@jbrowse/core 2.1.7 → 2.2.0

package/assemblyManager/assemblyManager.d.ts

@@ -1,11 +1,14 @@
-import { Instance, IAnyType } from 'mobx-state-tree';
+import { IAnyType } from 'mobx-state-tree';
+import { Assembly } from './assembly';
 import PluginManager from '../PluginManager';
-export default function assemblyManagerFactory(assemblyConfigType: IAnyType, pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+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: Error | undefined;
-        regions: import("./assembly").BasicRegion[] | undefined;
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
             [x: string]: string;
         } | undefined;
@@ -16,41 +19,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     } & {
         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 refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: Error): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCase: {
+        }, lcAliases: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
-        afterAttach(): 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<{
@@ -61,11 +58,13 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
-    get(assemblyName: string): ({
+    get(asmName: string): ({
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: Error | undefined;
-        regions: import("./assembly").BasicRegion[] | undefined;
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
             [x: string]: string;
         } | undefined;
@@ -76,41 +75,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     } & {
         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 refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: Error): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCase: {
+        }, lcAliases: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
-        afterAttach(): 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<{
@@ -122,8 +115,10 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
-        error: Error | undefined;
-        regions: import("./assembly").BasicRegion[] | undefined;
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
             [x: string]: string;
         } | undefined;
@@ -134,41 +129,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     } & {
         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 refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: Error): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCase: {
+        }, lcAliases: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
-        afterAttach(): 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<{
@@ -178,23 +167,21 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             [x: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
-    readonly assemblyNamesList: string[];
+    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("../configuration").AnyConfigurationSchemaType> & {
-        name: string;
-    })[];
+    } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
     readonly rpcManager: any;
-    readonly pluginManager: any;
-    readonly allPossibleRefNames: string[] | undefined;
 } & {
     waitForAssembly(assemblyName: string): Promise<({
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: Error | undefined;
-        regions: import("./assembly").BasicRegion[] | undefined;
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
             [x: string]: string;
         } | undefined;
@@ -205,41 +192,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     } & {
         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 refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: Error): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCase: {
+        }, lcAliases: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
-        afterAttach(): 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<{
@@ -251,8 +232,10 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
-        error: Error | undefined;
-        regions: import("./assembly").BasicRegion[] | undefined;
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("./assembly").BasicRegion[] | undefined;
         refNameAliases: {
             [x: string]: string;
         } | undefined;
@@ -263,41 +246,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     } & {
         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 refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: Error): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("./assembly").Loading): void;
+        setError(e: unknown): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCase: {
+        }, lcAliases: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("../util").Feature[]): void;
-        afterAttach(): 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<{
@@ -319,126 +296,11 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
     }): Promise<{
         [x: string]: string;
     } | undefined>;
-    isValidRefName(refName: string, assemblyName?: string): boolean;
+    isValidRefName(refName: string, assemblyName: string): boolean;
 } & {
-    removeAssembly(asm: {
-        configuration: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: Error | undefined;
-        regions: import("./assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("../util").Feature[] | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly aliases: string[];
-        readonly displayName: string | undefined;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly refNames: string[] | undefined;
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
-        readonly refNameColors: string[];
-    } & {
-        getCanonicalRefName(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-    } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: Error): void;
-        setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }, lowerCase: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util").Feature[]): void;
-        afterAttach(): void;
-    } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
-    }, {
-        error: Error | undefined;
-        regions: import("./assembly").BasicRegion[] | undefined;
-        refNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        lowerCaseRefNameAliases: {
-            [x: string]: string;
-        } | undefined;
-        cytobands: import("../util").Feature[] | undefined;
-    } & {
-        readonly initialized: boolean;
-        readonly name: string;
-        readonly aliases: string[];
-        readonly displayName: string | undefined;
-        hasName(name: string): boolean;
-        readonly allAliases: string[];
-        readonly refNames: string[] | undefined;
-        readonly allRefNames: string[] | undefined;
-        readonly lowerCaseRefNames: string[] | undefined;
-        readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
-        readonly refNameColors: string[];
-    } & {
-        getCanonicalRefName(refName: string): string;
-        getRefNameColor(refName: string): string | undefined;
-        isValidRefName(refName: string): boolean;
-    } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("../util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("../util").Feature[];
-        }): void;
-        setError(e: Error): void;
-        setRegions(regions: import("../util").Region[]): void;
-        setRefNameAliases(aliases: {
-            [x: string]: string;
-        }, lowerCase: {
-            [x: string]: string;
-        }): void;
-        setCytobands(cytobands: import("../util").Feature[]): void;
-        afterAttach(): void;
-    } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<import("./assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
-            [x: string]: string;
-        }>;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
     afterAttach(): void;
-    addAssembly(assemblyConfig: Instance<typeof assemblyConfigType> | string): void;
-    replaceAssembly(idx: number, assemblyConfig: Instance<typeof assemblyConfigType> | string): void;
+    removeAssembly(asm: Assembly): void;
+    addAssembly(configuration: any): void;
+    replaceAssembly(idx: number, configuration: any): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default assemblyManagerFactory;

package/assemblyManager/assemblyManager.js

@@ -3,20 +3,19 @@ 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 util_1 = require("../util");
+const mobx_1 = require("mobx");
 const configuration_1 = require("../configuration");
 const assembly_1 = __importDefault(require("./assembly"));
-function assemblyManagerFactory(assemblyConfigType, pluginManager) {
-    const Assembly = (0, assembly_1.default)(assemblyConfigType, pluginManager);
+function assemblyManagerFactory(conf, pm) {
     return mobx_state_tree_1.types
         .model({
-        assemblies: mobx_state_tree_1.types.array(Assembly),
+        assemblies: mobx_state_tree_1.types.array((0, assembly_1.default)(conf, pm)),
     })
         .views(self => ({
-        get(assemblyName) {
-            return self.assemblies.find(assembly => assembly.hasName(assemblyName));
+        get(asmName) {
+            return self.assemblies.find(asm => asm.hasName(asmName));
         },
         get assemblyNamesList() {
             return this.assemblyList.map(asm => asm.name);
@@ -37,20 +36,6 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
             // eslint-disable-next-line @typescript-eslint/no-explicit-any
             return (0, mobx_state_tree_1.getParent)(self).rpcManager;
         },
-        get pluginManager() {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            return (0, mobx_state_tree_1.getParent)(self).pluginManager;
-        },
-        get allPossibleRefNames() {
-            let refNames = [];
-            for (const assembly of self.assemblies) {
-                if (!assembly.allRefNames) {
-                    return undefined;
-                }
-                refNames = refNames.concat(assembly.allRefNames);
-            }
-            return refNames;
-        },
     }))
         .views(self => ({
         // use this method instead of assemblyManager.get(assemblyName)
@@ -72,6 +57,7 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
             if (!assembly) {
                 return undefined;
             }
+            await assembly.load();
             await (0, util_1.when)(() => Boolean((assembly === null || assembly === void 0 ? void 0 : assembly.regions) && assembly.refNameAliases) ||
                 !!(assembly === null || assembly === void 0 ? void 0 : assembly.error));
             if (assembly.error) {
@@ -94,23 +80,14 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
             return {};
         },
         isValidRefName(refName, assemblyName) {
-            if (assemblyName) {
-                const assembly = self.get(assemblyName);
-                if (assembly) {
-                    return assembly.isValidRefName(refName);
-                }
-                throw new Error(`isValidRefName for ${assemblyName} failed, assembly does not exist`);
-            }
-            if (!self.allPossibleRefNames) {
-                throw new Error(`isValidRefName not available, assemblyManager has not yet finished loading. If you are looking for a refname in a specific assembly, pass assembly argument`);
+            const assembly = self.get(assemblyName);
+            if (assembly) {
+                return assembly.isValidRefName(refName);
             }
-            return self.allPossibleRefNames.includes(refName);
+            throw new Error(`isValidRefName for ${assemblyName} failed, assembly does not exist`);
         },
     }))
         .actions(self => ({
-        removeAssembly(asm) {
-            self.assemblies.remove(asm);
-        },
         afterAttach() {
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(
             // have to slice it to be properly reacted to
@@ -128,16 +105,17 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
                 });
             }, { fireImmediately: true, name: 'assemblyManagerAfterAttach' }));
         },
+        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
-        addAssembly(assemblyConfig) {
-            self.assemblies.push({ configuration: assemblyConfig });
+        addAssembly(configuration) {
+            self.assemblies.push({ configuration });
         },
-        replaceAssembly(idx, assemblyConfig) {
-            self.assemblies[idx] = (0, mobx_state_tree_1.cast)({
-                configuration: assemblyConfig,
-            });
+        replaceAssembly(idx, configuration) {
+            self.assemblies[idx] = (0, mobx_state_tree_1.cast)({ configuration });
         },
     }));
 }

package/data_adapters/CytobandAdapter.js

@@ -8,7 +8,14 @@ const simpleFeature_1 = __importDefault(require("../util/simpleFeature"));
 const configuration_1 = require("../configuration");
 const io_1 = require("../util/io");
 const BaseAdapter_1 = require("./BaseAdapter");
+/**
+ * #config CytobandAdapter
+ */
+function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const configSchema = (0, configuration_1.ConfigurationSchema)('CytobandAdapter', {
+    /**
+     * #slot
+     */
     cytobandLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/cytoband.txt.gz' },

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.1.7",
+  "version": "2.2.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -73,5 +73,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "a1344081f61e22e0f597517efa7386023eef9f33"
+  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
 }