@jbrowse/plugin-config 1.7.9 → 2.0.0

package/dist/FromConfigAdapter/FromConfigAdapter.js

@@ -1,215 +1,183 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-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 _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 _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
-
-function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
-
-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 _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 __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 __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 __values = (this && this.__values) || function(o) {
+    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
+    if (m) return m.call(o);
+    if (o && typeof o.length === "number") return {
+        next: function () {
+            if (o && i >= o.length) o = void 0;
+            return { value: o && o[i++], done: !o };
+        }
+    };
+    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
+};
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var configuration_1 = require("@jbrowse/core/configuration");
 /**
  * Adapter that just returns the features defined in its `features` configuration
  * key, like:
  *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
  */
-var FromConfigAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(FromConfigAdapter, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(FromConfigAdapter);
-
-  function FromConfigAdapter(conf, getSubAdapter, pluginManager) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, FromConfigAdapter);
-    _this = _super.call(this, conf, getSubAdapter, pluginManager);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "features", void 0);
-    var feats = (0, _configuration.readConfObject)(conf, 'features');
-    _this.features = FromConfigAdapter.makeFeatures(feats || []);
-    return _this;
-  }
-
-  (0, _createClass2.default)(FromConfigAdapter, [{
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                return _context.abrupt("return", (0, _toConsumableArray2.default)(this.features.keys()));
-
-              case 1:
-              case "end":
-                return _context.stop();
+var FromConfigAdapter = /** @class */ (function (_super) {
+    __extends(FromConfigAdapter, _super);
+    function FromConfigAdapter(conf, getSubAdapter, pluginManager) {
+        var _this = _super.call(this, conf, getSubAdapter, pluginManager) || this;
+        var feats = (0, configuration_1.readConfObject)(conf, 'features');
+        _this.features = FromConfigAdapter.makeFeatures(feats || []);
+        return _this;
+    }
+    FromConfigAdapter.makeFeatures = function (fdata) {
+        var e_1, _a;
+        var features = new Map();
+        for (var i = 0; i < fdata.length; i += 1) {
+            if (fdata[i]) {
+                var f = this.makeFeature(fdata[i]);
+                var refName = f.get('refName');
+                var bucket = features.get(refName);
+                if (!bucket) {
+                    bucket = [];
+                    features.set(refName, bucket);
+                }
+                bucket.push(f);
             }
-          }
-        }, _callee, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "getRefNameAliases",
-    value: function () {
-      var _getRefNameAliases = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                return _context2.abrupt("return", Array.from(this.features.values()).map(function (featureArray) {
-                  return {
-                    refName: featureArray[0].get('refName'),
-                    aliases: featureArray[0].get('aliases')
-                  };
-                }));
-
-              case 1:
-              case "end":
-                return _context2.stop();
+        }
+        try {
+            // sort the features on each reference sequence by start coordinate
+            for (var _b = __values(features.values()), _c = _b.next(); !_c.done; _c = _b.next()) {
+                var refFeatures = _c.value;
+                refFeatures.sort(function (a, b) { return a.get('start') - b.get('start'); });
             }
-          }
-        }, _callee2, this);
-      }));
-
-      function getRefNameAliases() {
-        return _getRefNameAliases.apply(this, arguments);
-      }
-
-      return getRefNameAliases;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(region) {
-      var _this2 = this;
-
-      var refName = region.refName,
-          start = region.start,
-          end = region.end;
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(observer) {
-          var features, i, f;
-          return _regenerator.default.wrap(function _callee3$(_context3) {
-            while (1) {
-              switch (_context3.prev = _context3.next) {
-                case 0:
-                  features = _this2.features.get(refName) || [];
-
-                  for (i = 0; i < features.length; i++) {
+        }
+        catch (e_1_1) { e_1 = { error: e_1_1 }; }
+        finally {
+            try {
+                if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
+            }
+            finally { if (e_1) throw e_1.error; }
+        }
+        return features;
+    };
+    FromConfigAdapter.makeFeature = function (data) {
+        return new simpleFeature_1.default(data);
+    };
+    FromConfigAdapter.prototype.getRefNames = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                return [2 /*return*/, __spreadArray([], __read(this.features.keys()), false)];
+            });
+        });
+    };
+    FromConfigAdapter.prototype.getRefNameAliases = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                return [2 /*return*/, Array.from(this.features.values()).map(function (featureArray) { return ({
+                        refName: featureArray[0].get('refName'),
+                        aliases: featureArray[0].get('aliases'),
+                    }); })];
+            });
+        });
+    };
+    FromConfigAdapter.prototype.getFeatures = function (region) {
+        var _this = this;
+        var refName = region.refName, start = region.start, end = region.end;
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var features, i, f;
+            return __generator(this, function (_a) {
+                features = this.features.get(refName) || [];
+                for (i = 0; i < features.length; i++) {
                     f = features[i];
-
                     if (f.get('end') > start && f.get('start') < end) {
-                      observer.next(f);
+                        observer.next(f);
                     }
-                  }
-
-                  observer.complete();
-
-                case 3:
-                case "end":
-                  return _context3.stop();
-              }
-            }
-          }, _callee3);
-        }));
-
-        return function (_x) {
-          return _ref.apply(this, arguments);
-        };
-      }());
-    }
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }], [{
-    key: "makeFeatures",
-    value: function makeFeatures(fdata) {
-      var features = new Map();
-
-      for (var i = 0; i < fdata.length; i += 1) {
-        if (fdata[i]) {
-          var f = this.makeFeature(fdata[i]);
-          var refName = f.get('refName');
-          var bucket = features.get(refName);
-
-          if (!bucket) {
-            bucket = [];
-            features.set(refName, bucket);
-          }
-
-          bucket.push(f);
-        }
-      } // sort the features on each reference sequence by start coordinate
-
-
-      var _iterator = _createForOfIteratorHelper(features.values()),
-          _step;
-
-      try {
-        for (_iterator.s(); !(_step = _iterator.n()).done;) {
-          var refFeatures = _step.value;
-          refFeatures.sort(function (a, b) {
-            return a.get('start') - b.get('start');
-          });
-        }
-      } catch (err) {
-        _iterator.e(err);
-      } finally {
-        _iterator.f();
-      }
-
-      return features;
-    }
-  }, {
-    key: "makeFeature",
-    value: function makeFeature(data) {
-      return new _simpleFeature.default(data);
-    }
-  }]);
-  return FromConfigAdapter;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
-exports.default = FromConfigAdapter;
+                }
+                observer.complete();
+                return [2 /*return*/];
+            });
+        }); });
+    };
+    FromConfigAdapter.prototype.freeResources = function ( /* { region } */) { };
+    return FromConfigAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = FromConfigAdapter;
+//# sourceMappingURL=FromConfigAdapter.js.map

package/dist/FromConfigAdapter/FromConfigAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"FromConfigAdapter.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/FromConfigAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uEAAgF;AAChF,mFAGyC;AACzC,gDAA0D;AAG1D,6DAA4D;AAI5D;;;;GAIG;AAEH;IAA+C,qCAAsB;IAGnE,2BACE,IAA2B,EAC3B,aAAiC,EACjC,aAA6B;QAH/B,YAKE,kBAAM,IAAI,EAAE,aAAa,EAAE,aAAa,CAAC,SAG1C;QAFC,IAAM,KAAK,GAAG,IAAA,8BAAc,EAAC,IAAI,EAAE,UAAU,CAA8B,CAAA;QAC3E,KAAI,CAAC,QAAQ,GAAG,iBAAiB,CAAC,YAAY,CAAC,KAAK,IAAI,EAAE,CAAC,CAAA;;IAC7D,CAAC;IAEM,8BAAY,GAAnB,UAAoB,KAAgC;;QAClD,IAAM,QAAQ,GAAG,IAAI,GAAG,EAAqB,CAAA;QAC7C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YACxC,IAAI,KAAK,CAAC,CAAC,CAAC,EAAE;gBACZ,IAAM,CAAC,GAAG,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;gBACpC,IAAM,OAAO,GAAG,CAAC,CAAC,GAAG,CAAC,SAAS,CAAW,CAAA;gBAC1C,IAAI,MAAM,GAAG,QAAQ,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;gBAClC,IAAI,CAAC,MAAM,EAAE;oBACX,MAAM,GAAG,EAAE,CAAA;oBACX,QAAQ,CAAC,GAAG,CAAC,OAAO,EAAE,MAAM,CAAC,CAAA;iBAC9B;gBAED,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;aACf;SACF;;YAED,mEAAmE;YACnE,KAA0B,IAAA,KAAA,SAAA,QAAQ,CAAC,MAAM,EAAE,CAAA,gBAAA,4BAAE;gBAAxC,IAAM,WAAW,WAAA;gBACpB,WAAW,CAAC,IAAI,CAAC,UAAC,CAAC,EAAE,CAAC,IAAK,OAAA,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAA/B,CAA+B,CAAC,CAAA;aAC5D;;;;;;;;;QAED,OAAO,QAAQ,CAAA;IACjB,CAAC;IAEM,6BAAW,GAAlB,UAAmB,IAA6B;QAC9C,OAAO,IAAI,uBAAa,CAAC,IAAI,CAAC,CAAA;IAChC,CAAC;IAEK,uCAAW,GAAjB;;;gBACE,+CAAW,IAAI,CAAC,QAAQ,CAAC,IAAI,EAAE,WAAC;;;KACjC;IAEK,6CAAiB,GAAvB;;;gBACE,sBAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,UAAA,YAAY,IAAI,OAAA,CAAC;wBAC7D,OAAO,EAAE,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;wBACvC,OAAO,EAAE,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;qBACxC,CAAC,EAH4D,CAG5D,CAAC,EAAA;;;KACJ;IAED,uCAAW,GAAX,UAAY,MAAwB;QAApC,iBAcC;QAbS,IAAA,OAAO,GAAiB,MAAM,QAAvB,EAAE,KAAK,GAAU,MAAM,MAAhB,EAAE,GAAG,GAAK,MAAM,IAAX,CAAW;QAEtC,OAAO,IAAA,uBAAgB,EAAU,UAAM,QAAQ;;;gBACvC,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;gBACjD,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;oBAClC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;oBAErB,IAAI,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,KAAK,IAAI,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,GAAG,EAAE;wBAChD,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;qBACjB;iBACF;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;;;aACpB,CAAC,CAAA;IACJ,CAAC;IAED,yCAAa,GAAb,WAAc,gBAAgB,IAAS,CAAC;IAC1C,wBAAC;AAAD,CAAC,AArED,CAA+C,oCAAsB,GAqEpE"}