@jbrowse/plugin-wiggle 1.7.11 → 2.0.0

package/dist/WiggleRPC/rpcMethods.js

@@ -1,295 +1,189 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
 exports.WiggleGetMultiRegionStats = exports.WiggleGetGlobalStats = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
-
-var _get2 = _interopRequireDefault(require("@babel/runtime/helpers/get"));
-
-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 _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _dataAdapterCache = require("@jbrowse/core/data_adapters/dataAdapterCache");
-
-var _RpcMethodType3 = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
-
-var _util = require("@jbrowse/core/util");
-
-var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _serializableFilterChain = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
-
-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 _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; } }
-
-var WiggleGetGlobalStats = /*#__PURE__*/function (_RpcMethodType) {
-  (0, _inherits2.default)(WiggleGetGlobalStats, _RpcMethodType);
-
-  var _super = _createSuper(WiggleGetGlobalStats);
-
-  function WiggleGetGlobalStats() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, WiggleGetGlobalStats);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+var dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+var RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
+var util_1 = require("@jbrowse/core/util");
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
+var WiggleGetGlobalStats = /** @class */ (function (_super) {
+    __extends(WiggleGetGlobalStats, _super);
+    function WiggleGetGlobalStats() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.name = 'WiggleGetGlobalStats';
+        return _this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'WiggleGetGlobalStats');
-    return _this;
-  }
-
-  (0, _createClass2.default)(WiggleGetGlobalStats, [{
-    key: "deserializeArguments",
-    value: // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    function () {
-      var _deserializeArguments = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(args, rpcDriverClassName) {
-        var l;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return (0, _get2.default)((0, _getPrototypeOf2.default)(WiggleGetGlobalStats.prototype), "deserializeArguments", this).call(this, args, rpcDriverClassName);
-
-              case 2:
-                l = _context.sent;
-                return _context.abrupt("return", _objectSpread(_objectSpread({}, l), {}, {
-                  filters: args.filters ? new _serializableFilterChain.default({
-                    filters: args.filters
-                  }) : undefined
-                }));
-
-              case 4:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function deserializeArguments(_x, _x2) {
-        return _deserializeArguments.apply(this, arguments);
-      }
-
-      return deserializeArguments;
-    }()
-  }, {
-    key: "execute",
-    value: function () {
-      var _execute = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(args, rpcDriverClassName) {
-        var deserializedArgs, adapterConfig, sessionId, _yield$getAdapter, dataAdapter;
-
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.deserializeArguments(args, rpcDriverClassName);
-
-              case 2:
-                deserializedArgs = _context2.sent;
-                adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId;
-                _context2.next = 6;
-                return (0, _dataAdapterCache.getAdapter)(this.pluginManager, sessionId, adapterConfig);
-
-              case 6:
-                _yield$getAdapter = _context2.sent;
-                dataAdapter = _yield$getAdapter.dataAdapter;
-                return _context2.abrupt("return", dataAdapter.getGlobalStats(deserializedArgs));
-
-              case 9:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function execute(_x3, _x4) {
-        return _execute.apply(this, arguments);
-      }
-
-      return execute;
-    }()
-  }]);
-  return WiggleGetGlobalStats;
-}(_RpcMethodType3.default);
-
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    WiggleGetGlobalStats.prototype.deserializeArguments = function (args, rpcDriverClassName) {
+        return __awaiter(this, void 0, void 0, function () {
+            var l;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, _super.prototype.deserializeArguments.call(this, args, rpcDriverClassName)];
+                    case 1:
+                        l = _a.sent();
+                        return [2 /*return*/, __assign(__assign({}, l), { filters: args.filters
+                                    ? new serializableFilterChain_1.default({
+                                        filters: args.filters,
+                                    })
+                                    : undefined })];
+                }
+            });
+        });
+    };
+    WiggleGetGlobalStats.prototype.execute = function (args, rpcDriverClassName) {
+        return __awaiter(this, void 0, void 0, function () {
+            var deserializedArgs, adapterConfig, sessionId, dataAdapter;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.deserializeArguments(args, rpcDriverClassName)];
+                    case 1:
+                        deserializedArgs = _a.sent();
+                        adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId;
+                        return [4 /*yield*/, (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)
+                            // @ts-ignore
+                        ];
+                    case 2:
+                        dataAdapter = (_a.sent()).dataAdapter;
+                        // @ts-ignore
+                        return [2 /*return*/, dataAdapter.getGlobalStats(deserializedArgs)];
+                }
+            });
+        });
+    };
+    return WiggleGetGlobalStats;
+}(RpcMethodType_1.default));
 exports.WiggleGetGlobalStats = WiggleGetGlobalStats;
-
-var WiggleGetMultiRegionStats = /*#__PURE__*/function (_RpcMethodType2) {
-  (0, _inherits2.default)(WiggleGetMultiRegionStats, _RpcMethodType2);
-
-  var _super2 = _createSuper(WiggleGetMultiRegionStats);
-
-  function WiggleGetMultiRegionStats() {
-    var _this2;
-
-    (0, _classCallCheck2.default)(this, WiggleGetMultiRegionStats);
-
-    for (var _len2 = arguments.length, args = new Array(_len2), _key2 = 0; _key2 < _len2; _key2++) {
-      args[_key2] = arguments[_key2];
+var WiggleGetMultiRegionStats = /** @class */ (function (_super) {
+    __extends(WiggleGetMultiRegionStats, _super);
+    function WiggleGetMultiRegionStats() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.name = 'WiggleGetMultiRegionStats';
+        return _this;
     }
-
-    _this2 = _super2.call.apply(_super2, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this2), "name", 'WiggleGetMultiRegionStats');
-    return _this2;
-  }
-
-  (0, _createClass2.default)(WiggleGetMultiRegionStats, [{
-    key: "deserializeArguments",
-    value: // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    function () {
-      var _deserializeArguments2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(args, rpcDriverClassName) {
-        var l;
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return (0, _get2.default)((0, _getPrototypeOf2.default)(WiggleGetMultiRegionStats.prototype), "deserializeArguments", this).call(this, args, rpcDriverClassName);
-
-              case 2:
-                l = _context3.sent;
-                return _context3.abrupt("return", _objectSpread(_objectSpread({}, l), {}, {
-                  filters: args.filters ? new _serializableFilterChain.default({
-                    filters: args.filters
-                  }) : undefined
-                }));
-
-              case 4:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function deserializeArguments(_x5, _x6) {
-        return _deserializeArguments2.apply(this, arguments);
-      }
-
-      return deserializeArguments;
-    }()
-  }, {
-    key: "serializeArguments",
-    value: function () {
-      var _serializeArguments = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(args, rpcDriverClassName) {
-        var _this$pluginManager$r, _this$pluginManager$r2;
-
-        var assemblyManager, renamedArgs;
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                assemblyManager = (_this$pluginManager$r = this.pluginManager.rootModel) === null || _this$pluginManager$r === void 0 ? void 0 : (_this$pluginManager$r2 = _this$pluginManager$r.session) === null || _this$pluginManager$r2 === void 0 ? void 0 : _this$pluginManager$r2.assemblyManager;
-
-                if (assemblyManager) {
-                  _context4.next = 3;
-                  break;
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    WiggleGetMultiRegionStats.prototype.deserializeArguments = function (args, rpcDriverClassName) {
+        return __awaiter(this, void 0, void 0, function () {
+            var l;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, _super.prototype.deserializeArguments.call(this, args, rpcDriverClassName)];
+                    case 1:
+                        l = _a.sent();
+                        return [2 /*return*/, __assign(__assign({}, l), { filters: args.filters
+                                    ? new serializableFilterChain_1.default({
+                                        filters: args.filters,
+                                    })
+                                    : undefined })];
                 }
-
-                return _context4.abrupt("return", args);
-
-              case 3:
