^2.2.0",
     "cypress-image-diff-js": "^2.3.0",
@@ -90,31 +108,36 @@
     "fake-indexeddb": "^4.0.2",
     "jest": "^29.6.2",
     "jest-fetch-mock": "^3.0.3",
+    "jest-util": "^30.2.0",
     "librpc-web-mod": "^1.1.9",
+    "lodash.merge": "^4.6.2",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.4.0",
     "npm-run-all": "^4.1.5",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
     "rimraf": "^3.0.2",
-    "rollup": "^2.79.2",
+    "rollup": "^4.57.0",
+    "rollup-plugin-external-globals": "^0.13.0",
+    "rollup-plugin-polyfill-node": "^0.13.0",
+    "rollup-plugin-sourcemaps": "^0.6.3",
+    "rollup-plugin-terser": "^7.0.2",
     "rxjs": "^7.4.0",
     "serve": "^14.0.1",
     "shx": "^0.3.3",
     "start-server-and-test": "^1.11.7",
-    "ts-jest": "^29.1.1",
+    "ts-jest": "^29.4.6",
     "ts-node": "^10.3.0",
     "tss-react": "^4.6.1",
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^3.0.1",
-    "@mui/material": "^7.0.0",
+    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.7",
     "mobx": "^6.6.1",
     "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.4.0",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",

package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx

@@ -1,5 +1,6 @@
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 import { isAbortException } from '@jbrowse/core/util/aborting'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import {
   Button,
   DialogActions,
@@ -8,7 +9,6 @@ import {
   Divider,
 } from '@mui/material'
 import React, { useEffect, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { Dialog } from '../../components/Dialog'
 import { createFetchErrorMessage } from '../../util'
@@ -57,7 +57,12 @@ export const AuthTypeSelector = ({
       }
     })
     return () => {
-      controller.abort('AuthTypeSelector')
+      controller.abort(
+        new DOMException(
+          'Error retrieving valid authentication types',
+          'AbortError',
+        ),
+      )
     }
   }, [baseURL])
 

package/src/ApolloInternetAccount/components/LoginButtons.tsx

@@ -1,7 +1,7 @@
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import AccountCircleIcon from '@mui/icons-material/AccountCircle'
 import { Button, type ButtonProps } from '@mui/material'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { Google, Microsoft } from './LoginIcons'
 

package/src/ApolloInternetAccount/configSchema.ts

@@ -1,6 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { BaseInternetAccountConfig } from '@jbrowse/core/pluggableElementTypes'
-import { type Instance } from 'mobx-state-tree'
+import type { Instance } from '@jbrowse/mobx-state-tree'
 
 const ApolloConfigSchema = ConfigurationSchema(
   'ApolloInternetAccount',

package/src/ApolloInternetAccount/model.ts

@@ -22,17 +22,23 @@ import {
   isAbstractMenuManager,
   isElectron,
 } from '@jbrowse/core/util'
+import {
+  type Instance,
+  flow,
+  getRoot,
+  isAlive,
+  types,
+} from '@jbrowse/mobx-state-tree'
 import { autorun } from 'mobx'
-import { type Instance, flow, getRoot, isAlive, types } from 'mobx-state-tree'
 import { io } from 'socket.io-client'
 
 import { addTopLevelAdminMenus } from '../menus/topLevelMenuAdmin'
-import { type Collaborator } from '../session'
-import { type ApolloRootModel } from '../types'
+import type { Collaborator } from '../session'
+import type { ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
 
 import { AuthTypeSelector } from './components/AuthTypeSelector'
-import { type ApolloInternetAccountConfigModel } from './configSchema'
+import type { ApolloInternetAccountConfigModel } from './configSchema'
 
 type AuthType = 'google' | 'microsoft' | 'guest'
 
@@ -101,7 +107,6 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
           if (
             event.data.name !== `JBrowseAuthWindow-${self.internetAccountId}`
           ) {
-            this.deleteMessageChannel()
             return
           }
           const redirectUriWithInfo = event.data.redirectUri
@@ -503,7 +508,9 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
       beforeDestroy() {
         self.removeBeforeUnloadListener()
         self.removeVisibilityChangeListener()
-        self.controller.abort('internet account beforeDestroy')
+        self.controller.abort(
+          new DOMException('Cleaning up Apollo connection', 'AbortError'),
+        )
         self.socket.close()
       },
     }))

package/src/ApolloJobModel.ts

@@ -5,15 +5,15 @@ import {
   getSession,
   isSessionModelWithWidgets,
 } from '@jbrowse/core/util'
-import { types } from 'mobx-state-tree'
+import { types } from '@jbrowse/mobx-state-tree'
 
-interface JobsEntry {
+export interface JobsEntry {
   name: string
   cancelCallback?: () => void
   progressPct?: number
   statusMessage?: string
 }
-interface JobsListModel {
+export interface JobsListModel {
   id: number
   type: 'JobsListWidget'
   jobs: JobsEntry[]

package/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts

@@ -6,9 +6,9 @@ import {
 import type RpcServer from 'librpc-web-mod/dist/server'
 import { nanoid } from 'nanoid'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
-import { type RefNameAliases } from './../BackendDrivers/BackendDriver'
+import type { RefNameAliases } from './../BackendDrivers/BackendDriver'
 
 declare global {
   const rpcServer: RpcServer

package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts

@@ -7,10 +7,10 @@ import { readConfObject } from '@jbrowse/core/configuration'
 import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import SimpleFeature, { type Feature } from '@jbrowse/core/util/simpleFeature'
-import { type NoAssemblyRegion, type Region } from '@jbrowse/core/util/types'
+import type { NoAssemblyRegion, Region } from '@jbrowse/core/util/types'
 import { nanoid } from 'nanoid'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
 
