@jbrowse/core 1.5.3 → 1.5.4

package/BaseFeatureWidget/BaseFeatureDetail.d.ts

@@ -4,19 +4,21 @@ import { BaseCardProps, BaseProps } from './types';
 import { SimpleFeatureSerialized } from '../util/simpleFeature';
 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, }: {
+export declare const FieldName: ({ description, name, prefix, width, }: {
     description?: React.ReactNode;
     name: string;
     prefix?: string[] | undefined;
+    width?: number | undefined;
 }) => JSX.Element;
 export declare const BasicValue: ({ value }: {
     value: string | React.ReactNode;
 }) => JSX.Element;
-export declare const SimpleValue: ({ name, value, description, prefix, }: {
+export declare const SimpleValue: ({ name, value, description, prefix, width, }: {
     description?: React.ReactNode;
     name: string;
     value: any;
     prefix?: string[] | undefined;
+    width?: number | undefined;
 }) => JSX.Element | null;
 export declare const BaseCoreDetails: (props: BaseProps) => JSX.Element;
 interface AttributeProps {

package/BaseFeatureWidget/BaseFeatureDetail.js

@@ -55,11 +55,12 @@ function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "functio
 
 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 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; }
+
+var MAX_FIELD_NAME_WIDTH = 170; // these are always omitted as too detailed
 
-// these are always omitted as too detailed
 var globalOmit = ['length', 'position', 'subfeatures', 'uniqueId', 'exonFrames', 'parentId', 'thickStart', 'thickEnd']; // coreDetails are omitted in some circumstances
 
 var coreDetails = ['name', 'start', 'end', 'strand', 'refName', 'description', 'type'];
@@ -84,7 +85,6 @@ var useStyles = (0, _styles.makeStyles)(function (theme) {
     fieldName: {
       wordBreak: 'break-all',
       minWidth: '90px',
-      maxWidth: '150px',
       borderBottom: '1px solid #0003',
       background: theme.palette.grey[200],
       marginRight: theme.spacing(1),
@@ -146,7 +146,8 @@ var FieldName = function FieldName(_ref2) {
   var description = _ref2.description,
       name = _ref2.name,
       _ref2$prefix = _ref2.prefix,
-      prefix = _ref2$prefix === void 0 ? [] : _ref2$prefix;
+      prefix = _ref2$prefix === void 0 ? [] : _ref2$prefix,
+      width = _ref2.width;
   var classes = useStyles();
   var val = [].concat((0, _toConsumableArray2.default)(prefix), [name]).join('.');
   return description ? /*#__PURE__*/_react.default.createElement(_core.Tooltip, {
@@ -155,7 +156,10 @@ var FieldName = function FieldName(_ref2) {
   }, /*#__PURE__*/_react.default.createElement("div", {
     className: (0, _clsx.default)(classes.fieldDescription, classes.fieldName)
   }, val)) : /*#__PURE__*/_react.default.createElement("div", {
-    className: classes.fieldName
+    className: classes.fieldName,
+    style: {
+      width: width
+    }
   }, val);
 };
 
@@ -177,14 +181,16 @@ var SimpleValue = function SimpleValue(_ref4) {
   var name = _ref4.name,
       value = _ref4.value,
       description = _ref4.description,
-      prefix = _ref4.prefix;
+      prefix = _ref4.prefix,
+      width = _ref4.width;
   var classes = useStyles();
   return value !== null && value !== undefined ? /*#__PURE__*/_react.default.createElement("div", {
     className: classes.field
   }, /*#__PURE__*/_react.default.createElement(FieldName, {
     prefix: prefix,
     description: description,
-    name: name
+    name: name,
+    width: width
   }), /*#__PURE__*/_react.default.createElement(BasicValue, {
     value: value
   })) : null;
@@ -371,6 +377,17 @@ function accessNested(arr) {
   return typeof obj === 'string' ? obj : typeof ((_obj = obj) === null || _obj === void 0 ? void 0 : _obj.Description) === 'string' ? obj.Description : undefined;
 }
 