-                _context4.next = 5;
-                return (0, _util.renameRegionsIfNeeded)(assemblyManager, _objectSpread(_objectSpread({}, args), {}, {
-                  filters: args.filters && args.filters.toJSON().filters
-                }));
-
-              case 5:
-                renamedArgs = _context4.sent;
-                return _context4.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(WiggleGetMultiRegionStats.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
-
-              case 7:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function serializeArguments(_x7, _x8) {
-        return _serializeArguments.apply(this, arguments);
-      }
-
-      return serializeArguments;
-    }()
-  }, {
-    key: "execute",
-    value: function () {
-      var _execute2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(args, rpcDriverClassName) {
-        var deserializedArgs, regions, adapterConfig, sessionId, _yield$getAdapter2, dataAdapter;
-
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
-                _context5.next = 2;
-                return this.deserializeArguments(args, rpcDriverClassName);
-
-              case 2:
-                deserializedArgs = _context5.sent;
-                regions = deserializedArgs.regions, adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId;
-                _context5.next = 6;
-                return (0, _dataAdapterCache.getAdapter)(this.pluginManager, sessionId, adapterConfig);
-
-              case 6:
-                _yield$getAdapter2 = _context5.sent;
-                dataAdapter = _yield$getAdapter2.dataAdapter;
-
-                if (!(dataAdapter instanceof _BaseAdapter.BaseFeatureDataAdapter)) {
-                  _context5.next = 10;
-                  break;
+            });
+        });
+    };
+    WiggleGetMultiRegionStats.prototype.serializeArguments = function (args, rpcDriverClassName) {
+        var _a, _b;
+        return __awaiter(this, void 0, void 0, function () {
+            var assemblyManager, renamedArgs;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0:
+                        assemblyManager = (_b = (_a = this.pluginManager.rootModel) === null || _a === void 0 ? void 0 : _a.session) === null || _b === void 0 ? void 0 : _b.assemblyManager;
+                        if (!assemblyManager) {
+                            return [2 /*return*/, args];
+                        }
+                        return [4 /*yield*/, (0, util_1.renameRegionsIfNeeded)(assemblyManager, __assign(__assign({}, args), { filters: args.filters && args.filters.toJSON().filters }))];
+                    case 1:
+                        renamedArgs = _c.sent();
+                        return [2 /*return*/, _super.prototype.serializeArguments.call(this, renamedArgs, rpcDriverClassName)];
                 }
-
-                return _context5.abrupt("return", dataAdapter.getMultiRegionStats(regions, deserializedArgs));
-
-              case 10:
-                throw new Error('Data adapter not found');
-
-              case 11:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function execute(_x9, _x10) {
-        return _execute2.apply(this, arguments);
-      }
-
-      return execute;
-    }()
-  }]);
-  return WiggleGetMultiRegionStats;
-}(_RpcMethodType3.default);
-
-exports.WiggleGetMultiRegionStats = WiggleGetMultiRegionStats;
+            });
+        });
+    };
+    WiggleGetMultiRegionStats.prototype.execute = function (args, rpcDriverClassName) {
+        return __awaiter(this, void 0, void 0, function () {
+            var deserializedArgs, regions, adapterConfig, sessionId, dataAdapter;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.deserializeArguments(args, rpcDriverClassName)];
+                    case 1:
+                        deserializedArgs = _a.sent();
+                        regions = deserializedArgs.regions, adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId;
+                        return [4 /*yield*/, (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)];
+                    case 2:
+                        dataAdapter = (_a.sent()).dataAdapter;
+                        if (dataAdapter instanceof BaseAdapter_1.BaseFeatureDataAdapter) {
+                            return [2 /*return*/, dataAdapter.getMultiRegionStats(regions, deserializedArgs)];
+                        }
+                        throw new Error('Data adapter not found');
+                }
+            });
+        });
+    };
+    return WiggleGetMultiRegionStats;
+}(RpcMethodType_1.default));
+exports.WiggleGetMultiRegionStats = WiggleGetMultiRegionStats;
+//# sourceMappingURL=rpcMethods.js.map

package/dist/WiggleRPC/rpcMethods.js.map

@@ -0,0 +1 @@
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