@jbrowse/product-core 2.11.2 → 2.12.1

package/dist/Session/Tracks.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isSessionWithTracks = exports.TracksManagerSessionMixin = void 0;
+exports.TracksManagerSessionMixin = TracksManagerSessionMixin;
+exports.isSessionWithTracks = isSessionWithTracks;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseSession_1 = require("./BaseSession");
 const ReferenceManagement_1 = require("./ReferenceManagement");
@@ -43,9 +44,7 @@ function TracksManagerSessionMixin(pluginManager) {
         },
     }));
 }
-exports.TracksManagerSessionMixin = TracksManagerSessionMixin;
 /** Type guard for SessionWithTracks */
 function isSessionWithTracks(thing) {
     return (0, BaseSession_1.isBaseSession)(thing) && 'tracks' in thing;
 }
-exports.isSessionWithTracks = isSessionWithTracks;

package/dist/rpcWorker.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.initializeWorker = void 0;
+exports.initializeWorker = initializeWorker;
 const librpc_web_mod_1 = __importDefault(require("librpc-web-mod"));
 const PluginManager_1 = __importDefault(require("@jbrowse/core/PluginManager"));
 const remoteAbortSignals_1 = require("@jbrowse/core/rpc/remoteAbortSignals");
@@ -69,4 +69,3 @@ async function initializeWorker(corePlugins, opts) {
     }
     /* do nothing */
 }
-exports.initializeWorker = initializeWorker;

package/dist/ui/AboutDialog.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.AboutDialog = void 0;
+exports.AboutDialog = AboutDialog;
 const react_1 = __importDefault(require("react"));
 const Dialog_1 = __importDefault(require("@jbrowse/core/ui/Dialog"));
 const util_1 = require("@jbrowse/core/util");
@@ -17,4 +17,3 @@ function AboutDialog({ config, handleClose, }) {
     return (react_1.default.createElement(Dialog_1.default, { open: true, onClose: handleClose, title: trackName, maxWidth: "xl" },
         react_1.default.createElement(AboutComponent, { config: config })));
 }
-exports.AboutDialog = AboutDialog;

package/dist/ui/AboutDialogContents.d.ts

@@ -1,5 +1,6 @@
 import React from 'react';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export default function AboutContents({ config, }: {
+declare const AboutDialogContents: ({ config, }: {
     config: AnyConfigurationModel;
-}): React.JSX.Element;
+}) => React.JSX.Element;
+export default AboutDialogContents;