+function generateMaxWidth(array, prefix) {
+  // @ts-ignore
+  var arr = [];
+  array.forEach(function (key, value) {
+    var val = [].concat((0, _toConsumableArray2.default)(prefix), [key[0]]).join('.');
+    arr.push((0, _util.measureText)(val, 12));
+  }); // @ts-ignore
+
+  return Math.ceil(Math.max.apply(Math, arr)) + 10;
+}
+
 var Attributes = function Attributes(props) {
   var attributes = props.attributes,
       _props$omit = props.omit,
@@ -383,16 +400,24 @@ var Attributes = function Attributes(props) {
       _props$prefix = props.prefix,
       prefix = _props$prefix === void 0 ? [] : _props$prefix;
   var omits = [].concat((0, _toConsumableArray2.default)(omit), globalOmit);
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, Object.entries(attributes).filter(function (_ref14) {
+  var maxLabelWidth = generateMaxWidth(Object.entries(attributes).filter(function (_ref14) {
     var _ref15 = (0, _slicedToArray2.default)(_ref14, 2),
         k = _ref15[0],
         v = _ref15[1];
 
     return v !== undefined && !omits.includes(k);
-  }).map(function (_ref16) {
+  }), prefix);
+  var labelWidth = maxLabelWidth <= MAX_FIELD_NAME_WIDTH ? maxLabelWidth : MAX_FIELD_NAME_WIDTH;
+  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, Object.entries(attributes).filter(function (_ref16) {
     var _ref17 = (0, _slicedToArray2.default)(_ref16, 2),
-        key = _ref17[0],
-        value = _ref17[1];
+        k = _ref17[0],
+        v = _ref17[1];
+
+    return v !== undefined && !omits.includes(k);
+  }).map(function (_ref18) {
+    var _ref19 = (0, _slicedToArray2.default)(_ref18, 2),
+        key = _ref19[0],
+        value = _ref19[1];
 
     if (Array.isArray(value) && value.length > 2 && value.every(function (val) {
       return (0, _isObject.default)(val);
@@ -432,7 +457,8 @@ var Attributes = function Attributes(props) {
       name: key,
       value: formatter(value, key),
       description: description,
-      prefix: prefix
+      prefix: prefix,
+      width: labelWidth
     });
   }));
 };
@@ -480,8 +506,8 @@ var FeatureDetails = function FeatureDetails(props) {
   }, props, {
     omit: [].concat((0, _toConsumableArray2.default)(omit), coreDetails)
   })), sequenceTypes.includes(feature.type) ? /*#__PURE__*/_react.default.createElement(_reactErrorBoundary.ErrorBoundary, {
-    FallbackComponent: function FallbackComponent(_ref18) {
-      var error = _ref18.error;
+    FallbackComponent: function FallbackComponent(_ref20) {
+      var error = _ref20.error;
       return /*#__PURE__*/_react.default.createElement(_core.Typography, {
         color: "error"
       }, "Failed to fetch sequence for feature: ", "".concat(error));

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -38,9 +38,9 @@ function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "functio
 
 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 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; }
 
 var useStyles = (0, _core.makeStyles)(function (theme) {
   return {
@@ -192,7 +192,8 @@ var SequencePanel = /*#__PURE__*/_react.default.forwardRef(function (_ref4, ref)
   }, /*#__PURE__*/_react.default.createElement("div", {
     style: {
       fontFamily: 'monospace',
-      wordWrap: 'break-word'
+      wordWrap: 'break-word',
+      maxWidth: 600
     }
   }, ">".concat(feature.name || feature.id || 'unknown', "-").concat(mode, "\n"), mode === 'cds' ? /*#__PURE__*/_react.default.createElement(GeneCDS, {
     cds: cds,

package/BaseFeatureWidget/util.js

@@ -15,9 +15,9 @@ var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
-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 stitch(subfeats, sequence) {
   return subfeats.map(function (sub) {

package/PluginLoader.js

@@ -12,10 +12,10 @@ exports.isCJSPluginDefinition = isCJSPluginDefinition;
 exports.isESMPluginDefinition = isESMPluginDefinition;
 exports.isUMDPluginDefinition = isUMDPluginDefinition;
 
