@jbrowse/plugin-gff3 1.7.9 → 2.0.0

package/dist/Gff3Adapter/Gff3Adapter.js

@@ -1,402 +1,295 @@
 "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 _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _io = require("@jbrowse/core/util/io");
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _intervalTree = _interopRequireDefault(require("@flatten-js/interval-tree"));
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _bgzfFilehandle = require("@gmod/bgzf-filehandle");
-
-var _gff = _interopRequireDefault(require("@gmod/gff"));
-
-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 __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 __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 io_1 = require("@jbrowse/core/util/io");
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+var bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+var gff_1 = __importDefault(require("@gmod/gff"));
 function isGzip(buf) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
 }
-
-var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(_default, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(_default);
-
-  function _default() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, _default);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+var default_1 = /** @class */ (function (_super) {
+    __extends(default_1, _super);
+    function default_1() {
+        return _super !== null && _super.apply(this, arguments) || this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "gffFeatures", void 0);
-    return _this;
-  }
-
-  (0, _createClass2.default)(_default, [{
-    key: "loadDataP",
-    value: function () {
-      var _loadDataP = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var _this2 = this;
-
-        var buffer, buf, data, lines, headerLines, i, header, feats, intervalTree;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return (0, _io.openLocation)((0, _configuration.readConfObject)(this.config, 'gffLocation'), this.pluginManager).readFile();
-
-              case 2:
-                buffer = _context.sent;
-
-                if (!isGzip(buffer)) {
-                  _context.next = 9;
-                  break;
+    default_1.prototype.loadDataP = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var pm, buf, buffer, _a, data, lines, headerLines, i, header, feats, intervalTree;
+            var _this = this;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        pm = this.pluginManager;
+                        return [4 /*yield*/, (0, io_1.openLocation)(this.getConf('gffLocation'), pm).readFile()];
+                    case 1:
+                        buf = _b.sent();
+                        if (!isGzip(buf)) return [3 /*break*/, 3];
+                        return [4 /*yield*/, (0, bgzf_filehandle_1.unzip)(buf)];
+                    case 2:
+                        _a = _b.sent();
+                        return [3 /*break*/, 4];
+                    case 3:
+                        _a = buf;
+                        _b.label = 4;
+                    case 4:
+                        buffer = _a;
+                        // 512MB  max chrome string length is 512MB
+                        if (buffer.length > 536870888) {
+                            throw new Error('Data exceeds maximum string length (512MB)');
+                        }
+                        data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+                        lines = data.split('\n');
+                        headerLines = [];
+                        for (i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
+                            headerLines.push(lines[i]);
+                        }
+                        header = headerLines.join('\n');
+                        feats = gff_1.default.parseStringSync(data, {
+                            parseFeatures: true,
+                            parseComments: false,
+                            parseDirectives: false,
+                            parseSequences: false,
+                        });
+                        intervalTree = feats
+                            .flat()
+                            .map(function (f, i) {
+                            return new simpleFeature_1.default({
+                                data: _this.featureData(f),
+                                id: "".concat(_this.id, "-offset-").concat(i),
+                            });
+                        })
+                            .reduce(function (acc, obj) {
+                            var key = obj.get('refName');
+                            if (!acc[key]) {
+                                acc[key] = new interval_tree_1.default();
+                            }
+                            acc[key].insert([obj.get('start'), obj.get('end')], obj);
+                            return acc;
+                        }, {});
+                        return [2 /*return*/, { header: header, intervalTree: intervalTree }];
                 }
-
-                _context.next = 6;
-                return (0, _bgzfFilehandle.unzip)(buffer);
-
-              case 6:
-                _context.t0 = _context.sent;
-                _context.next = 10;
-                break;
-
-              case 9:
-                _context.t0 = buffer;
-
-              case 10:
-                buf = _context.t0;
-
-                if (!(buf.length > 536870888)) {
-                  _context.next = 13;
-                  break;
+            });
+        });
+    };
+    default_1.prototype.loadData = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
+                if (!this.gffFeatures) {
+                    this.gffFeatures = this.loadDataP().catch(function (e) {
+                        _this.gffFeatures = undefined;
+                        throw e;
+                    });
                 }
-
-                throw new Error('Data exceeds maximum string length (512MB)');