package/dist/ui/AboutDialogContents.js

@@ -27,6 +27,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
+const mobx_react_1 = require("mobx-react");
 const clone_1 = __importDefault(require("clone"));
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const material_1 = require("@mui/material");
@@ -35,10 +36,14 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const FileInfoPanel_1 = __importDefault(require("./FileInfoPanel"));
+const RefNameInfoDialog_1 = __importDefault(require("./RefNameInfoDialog"));
 const useStyles = (0, mui_1.makeStyles)()({
     content: {
         minWidth: 800,
     },
+    button: {
+        float: 'right',
+    },
 });
 function removeAttr(obj, attr) {
     for (const prop in obj) {
@@ -51,11 +56,12 @@ function removeAttr(obj, attr) {
     }
     return obj;
 }
-function AboutContents({ config, }) {
+const AboutDialogContents = (0, mobx_react_1.observer)(function ({ config, }) {
     const [copied, setCopied] = (0, react_1.useState)(false);
     const conf = (0, configuration_1.readConfObject)(config);
     const session = (0, util_1.getSession)(config);
     const { classes } = useStyles();
+    const [showRefNames, setShowRefNames] = (0, react_1.useState)(false);
     const hideUris = (0, configuration_1.getConf)(session, ['formatAbout', 'hideUris']) ||
         (0, configuration_1.readConfObject)(config, ['formatAbout', 'hideUris']);
     const { pluginManager } = (0, util_1.getEnv)(session);
@@ -69,15 +75,18 @@ function AboutContents({ config, }) {
     const ExtraPanel = pluginManager.evaluateExtensionPoint('Core-extraAboutPanel', null, { session, config });
     return (react_1.default.createElement("div", { className: classes.content },
         react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "Configuration" },
-            !hideUris ? (react_1.default.createElement(material_1.Button, { variant: "contained", style: { float: 'right' }, onClick: () => {
-                    const snap = removeAttr((0, clone_1.default)(conf), 'baseUri');
-                    (0, copy_to_clipboard_1.default)(JSON.stringify(snap, null, 2));
-                    setCopied(true);
-                    setTimeout(() => setCopied(false), 1000);
-                } }, copied ? 'Copied to clipboard!' : 'Copy config')) : null,
+            !hideUris ? (react_1.default.createElement("span", { className: classes.button },
+                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => setShowRefNames(true) }, "Show ref names"),
+                react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
+                        const snap = removeAttr((0, clone_1.default)(conf), 'baseUri');
+                        (0, copy_to_clipboard_1.default)(JSON.stringify(snap, null, 2));
+                        setCopied(true);
+                        setTimeout(() => setCopied(false), 1000);
+                    } }, copied ? 'Copied to clipboard!' : 'Copy config'))) : null,
             react_1.default.createElement(BaseFeatureDetail_1.Attributes, { attributes: confPostExt, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris })),
         ExtraPanel ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: ExtraPanel.name },
             react_1.default.createElement(ExtraPanel.Component, { config: config }))) : null,
-        react_1.default.createElement(FileInfoPanel_1.default, { config: config })));
-}
-exports.default = AboutContents;
+        react_1.default.createElement(FileInfoPanel_1.default, { config: config }),
+        showRefNames ? (react_1.default.createElement(RefNameInfoDialog_1.default, { config: config, onClose: () => setShowRefNames(false) })) : null));
+});
+exports.default = AboutDialogContents;

package/dist/ui/FileInfoPanel.js

@@ -23,6 +23,7 @@ var __importStar = (this && this.__importStar) || function (mod) {
     return result;
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = FileInfoPanel;
 const react_1 = __importStar(require("react"));
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
@@ -59,4 +60,3 @@ function FileInfoPanel({ config, }) {
         : info || {};
     return info !== null ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "File info" }, error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : info === undefined ? (react_1.default.createElement(ui_1.LoadingEllipses, { message: "Loading file data" })) : (react_1.default.createElement(BaseFeatureDetail_1.Attributes, { attributes: details })))) : null;
 }
-exports.default = FileInfoPanel;

package/dist/ui/RefNameInfoDialog.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+declare const RefNameInfoDialog: ({ config, onClose, }: {
+    config: AnyConfigurationModel;
+    onClose: () => void;
+}) => React.JSX.Element;
+export default RefNameInfoDialog;

