@jbrowse/core 2.4.1 → 2.5.0

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 +50,27 @@ 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>>;
 }, {
+    /**
+     * #method
+     */
     get(asmName: string): ({
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -66,10 +79,10 @@ 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 +96,12 @@ 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 +109,21 @@ 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 +133,10 @@ 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 +150,12 @@ 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 +163,44 @@ 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 +209,10 @@ 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 +226,12 @@ 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 +239,21 @@ 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 +263,10 @@ 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 +280,12 @@ 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 +293,71 @@ 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 +8,38 @@ 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 => ({
+        /**
+         * #method
+         */
         get(asmName) {
             return self.assemblies.find(asm => asm.hasName(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 +58,11 @@ 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 +88,9 @@ function assemblyManagerFactory(conf, pm) {
             }
             return assembly;
         },
+        /**
+         * #method
+         */
         async getRefNameMapForAdapter(adapterConf, assemblyName, opts) {
             if (assemblyName) {
                 const asm = await this.waitForAssembly(assemblyName);
@@ -72,6 +98,9 @@ function assemblyManagerFactory(conf, pm) {
             }
             return {};
         },
+        /**
+         * #method
+         */
         async getReverseRefNameMapForAdapter(adapterConf, assemblyName, opts) {
             if (assemblyName) {
                 const asm = await this.waitForAssembly(assemblyName);
@@ -79,6 +108,9 @@ function assemblyManagerFactory(conf, pm) {
             }
             return {};
         },
+        /**
+         * #method
+         */
         isValidRefName(refName, assemblyName) {
             const assembly = self.get(assemblyName);
             if (assembly) {
@@ -89,31 +121,47 @@ 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/configuration/configurationSchema.d.ts

@@ -1,29 +1,29 @@
-import { Instance, IAnyType } from 'mobx-state-tree';
+import { IAnyType } from 'mobx-state-tree';
 import { ConfigSlotDefinition } from './configurationSlot';
+import { AnyConfigurationSchemaType } from './types';
+export type { AnyConfigurationSchemaType, AnyConfigurationModel, AnyConfigurationSlot, AnyConfigurationSlotType, } from './types';
 export interface ConfigurationSchemaDefinition {
     [n: string]: ConfigSlotDefinition | ConfigurationSchemaDefinition | string | number | IAnyType;
 }
-interface ConfigurationSchemaOptions {
+export interface ConfigurationSchemaOptions<BASE_SCHEMA extends AnyConfigurationSchemaType | undefined, EXPLICIT_IDENTIFIER extends string | undefined> {
     explicitlyTyped?: boolean;
-    explicitIdentifier?: string;
+    explicitIdentifier?: EXPLICIT_IDENTIFIER;
     implicitIdentifier?: string | boolean;
-    baseConfiguration?: AnyConfigurationSchemaType;
+    baseConfiguration?: BASE_SCHEMA;
     actions?: (self: unknown) => any;
     views?: (self: unknown) => any;
     extend?: (self: unknown) => any;
     preProcessSnapshot?: (snapshot: {}) => {};
 }
-declare function makeConfigurationSchemaModel<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions>(modelName: string, schemaDefinition: DEFINITION, options: OPTIONS): import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<Record<string, any>, {
+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: unknown): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-export interface AnyConfigurationSchemaType extends ReturnType<typeof makeConfigurationSchemaModel> {
+export interface ConfigurationSchemaType<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions<any, any>> extends ReturnType<typeof makeConfigurationSchemaModel<DEFINITION, OPTIONS>> {
     isJBrowseConfigurationSchema: boolean;
-    jbrowseSchemaDefinition: ConfigurationSchemaDefinition;
-    jbrowseSchemaOptions: ConfigurationSchemaOptions;
+    jbrowseSchemaDefinition: DEFINITION;
+    jbrowseSchemaOptions: OPTIONS;
     type: string;
+    [key: string]: unknown;
 }
-export type AnyConfigurationModel = Instance<AnyConfigurationSchemaType>;
-export type ConfigurationModel<SCHEMA extends AnyConfigurationSchemaType> = Instance<SCHEMA>;
-export declare function ConfigurationSchema<DEFINITION extends ConfigurationSchemaDefinition, OPTIONS extends ConfigurationSchemaOptions>(modelName: string, inputSchemaDefinition: DEFINITION, inputOptions?: OPTIONS): AnyConfigurationSchemaType;
-export declare function ConfigurationReference(schemaType: IAnyType): import("mobx-state-tree").ITypeUnion<any, any, any>;
-export {};
+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;

