@jbrowse/core 1.5.0 → 1.5.4

package/assemblyManager/assemblyManager.d.ts

@@ -1,4 +1,4 @@
-import { IAnyType, Instance } from 'mobx-state-tree';
+import { Instance, IAnyType } from 'mobx-state-tree';
 import PluginManager from '../PluginManager';
 export default function assemblyManagerFactory(assemblyConfigType: IAnyType, pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -9,6 +9,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
+        cytobands: import("../util/simpleFeature").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -25,25 +26,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            cytobands: import("../util/simpleFeature").Feature[];
         }): void;
-        setError(error: Error): void;
+        setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
+        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: Record<string, string>;
-            reverseMap: Record<string, string>;
+            forwardMap: {
+                [k: string]: string;
+            };
+            reverseMap: {
+                [k: string]: string;
+            };
+        }>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
         }>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 }, {
     get(assemblyName: string): (import("mobx-state-tree").ModelInstanceTypeProps<{
@@ -54,6 +65,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
+        cytobands: import("../util/simpleFeature").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -70,25 +82,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            cytobands: import("../util/simpleFeature").Feature[];
         }): void;
-        setError(error: Error): void;
+        setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
+        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: Record<string, string>;
-            reverseMap: Record<string, string>;
+            forwardMap: {
+                [k: string]: string;
+            };
+            reverseMap: {
+                [k: string]: string;
+            };
+        }>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
         }>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
@@ -97,6 +119,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
+        cytobands: import("../util/simpleFeature").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -113,25 +136,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            cytobands: import("../util/simpleFeature").Feature[];
         }): void;
-        setError(error: Error): void;
+        setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
+        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: Record<string, string>;
-            reverseMap: Record<string, string>;
+            forwardMap: {
+                [k: string]: string;
+            };
+            reverseMap: {
+                [k: string]: string;
+            };
+        }>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
         }>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     readonly assemblyNamesList: string[];
     readonly assemblyList: (import("mobx-state-tree").ModelInstanceTypeProps<Record<string, any>> & {
@@ -151,6 +184,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
+        cytobands: import("../util/simpleFeature").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -167,25 +201,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            cytobands: import("../util/simpleFeature").Feature[];
         }): void;
-        setError(error: Error): void;
+        setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
+        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: Record<string, string>;
-            reverseMap: Record<string, string>;
+            forwardMap: {
+                [k: string]: string;
+            };
+            reverseMap: {
+                [k: string]: string;
+            };
+        }>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
         }>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
@@ -194,6 +238,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
+        cytobands: import("../util/simpleFeature").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -210,34 +255,48 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            cytobands: import("../util/simpleFeature").Feature[];
         }): void;
-        setError(error: Error): void;
+        setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
+        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: Record<string, string>;
-            reverseMap: Record<string, string>;
+            forwardMap: {
+                [k: string]: string;
+            };
+            reverseMap: {
+                [k: string]: string;
+            };
+        }>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
         }>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined>;
     getRefNameMapForAdapter(adapterConf: unknown, assemblyName: string, opts: {
         signal?: AbortSignal;
         sessionId: string;
-    }): Promise<Record<string, string> | undefined>;
+    }): Promise<{
+        [k: string]: string;
+    } | undefined>;
     getReverseRefNameMapForAdapter(adapterConf: unknown, assemblyName: string, opts: {
         signal?: AbortSignal;
         sessionId: string;
-    }): Promise<Record<string, string> | undefined>;
+    }): Promise<{
+        [k: string]: string;
+    } | undefined>;
     isValidRefName(refName: string, assemblyName?: string | undefined): boolean;
 } & {
     removeAssembly(asm: import("mobx-state-tree").ModelInstanceTypeProps<{
@@ -248,6 +307,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
+        cytobands: import("../util/simpleFeature").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -264,25 +324,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            cytobands: import("../util/simpleFeature").Feature[];
         }): void;
-        setError(error: Error): void;
+        setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
+        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: Record<string, string>;
-            reverseMap: Record<string, string>;
+            forwardMap: {
+                [k: string]: string;
+            };
+            reverseMap: {
+                [k: string]: string;
+            };
+        }>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
         }>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
     }, {
@@ -291,6 +361,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
+        cytobands: import("../util/simpleFeature").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -307,25 +378,35 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         isValidRefName(refName: string): boolean;
     } & {
         setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, }: {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
             adapterRegionsWithAssembly: import("../util").Region[];
             refNameAliases: {
                 [x: string]: string;
             };
+            cytobands: import("../util/simpleFeature").Feature[];
         }): void;
-        setError(error: Error): void;
+        setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
+        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
-            forwardMap: Record<string, string>;
-            reverseMap: Record<string, string>;
+            forwardMap: {
+                [k: string]: string;
+            };
+            reverseMap: {
+                [k: string]: string;
+            };
+        }>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<{
+            [k: string]: string;
         }>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("./assembly").BaseOptions): Promise<Record<string, string>>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>): void;
     afterAttach(): void;
     addAssembly(assemblyConfig: Instance<typeof assemblyConfigType> | string): void;

package/assemblyManager/index.d.ts

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

package/assemblyManager/index.js

@@ -5,19 +5,19 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-Object.defineProperty(exports, "default", {
+Object.defineProperty(exports, "assemblyConfigSchemaFactory", {
   enumerable: true,
   get: function get() {
-    return _assemblyManager.default;
+    return _assemblyConfigSchema.default;
   }
 });
-Object.defineProperty(exports, "assemblyConfigSchemas", {
+Object.defineProperty(exports, "default", {
   enumerable: true,
   get: function get() {
-    return _assemblyConfigSchemas.default;
+    return _assemblyManager.default;
   }
 });
 
 var _assemblyManager = _interopRequireDefault(require("./assemblyManager"));
 
-var _assemblyConfigSchemas = _interopRequireDefault(require("./assemblyConfigSchemas"));
+var _assemblyConfigSchema = _interopRequireDefault(require("./assemblyConfigSchema"));

package/configuration/configurationSchema.js

@@ -5,8 +5,8 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.ConfigurationSchema = ConfigurationSchema;
 exports.ConfigurationReference = ConfigurationReference;
+exports.ConfigurationSchema = ConfigurationSchema;
 
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
@@ -22,9 +22,9 @@ var _configurationSlot = _interopRequireDefault(require("./configurationSlot"));
 
 var _util = require("./util");
 
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
 
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 function isEmptyObject(thing) {
   return (0, _typeof2.default)(thing) === 'object' && !Array.isArray(thing) && thing !== null && Object.keys(thing).length === 0;
@@ -141,7 +141,9 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
   });
 
   if (Object.keys(volatileConstants).length) {
-    completeModel = completeModel.volatile(function () {
+    completeModel = completeModel.volatile(function
+      /* self */
+    () {
       return volatileConstants;
     });
   }
@@ -199,9 +201,7 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
     completeModel = completeModel.preProcessSnapshot(options.preProcessSnapshot);
   }
 
-  var schemaType = _mobxStateTree.types.optional(completeModel, modelDefault);
-
-  return schemaType;
+  return _mobxStateTree.types.optional(completeModel, modelDefault);
 }
 
 function ConfigurationSchema(modelName, inputSchemaDefinition, inputOptions) {

package/configuration/configurationSlot.js

@@ -16,7 +16,9 @@ var _jexlStrings = require("../util/jexlStrings");
 var _mst = require("../util/types/mst");
 
 /* eslint-disable @typescript-eslint/no-explicit-any */
-function isValidColorString() {
+function
+  /* str */
+isValidColorString() {
   // TODO: check all the crazy cases for whether it's a valid HTML/CSS color string
   return true;
 }

package/configuration/index.js

@@ -7,16 +7,16 @@ var _exportNames = {
   ConfigurationSchema: true,
   ConfigurationReference: true
 };
-Object.defineProperty(exports, "ConfigurationSchema", {
+Object.defineProperty(exports, "ConfigurationReference", {
   enumerable: true,
   get: function get() {
-    return _configurationSchema.ConfigurationSchema;
+    return _configurationSchema.ConfigurationReference;
   }
 });
-Object.defineProperty(exports, "ConfigurationReference", {
+Object.defineProperty(exports, "ConfigurationSchema", {
   enumerable: true,
   get: function get() {
-    return _configurationSchema.ConfigurationReference;
+    return _configurationSchema.ConfigurationSchema;
   }
 });
 

package/configuration/util.js

@@ -5,13 +5,13 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.readConfObject = readConfObject;
 exports.getConf = getConf;
 exports.getTypeNamesFromExplicitlyTypedUnion = getTypeNamesFromExplicitlyTypedUnion;
 exports.isBareConfigurationSchemaType = isBareConfigurationSchemaType;
-exports.isConfigurationSchemaType = isConfigurationSchemaType;
 exports.isConfigurationModel = isConfigurationModel;
+exports.isConfigurationSchemaType = isConfigurationSchemaType;
 exports.isConfigurationSlotType = isConfigurationSlotType;
+exports.readConfObject = readConfObject;
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 

package/data_adapters/BaseAdapter.d.ts

@@ -2,7 +2,7 @@ import { Observable } from 'rxjs';
 import { Feature } from '../util/simpleFeature';
 import { AnyConfigurationModel } from '../configuration/configurationSchema';
 import { getSubAdapterType } from './dataAdapterCache';
-import { Region, NoAssemblyRegion } from '../util/types';
+import { AugmentedRegion as Region, NoAssemblyRegion } from '../util/types';
 import BaseResult from '../TextSearch/BaseResults';
 import PluginManager from '../PluginManager';
 export interface BaseOptions {
@@ -26,12 +26,12 @@ export interface AnyAdapter {
 }
 export declare type AnyDataAdapter = BaseAdapter | BaseFeatureDataAdapter | BaseRefNameAliasAdapter | BaseTextSearchAdapter | RegionsAdapter | SequenceAdapter;
 export declare abstract class BaseAdapter {
+    config: AnyConfigurationModel;
+    getSubAdapter?: getSubAdapterType | undefined;
+    pluginManager?: PluginManager | undefined;
     id: string;
     static capabilities: string[];
-    config: AnyConfigurationModel;
-    getSubAdapter?: getSubAdapterType;
-    pluginManager: PluginManager | undefined;
-    constructor(config?: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    constructor(config?: AnyConfigurationModel, getSubAdapter?: getSubAdapterType | undefined, pluginManager?: PluginManager | undefined);
     /**
      * Called to provide a hint that data tied to a certain region will not be
      * needed for the forseeable future and can be purged from caches, etc

package/data_adapters/BaseAdapter.js

@@ -5,12 +5,12 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.isSequenceAdapter = isSequenceAdapter;
-exports.isRegionsAdapter = isRegionsAdapter;
+exports.BaseFeatureDataAdapter = exports.BaseAdapter = void 0;
 exports.isFeatureAdapter = isFeatureAdapter;
 exports.isRefNameAliasAdapter = isRefNameAliasAdapter;
+exports.isRegionsAdapter = isRegionsAdapter;
+exports.isSequenceAdapter = isSequenceAdapter;
 exports.isTextSearchAdapter = isTextSearchAdapter;
-exports.BaseFeatureDataAdapter = exports.BaseAdapter = void 0;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -18,14 +18,14 @@ var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers
 
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
 var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
 
 var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
 
 var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
 
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
@@ -50,20 +50,12 @@ function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflec
 
 function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
 
-var BaseAdapter = function BaseAdapter() {
-  var config = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : (0, _configurationSchema.ConfigurationSchema)('empty', {}).create();
-  var getSubAdapter = arguments.length > 1 ? arguments[1] : undefined;
-  var pluginManager = arguments.length > 2 ? arguments[2] : undefined;
+var BaseAdapter = /*#__PURE__*/(0, _createClass2.default)(function BaseAdapter(config = (0, _configurationSchema.ConfigurationSchema)('empty', {}).create(), getSubAdapter, pluginManager) {
   (0, _classCallCheck2.default)(this, BaseAdapter);
   (0, _defineProperty2.default)(this, "id", void 0);
-  (0, _defineProperty2.default)(this, "config", void 0);
-  (0, _defineProperty2.default)(this, "getSubAdapter", void 0);
-  (0, _defineProperty2.default)(this, "pluginManager", void 0);
-  this.config = config;
-  this.getSubAdapter = getSubAdapter;
-  this.pluginManager = pluginManager; // note: we use switch on jest here for more simple feature IDs
-  // in test environment
 
+  // note: we use switch on jest here for more simple feature IDs
+  // in test environment
   if (typeof jest === 'undefined') {
     var data = (0, _mobxStateTree.isStateTreeNode)(config) ? (0, _mobxStateTree.getSnapshot)(config) : config;
     this.id = "".concat((0, _idMaker.default)(data));
@@ -76,13 +68,12 @@ var BaseAdapter = function BaseAdapter() {
  * needed for the forseeable future and can be purged from caches, etc
  * @param region - Region
  */
-;
+);
 /**
  * Base class for feature adapters to extend. Defines some methods that
  * subclasses must implement.
  */
 
-
 exports.BaseAdapter = BaseAdapter;
 (0, _defineProperty2.default)(BaseAdapter, "capabilities", []);
 

package/data_adapters/CytobandAdapter.d.ts

@@ -0,0 +1,8 @@
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { BaseAdapter } from './BaseAdapter';
+declare const configSchema: import("../configuration/configurationSchema").AnyConfigurationSchemaType;
+declare class CytobandAdapter extends BaseAdapter {
+    getData(): Promise<SimpleFeature[]>;
+    freeResources(): void;
+}
+export { configSchema, CytobandAdapter as DataAdapter };