@jbrowse/plugin-sequence 1.7.3 → 1.7.6

package/dist/index.js

@@ -7,7 +7,7 @@ var _typeof = require("@babel/runtime/helpers/typeof");
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
@@ -55,37 +55,37 @@ var _referenceSeqTrackConfig = require("./referenceSeqTrackConfig");
 
 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 _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); 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 = 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 _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); }; }
+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); }; }
 
 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; } }
 
 /* adjust in both directions */
 var DivSequenceRenderer = /*#__PURE__*/function (_FeatureRendererType) {
-  (0, _inherits2["default"])(DivSequenceRenderer, _FeatureRendererType);
+  (0, _inherits2.default)(DivSequenceRenderer, _FeatureRendererType);
 
   var _super = _createSuper(DivSequenceRenderer);
 
   function DivSequenceRenderer() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, DivSequenceRenderer);
+    (0, _classCallCheck2.default)(this, DivSequenceRenderer);
 
     for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
       args[_key] = arguments[_key];
     }
 
     _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "supportsSVG", true);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "supportsSVG", true);
     return _this;
   }
 
-  (0, _createClass2["default"])(DivSequenceRenderer, [{
+  (0, _createClass2.default)(DivSequenceRenderer, [{
     key: "getExpandedRegion",
     value: function getExpandedRegion(region) {
       return _objectSpread(_objectSpread({}, region), {}, {
@@ -95,32 +95,32 @@ var DivSequenceRenderer = /*#__PURE__*/function (_FeatureRendererType) {
     }
   }]);
   return DivSequenceRenderer;
-}(_FeatureRendererType2["default"]);
+}(_FeatureRendererType2.default);
 
 var SequencePlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2["default"])(SequencePlugin, _Plugin);
+  (0, _inherits2.default)(SequencePlugin, _Plugin);
 
   var _super2 = _createSuper(SequencePlugin);
 
   function SequencePlugin() {
     var _this2;
 
-    (0, _classCallCheck2["default"])(this, SequencePlugin);
+    (0, _classCallCheck2.default)(this, SequencePlugin);
 
     for (var _len2 = arguments.length, args = new Array(_len2), _key2 = 0; _key2 < _len2; _key2++) {
       args[_key2] = arguments[_key2];
     }
 
     _this2 = _super2.call.apply(_super2, [this].concat(args));
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this2), "name", 'SequencePlugin');
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this2), "name", 'SequencePlugin');
     return _this2;
   }
 
-  (0, _createClass2["default"])(SequencePlugin, [{
+  (0, _createClass2.default)(SequencePlugin, [{
     key: "install",
     value: function install(pluginManager) {
       pluginManager.addAdapterType(function () {
-        return new _AdapterType["default"]({
+        return new _AdapterType.default({
           name: 'TwoBitAdapter',
           configSchema: _TwoBitAdapter.configSchema,
           adapterMetadata: {
@@ -133,7 +133,7 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
             return Promise.resolve().then(function () {
               return _interopRequireWildcard(require('./TwoBitAdapter/TwoBitAdapter'));
             }).then(function (r) {
-              return r["default"];
+              return r.default;
             });
           }
         });
@@ -167,7 +167,7 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
         };
       });
       pluginManager.addAdapterType(function () {
-        return new _AdapterType["default"]({
+        return new _AdapterType.default({
           name: 'ChromSizesAdapter',
           configSchema: _ChromSizesAdapter.configSchema,
           adapterMetadata: {
@@ -180,13 +180,13 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
             return Promise.resolve().then(function () {
               return _interopRequireWildcard(require('./ChromSizesAdapter/ChromSizesAdapter'));
             }).then(function (r) {
-              return r["default"];
+              return r.default;
             });
           }
         });
       });
       pluginManager.addAdapterType(function () {
-        return new _AdapterType["default"]({
+        return new _AdapterType.default({
           name: 'IndexedFastaAdapter',
           configSchema: _IndexedFastaAdapter.configSchema,
           adapterMetadata: {
@@ -199,7 +199,7 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
             return Promise.resolve().then(function () {
               return _interopRequireWildcard(require('./IndexedFastaAdapter/IndexedFastaAdapter'));
             }).then(function (r) {
-              return r["default"];
+              return r.default;
             });
           }
         });
@@ -234,7 +234,7 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
         };
       });
       pluginManager.addAdapterType(function () {
-        return new _AdapterType["default"]({
+        return new _AdapterType.default({
           name: 'BgzipFastaAdapter',
           configSchema: _BgzipFastaAdapter.configSchema,
           adapterMetadata: {
@@ -247,7 +247,7 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
             return Promise.resolve().then(function () {
               return _interopRequireWildcard(require('./BgzipFastaAdapter/BgzipFastaAdapter'));
             }).then(function (r) {
-              return r["default"];
+              return r.default;
             });
           }
         });
@@ -282,7 +282,7 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
         };
       });
       pluginManager.addAdapterType(function () {
-        return new _AdapterType["default"](_objectSpread({
+        return new _AdapterType.default(_objectSpread({
           name: 'GCContentAdapter',
           adapterMetadata: {
             category: null,
@@ -290,11 +290,11 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
             displayName: null,
             description: null
           }
-        }, pluginManager.load(_GCContentAdapter["default"])));
+        }, pluginManager.load(_GCContentAdapter.default)));
       });
       pluginManager.addTrackType(function () {
         var configSchema = (0, _referenceSeqTrackConfig.createReferenceSeqTrackConfig)(pluginManager);
-        return new _TrackType["default"]({
+        return new _TrackType.default({
           name: 'ReferenceSequenceTrack',
           configSchema: configSchema,
           stateModel: (0, _models.createBaseTrackModel)(pluginManager, 'ReferenceSequenceTrack', configSchema)
@@ -322,6 +322,6 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
     }
   }]);
   return SequencePlugin;
-}(_Plugin2["default"]);
+}(_Plugin2.default);
 
