@jbrowse/core 3.6.5 → 4.0.0

package/assemblyManager/assemblyManager.d.ts

@@ -1,499 +0,0 @@
-import type { AnyConfigurationModel } from '../configuration';
-import type { Assembly } from './assembly';
-import type PluginManager from '../PluginManager';
-import type RpcManager from '../rpc/RpcManager';
-import type { IAnyType } from 'mobx-state-tree';
-type AdapterConf = Record<string, unknown>;
-declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): import("mobx-state-tree").IModelType<{
-    assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }, {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("../util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("./assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        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({ regions, refNameAliases, cytobands, }: {
-            regions: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util").Feature[]): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
-}, {
-    readonly assemblyNameMap: Record<string, {
-        configuration: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("../util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("./assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        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({ regions, refNameAliases, cytobands, }: {
-            regions: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util").Feature[]): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }, {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("../util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("./assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        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({ regions, refNameAliases, cytobands, }: {
-            regions: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util").Feature[]): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
-} & {
-    getCanonicalAssemblyName(asmName: string): string | undefined;
-    get(asmName: string): ({
-        configuration: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("../util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("./assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        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({ regions, refNameAliases, cytobands, }: {
-            regions: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util").Feature[]): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }, {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("../util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("./assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        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({ regions, refNameAliases, cytobands, }: {
-            regions: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util").Feature[]): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
-    readonly assemblyNamesList: any[];
-    readonly assemblyList: AnyConfigurationModel[];
-    readonly rpcManager: RpcManager;
-} & {
-    waitForAssembly(assemblyName: string): Promise<({
-        configuration: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("../util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("./assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        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({ regions, refNameAliases, cytobands, }: {
-            regions: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util").Feature[]): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }, {
-        error: unknown;
-        loadingP: Promise<void> | undefined;
-        volatileRegions: import("./assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("../util").Feature[] | undefined;
-    } & {
-        getConf(arg: string): any;
-        readonly lowerCaseRefNameAliases: {
-            [k: string]: string;
-        } | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly regions: import("./assembly").BasicRegion[] | undefined;
-        readonly aliases: string[];
-        readonly displayName: string;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly allRefNames: string[] | undefined;
-        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({ regions, refNameAliases, cytobands, }: {
-            regions: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: unknown): void;
-        setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util").Feature[]): void;
-        setLoadingP(p?: Promise<void>): void;
-        load(): Promise<void>;
-        loadPre(): Promise<void>;
-    } & {
-        getAdapterMapEntry(adapterConf: {
-            [x: string]: unknown;
-        }, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: {
-            [x: string]: unknown;
-        }, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        afterCreate(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
-    getRefNameMapForAdapter(adapterConf: AdapterConf, assemblyName: string | undefined, opts: {
-        stopToken?: string;
-        sessionId: string;
-    }): Promise<{
-        [x: string]: string;
-    } | undefined>;
-    getReverseRefNameMapForAdapter(adapterConf: AdapterConf, assemblyName: string | undefined, opts: {
-        stopToken?: string;
-        sessionId: string;
-    }): Promise<{
-        [x: string]: string;
-    } | undefined>;
-    isValidRefName(refName: string, assemblyName: string): boolean;
-} & {
-    afterAttach(): void;
-    removeAssembly(asm: Assembly): void;
-    addAssembly(configuration: any): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export default assemblyManagerFactory;

