@jbrowse/core 1.4.1 → 1.5.2

package/BaseFeatureWidget/BaseFeatureDetail.d.ts

@@ -2,7 +2,7 @@ import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { BaseCardProps, BaseProps } from './types';
 import { SimpleFeatureSerialized } from '../util/simpleFeature';
-export declare const useStyles: (props?: any) => Record<"expandIcon" | "expansionPanelDetails" | "field" | "fieldDescription" | "fieldName" | "fieldValue" | "fieldSubvalue", string>;
+export declare const useStyles: (props?: any) => import("@material-ui/styles").ClassNameMap<"expandIcon" | "expansionPanelDetails" | "field" | "fieldDescription" | "fieldName" | "fieldValue" | "fieldSubvalue">;
 export declare function BaseCard({ children, title, defaultExpanded, }: BaseCardProps): JSX.Element;
 export declare const FieldName: ({ description, name, prefix, }: {
     description?: React.ReactNode;
@@ -22,7 +22,7 @@ export declare const BaseCoreDetails: (props: BaseProps) => JSX.Element;
 interface AttributeProps {
     attributes: Record<string, any>;
     omit?: string[];
-    formatter?: (val: unknown, key: string) => JSX.Element;
+    formatter?: (val: unknown, key: string) => React.ReactElement;
     descriptions?: Record<string, React.ReactNode>;
     prefix?: string[];
 }
@@ -32,7 +32,7 @@ export interface BaseInputProps extends BaseCardProps {
     omit?: string[];
     model: any;
     descriptions?: Record<string, React.ReactNode>;
-    formatter?: (val: unknown, key: string) => JSX.Element;
+    formatter?: (val: unknown, key: string) => React.ReactElement;
 }
 export declare const FeatureDetails: (props: {
     model: IAnyStateTreeNode;
@@ -42,7 +42,7 @@ export declare const FeatureDetails: (props: {
     };
     depth?: number | undefined;
     omit?: string[] | undefined;
-    formatter?: ((val: unknown, key: string) => JSX.Element) | undefined;
+    formatter?: ((val: unknown, key: string) => React.ReactElement) | undefined;
 }) => JSX.Element;
 declare const BaseFeatureDetails: (props: BaseInputProps) => JSX.Element | null;
 export default BaseFeatureDetails;

package/BaseFeatureWidget/BaseFeatureDetail.js

@@ -2,23 +2,26 @@
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
+var _typeof = require("@babel/runtime/helpers/typeof");
+
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
+exports.BaseAttributes = exports.Attributes = void 0;
 exports.BaseCard = BaseCard;
-exports.default = exports.FeatureDetails = exports.BaseAttributes = exports.Attributes = exports.BaseCoreDetails = exports.SimpleValue = exports.BasicValue = exports.FieldName = exports.useStyles = void 0;
+exports.useStyles = exports.default = exports.SimpleValue = exports.FieldName = exports.FeatureDetails = exports.BasicValue = exports.BaseCoreDetails = void 0;
 
 var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
 
 var _extends2 = _interopRequireDefault(require("@babel/runtime/helpers/extends"));
 
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
 var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
-var _react = _interopRequireDefault(require("react"));
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+var _react = _interopRequireWildcard(require("react"));
 
 var _reactErrorBoundary = require("react-error-boundary");
 
@@ -28,7 +31,7 @@ var _ExpandMore = _interopRequireDefault(require("@material-ui/icons/ExpandMore"
 
 var _styles = require("@material-ui/core/styles");
 
-var _dataGrid = require("@material-ui/data-grid");
+var _xDataGrid = require("@mui/x-data-grid");
 
 var _mobxReact = require("mobx-react");
 
@@ -48,6 +51,10 @@ var _util2 = require("./util");
 
 var _excluded = ["id"];
 