-exports["default"] = SequencePlugin;
+exports.default = SequencePlugin;

package/dist/index.test.js

@@ -10,11 +10,11 @@ var _ = _interopRequireDefault(require("."));
 
 test('plugin in a stock JBrowse', function () {
   console.warn = jest.fn();
-  var pluginManager = new _PluginManager["default"]([new _["default"]()]);
+  var pluginManager = new _PluginManager.default([new _.default()]);
   pluginManager.createPluggableElements();
   pluginManager.configure();
   expect(function () {
-    return pluginManager.addPlugin(new _["default"]());
+    return pluginManager.addPlugin(new _.default());
   }).toThrow(/JBrowse already configured, cannot add plugins/);
   var TwoBitAdapter = pluginManager.getAdapterType('TwoBitAdapter');
   var config = TwoBitAdapter.configSchema.create({

package/dist/referenceSeqTrackConfig.js

@@ -15,7 +15,7 @@ var _configuration = require("@jbrowse/core/configuration");
 
 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 = 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 _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; }
 
 /*
 Note: this is primarily a copy of createBaseTrackConfig, except with a subset
@@ -26,6 +26,11 @@ function createReferenceSeqTrackConfig(pluginManager) {
   return (0, _configuration.ConfigurationSchema)('ReferenceSequenceTrack', {
     adapter: pluginManager.pluggableConfigSchemaType('adapter'),
     displays: _mobxStateTree.types.array(pluginManager.pluggableConfigSchemaType('display')),
+    name: {
+      type: 'string',
+      description: 'optional track name',
+      defaultValue: ''
+    },
     metadata: {
       type: 'frozen',
       description: 'anything to add about this track',

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sequence",
-  "version": "1.7.3",
+  "version": "1.7.6",
   "description": "JBrowse 2 sequence adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -33,10 +33,10 @@
     "postbuild": "tsc --build tsconfig.build.json"
   },
   "dependencies": {
+    "@babel/runtime": "^7.17.9",
     "@gmod/indexedfasta": "^2.0.2",
     "@gmod/twobit": "^1.1.12",
     "abortable-promise-cache": "^1.5.0",
-    "clsx": "^1.1.0",
     "generic-filehandle": "^2.2.2"
   },
   "peerDependencies": {
@@ -53,5 +53,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "09b13c85acf4ac68dd71ab23af87656c7552fdaf"
+  "gitHead": "dbd73f99714e395cf20877d5e05d26855857a0e3"
 }

package/src/referenceSeqTrackConfig.ts

@@ -14,6 +14,11 @@ export function createReferenceSeqTrackConfig(pluginManager: PluginManager) {
     {
       adapter: pluginManager.pluggableConfigSchemaType('adapter'),
       displays: types.array(pluginManager.pluggableConfigSchemaType('display')),
+      name: {
+        type: 'string',
+        description: 'optional track name',
+        defaultValue: '',
+      },
       metadata: {
         type: 'frozen',
         description: 'anything to add about this track',