package/assemblyManager/assemblyManager.js

@@ -1,134 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const configuration_1 = require("../configuration");
-const util_1 = require("../util");
-const assembly_1 = __importDefault(require("./assembly"));
-function assemblyManagerFactory(conf, pm) {
-    return mobx_state_tree_1.types
-        .model({
-        assemblies: mobx_state_tree_1.types.array((0, assembly_1.default)(conf, pm)),
-    })
-        .views(self => ({
-        get assemblyNameMap() {
-            const obj = {};
-            for (const assembly of self.assemblies) {
-                for (const name of assembly.allAliases) {
-                    obj[name] = assembly;
-                }
-            }
-            return obj;
-        },
-    }))
-        .views(self => ({
-        getCanonicalAssemblyName(asmName) {
-            var _a;
-            return (_a = self.assemblyNameMap[asmName]) === null || _a === void 0 ? void 0 : _a.name;
-        },
-        get(asmName) {
-            if (asmName) {
-                const assembly = self.assemblyNameMap[asmName];
-                if (assembly) {
-                    return assembly;
-                }
-                else if (!this.assemblyNamesList.includes(asmName)) {
-                    pm.evaluateExtensionPoint('Core-handleUnrecognizedAssembly', undefined, {
-                        assemblyName: asmName,
-                        session: (0, mobx_state_tree_1.getParent)(self).session,
-                    });
-                }
-            }
-            return undefined;
-        },
-        get assemblyNamesList() {
-            return this.assemblyList.map(asm => asm.name);
-        },
-        get assemblyList() {
-            const { jbrowse: { assemblies }, session: { sessionAssemblies = [], temporaryAssemblies = [] } = {}, } = (0, mobx_state_tree_1.getParent)(self);
-            return [
-                ...assemblies,
-                ...sessionAssemblies,
-                ...temporaryAssemblies,
-            ];
-        },
-        get rpcManager() {
-            return (0, mobx_state_tree_1.getParent)(self).rpcManager;
-        },
-    }))
-        .views(self => ({
-        async waitForAssembly(assemblyName) {
-            if (!assemblyName) {
-                throw new Error('no assembly name supplied to waitForAssembly');
-            }
-            let assembly = self.get(assemblyName);
-            if (!assembly) {
-                try {
-                    await (0, util_1.when)(() => Boolean(self.get(assemblyName)), {
-                        timeout: 10000,
-                    });
-                    assembly = self.get(assemblyName);
-                }
-                catch (e) {
-                }
-            }
-            if (!assembly) {
-                return undefined;
-            }
-            await assembly.load();
-            await (0, util_1.when)(() => !!(assembly.regions && assembly.refNameAliases) || !!assembly.error);
-            if (assembly.error) {
-                throw assembly.error;
-            }
-            return assembly;
-        },
-        async getRefNameMapForAdapter(adapterConf, assemblyName, opts) {
-            if (assemblyName) {
-                const asm = await this.waitForAssembly(assemblyName);
-                return asm === null || asm === void 0 ? void 0 : asm.getRefNameMapForAdapter(adapterConf, opts);
-            }
-            return {};
-        },
-        async getReverseRefNameMapForAdapter(adapterConf, assemblyName, opts) {
-            if (assemblyName) {
-                const asm = await this.waitForAssembly(assemblyName);
-                return asm === null || asm === void 0 ? void 0 : asm.getReverseRefNameMapForAdapter(adapterConf, opts);
-            }
-            return {};
-        },
-        isValidRefName(refName, assemblyName) {
-            const assembly = self.get(assemblyName);
-            if (assembly) {
-                return assembly.isValidRefName(refName);
-            }
-            throw new Error(`Failed to look up refName:${refName} on assemblyName:${assemblyName} (assembly does not exist)`);
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(() => self.assemblyList, assemblyConfs => {
-                for (const asm of self.assemblies) {
-                    if (!asm.configuration) {
-                        this.removeAssembly(asm);
-                    }
-                }
-                for (const conf of assemblyConfs) {
-                    const name = (0, configuration_1.readConfObject)(conf, 'name');
-                    if (!self.assemblies.some(a => a.name === name)) {
-                        this.addAssembly(conf);
-                    }
-                }
-            }, { fireImmediately: true, name: 'assemblyManagerAfterAttach' }));
-        },
-        removeAssembly(asm) {
-            self.assemblies.remove(asm);
-        },
-        addAssembly(configuration) {
-            self.assemblies.push({ configuration });
-        },
-    }));
-}
-exports.default = assemblyManagerFactory;

package/assemblyManager/index.d.ts

@@ -1,3 +0,0 @@
-export { default } from './assemblyManager';
-export { default as assemblyConfigSchemaFactory } from './assemblyConfigSchema';
-export type { BaseAssemblyConfigSchema } from './assemblyConfigSchema';

package/assemblyManager/index.js

@@ -1,10 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.assemblyConfigSchemaFactory = exports.default = void 0;
-var assemblyManager_1 = require("./assemblyManager");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(assemblyManager_1).default; } });
-var assemblyConfigSchema_1 = require("./assemblyConfigSchema");
-Object.defineProperty(exports, "assemblyConfigSchemaFactory", { enumerable: true, get: function () { return __importDefault(assemblyConfigSchema_1).default; } });

package/configuration/configurationSchema.d.ts

@@ -1,35 +0,0 @@
-import type { ConfigSlotDefinition } from './configurationSlot';
-import type { AnyConfigurationSchemaType } from './types';
-import type { IAnyType } from 'mobx-state-tree';
-export type { AnyConfigurationModel, AnyConfigurationSchemaType, AnyConfigurationSlot, AnyConfigurationSlotType, } from './types';
-export interface ConfigurationSchemaDefinition {
-    [n: string]: ConfigSlotDefinition | ConfigurationSchemaDefinition | string | number | IAnyType;
-}
-export interface ConfigurationSchemaOptions<BASE_SCHEMA extends AnyConfigurationSchemaType | undefined, EXPLICIT_IDENTIFIER extends string | undefined> {
-    explicitlyTyped?: boolean;
-    explicitIdentifier?: EXPLICIT_IDENTIFIER;
-    implicitIdentifier?: string | boolean;
-    baseConfiguration?: BASE_SCHEMA;
-    actions?: (self: unknown) => any;
-    views?: (self: unknown) => any;
-    extend?: (self: unknown) => any;
-    preProcessSnapshot?: (snapshot: Record<string, unknown>) => Record<string, unknown>;
-}
-declare function makeConfigurationSchemaModel<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions<any, any>>(modelName: string, schemaDefinition: DEFINITION, options: OPTIONS): import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<Record<string, 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")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-export interface ConfigurationSchemaType<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions<any, any>> extends ReturnType<typeof makeConfigurationSchemaModel<DEFINITION, OPTIONS>> {
-    isJBrowseConfigurationSchema: boolean;
-    jbrowseSchemaDefinition: DEFINITION;
-    jbrowseSchemaOptions: OPTIONS;
-    type: string;
-    [key: string]: unknown;
-}
-export declare function ConfigurationSchema<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions<BASE_SCHEMA, EXPLICIT_IDENTIFIER>, BASE_SCHEMA extends AnyConfigurationSchemaType | undefined = undefined, EXPLICIT_IDENTIFIER extends string | undefined = undefined>(modelName: string, inputSchemaDefinition: DEFINITION, inputOptions?: ConfigurationSchemaOptions<BASE_SCHEMA, EXPLICIT_IDENTIFIER>): ConfigurationSchemaType<DEFINITION, OPTIONS>;
-export declare function ConfigurationReference<SCHEMATYPE extends AnyConfigurationSchemaType>(schemaType: SCHEMATYPE): SCHEMATYPE;