package/dist/ui/RefNameInfoDialog.js

@@ -0,0 +1,110 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const configuration_1 = require("@jbrowse/core/configuration");
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const MAX_REF_NAMES = 10000;
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    container: {
+        minWidth: 800,
+    },
+    refNames: {
+        maxHeight: 300,
+        width: '100%',
+        overflow: 'auto',
+        flexGrow: 1,
+        background: theme.palette.background.default,
+    },
+}));
+const RefNameInfoDialog = (0, mobx_react_1.observer)(function ({ config, onClose, }) {
+    const [error, setError] = (0, react_1.useState)();
+    const [refNames, setRefNames] = (0, react_1.useState)();
+    const [copied, setCopied] = (0, react_1.useState)(false);
+    const { classes } = useStyles();
+    const session = (0, util_1.getSession)(config);
+    const { rpcManager } = session;
+    (0, react_1.useEffect)(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                const map = await Promise.all([...new Set((0, tracks_1.getConfAssemblyNames)(config))].map(async (assemblyName) => {
+                    const adapterConfig = (0, configuration_1.readConfObject)(config, 'adapter');
+                    return [
+                        assemblyName,
+                        (await rpcManager.call(config.trackId, 'CoreGetRefNames', {
+                            adapterConfig,
+                            // hack for synteny adapters
+                            regions: [{ assemblyName }],
+                        })),
+                    ];
+                }));
+                setRefNames(Object.fromEntries(map));
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+        })();
+    }, [config, rpcManager]);
+    const names = refNames ? Object.entries(refNames) : [];
+    const result = names
+        .flatMap(([assemblyName, refNames]) => {
+        return [
+            `--- ${assemblyName} ---`,
+            ...refNames.slice(0, MAX_REF_NAMES),
+            `${refNames.length > MAX_REF_NAMES
+                ? `\nToo many refNames to show in browser for ${assemblyName}, use "Copy ref names" button to copy to clipboard`
+                : ''}`,
+        ];
+    })
+        .filter(f => !!f)
+        .join('\n');
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, title: "Reference sequence names used in track", onClose: onClose },
+        react_1.default.createElement(material_1.DialogContent, { className: classes.container }, error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : refNames === undefined ? (react_1.default.createElement(ui_1.LoadingEllipses, { message: "Loading refNames" })) : (react_1.default.createElement(react_1.default.Fragment, null,
+            react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
+                    (0, copy_to_clipboard_1.default)(names
+                        .flatMap(([assemblyName, refNames]) => [
+                        `--- ${assemblyName} ---`,
+                        ...refNames,
+                    ])
+                        .filter(f => !!f)
+                        .join('\n'));
+                    setCopied(true);
+                    setTimeout(() => setCopied(false), 1000);
+                } }, copied ? 'Copied to clipboard!' : 'Copy ref names'),
+            react_1.default.createElement("pre", { className: classes.refNames }, result))))));
+});
+exports.default = RefNameInfoDialog;

