@jbrowse/core 2.4.2 → 2.6.0

package/assemblyManager/assemblyManager.d.ts

@@ -1,7 +1,17 @@
 import { IAnyType } from 'mobx-state-tree';
 import { Assembly } from './assembly';
 import PluginManager from '../PluginManager';
+import RpcManager from '../rpc/RpcManager';
+/**
+ * #stateModel AssemblyManager
+ */
 declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     * this is automatically managed by an autorun which looks in the parent
+     * session.assemblies, session.sessionAssemblies, and
+     * session.temporaryAssemblies
+     */
     assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
@@ -10,10 +20,10 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         lowerCaseRefNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -27,12 +37,12 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
+        readonly rpcManager: RpcManager;
         readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
     } & {
-        getCanonicalRefName(refName: string): string;
+        getCanonicalRefName(refName: string): string | undefined;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -40,24 +50,139 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }, lcAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void> | undefined): void;
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
+    readonly assemblyNameMap: {
+        [key: string]: ({
+            configuration: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            error: unknown;
+            loaded: boolean;
+            loadingP: Promise<void> | undefined;
+            volatileRegions: import("./assembly").BasicRegion[] | undefined;
+            refNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            lowerCaseRefNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            cytobands: import("../util").Feature[] | undefined;
+        } & {
+            readonly initialized: boolean;
+            readonly name: string;
+            readonly regions: import("./assembly").BasicRegion[] | undefined;
+            readonly aliases: string[];
+            readonly displayName: string | undefined;
+            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({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+            setError(e: unknown): void;
+            setRegions(regions: import("../util").Region[]): void;
+            setRefNameAliases(aliases: {
+                [x: string]: string | undefined;
+            }, lcAliases: {
+                [x: string]: string | undefined;
+            }): void;
+            setCytobands(cytobands: import("../util").Feature[]): void;
+            setLoadingP(p?: Promise<void> | undefined): void;
+            load(): Promise<void>;
+            loadPre(): Promise<void>;
+        } & {
+            getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../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("./assembly").BasicRegion[] | undefined;
+            refNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            lowerCaseRefNameAliases: {
+                [x: string]: string | undefined;
+            } | undefined;
+            cytobands: import("../util").Feature[] | undefined;
+        } & {
+            readonly initialized: boolean;
+            readonly name: string;
+            readonly regions: import("./assembly").BasicRegion[] | undefined;
+            readonly aliases: string[];
+            readonly displayName: string | undefined;
+            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({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+            setError(e: unknown): void;
+            setRegions(regions: import("../util").Region[]): void;
+            setRefNameAliases(aliases: {
+                [x: string]: string | undefined;
+            }, lcAliases: {
+                [x: string]: string | undefined;
+            }): void;
+            setCytobands(cytobands: import("../util").Feature[]): void;
+            setLoadingP(p?: Promise<void> | undefined): void;
+            load(): Promise<void>;
+            loadPre(): Promise<void>;
+        } & {
+            getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+            getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+            getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+                [x: string]: string | undefined;
+            }>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+    };
+} & {
+    /**
+     * #method
+     */
     get(asmName: string): ({
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -66,10 +191,10 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         lowerCaseRefNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -83,12 +208,12 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
+        readonly rpcManager: RpcManager;
         readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
     } & {
-        getCanonicalRefName(refName: string): string;
+        getCanonicalRefName(refName: string): string | undefined;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -96,21 +221,21 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }, lcAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void> | undefined): void;