 // declare global {
 //   var rpcServer: import('librpc-web-mod').RpcServer

package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts

@@ -1,15 +1,36 @@
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
-import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { readConfObject } from '@jbrowse/core/configuration'
 import {
   BaseAdapter,
   type BaseTextSearchAdapter,
   type BaseTextSearchArgs,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { type AbstractSessionModel, type UriLocation } from '@jbrowse/core/util'
+import type { AbstractSessionModel, UriLocation } from '@jbrowse/core/util'
 
-import { type ApolloSessionModel } from '../session'
+import type { ApolloSessionModel } from '../session'
+
+function getMatchedFeature(
+  query: string,
+  feature: AnnotationFeatureSnapshot,
+): AnnotationFeatureSnapshot | undefined {
+  // @ts-expect-error this actually has a bit more info that a plain snapshot
+  const { children, indexedIds, ...featureWithoutChildren } = feature
+  const featureString = JSON.stringify(featureWithoutChildren)
+  if (featureString.includes(query)) {
+    return feature
+  }
+  if (!children) {
+    return undefined
+  }
+  for (const subFeature of Object.values(children)) {
+    const matchedFeature = getMatchedFeature(query, subFeature)
+    if (matchedFeature) {
+      return matchedFeature
+    }
+  }
+}
 
 export class ApolloTextSearchAdapter
   extends BaseAdapter
@@ -33,11 +54,13 @@ export class ApolloTextSearchAdapter
     query: string,
   ) {
     return features.map((feature) => {
+      const matchedObject = getMatchedFeature(query, feature) ?? feature
       const refName = assembly.getCanonicalRefName(feature.refSeq)
       return new BaseResult({
         label: query,
         trackId: this.trackId,
-        locString: `${refName}:${feature.min + 1}..${feature.max}`,
+        locString: `${refName}:${matchedObject.min + 1}..${matchedObject.max}`,
+        matchedObject,
       })
     })
   }

package/src/BackendDrivers/BackendDriver.ts

@@ -1,13 +1,13 @@
-import { type Change, type ClientDataStore } from '@apollo-annotation/common'
-import {
-  type AnnotationFeatureSnapshot,
-  type CheckResultSnapshot,
+import type { Change, ClientDataStore } from '@apollo-annotation/common'
+import type {
+  AnnotationFeatureSnapshot,
+  CheckResultSnapshot,
 } from '@apollo-annotation/mst'
-import { type ValidationResultSet } from '@apollo-annotation/shared'
-import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
-import { type Region } from '@jbrowse/core/util'
+import type { ValidationResultSet } from '@apollo-annotation/shared'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import type { Region } from '@jbrowse/core/util'
 
-import { type SubmitOpts } from '../ChangeManager'
+import type { SubmitOpts } from '../ChangeManager'
 
 export interface RefNameAliases {
   refName: string

package/src/BackendDrivers/CollaborationServerDriver.ts

@@ -10,10 +10,10 @@ import {
   type FeatureChange,
   isFeatureChange,
 } from '@apollo-annotation/common'
-import {
-  type AnnotationFeatureSnapshot,
-  type ApolloRefSeqI,
-  type CheckResultSnapshot,
+import type {
+  AnnotationFeatureSnapshot,
+  ApolloRefSeqI,
+  CheckResultSnapshot,
 } from '@apollo-annotation/mst'
 import {
   type ChangeMessage,
@@ -21,9 +21,9 @@ import {
   makeUserSessionId,
 } from '@apollo-annotation/shared'
 import { getConf } from '@jbrowse/core/configuration'
-import { type BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
+import type { BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
 import { type Region, getSession } from '@jbrowse/core/util'
-import { type Socket } from 'socket.io-client'
+import type { Socket } from 'socket.io-client'
 
 import { ChangeManager, type SubmitOpts } from '../ChangeManager'
 import { createFetchErrorMessage } from '../util'

package/src/BackendDrivers/DesktopFileDriver.ts

@@ -4,9 +4,9 @@ import {
   type Change,
   isAssemblySpecificChange,
 } from '@apollo-annotation/common'
-import {
-  type AnnotationFeatureSnapshot,
-  type CheckResultSnapshot,
+import type {
+  AnnotationFeatureSnapshot,
+  CheckResultSnapshot,
 } from '@apollo-annotation/mst'
 import {
   ValidationResultSet,
@@ -16,7 +16,7 @@ import {
 import { type GFF3Item, formatSync } from '@gmod/gff'
 import { getConf } from '@jbrowse/core/configuration'
 import { type Region, getSession } from '@jbrowse/core/util'
-import { getSnapshot } from 'mobx-state-tree'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 
 import { checkFeatures, loadAssemblyIntoClient } from '../util'
 

package/src/BackendDrivers/InMemoryFileDriver.ts

@@ -1,17 +1,14 @@
 /* eslint-disable @typescript-eslint/require-await */
-import {
-  type AssemblySpecificChange,
-  type Change,
-} from '@apollo-annotation/common'
-import {
-  type AnnotationFeatureSnapshot,
-  type CheckResultSnapshot,
+import type { AssemblySpecificChange, Change } from '@apollo-annotation/common'
+import type {
+  AnnotationFeatureSnapshot,
+  CheckResultSnapshot,
 } from '@apollo-annotation/mst'
 import { ValidationResultSet } from '@apollo-annotation/shared'
 import { getConf } from '@jbrowse/core/configuration'
 import { type Region, getSession } from '@jbrowse/core/util'
 
-import { type SubmitOpts } from '../ChangeManager'
+import type { SubmitOpts } from '../ChangeManager'
 import { checkFeatures } from '../util'
 
 import { BackendDriver, type RefNameAliases } from './BackendDriver'