+function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
 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 _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; }
@@ -108,8 +115,19 @@ function BaseCard(_ref) {
       _ref$defaultExpanded = _ref.defaultExpanded,
       defaultExpanded = _ref$defaultExpanded === void 0 ? true : _ref$defaultExpanded;
   var classes = useStyles();
+
+  var _useState = (0, _react.useState)(defaultExpanded),
+      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
+      expanded = _useState2[0],
+      setExpanded = _useState2[1];
+
   return /*#__PURE__*/_react.default.createElement(_core.Accordion, {
-    defaultExpanded: defaultExpanded,
+    expanded: expanded,
+    onChange: function onChange() {
+      return setExpanded(function (s) {
+        return !s;
+      });
+    },
     TransitionProps: {
       unmountOnExit: true
     }
@@ -178,7 +196,8 @@ var ArrayValue = function ArrayValue(_ref5) {
   var name = _ref5.name,
       value = _ref5.value,
       description = _ref5.description,
-      prefix = _ref5.prefix;
+      _ref5$prefix = _ref5.prefix,
+      prefix = _ref5$prefix === void 0 ? [] : _ref5$prefix;
   var classes = useStyles();
   return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, value.length === 1 ? (0, _isObject.default)(value[0]) ? /*#__PURE__*/_react.default.createElement(Attributes, {
     attributes: value[0],
@@ -323,7 +342,7 @@ var DataGridDetails = function DataGridDetails(_ref11) {
         height: Math.min(rows.length, 100) * 20 + 50 + (rows.length < 100 ? 0 : 50),
         width: '100%'
       }
-    }, /*#__PURE__*/_react.default.createElement(_dataGrid.DataGrid, {
+    }, /*#__PURE__*/_react.default.createElement(_xDataGrid.DataGrid, {
       disableSelectionOnClick: true,
       rowHeight: 20,
       headerHeight: 25,

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -7,8 +7,8 @@ var _typeof = require("@babel/runtime/helpers/typeof");
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = SequenceFeatureDetails;
 exports.SequencePanel = void 0;
+exports.default = SequenceFeatureDetails;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -366,35 +366,35 @@ function SequenceFeatureDetails(_ref6) {
 
     ;
     (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-      var _ref10, s, e, refName, seq, upstream, downstream;
+      var _ref10, start, end, refName, seq, up, down;
 
       return _regenerator.default.wrap(function _callee$(_context) {
         while (1) {
           switch (_context.prev = _context.next) {
             case 0:
               _context.prev = 0;
-              _ref10 = feature, s = _ref10.start, e = _ref10.end, refName = _ref10.refName;
+              _ref10 = feature, start = _ref10.start, end = _ref10.end, refName = _ref10.refName;
               _context.next = 4;
-              return fetchSeq(s, e, refName);
+              return fetchSeq(start, end, refName);
 
             case 4:
               seq = _context.sent;
               _context.next = 7;
-              return fetchSeq(Math.max(0, s - 500), s, refName);
+              return fetchSeq(Math.max(0, start - 500), start, refName);
 
             case 7:
-              upstream = _context.sent;
+              up = _context.sent;
               _context.next = 10;
-              return fetchSeq(e, e + 500, refName);
+              return fetchSeq(end, end + 500, refName);
 
             case 10:
-              downstream = _context.sent;
+              down = _context.sent;
 
               if (!finished) {
                 setSequence({
                   seq: seq,
-                  upstream: upstream,
-                  downstream: downstream
+                  upstream: up,
+                  downstream: down
                 });
               }
 

package/BaseFeatureWidget/index.js

@@ -3,8 +3,8 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.stateModelFactory = exports.default = stateModelFactory;
 exports.configSchema = void 0;
+exports.stateModelFactory = exports.default = stateModelFactory;
 
 var _mobxStateTree = require("mobx-state-tree");
 

package/BaseFeatureWidget/types.d.ts

@@ -1,4 +1,4 @@
-/// <reference types="react" />
+import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 import { SimpleFeatureSerialized } from '../util/simpleFeature';
 import { AbstractViewModel } from '../util';

package/BaseFeatureWidget/util.js

@@ -5,11 +5,11 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.stitch = stitch;
-exports.dedupe = dedupe;
-exports.revlist = revlist;
 exports.calculateUTRs = calculateUTRs;
+exports.dedupe = dedupe;
 exports.ellipses = ellipses;
+exports.revlist = revlist;
+exports.stitch = stitch;
 
 var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 

package/CorePlugin.d.ts

@@ -1,6 +1,5 @@
 import Plugin from './Plugin';
 import PluginManager from './PluginManager';
-/** the core plugin, which registers types that ALL JBrowse applications are expected to need. */
 export default class CorePlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/CorePlugin.js