-
-              case 13:
-                data = new TextDecoder('utf8', {
-                  fatal: true
-                }).decode(buf);
-                lines = data.split('\n');
-                headerLines = [];
-
-                for (i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
-                  headerLines.push(lines[i]);
+                return [2 /*return*/, this.gffFeatures];
+            });
+        });
+    };
+    default_1.prototype.getRefNames = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var intervalTree;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.loadData()];
+                    case 1:
+                        intervalTree = (_a.sent()).intervalTree;
+                        return [2 /*return*/, Object.keys(intervalTree)];
                 }
-
-                header = headerLines.join('\n');
-                feats = _gff.default.parseStringSync(data, {
-                  parseFeatures: true,
-                  parseComments: false,
-                  parseDirectives: false,
-                  parseSequences: false
-                });
-                intervalTree = feats.flat().map(function (f, i) {
-                  return new _simpleFeature.default({
-                    data: _this2.featureData(f),
-                    id: "".concat(_this2.id, "-offset-").concat(i)
-                  });
-                }).reduce(function (acc, obj) {
-                  var key = obj.get('refName');
-
-                  if (!acc[key]) {
-                    acc[key] = new _intervalTree.default();
-                  }
-
-                  acc[key].insert([obj.get('start'), obj.get('end')], obj);
-                  return acc;
-                }, {});
-                return _context.abrupt("return", {
-                  header: header,
-                  intervalTree: intervalTree
-                });
-
-              case 21:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function loadDataP() {
-        return _loadDataP.apply(this, arguments);
-      }
-
-      return loadDataP;
-    }()
-  }, {
-    key: "loadData",
-    value: function () {
-      var _loadData = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        var _this3 = this;
-
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                if (!this.gffFeatures) {
-                  this.gffFeatures = this.loadDataP().catch(function (e) {
-                    _this3.gffFeatures = undefined;
-                    throw e;
-                  });
+            });
+        });
+    };
+    default_1.prototype.getHeader = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var header;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.loadData()];
+                    case 1:
+                        header = (_a.sent()).header;
+                        return [2 /*return*/, header];
                 }
-
-                return _context2.abrupt("return", this.gffFeatures);
-
-              case 2:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function loadData() {
-        return _loadData.apply(this, arguments);
-      }
-
-      return loadData;
-    }()
-  }, {
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-        var opts,
-            _yield$this$loadData,
-            intervalTree,
-            _args3 = arguments;
-
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                opts = _args3.length > 0 && _args3[0] !== undefined ? _args3[0] : {};
-                _context3.next = 3;
-                return this.loadData();
-
-              case 3:
-                _yield$this$loadData = _context3.sent;
-                intervalTree = _yield$this$loadData.intervalTree;
-                return _context3.abrupt("return", Object.keys(intervalTree));
-
-              case 6:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
-        var _yield$this$loadData2, header;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.loadData();
-
-              case 2:
-                _yield$this$loadData2 = _context4.sent;
-                header = _yield$this$loadData2.header;
-                return _context4.abrupt("return", header);
-
-              case 5:
-              case "end":
-                return _context4.stop();
+            });
+        });
+    };
+    default_1.prototype.getFeatures = function (query, opts) {
+        var _this = this;
+        if (opts === void 0) { opts = {}; }
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var start, end, refName, intervalTree, e_1;
+            var _a;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _b.trys.push([0, 2, , 3]);
+                        start = query.start, end = query.end, refName = query.refName;
+                        return [4 /*yield*/, this.loadData()];
+                    case 1:
+                        intervalTree = (_b.sent()).intervalTree;
+                        (_a = intervalTree[refName]) === null || _a === void 0 ? void 0 : _a.search([start, end]).forEach(function (f) { return observer.next(f); });
+                        observer.complete();
+                        return [3 /*break*/, 3];
+                    case 2:
+                        e_1 = _b.sent();
+                        observer.error(e_1);
+                        return [3 /*break*/, 3];
+                    case 3: return [2 /*return*/];
+                }
+            });
+        }); }, opts.signal);
+    };
+    default_1.prototype.featureData = function (data) {
+        var _this = this;
+        var f = __assign({}, data);
+        f.start -= 1; // convert to interbase
+        if (data.strand === '+') {
+            f.strand = 1;
+        }
+        else if (data.strand === '-') {
+            f.strand = -1;
+        }
+        else if (data.strand === '.') {
+            f.strand = 0;
+        }
+        else {
+            f.strand = undefined;