package/esm/RootModel/BaseRootModel.d.ts

@@ -72,14 +72,16 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         } & {
             setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
             setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+            setRegions(regions: import("@jbrowse/core/util" /**
+             * #action
+             */).Region[]): void;
             setRefNameAliases(aliases: {
                 [x: string]: string | undefined;
             }, lcAliases: {
                 [x: string]: string | undefined;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setLoadingP(p?: Promise<void> | undefined): void;
+            setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
@@ -143,7 +145,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setLoadingP(p?: Promise<void> | undefined): void;
+            setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
@@ -205,7 +207,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setLoadingP(p?: Promise<void> | undefined): void;
+            setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
@@ -269,7 +271,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setLoadingP(p?: Promise<void> | undefined): void;
+            setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
@@ -331,7 +333,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setLoadingP(p?: Promise<void> | undefined): void;
+            setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
@@ -350,11 +352,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
             }>;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
         readonly assemblyNamesList: any[];
-        readonly assemblyList: ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: unknown): any;
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+        readonly assemblyList: import("@jbrowse/core/configuration").AnyConfigurationModel[];
         readonly rpcManager: RpcManager;
     } & {
         waitForAssembly(assemblyName: string): Promise<({
@@ -402,7 +400,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setLoadingP(p?: Promise<void> | undefined): void;
+            setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
@@ -464,7 +462,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
                 [x: string]: string | undefined;
             }): void;
             setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setLoadingP(p?: Promise<void> | undefined): void;
+            setLoadingP(p?: Promise<void>): void;
             load(): Promise<void>;
             loadPre(): Promise<void>;
         } & {
@@ -485,7 +483,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, assemblyName: string | undefined, opts: {
-            signal?: AbortSignal | undefined;
+            signal?: AbortSignal;
             sessionId: string;
         }): Promise<{
             [x: string]: string | undefined;
@@ -493,7 +491,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, assemblyName: string | undefined, opts: {
-            signal?: AbortSignal | undefined;
+            signal?: AbortSignal;
             sessionId: string;
         }): Promise<{
             [x: string]: string | undefined;
@@ -501,135 +499,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         isValidRefName(refName: string, assemblyName: string): boolean;
     } & {
         afterAttach(): void;
-        removeAssembly(asm: {
-            configuration: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            error: unknown;
-            loaded: boolean;
-            loadingP: Promise<void> | undefined;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: {
-                [x: string]: string | undefined;
-            } | undefined;
-            lowerCaseRefNameAliases: {
-                [x: string]: string | undefined;
-            } | undefined;
-            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-        } & {
-            getConf(arg: string): any;
-        } & {
-            readonly initialized: boolean;
-            readonly name: string;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            readonly aliases: string[];
-            readonly displayName: string | undefined;
-            hasName(name: string): boolean;
-            readonly allAliases: string[];
-            readonly allRefNames: string[] | undefined; /**
-             * #action
-             */
-            readonly lowerCaseRefNames: string[] | undefined;
-            readonly allRefNamesWithLowerCase: string[] | undefined;
-            readonly rpcManager: RpcManager;
-            readonly refNameColors: string[];
-        } & {
-            readonly refNames: string[] | undefined;
-        } & {
-            getCanonicalRefName(refName: string): string | undefined;
-            getRefNameColor(refName: string): string | undefined;
-            isValidRefName(refName: string): boolean;
-        } & {
-            setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-            setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-            setRefNameAliases(aliases: {
-                [x: string]: string | undefined;
-            }, lcAliases: {
-                [x: string]: string | undefined;
-            }): void;
-            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setLoadingP(p?: Promise<void> | undefined): void;
-            load(): Promise<void>;
-            loadPre(): Promise<void>;
-        } & {
-            getAdapterMapEntry(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-            getRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string | undefined;
-            }>;
-            getReverseRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string | undefined;
-            }>;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-        }, {
-            error: unknown;
-            loaded: boolean;
-            loadingP: Promise<void> | undefined;
-            volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            refNameAliases: {
-                [x: string]: string | undefined;
-            } | undefined;
-            lowerCaseRefNameAliases: {
-                [x: string]: string | undefined;
-            } | undefined;
-            cytobands: import("@jbrowse/core/util").Feature[] | undefined;
-        } & {
-            getConf(arg: string): any;
-        } & {
-            readonly initialized: boolean;
-            readonly name: string;
-            readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
-            readonly aliases: string[];
-            readonly displayName: string | undefined;
-            hasName(name: string): boolean;
-            readonly allAliases: string[];
-            readonly allRefNames: string[] | undefined; /**
-             * #action
-             */
-            readonly lowerCaseRefNames: string[] | undefined;
-            readonly allRefNamesWithLowerCase: string[] | undefined;
-            readonly rpcManager: RpcManager;
-            readonly refNameColors: string[];
-        } & {
-            readonly refNames: string[] | undefined;
-        } & {
-            getCanonicalRefName(refName: string): string | undefined;
-            getRefNameColor(refName: string): string | undefined;
-            isValidRefName(refName: string): boolean;
-        } & {
-            setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
-            setError(e: unknown): void;
-            setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-            setRefNameAliases(aliases: {
-                [x: string]: string | undefined;
-            }, lcAliases: {
-                [x: string]: string | undefined;
-            }): void;
-            setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-            setLoadingP(p?: Promise<void> | undefined): void;
-            load(): Promise<void>;
-            loadPre(): Promise<void>;
-        } & {
-            getAdapterMapEntry(adapterConf: {
-                [x: string]: unknown;
-            }, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-            getRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string | undefined;
-            }>;
-            getReverseRefNameMapForAdapter(adapterConf: {
-                [x: string]: unknown;
-            }, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
-                [x: string]: string | undefined;
-            }>;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
+        removeAssembly(asm: import("@jbrowse/core/assemblyManager/assembly").Assembly): void;
         addAssembly(configuration: any): void;
         replaceAssembly(idx: number, configuration: any): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;

package/esm/Session/BaseSession.d.ts

@@ -60,14 +60,20 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
     readonly assemblies: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: unknown): any;
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [x: string]: any;
+            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         aliases: {
             type: string;
             defaultValue: never[];
             description: string;
         };
-        sequence: AnyConfigurationSchemaType;
+        sequence: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
         refNameColors: {
             type: string;
             defaultValue: never[];
@@ -77,12 +83,8 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
             adapter: import("mobx-state-tree").IAnyModelType;
         }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
         cytobands: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-            adapter: import("mobx-state-tree").IAnyModelType; /**
-             * #getter
-             */
-        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>; /**
-         * #getter
-         */
+            adapter: import("mobx-state-tree").IAnyModelType;
+        }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
         displayName: {
             type: string;
             defaultValue: string;