package/configuration/configurationSchema.js

@@ -4,6 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ConfigurationReference = exports.ConfigurationSchema = void 0;
+/* eslint-disable @typescript-eslint/no-explicit-any */
 const mobx_state_tree_1 = require("mobx-state-tree");
 const mst_1 = require("../util/types/mst");
 const configurationSlot_1 = __importDefault(require("./configurationSlot"));
@@ -41,7 +42,6 @@ function preprocessConfigurationSchemaArguments(modelName, inputSchemaDefinition
 }
 function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
     // now assemble the MST model of the configuration schema
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const modelDefinition = {};
     let identifier;
     if (options.explicitlyTyped) {
@@ -70,7 +70,6 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
             identifier = 'id';
         }
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     const volatileConstants = {
         isJBrowseConfigurationSchema: true,
         jbrowseSchema: {
@@ -181,6 +180,9 @@ function ConfigurationSchema(modelName, inputSchemaDefinition, inputOptions) {
 }
 exports.ConfigurationSchema = ConfigurationSchema;
 function ConfigurationReference(schemaType) {
+    // we cast this to SCHEMATYPE, because the reference *should* behave just
+    // like the object it points to. It won't be undefined (this is a
+    // `reference`, not a `safeReference`)
     return mobx_state_tree_1.types.union(mobx_state_tree_1.types.reference(schemaType), schemaType);
 }
 exports.ConfigurationReference = ConfigurationReference;

package/configuration/configurationSlot.d.ts

@@ -1,5 +1,6 @@
 import { IAnyModelType, IAnyComplexType } from 'mobx-state-tree';
 export interface ConfigSlotDefinition {
+    /** human-readable description of the slot's meaning */
     description?: string;
     /** custom base MST model for the slot's value */
     model?: IAnyModelType | IAnyComplexType;

package/configuration/index.d.ts

@@ -1,3 +1,3 @@
 export { ConfigurationSchema, ConfigurationReference, } from './configurationSchema';
-export type { AnyConfigurationModel, AnyConfigurationSchemaType, } from './configurationSchema';
+export type { AnyConfigurationSchemaType, AnyConfigurationModel, AnyConfigurationSlot, AnyConfigurationSlotType, } from './types';
 export * from './util';

package/configuration/types.d.ts

@@ -0,0 +1,13 @@
+import type { IStateTreeNode, Instance } from 'mobx-state-tree';
+import type { ConfigurationSchemaType, ConfigurationSchemaOptions } from './configurationSchema';
+import type ConfigSlot from './configurationSlot';
+export type GetOptions<SCHEMA> = SCHEMA extends ConfigurationSchemaType<any, infer OPTIONS> ? OPTIONS : never;
+export type GetBase<SCHEMA> = SCHEMA extends undefined ? never : GetOptions<SCHEMA> extends ConfigurationSchemaOptions<undefined, any> ? undefined : GetOptions<SCHEMA> extends ConfigurationSchemaOptions<infer BASE extends AnyConfigurationSchemaType, any> ? BASE : never;
+export type GetExplicitIdentifier<SCHEMA> = GetOptions<SCHEMA> extends ConfigurationSchemaOptions<any, infer EXPLICIT_IDENTIFIER extends string> ? EXPLICIT_IDENTIFIER : never;
+export type ConfigurationSchemaForModel<MODEL> = MODEL extends IStateTreeNode<infer SCHEMA extends AnyConfigurationSchemaType> ? SCHEMA : never;
+export type ConfigurationSlotName<SCHEMA> = SCHEMA extends undefined ? never : SCHEMA extends ConfigurationSchemaType<infer D, any> ? (keyof D & string) | GetExplicitIdentifier<SCHEMA> | (GetBase<SCHEMA> extends ConfigurationSchemaType<any, any> ? ConfigurationSlotName<GetBase<SCHEMA>> : never) : never;
+export type AnyConfigurationSchemaType = ConfigurationSchemaType<any, any>;
+export type AnyConfigurationModel = Instance<AnyConfigurationSchemaType>;
+export type AnyConfigurationSlotType = ReturnType<typeof ConfigSlot>;
+export type AnyConfigurationSlot = Instance<AnyConfigurationSlotType>;
+export type ConfigurationModel<SCHEMA extends AnyConfigurationSchemaType> = Instance<SCHEMA>;

package/configuration/types.js

@@ -0,0 +1,2 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });