@jbrowse/core 1.5.0 → 1.5.4

package/ReExports/material-ui-colors.js

@@ -5,118 +5,118 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-Object.defineProperty(exports, "red", {
+Object.defineProperty(exports, "amber", {
   enumerable: true,
   get: function get() {
-    return _red.default;
+    return _amber.default;
   }
 });
-Object.defineProperty(exports, "pink", {
+Object.defineProperty(exports, "blue", {
   enumerable: true,
   get: function get() {
-    return _pink.default;
+    return _blue.default;
   }
 });
-Object.defineProperty(exports, "purple", {
+Object.defineProperty(exports, "blueGrey", {
   enumerable: true,
   get: function get() {
-    return _purple.default;
+    return _blueGrey.default;
   }
 });
-Object.defineProperty(exports, "deepPurple", {
+Object.defineProperty(exports, "brown", {
   enumerable: true,
   get: function get() {
-    return _deepPurple.default;
+    return _brown.default;
   }
 });
-Object.defineProperty(exports, "indigo", {
+Object.defineProperty(exports, "cyan", {
   enumerable: true,
   get: function get() {
-    return _indigo.default;
+    return _cyan.default;
   }
 });
-Object.defineProperty(exports, "blue", {
+Object.defineProperty(exports, "deepOrange", {
   enumerable: true,
   get: function get() {
-    return _blue.default;
+    return _deepOrange.default;
   }
 });
-Object.defineProperty(exports, "lightBlue", {
+Object.defineProperty(exports, "deepPurple", {
   enumerable: true,
   get: function get() {
-    return _lightBlue.default;
+    return _deepPurple.default;
   }
 });
-Object.defineProperty(exports, "cyan", {
+Object.defineProperty(exports, "green", {
   enumerable: true,
   get: function get() {
-    return _cyan.default;
+    return _green.default;
   }
 });
-Object.defineProperty(exports, "teal", {
+Object.defineProperty(exports, "grey", {
   enumerable: true,
   get: function get() {
-    return _teal.default;
+    return _grey.default;
   }
 });
-Object.defineProperty(exports, "green", {
+Object.defineProperty(exports, "indigo", {
   enumerable: true,
   get: function get() {
-    return _green.default;
+    return _indigo.default;
   }
 });
-Object.defineProperty(exports, "lightGreen", {
+Object.defineProperty(exports, "lightBlue", {
   enumerable: true,
   get: function get() {
-    return _lightGreen.default;
+    return _lightBlue.default;
   }
 });
-Object.defineProperty(exports, "lime", {
+Object.defineProperty(exports, "lightGreen", {
   enumerable: true,
   get: function get() {
-    return _lime.default;
+    return _lightGreen.default;
   }
 });
-Object.defineProperty(exports, "yellow", {
+Object.defineProperty(exports, "lime", {
   enumerable: true,
   get: function get() {
-    return _yellow.default;
+    return _lime.default;
   }
 });
-Object.defineProperty(exports, "amber", {
+Object.defineProperty(exports, "orange", {
   enumerable: true,
   get: function get() {
-    return _amber.default;
+    return _orange.default;
   }
 });
-Object.defineProperty(exports, "orange", {
+Object.defineProperty(exports, "pink", {
   enumerable: true,
   get: function get() {
-    return _orange.default;
+    return _pink.default;
   }
 });
-Object.defineProperty(exports, "deepOrange", {
+Object.defineProperty(exports, "purple", {
   enumerable: true,
   get: function get() {
-    return _deepOrange.default;
+    return _purple.default;
   }
 });
-Object.defineProperty(exports, "brown", {
+Object.defineProperty(exports, "red", {
   enumerable: true,
   get: function get() {
-    return _brown.default;
+    return _red.default;
   }
 });
-Object.defineProperty(exports, "grey", {
+Object.defineProperty(exports, "teal", {
   enumerable: true,
   get: function get() {
-    return _grey.default;
+    return _teal.default;
   }
 });
-Object.defineProperty(exports, "blueGrey", {
+Object.defineProperty(exports, "yellow", {
   enumerable: true,
   get: function get() {
-    return _blueGrey.default;
+    return _yellow.default;
   }
 });
 

package/ReExports/modules.d.ts

@@ -11,22 +11,18 @@ import * as MUILab from '@material-ui/lab';
 import * as MUIDataGrid from '@mui/x-data-grid';
 import * as BaseAdapterExports from '../data_adapters/BaseAdapter';
 import * as BaseFeatureDetail from '../BaseFeatureWidget/BaseFeatureDetail';
-import ViewType from '../pluggableElementTypes/ViewType';
-import AdapterType from '../pluggableElementTypes/AdapterType';
-import DisplayType from '../pluggableElementTypes/DisplayType';
-import TrackType from '../pluggableElementTypes/TrackType';
-import WidgetType from '../pluggableElementTypes/WidgetType';
+import * as pluggableElementTypes from '../pluggableElementTypes';
 import * as pluggableElementTypeModels from '../pluggableElementTypes/models';
 import * as ServerSideRendererType from '../pluggableElementTypes/renderers/ServerSideRendererType';
-import CircularChordRendererType from '../pluggableElementTypes/renderers/CircularChordRendererType';
 import * as BoxRendererType from '../pluggableElementTypes/renderers/BoxRendererType';
 import * as FeatureRendererType from '../pluggableElementTypes/renderers/FeatureRendererType';
 import * as RendererType from '../pluggableElementTypes/renderers/RendererType';
 import * as Configuration from '../configuration';
-import * as Plugin from '../Plugin';
+import Plugin from '../Plugin';
 import * as coreUi from '../ui';
 import * as coreUtil from '../util';
 import * as coreColor from '../util/color';
+import * as coreLayouts from '../util/layouts';
 import * as trackUtils from '../util/tracks';
 import * as coreIo from '../util/io';
 import * as coreMstReflection from '../util/mst-reflection';
@@ -117,14 +113,15 @@ declare const libs: {
     '@material-ui/lab/ToggleButton': MUICore.ExtendButtonBase<MUILab.ToggleButtonTypeMap<{}, "button">>;
     '@material-ui/lab/ToggleButtonGroup': typeof MUILab.ToggleButtonGroup;
     '@jbrowse/core/Plugin': typeof Plugin;
-    '@jbrowse/core/pluggableElementTypes/ViewType': typeof ViewType;
-    '@jbrowse/core/pluggableElementTypes/AdapterType': typeof AdapterType;
-    '@jbrowse/core/pluggableElementTypes/DisplayType': typeof DisplayType;
-    '@jbrowse/core/pluggableElementTypes/TrackType': typeof TrackType;
-    '@jbrowse/core/pluggableElementTypes/WidgetType': typeof WidgetType;
+    '@jbrowse/core/pluggableElementTypes': typeof pluggableElementTypes;
+    '@jbrowse/core/pluggableElementTypes/ViewType': typeof pluggableElementTypes.ViewType;
+    '@jbrowse/core/pluggableElementTypes/AdapterType': typeof pluggableElementTypes.AdapterType;
+    '@jbrowse/core/pluggableElementTypes/DisplayType': typeof pluggableElementTypes.DisplayType;
+    '@jbrowse/core/pluggableElementTypes/TrackType': typeof pluggableElementTypes.TrackType;
+    '@jbrowse/core/pluggableElementTypes/WidgetType': typeof pluggableElementTypes.WidgetType;
     '@jbrowse/core/pluggableElementTypes/models': typeof pluggableElementTypeModels;
     '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType': typeof ServerSideRendererType;
-    '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType': typeof CircularChordRendererType;
+    '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType': typeof pluggableElementTypes.CircularChordRendererType;
     '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType': typeof BoxRendererType;
     '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType': typeof FeatureRendererType;
     '@jbrowse/core/pluggableElementTypes/renderers/RendererType': typeof RendererType;
@@ -133,6 +130,7 @@ declare const libs: {
     '@jbrowse/core/ui': typeof coreUi;
     '@jbrowse/core/util': typeof coreUtil;
     '@jbrowse/core/util/color': typeof coreColor;
+    '@jbrowse/core/util/layouts': typeof coreLayouts;
     '@jbrowse/core/util/tracks': typeof trackUtils;
     '@jbrowse/core/util/Base1DViewModel': mst.IModelType<{
         displayedRegions: mst.IArrayType<mst.IModelType<{

package/ReExports/modules.js

@@ -101,6 +101,8 @@ var BaseFeatureDetail = _interopRequireWildcard(require("../BaseFeatureWidget/Ba
 
 var _Base1DViewModel = _interopRequireDefault(require("../util/Base1DViewModel"));
 
+var pluggableElementTypes = _interopRequireWildcard(require("../pluggableElementTypes"));
+
 var _ViewType = _interopRequireDefault(require("../pluggableElementTypes/ViewType"));
 
 var _AdapterType = _interopRequireDefault(require("../pluggableElementTypes/AdapterType"));
@@ -125,7 +127,7 @@ var RendererType = _interopRequireWildcard(require("../pluggableElementTypes/ren
 
 var Configuration = _interopRequireWildcard(require("../configuration"));
 
-var Plugin = _interopRequireWildcard(require("../Plugin"));
+var _Plugin = _interopRequireDefault(require("../Plugin"));
 
 var coreUi = _interopRequireWildcard(require("../ui"));
 
@@ -133,6 +135,8 @@ var coreUtil = _interopRequireWildcard(require("../util"));
 
 var coreColor = _interopRequireWildcard(require("../util/color"));
 
+var coreLayouts = _interopRequireWildcard(require("../util/layouts"));
+
 var trackUtils = _interopRequireWildcard(require("../util/tracks"));
 
 var coreIo = _interopRequireWildcard(require("../util/io"));
@@ -205,7 +209,8 @@ var libs = {
   // @material-ui lab
   '@material-ui/lab/ToggleButton': _ToggleButton.default,
   '@material-ui/lab/ToggleButtonGroup': _ToggleButtonGroup.default,
-  '@jbrowse/core/Plugin': Plugin,
+  '@jbrowse/core/Plugin': _Plugin.default,
+  '@jbrowse/core/pluggableElementTypes': pluggableElementTypes,
   '@jbrowse/core/pluggableElementTypes/ViewType': _ViewType.default,
   '@jbrowse/core/pluggableElementTypes/AdapterType': _AdapterType.default,
   '@jbrowse/core/pluggableElementTypes/DisplayType': _DisplayType.default,
@@ -222,6 +227,7 @@ var libs = {
   '@jbrowse/core/ui': coreUi,
   '@jbrowse/core/util': coreUtil,
   '@jbrowse/core/util/color': coreColor,
+  '@jbrowse/core/util/layouts': coreLayouts,
   '@jbrowse/core/util/tracks': trackUtils,
   '@jbrowse/core/util/Base1DViewModel': _Base1DViewModel.default,
   '@jbrowse/core/util/io': coreIo,

package/TextSearch/BaseResults.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.RefSequenceResult = exports.default = void 0;
+exports.default = exports.RefSequenceResult = void 0;
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
 

package/TextSearch/TextSearchManager.d.ts

@@ -4,8 +4,8 @@ import PluginManager from '../PluginManager';
 import QuickLRU from '../util/QuickLRU';
 import { SearchType, BaseTextSearchAdapter } from '../data_adapters/BaseAdapter';
 export interface BaseArgs {
-    searchType: SearchType;
     queryString: string;
+    searchType?: SearchType;
     signal?: AbortSignal;
     limit?: number;
     pageNumber?: number;
@@ -16,8 +16,8 @@ export interface SearchScope {
     tracks?: Array<string>;
 }
 export default class TextSearchManager {
-    adapterCache: QuickLRU;
     pluginManager: PluginManager;
+    adapterCache: QuickLRU;
     constructor(pluginManager: PluginManager);
     /**
      * Instantiate/initialize list of relevant adapters

package/TextSearch/TextSearchManager.js

@@ -28,8 +28,6 @@ var TextSearchManager = /*#__PURE__*/function () {
   function TextSearchManager(pluginManager) {
     (0, _classCallCheck2.default)(this, TextSearchManager);
     (0, _defineProperty2.default)(this, "adapterCache", void 0);
-    (0, _defineProperty2.default)(this, "pluginManager", void 0);
-    this.pluginManager = pluginManager;
     this.adapterCache = new _QuickLRU.default({
       maxSize: 15
     });

package/assemblyManager/assembly.d.ts

@@ -1,4 +1,5 @@
-import { IAnyType, Instance } from 'mobx-state-tree';
+import { Instance, IAnyType } from 'mobx-state-tree';
+import { Feature } from '../util/simpleFeature';
 import PluginManager from '../PluginManager';
 import { Region } from '../util/types';
 declare type RefNameAliases = Record<string, string>;
@@ -21,6 +22,7 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pluginMana
     refNameAliases: {
         [key: string]: string;
     } | undefined;
+    cytobands: Feature[] | undefined;
 } & {
     readonly initialized: boolean;
     readonly name: string;
@@ -37,27 +39,38 @@ export default function assemblyFactory(assemblyConfigType: IAnyType, pluginMana
     isValidRefName(refName: string): boolean;
 } & {
     setLoading(): void;
-    setLoaded({ adapterRegionsWithAssembly, refNameAliases, }: {
+    setLoaded({ adapterRegionsWithAssembly, refNameAliases, cytobands, }: {
         adapterRegionsWithAssembly: Region[];
         refNameAliases: RefNameAliases;
+        cytobands: Feature[];
     }): void;
-    setError(error: Error): void;
+    setError(e: Error): void;
     setRegions(regions: Region[]): void;
     setRefNameAliases(refNameAliases: RefNameAliases): void;
+    setCytobands(cytobands: Feature[]): void;
     afterAttach(): void;
 } & {
     getAdapterMapEntry(adapterConf: unknown, options: BaseOptions): Promise<{
-        forwardMap: Record<string, string>;
-        reverseMap: Record<string, string>;
+        forwardMap: {
+            [k: string]: string;
+        };
+        reverseMap: {
+            [k: string]: string;
+        };
     }>;
     /**
      * get Map of `canonical-name -> adapter-specific-name`
      */
-    getRefNameMapForAdapter(adapterConf: unknown, opts: BaseOptions): Promise<Record<string, string>>;
+    getRefNameMapForAdapter(adapterConf: unknown, opts: BaseOptions): Promise<{
+        [k: string]: string;
+    }>;
     /**
      * get Map of `adapter-specific-name -> canonical-name`
      */
-    getReverseRefNameMapForAdapter(adapterConf: unknown, opts: BaseOptions): Promise<Record<string, string>>;
+    getReverseRefNameMapForAdapter(adapterConf: unknown, opts: BaseOptions): Promise<{
+        [k: string]: string;
+    }>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export declare type Assembly = Instance<ReturnType<typeof assemblyFactory>>;
+export declare type AssemblyModel = ReturnType<typeof assemblyFactory>;
+export declare type Assembly = Instance<AssemblyModel>;
 export {};