@@ -29,10 +29,14 @@ var _BaseFeatureWidget = require("./BaseFeatureWidget");
 
 var _Plugin2 = _interopRequireDefault(require("./Plugin"));
 
+var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+
 var coreRpcMethods = _interopRequireWildcard(require("./rpc/coreRpcMethods"));
 
 var _WidgetType = _interopRequireDefault(require("./pluggableElementTypes/WidgetType"));
 
+var _CytobandAdapter = require("./data_adapters/CytobandAdapter");
+
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
 function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
@@ -41,7 +45,8 @@ 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; } }
 
-/** the core plugin, which registers types that ALL JBrowse applications are expected to need. */
+// the core plugin, which registers types that ALL JBrowse applications are
+// expected to need.
 var CorePlugin = /*#__PURE__*/function (_Plugin) {
   (0, _inherits2.default)(CorePlugin, _Plugin);
 
@@ -70,6 +75,13 @@ var CorePlugin = /*#__PURE__*/function (_Plugin) {
           return new RpcMethod(pluginManager);
         });
       });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType.default({
+          name: 'CytobandAdapter',
+          configSchema: _CytobandAdapter.configSchema,
+          AdapterClass: _CytobandAdapter.DataAdapter
+        });
+      });
       pluginManager.addWidgetType(function () {
         return new _WidgetType.default({
           name: 'BaseFeatureWidget',

package/PluginLoader.d.ts

@@ -1,19 +1,41 @@
-/// <reference types="node" />
 import { PluginConstructor } from './Plugin';
 export declare const PluginSourceConfigurationSchema: import("./configuration/configurationSchema").AnyConfigurationSchemaType;
-export interface PluginDefinition {
-    name?: string;
+export interface UMDPluginDefinition {
+    umdUrl: string;
+    name: string;
+}
+export interface LegacyUMDPluginDefinition {
     url: string;
+    name: string;
+}
+export declare function isUMDPluginDefinition(pluginDefinition: PluginDefinition): pluginDefinition is UMDPluginDefinition | LegacyUMDPluginDefinition;
+export interface ESMPluginDefinition {
+    esmUrl: string;
+}
+export declare function isESMPluginDefinition(pluginDefinition: PluginDefinition): pluginDefinition is ESMPluginDefinition;
+export interface CJSPluginDefinition {
+    cjsUrl: string;
+}
+export declare function isCJSPluginDefinition(pluginDefinition: PluginDefinition): pluginDefinition is CJSPluginDefinition;
+export interface PluginDefinition extends Partial<UMDPluginDefinition>, Partial<LegacyUMDPluginDefinition>, Partial<ESMPluginDefinition>, Partial<CJSPluginDefinition> {
 }
 export interface PluginRecord {
     plugin: PluginConstructor;
     definition: PluginDefinition;
 }
+export interface LoadedPlugin {
+    default: PluginConstructor;
+}
 export default class PluginLoader {
     definitions: PluginDefinition[];
     constructor(pluginDefinitions?: PluginDefinition[]);
     loadScript(scriptUrl: string): Promise<void>;
+    loadCJSPlugin(pluginDefinition: CJSPluginDefinition): Promise<LoadedPlugin>;
+    loadESMPlugin(pluginDefinition: ESMPluginDefinition): Promise<LoadedPlugin>;
+    loadUMDPlugin(pluginDefinition: UMDPluginDefinition | LegacyUMDPluginDefinition): Promise<{
+        default: PluginConstructor;
+    }>;
     loadPlugin(definition: PluginDefinition): Promise<PluginConstructor>;
-    installGlobalReExports(target: WindowOrWorkerGlobalScope | NodeJS.Global): void;
+    installGlobalReExports(target: WindowOrWorkerGlobalScope): void;
     load(): Promise<PluginRecord[]>;
 }