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../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>>;
@@ -120,10 +245,10 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         lowerCaseRefNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -137,12 +262,12 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
+        readonly rpcManager: RpcManager;
         readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
     } & {
-        getCanonicalRefName(refName: string): string;
+        getCanonicalRefName(refName: string): string | undefined;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -150,31 +275,44 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }, lcAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void> | undefined): void;
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+    /**
+     * #getter
+     */
     readonly assemblyNamesList: any[];
+    /**
+     * #getter
+     * looks at jbrowse.assemblies, session.sessionAssemblies, and
+     * session.temporaryAssemblies to load from
+     */
     readonly assemblyList: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
-    readonly rpcManager: any;
+    readonly rpcManager: RpcManager;
 } & {
+    /**
+     * #method
+     * use this method instead of assemblyManager.get(assemblyName)
+     * to get an assembly with regions loaded
+     */
     waitForAssembly(assemblyName: string): Promise<({
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -183,10 +321,10 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         lowerCaseRefNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -200,12 +338,12 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
+        readonly rpcManager: RpcManager;
         readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
     } & {
-        getCanonicalRefName(refName: string): string;
+        getCanonicalRefName(refName: string): string | undefined;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -213,21 +351,21 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }, lcAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void> | undefined): void;
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../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>>;
@@ -237,10 +375,10 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         loadingP: Promise<void> | undefined;
         volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         lowerCaseRefNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         cytobands: import("../util").Feature[] | undefined;
     } & {
@@ -254,12 +392,12 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
+        readonly rpcManager: RpcManager;
         readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
     } & {
-        getCanonicalRefName(refName: string): string;
+        getCanonicalRefName(refName: string): string | undefined;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -267,40 +405,71 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
         setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }, lcAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
         setLoadingP(p?: Promise<void> | undefined): void;
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getAdapterMapEntry(adapterConf: unknown, options: import("../data_adapters/BaseAdapter").BaseOptions): Promise<import("./assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("../data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
+    /**
+     * #method
+     */
     getRefNameMapForAdapter(adapterConf: unknown, assemblyName: string | undefined, opts: {
         signal?: AbortSignal;
         sessionId: string;
     }): Promise<{
-        [x: string]: string;
+        [x: string]: string | undefined;
     } | undefined>;
+    /**
+     * #method
+     */
     getReverseRefNameMapForAdapter(adapterConf: unknown, assemblyName: string | undefined, opts: {
         signal?: AbortSignal;
         sessionId: string;
     }): Promise<{
-        [x: string]: string;
+        [x: string]: string | undefined;
     } | undefined>;
+    /**
+     * #method
+     */
     isValidRefName(refName: string, assemblyName: string): boolean;
 } & {
     afterAttach(): void;
+    /**
+     * #action
+     * private: you would generally want to add to manipulate
+     * jbrowse.assemblies, session.sessionAssemblies, or
+     * session.temporaryAssemblies instead of using this directly
+     */
     removeAssembly(asm: Assembly): void;
+    /**
+     * #action
+     * private: you would generally want to add to manipulate
+     * jbrowse.assemblies, session.sessionAssemblies, or
+     * session.temporaryAssemblies instead of using this directly
+     *
+     * this can take an active instance of an assembly, in which case it is
+     * referred to, or it can take an identifier e.g. assembly name, which is
+     * used as a reference. snapshots cannot be used
+     */
     addAssembly(configuration: any): void;
+    /**
+     * #action
+     * private: you would generally want to add to manipulate
+     * jbrowse.assemblies, session.sessionAssemblies, or
+     * session.temporaryAssemblies instead of using this directly
+     */
     replaceAssembly(idx: number, configuration: any): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default assemblyManagerFactory;