+        }
+        f.phase = Number(data.phase);
+        f.refName = data.seq_id;
+        if (data.score === null) {
+            delete f.score;
+        }
+        if (data.phase === null) {
+            delete f.score;
+        }
+        var defaultFields = [
+            'start',
+            'end',
+            'seq_id',
+            'score',
+            'type',
+            'source',
+            'phase',
+            'strand',
+        ];
+        var dataAttributes = data.attributes || {};
+        Object.keys(dataAttributes).forEach(function (a) {
+            var _a, _b;
+            var b = a.toLowerCase();
+            if (defaultFields.includes(b)) {
+                // add "suffix" to tag name if it already exists
+                // reproduces behavior of NCList
+                b += '2';
             }
-          }
-        }, _callee4, this);
-      }));
-
-      function getHeader() {
-        return _getHeader.apply(this, arguments);
-      }
-
-      return getHeader;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(query) {
-      var _this4 = this;
-
-      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(observer) {
-          var _intervalTree$refName, start, end, refName, _yield$_this4$loadDat, intervalTree;
-
-          return _regenerator.default.wrap(function _callee5$(_context5) {
-            while (1) {
-              switch (_context5.prev = _context5.next) {
-                case 0:
-                  _context5.prev = 0;
-                  start = query.start, end = query.end, refName = query.refName;
-                  _context5.next = 4;
-                  return _this4.loadData();
-
-                case 4:
-                  _yield$_this4$loadDat = _context5.sent;
-                  intervalTree = _yield$_this4$loadDat.intervalTree;
-                  (_intervalTree$refName = intervalTree[refName]) === null || _intervalTree$refName === void 0 ? void 0 : _intervalTree$refName.search([start, end]).forEach(function (f) {
-                    return observer.next(f);
-                  });
-                  observer.complete();
-                  _context5.next = 13;
-                  break;
-
-                case 10:
-                  _context5.prev = 10;
-                  _context5.t0 = _context5["catch"](0);
-                  observer.error(_context5.t0);
-
-                case 13:
-                case "end":
-                  return _context5.stop();
-              }
+            if (dataAttributes[a] !== null) {
+                var attr = dataAttributes[a];
+                if (Array.isArray(attr) && attr.length === 1) {
+                    ;
+                    _a = attr, _b = __read(_a, 1), attr = _b[0];
+                }
+                f[b] = attr;
             }
-          }, _callee5, null, [[0, 10]]);
-        }));
-
-        return function (_x) {
-          return _ref.apply(this, arguments);
-        };
-      }(), opts.signal);
-    }
-  }, {
-    key: "featureData",
-    value: function featureData(data) {
-      var _this5 = this;
-
-      var f = _objectSpread({}, data);
-
-      f.start -= 1; // convert to interbase
-
-      if (data.strand === '+') {
-        f.strand = 1;
-      } else if (data.strand === '-') {
-        f.strand = -1;
-      } else if (data.strand === '.') {
-        f.strand = 0;
-      } else {
-        f.strand = undefined;
-      }
-
-      f.phase = Number(data.phase);
-      f.refName = data.seq_id;
-
-      if (data.score === null) {
-        delete f.score;
-      }
-
-      if (data.phase === null) {
-        delete f.score;
-      }
-
-      var defaultFields = ['start', 'end', 'seq_id', 'score', 'type', 'source', 'phase', 'strand'];
-      var dataAttributes = data.attributes || {};
-      Object.keys(dataAttributes).forEach(function (a) {
-        var b = a.toLowerCase();
-
-        if (defaultFields.includes(b)) {
-          // add "suffix" to tag name if it already exists
-          // reproduces behavior of NCList
-          b += '2';
+        });
+        f.refName = f.seq_id;
+        // the SimpleFeature constructor takes care of recursively inflating subfeatures
+        if (data.child_features && data.child_features.length) {
+            f.subfeatures = data.child_features
+                .map(function (childLocs) { return childLocs.map(function (childLoc) { return _this.featureData(childLoc); }); })
+                .flat();
         }
-
-        if (dataAttributes[a] !== null) {
-          var attr = dataAttributes[a];
-
-          if (Array.isArray(attr) && attr.length === 1) {
-            ;
-            var _attr = attr;
-
-            var _attr2 = (0, _slicedToArray2.default)(_attr, 1);
-
-            attr = _attr2[0];
-          }
-
-          f[b] = attr;
-        }
-      });
-      f.refName = f.seq_id; // the SimpleFeature constructor takes care of recursively inflating subfeatures
-
-      if (data.child_features && data.child_features.length) {
-        f.subfeatures = data.child_features.map(function (childLocs) {
-          return childLocs.map(function (childLoc) {
-            return _this5.featureData(childLoc);
-          });
-        }).flat();
-      }
-
-      delete f.child_features;
-      delete f.data;
-      delete f.derived_features;
-      delete f.attributes;
-      delete f.seq_id;
-      return f;
-    }
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }]);
-  return _default;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
-exports.default = _default;
+        delete f.child_features;
+        delete f.data;
+        delete f.derived_features;
+        delete f.attributes;
+        delete f.seq_id;
+        return f;
+    };
+    default_1.prototype.freeResources = function ( /* { region } */) { };
+    return default_1;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = default_1;
+//# sourceMappingURL=Gff3Adapter.js.map