@jbrowse/plugin-sequence 1.7.11 → 2.1.0

package/dist/TwoBitAdapter/TwoBitAdapter.js

@@ -1,289 +1,193 @@
 "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 _io = require("@jbrowse/core/util/io");
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _twobit = require("@gmod/twobit");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-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 TwoBitAdapter = /*#__PURE__*/function (_BaseSequenceAdapter) {
-  (0, _inherits2.default)(TwoBitAdapter, _BaseSequenceAdapter);
-
-  var _super = _createSuper(TwoBitAdapter);
-
-  function TwoBitAdapter(config, getSubAdapter, pluginManager) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, TwoBitAdapter);
-    _this = _super.call(this, config, getSubAdapter, pluginManager);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "twobit", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "chromSizesData", void 0);
-    _this.chromSizesData = _this.initChromSizes();
-    _this.twobit = new _twobit.TwoBitFile({
-      filehandle: (0, _io.openLocation)((0, _configuration.readConfObject)(config, 'twoBitLocation'), _this.pluginManager)
+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());
     });
-    return _this;
-  }
-
-  (0, _createClass2.default)(TwoBitAdapter, [{
-    key: "initChromSizes",
-    value: // the chromSizesData can be used to speed up loading since TwoBit has to do
-    // many range requests at startup to perform the getRegions request
-    function () {
-      var _initChromSizes = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var conf, file, data;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                conf = (0, _configuration.readConfObject)(this.config, 'chromSizesLocation'); // check against default and empty in case someone makes the field blank in
-                // config editor, may want better way to check "optional config slots" in
-                // future
-
-                if (!(conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '')) {
-                  _context.next = 7;
-                  break;
-                }
-
-                file = (0, _io.openLocation)(conf, this.pluginManager);
-                _context.next = 5;
-                return file.readFile('utf8');
-
-              case 5:
-                data = _context.sent;
-                return _context.abrupt("return", Object.fromEntries(data === null || data === void 0 ? void 0 : data.split('\n').filter(function (line) {
-                  return !!line.trim();
-                }).map(function (line) {
-                  var _line$split = line.split('\t'),
-                      _line$split2 = (0, _slicedToArray2.default)(_line$split, 2),
-                      name = _line$split2[0],
-                      length = _line$split2[1];
-
-                  return [name, +length];
-                })));
-
-              case 7:
-                return _context.abrupt("return", undefined);
-
-              case 8:
-              case "end":
-                return _context.stop();
+};
+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;
             }
-          }
-        }, _callee, this);
-      }));
-
-      function initChromSizes() {
-        return _initChromSizes.apply(this, arguments);
-      }
-
-      return initChromSizes;
-    }()
-  }, {
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        var chromSizesData;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.chromSizesData;
-
-              case 2:
-                chromSizesData = _context2.sent;
-
-                if (!chromSizesData) {
-                  _context2.next = 5;
-                  break;
+            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 simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+var twobit_1 = require("@gmod/twobit");
+var configuration_1 = require("@jbrowse/core/configuration");
+var TwoBitAdapter = /** @class */ (function (_super) {
+    __extends(TwoBitAdapter, _super);
+    function TwoBitAdapter(config, getSubAdapter, pluginManager) {
+        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
+        _this.chromSizesData = _this.initChromSizes();
+        _this.twobit = new twobit_1.TwoBitFile({
+            filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(config, 'twoBitLocation'), _this.pluginManager),
+        });
+        return _this;
+    }
+    TwoBitAdapter.prototype.initChromSizes = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var conf, file, data;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        conf = (0, configuration_1.readConfObject)(this.config, 'chromSizesLocation');
+                        if (!(conf.uri !== '/path/to/default.chrom.sizes' && conf.uri !== '')) return [3 /*break*/, 2];
+                        file = (0, io_1.openLocation)(conf, this.pluginManager);
+                        return [4 /*yield*/, file.readFile('utf8')];
+                    case 1:
+                        data = _a.sent();
+                        return [2 /*return*/, Object.fromEntries(data === null || data === void 0 ? void 0 : data.split('\n').filter(function (line) { return !!line.trim(); }).map(function (line) {
+                                var _a = __read(line.split('\t'), 2), name = _a[0], length = _a[1];
+                                return [name, +length];
+                            }))];
+                    case 2: return [2 /*return*/, undefined];
                 }
-
-                return _context2.abrupt("return", Object.keys(chromSizesData));
-
-              case 5:
-                return _context2.abrupt("return", this.twobit.getSequenceNames());
-
-              case 6:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "getRegions",
-    value: function () {
-      var _getRegions = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-        var chromSizesData, refSizes;
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return this.chromSizesData;
-
-              case 2:
-                chromSizesData = _context3.sent;
-
-                if (!chromSizesData) {
-                  _context3.next = 5;
-                  break;
+            });
+        });
+    };
+    TwoBitAdapter.prototype.getRefNames = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var chromSizesData;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.chromSizesData];
+                    case 1:
+                        chromSizesData = _a.sent();
+                        if (chromSizesData) {
+                            return [2 /*return*/, Object.keys(chromSizesData)];
+                        }
+                        return [2 /*return*/, this.twobit.getSequenceNames()];
                 }
-
-                return _context3.abrupt("return", Object.keys(chromSizesData).map(function (refName) {
-                  return {
-                    refName: refName,
-                    start: 0,
-                    end: chromSizesData[refName]
-                  };
-                }));
-
-              case 5:
-                _context3.next = 7;
-                return this.twobit.getSequenceSizes();
-
-              case 7:
-                refSizes = _context3.sent;
-                return _context3.abrupt("return", Object.keys(refSizes).map(function (refName) {
-                  return {
-                    refName: refName,
-                    start: 0,
-                    end: refSizes[refName]
-                  };
-                }));
-
-              case 9:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getRegions() {
-        return _getRegions.apply(this, arguments);
-      }
-
-      return getRegions;
-    }()
+            });
+        });
+    };
+    TwoBitAdapter.prototype.getRegions = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var chromSizesData, refSizes;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.chromSizesData];
+                    case 1:
+                        chromSizesData = _a.sent();
+                        if (chromSizesData) {
+                            return [2 /*return*/, Object.keys(chromSizesData).map(function (refName) { return ({
+                                    refName: refName,
+                                    start: 0,
+                                    end: chromSizesData[refName],
+                                }); })];
+                        }
+                        return [4 /*yield*/, this.twobit.getSequenceSizes()];
+                    case 2:
+                        refSizes = _a.sent();
+                        return [2 /*return*/, Object.keys(refSizes).map(function (refName) { return ({
+                                refName: refName,
+                                start: 0,
+                                end: refSizes[refName],
+                            }); })];
+                }
+            });
+        });
+    };
     /**
      * Fetch features for a certain region
      * @param param -
      * @returns Observable of Feature objects in the region
      */
-
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(_ref) {
-      var _this2 = this;
-
-      var refName = _ref.refName,
-          start = _ref.start,
-          end = _ref.end;
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(observer) {
-          var size, regionEnd, seq;
-          return _regenerator.default.wrap(function _callee4$(_context4) {
-            while (1) {
-              switch (_context4.prev = _context4.next) {
-                case 0:
-                  _context4.next = 2;
-                  return _this2.twobit.getSequenceSize(refName);
-
-                case 2:
-                  size = _context4.sent;
-                  regionEnd = size !== undefined ? Math.min(size, end) : end;
-                  _context4.next = 6;
-                  return _this2.twobit.getSequence(refName, start, regionEnd);
-
-                case 6:
-                  seq = _context4.sent;
-
-                  if (seq) {
-                    observer.next(new _simpleFeature.default({
-                      id: "".concat(refName, " ").concat(start, "-").concat(regionEnd),
-                      data: {
-                        refName: refName,
-                        start: start,
-                        end: regionEnd,
-                        seq: seq
-                      }
-                    }));
-                  }
-
-                  observer.complete();
-
-                case 9:
-                case "end":
-                  return _context4.stop();
-              }
-            }
-          }, _callee4);
-        }));
-
-        return function (_x) {
-          return _ref2.apply(this, arguments);
-        };
-      }());
-    }
+    TwoBitAdapter.prototype.getFeatures = function (_a) {
+        var _this = this;
+        var refName = _a.refName, start = _a.start, end = _a.end;
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var size, regionEnd, seq;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.twobit.getSequenceSize(refName)];
+                    case 1:
+                        size = _a.sent();
+                        regionEnd = size !== undefined ? Math.min(size, end) : end;
+                        return [4 /*yield*/, this.twobit.getSequence(refName, start, regionEnd)];
+                    case 2:
+                        seq = _a.sent();
+                        if (seq) {
+                            observer.next(new simpleFeature_1.default({
+                                id: "".concat(refName, " ").concat(start, "-").concat(regionEnd),
+                                data: { refName: refName, start: start, end: regionEnd, seq: seq },
+                            }));
+                        }
+                        observer.complete();
+                        return [2 /*return*/];
+                }
+            });
+        }); });
+    };
     /**
      * called to provide a hint that data tied to a certain region
      * will not be needed for the forseeable future and can be purged
      * from caches, etc
      */
-
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }]);
-  return TwoBitAdapter;
-}(_BaseAdapter.BaseSequenceAdapter);
-
-exports.default = TwoBitAdapter;
+    TwoBitAdapter.prototype.freeResources = function ( /* { region } */) { };
+    return TwoBitAdapter;
+}(BaseAdapter_1.BaseSequenceAdapter));
+exports.default = TwoBitAdapter;
+//# sourceMappingURL=TwoBitAdapter.js.map

package/dist/TwoBitAdapter/TwoBitAdapter.js.map

@@ -0,0 +1 @@
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package/dist/TwoBitAdapter/configSchema.js

@@ -1,30 +1,18 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('TwoBitAdapter', {
-  twoBitLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/my.2bit',
-      locationType: 'UriLocation'
-    }
-  },
-  chromSizesLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/default.chrom.sizes',
-      locationType: 'UriLocation'
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('TwoBitAdapter', {
+    twoBitLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.2bit', locationType: 'UriLocation' },
     },
-    description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time'
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+    chromSizesLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/default.chrom.sizes',
+            locationType: 'UriLocation',
+        },
+        description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time',
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/TwoBitAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,kBAAkB,EAAE,YAAY,EAAE,aAAa,EAAE;KACvE;IACD,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;QACD,WAAW,EACT,8GAA8G;KACjH;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/TwoBitAdapter/index.js

@@ -1,15 +1,9 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "configSchema", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = void 0;
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/TwoBitAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}