@jbrowse/plugin-config 1.7.11 → 2.1.0

package/dist/FromConfigAdapter/FromConfigRegionsAdapter.js

@@ -1,154 +1,163 @@
 "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 _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-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 _BaseAdapter2 = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _FromConfigAdapter = _interopRequireDefault(require("./FromConfigAdapter"));
-
-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 __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 configuration_1 = require("@jbrowse/core/configuration");
+var FromConfigAdapter_1 = __importDefault(require("./FromConfigAdapter"));
 /**
  * Adapter that just returns the features defined in its `features` configuration
  * key, like:
  *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
  */
-var FromConfigRegionsAdapter = /*#__PURE__*/function (_BaseAdapter) {
-  (0, _inherits2.default)(FromConfigRegionsAdapter, _BaseAdapter);
-
-  var _super = _createSuper(FromConfigRegionsAdapter);
-
-  function FromConfigRegionsAdapter(config, getSubAdapter, pluginManager) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, FromConfigRegionsAdapter);
-    _this = _super.call(this, config, getSubAdapter, pluginManager);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "features", void 0);
-    var features = (0, _configuration.readConfObject)(config, 'features');
-    _this.features = _FromConfigAdapter.default.makeFeatures(features || []);
-    return _this;
-  }
-  /**
-   * Get refName, start, and end for all features after collapsing any overlaps
-   */
-
-
-  (0, _createClass2.default)(FromConfigRegionsAdapter, [{
-    key: "getRegions",
-    value: function () {
-      var _getRegions = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var regions, _iterator, _step, _step$value, refName, features, currentRegion, _iterator2, _step2, feature;
-
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                regions = []; // recall: features are stored in this object sorted by start coordinate
-
-                _iterator = _createForOfIteratorHelper(this.features);
-
+var FromConfigRegionsAdapter = /** @class */ (function (_super) {
+    __extends(FromConfigRegionsAdapter, _super);
+    function FromConfigRegionsAdapter(config, getSubAdapter, pluginManager) {
+        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
+        var features = (0, configuration_1.readConfObject)(config, 'features');
+        _this.features = FromConfigAdapter_1.default.makeFeatures(features || []);
+        return _this;
+    }
+    /**
+     * Get refName, start, and end for all features after collapsing any overlaps
+     */
+    FromConfigRegionsAdapter.prototype.getRegions = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var regions, _a, _b, _c, refName, features, currentRegion, features_1, features_1_1, feature;
+            var e_1, _d, e_2, _e;
+            return __generator(this, function (_f) {
+                regions = [];
                 try {
-                  for (_iterator.s(); !(_step = _iterator.n()).done;) {
-                    _step$value = (0, _slicedToArray2.default)(_step.value, 2), refName = _step$value[0], features = _step$value[1];
-                    currentRegion = void 0;
-                    _iterator2 = _createForOfIteratorHelper(features);
-
-                    try {
-                      for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
-                        feature = _step2.value;
-
-                        if (currentRegion && currentRegion.end >= feature.get('start') && currentRegion.start <= feature.get('end')) {
-                          currentRegion.end = feature.get('end');
-                        } else {
-                          if (currentRegion) {
+                    // recall: features are stored in this object sorted by start coordinate
+                    for (_a = __values(this.features), _b = _a.next(); !_b.done; _b = _a.next()) {
+                        _c = __read(_b.value, 2), refName = _c[0], features = _c[1];
+                        currentRegion = void 0;
+                        try {
+                            for (features_1 = (e_2 = void 0, __values(features)), features_1_1 = features_1.next(); !features_1_1.done; features_1_1 = features_1.next()) {
+                                feature = features_1_1.value;
+                                if (currentRegion &&
+                                    currentRegion.end >= feature.get('start') &&
+                                    currentRegion.start <= feature.get('end')) {
+                                    currentRegion.end = feature.get('end');
+                                }
+                                else {
+                                    if (currentRegion) {
+                                        regions.push(currentRegion);
+                                    }
+                                    currentRegion = {
+                                        refName: refName,
+                                        start: feature.get('start'),
+                                        end: feature.get('end'),
+                                    };
+                                }
+                            }
+                        }
+                        catch (e_2_1) { e_2 = { error: e_2_1 }; }
+                        finally {
+                            try {
+                                if (features_1_1 && !features_1_1.done && (_e = features_1.return)) _e.call(features_1);
+                            }
+                            finally { if (e_2) throw e_2.error; }
+                        }
+                        if (currentRegion) {
                             regions.push(currentRegion);
-                          }
-
-                          currentRegion = {
-                            refName: refName,
-                            start: feature.get('start'),
-                            end: feature.get('end')
-                          };
                         }
-                      }
-                    } catch (err) {
-                      _iterator2.e(err);
-                    } finally {
-                      _iterator2.f();
                     }
-
-                    if (currentRegion) {
-                      regions.push(currentRegion);
+                }
+                catch (e_1_1) { e_1 = { error: e_1_1 }; }
+                finally {
+                    try {
+                        if (_b && !_b.done && (_d = _a.return)) _d.call(_a);
                     }
-                  } // sort the regions by refName
-
-                } catch (err) {
-                  _iterator.e(err);
-                } finally {
-                  _iterator.f();
+                    finally { if (e_1) throw e_1.error; }
                 }
-
-                regions.sort(function (a, b) {
-                  return a.refName.localeCompare(b.refName);
-                });
-                return _context.abrupt("return", regions);
-
-              case 5:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getRegions() {
-        return _getRegions.apply(this, arguments);
-      }
-
-      return getRegions;
-    }()
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }]);
-  return FromConfigRegionsAdapter;
-}(_BaseAdapter2.BaseAdapter);
-
-exports.default = FromConfigRegionsAdapter;
+                // sort the regions by refName
+                regions.sort(function (a, b) { return a.refName.localeCompare(b.refName); });
+                return [2 /*return*/, regions];
+            });
+        });
+    };
+    FromConfigRegionsAdapter.prototype.freeResources = function ( /* { region } */) { };
+    return FromConfigRegionsAdapter;
+}(BaseAdapter_1.BaseAdapter));
+exports.default = FromConfigRegionsAdapter;
+//# sourceMappingURL=FromConfigRegionsAdapter.js.map

package/dist/FromConfigAdapter/FromConfigRegionsAdapter.js.map

@@ -0,0 +1 @@
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package/dist/FromConfigAdapter/FromConfigSequenceAdapter.d.ts

@@ -1,7 +1,8 @@
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import FromConfigAdapter from './FromConfigAdapter';
-export default class FromConfigSequenceAdapter extends FromConfigAdapter {
+import { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+export default class FromConfigSequenceAdapter extends FromConfigAdapter implements RegionsAdapter {
     /**
      * Fetch features for a certain region
      * @param region - Region