package/assemblyManager/assemblyManager.js

@@ -8,18 +8,49 @@ const util_1 = require("../util");
 const mobx_1 = require("mobx");
 const configuration_1 = require("../configuration");
 const assembly_1 = __importDefault(require("./assembly"));
+/**
+ * #stateModel AssemblyManager
+ */
 function assemblyManagerFactory(conf, pm) {
     return mobx_state_tree_1.types
         .model({
+        /**
+         * #property
+         * this is automatically managed by an autorun which looks in the parent
+         * session.assemblies, session.sessionAssemblies, and
+         * session.temporaryAssemblies
+         */
         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 => ({
+        /**
+         * #method
+         */
         get(asmName) {
-            return self.assemblies.find(asm => asm.hasName(asmName));
+            return self.assemblyNameMap[asmName];
         },
+        /**
+         * #getter
+         */
         get assemblyNamesList() {
             return this.assemblyList.map(asm => asm.name);
         },
+        /**
+         * #getter
+         * looks at jbrowse.assemblies, session.sessionAssemblies, and
+         * session.temporaryAssemblies to load from
+         */
         get assemblyList() {
             // name is the explicit identifier and can be accessed without getConf,
             // hence the union with {name:string}
@@ -38,8 +69,11 @@ function assemblyManagerFactory(conf, pm) {
         },
     }))
         .views(self => ({
-        // use this method instead of assemblyManager.get(assemblyName)
-        // get an assembly with regions loaded
+        /**
+         * #method
+         * use this method instead of assemblyManager.get(assemblyName)
+         * to get an assembly with regions loaded
+         */
         async waitForAssembly(assemblyName) {
             if (!assemblyName) {
                 throw new Error('no assembly name supplied to waitForAssembly');
@@ -65,6 +99,9 @@ function assemblyManagerFactory(conf, pm) {
             }
             return assembly;
         },
+        /**
+         * #method
+         */
         async getRefNameMapForAdapter(adapterConf, assemblyName, opts) {
             if (assemblyName) {
                 const asm = await this.waitForAssembly(assemblyName);
@@ -72,6 +109,9 @@ function assemblyManagerFactory(conf, pm) {
             }
             return {};
         },
+        /**
+         * #method
+         */
         async getReverseRefNameMapForAdapter(adapterConf, assemblyName, opts) {
             if (assemblyName) {
                 const asm = await this.waitForAssembly(assemblyName);
@@ -79,6 +119,9 @@ function assemblyManagerFactory(conf, pm) {
             }
             return {};
         },
+        /**
+         * #method
+         */
         isValidRefName(refName, assemblyName) {
             const assembly = self.get(assemblyName);
             if (assembly) {
@@ -89,31 +132,47 @@ function assemblyManagerFactory(conf, pm) {
     }))
         .actions(self => ({
         afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(
-            // have to slice it to be properly reacted to
-            () => self.assemblyList, assemblyConfigs => {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(() => self.assemblyList, assemblyConfs => {
                 self.assemblies.forEach(asm => {
                     if (!asm.configuration) {
                         this.removeAssembly(asm);
                     }
                 });
-                assemblyConfigs.forEach(assemblyConfig => {
-                    const existingAssemblyIdx = self.assemblies.findIndex(assembly => assembly.name === (0, configuration_1.readConfObject)(assemblyConfig, 'name'));
-                    if (existingAssemblyIdx === -1) {
-                        this.addAssembly(assemblyConfig);
+                assemblyConfs.forEach(conf => {
+                    if (!self.assemblies.some(a => a.name === (0, configuration_1.readConfObject)(conf, 'name'))) {
+                        this.addAssembly(conf);
                     }
                 });
             }, { fireImmediately: true, name: 'assemblyManagerAfterAttach' }));
         },
+        /**
+         * #action
+         * private: you would generally want to add to manipulate
+         * jbrowse.assemblies, session.sessionAssemblies, or
+         * session.temporaryAssemblies instead of using this directly
+         */
         removeAssembly(asm) {
             self.assemblies.remove(asm);
         },
-        // this can take an active instance of an assembly, in which case it is
-        // referred to, or it can take an identifier e.g. assembly name, which is
-        // used as a reference. snapshots cannot be used
+        /**
+         * #action
+         * private: you would generally want to add to manipulate
+         * jbrowse.assemblies, session.sessionAssemblies, or
+         * session.temporaryAssemblies instead of using this directly
+         *
+         * this can take an active instance of an assembly, in which case it is
+         * referred to, or it can take an identifier e.g. assembly name, which is
+         * used as a reference. snapshots cannot be used
+         */
         addAssembly(configuration) {
             self.assemblies.push({ configuration });
         },
+        /**
+         * #action
+         * private: you would generally want to add to manipulate
+         * jbrowse.assemblies, session.sessionAssemblies, or
+         * session.temporaryAssemblies instead of using this directly
+         */
         replaceAssembly(idx, configuration) {
             self.assemblies[idx] = (0, mobx_state_tree_1.cast)({ configuration });
         },

package/assemblyManager/index.d.ts

@@ -1,2 +1,3 @@
 export { default } from './assemblyManager';
 export { default as assemblyConfigSchemaFactory } from './assemblyConfigSchema';
+export type { BaseAssemblyConfigSchema } from './assemblyConfigSchema';