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));

package/PluginManager.d.ts

@@ -28,16 +28,16 @@ declare class PhasedScheduler<PhaseName extends string> {
 declare type PluggableElementTypeGroup = 'renderer' | 'adapter' | 'display' | 'track' | 'connection' | 'view' | 'widget' | 'rpc method' | 'internet account' | 'text search adapter';
 /** internal class that holds the info for a certain element type */
 declare class TypeRecord<ElementClass extends PluggableElementBase> {
-    registeredTypes: {
-        [name: string]: ElementClass;
-    };
+    typeName: string;
     baseClass: {
         new (...args: any[]): ElementClass;
     } | (Function & {
         prototype: ElementClass;
     });
-    typeName: string;
-    constructor(typeName: string, elementType: {
+    registeredTypes: {
+        [name: string]: ElementClass;
+    };
+    constructor(typeName: string, baseClass: {
         new (...args: any[]): ElementClass;
     } | (Function & {
         prototype: ElementClass;

package/PluginManager.js

@@ -107,13 +107,9 @@ var PhasedScheduler = /*#__PURE__*/function () {
 
 /** internal class that holds the info for a certain element type */
 var TypeRecord = /*#__PURE__*/function () {
-  function TypeRecord(typeName, elementType) {
+  function TypeRecord(typeName, baseClass) {
     (0, _classCallCheck2.default)(this, TypeRecord);
     (0, _defineProperty2.default)(this, "registeredTypes", {});
-    (0, _defineProperty2.default)(this, "baseClass", void 0);
-    (0, _defineProperty2.default)(this, "typeName", void 0);
-    this.typeName = typeName;
-    this.baseClass = elementType;
   }
 
   (0, _createClass2.default)(TypeRecord, [{

package/TextSearch/TextSearchManager.d.ts

@@ -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.js

@@ -11,10 +11,10 @@ var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/sli
 
 var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
@@ -33,9 +33,9 @@ var _QuickLRU = _interopRequireDefault(require("../util/QuickLRU"));
 
 var _excluded = ["signal", "statusCallback"];
 
-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; }
 
 // Based on the UCSC Genome Browser chromosome color palette:
 // https://github.com/ucscGenomeBrowser/kent/blob/a50ed53aff81d6fb3e34e6913ce18578292bc24e/src/hg/inc/chromColors.h

package/configuration/configurationSchema.js

@@ -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;

package/data_adapters/BaseAdapter.d.ts

@@ -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

@@ -12,13 +12,11 @@ exports.isRegionsAdapter = isRegionsAdapter;
 exports.isSequenceAdapter = isSequenceAdapter;
 exports.isTextSearchAdapter = isTextSearchAdapter;
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
 
@@ -26,6 +24,8 @@ var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime
 
 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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "1.5.3",
+  "version": "1.5.4",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -30,7 +30,7 @@
     "postpublish": "git push origin main --follow-tags"
   },
   "dependencies": {
-    "@babel/runtime": "^7.15.3",
+    "@babel/runtime": "^7.16.3",
     "@material-ui/icons": "^4.0.1",
     "abortable-promise-cache": "^1.1.3",
     "base64-js": "^1.3.0",
@@ -40,7 +40,7 @@
     "copy-to-clipboard": "^3.3.1",
     "deepmerge": "^4.2.2",
     "detect-node": "^2.1.0",
-    "dompurify": "^2.0.11",
+    "dompurify": "^2.3.4",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
     "file-uri-to-path": "^1.0.0",
@@ -54,13 +54,13 @@
     "object.fromentries": "^2.0.0",
     "rbush": "^3.0.1",
     "react-error-boundary": "^3.0.0",
-    "react-intersection-observer": "^8.31.0",
+    "react-intersection-observer": "^8.32.5",
     "react-measure": "^2.3.0",
     "sanitize-filename": "^1.6.3",
     "shortid": "^2.2.13",
     "svg-path-generator": "^1.1.0",
     "tenacious-fetch": "^2.1.0",
-    "util.promisify": "^1.0.0"
+    "util.promisify": "^1.1.1"
   },
   "peerDependencies": {
     "@material-ui/core": "^4.12.2",
@@ -78,5 +78,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "cea9023ebce8bbe5c08ae9e00c4e74fe3f02a7f1"
+  "gitHead": "0c398214590969168694b4ed8e20b595178b9efd"
 }

package/pluggableElementTypes/AdapterType.js

@@ -11,6 +11,8 @@ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"))
 
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -73,7 +75,7 @@ var AdapterType = /*#__PURE__*/function (_PluggableElementBase) {
     return _this;
   }
 
-  return AdapterType;
+  return (0, _createClass2.default)(AdapterType);
 }(_PluggableElementBase2.default);
 
 exports.default = AdapterType;

package/pluggableElementTypes/ConnectionType.js

@@ -7,6 +7,8 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -59,7 +61,7 @@ var ConnectionType = /*#__PURE__*/function (_PluggableElementBase) {
     return _this;
   }
 
-  return ConnectionType;
+  return (0, _createClass2.default)(ConnectionType);
 }(_PluggableElementBase2.default);
 
 exports.default = ConnectionType;

package/pluggableElementTypes/DisplayType.js

@@ -7,6 +7,8 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -76,7 +78,7 @@ var DisplayType = /*#__PURE__*/function (_PluggableElementBase) {
     return _this;
   }
 
-  return DisplayType;
+  return (0, _createClass2.default)(DisplayType);
 }(_PluggableElementBase2.default);
 
 exports.default = DisplayType;

package/pluggableElementTypes/InternetAccountType.js

@@ -7,6 +7,8 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -58,7 +60,7 @@ var InternetAccountType = /*#__PURE__*/function (_PluggableElementBase) {
     return _this;
   }
 
-  return InternetAccountType;
+  return (0, _createClass2.default)(InternetAccountType);
 }(_PluggableElementBase2.default);
 
 exports.default = InternetAccountType;

package/pluggableElementTypes/PluggableElementBase.js

@@ -7,14 +7,15 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
-var PluggableElementBase = function PluggableElementBase(args) {
+var PluggableElementBase = /*#__PURE__*/(0, _createClass2.default)(function PluggableElementBase(args) {
   (0, _classCallCheck2.default)(this, PluggableElementBase);
   (0, _defineProperty2.default)(this, "name", '');
   this.name = args.name;
-};
-
+});
 exports.default = PluggableElementBase;

package/pluggableElementTypes/RpcMethodType.js

@@ -7,12 +7,12 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
 var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
 
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
@@ -43,9 +43,9 @@ function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o =
 
 function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
 
-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 _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
 
@@ -63,9 +63,7 @@ var RpcMethodType = /*#__PURE__*/function (_PluggableElementBase) {
     _this = _super.call(this, {
       name: ''
     });
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "pluginManager", void 0);
     (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'UNKNOWN');
-    _this.pluginManager = pluginManager;
     return _this;
   }
 

package/pluggableElementTypes/TextSearchAdapterType.js

@@ -7,6 +7,8 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -49,7 +51,7 @@ var TextSearchAdapterType = /*#__PURE__*/function (_PluggableElementBase) {
     return _this;
   }
 
-  return TextSearchAdapterType;
+  return (0, _createClass2.default)(TextSearchAdapterType);
 }(_PluggableElementBase2.default);
 
 exports.default = TextSearchAdapterType;

package/pluggableElementTypes/WidgetType.js

@@ -7,6 +7,8 @@ Object.defineProperty(exports, "__esModule", {
 });
 exports.default = void 0;
 
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
 var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
@@ -58,7 +60,7 @@ var WidgetType = /*#__PURE__*/function (_PluggableElementBase) {
     return _this;
   }
 
-  return WidgetType;
+  return (0, _createClass2.default)(WidgetType);
 }(_PluggableElementBase2.default);
 
 exports.default = WidgetType;