@jbrowse/plugin-wiggle 1.7.10 → 2.0.1

package/dist/BigWigAdapter/BigWigAdapter.js

@@ -1,288 +1,180 @@
 "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 _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 _bbi = require("@gmod/bbi");
-
-var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _io = require("@jbrowse/core/util/io");
-
-var _util = require("@jbrowse/core/util");
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
-var _operators = require("rxjs/operators");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _stats = require("@jbrowse/core/util/stats");
-
-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 BigWigAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(BigWigAdapter, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(BigWigAdapter);
-
-  function BigWigAdapter(config, getSubAdapter, pluginManager) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, BigWigAdapter);
-    _this = _super.call(this, config, getSubAdapter, pluginManager);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "bigwig", void 0);
-    _this.bigwig = new _bbi.BigWig({
-      filehandle: (0, _io.openLocation)((0, _configuration.readConfObject)(config, 'bigWigLocation'), _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 __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());
     });
-    return _this;
-  }
-
-  (0, _createClass2.default)(BigWigAdapter, [{
-    key: "setup",
-    value: function () {
-      var _setup = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(opts) {
-        var _this2 = this;
-
-        var _ref, _ref$statusCallback, statusCallback;
-
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _ref = opts || {}, _ref$statusCallback = _ref.statusCallback, statusCallback = _ref$statusCallback === void 0 ? function () {} : _ref$statusCallback;
-                return _context.abrupt("return", (0, _util.updateStatus)('Downloading bigwig header', statusCallback, function () {
-                  return _this2.bigwig.getHeader(opts);
-                }));
-
-              case 2:
-              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);
-      }));
-
-      function setup(_x) {
-        return _setup.apply(this, arguments);
-      }
-
-      return setup;
-    }()
-  }, {
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(opts) {
-        var _yield$this$setup, refsByName;
-
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.setup(opts);
-
-              case 2:
-                _yield$this$setup = _context2.sent;
-                refsByName = _yield$this$setup.refsByName;
-                return _context2.abrupt("return", Object.keys(refsByName));
-
-              case 5:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getRefNames(_x2) {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "refIdToName",
-    value: function () {
-      var _refIdToName = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(refId) {
-        var _refsByNumber$refId;
-
-        var _yield$this$setup2, refsByNumber;
-
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return this.setup();
-
-              case 2:
-                _yield$this$setup2 = _context3.sent;
-                refsByNumber = _yield$this$setup2.refsByNumber;
-                return _context3.abrupt("return", (_refsByNumber$refId = refsByNumber[refId]) === null || _refsByNumber$refId === void 0 ? void 0 : _refsByNumber$refId.name);
-
-              case 5:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function refIdToName(_x3) {
-        return _refIdToName.apply(this, arguments);
-      }
-
-      return refIdToName;
-    }()
-  }, {
-    key: "getGlobalStats",
-    value: function () {
-      var _getGlobalStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(opts) {
-        var _yield$this$setup3, totalSummary;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.setup(opts);
-
-              case 2:
-                _yield$this$setup3 = _context4.sent;
-                totalSummary = _yield$this$setup3.totalSummary;
-                return _context4.abrupt("return", (0, _stats.rectifyStats)(totalSummary));
-
-              case 5:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function getGlobalStats(_x4) {
-        return _getGlobalStats.apply(this, arguments);
-      }
-
-      return getGlobalStats;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(region) {
-      var _this3 = this;
-
-      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-      var refName = region.refName,
-          start = region.start,
-          end = region.end;
-      var _opts$bpPerPx = opts.bpPerPx,
-          bpPerPx = _opts$bpPerPx === void 0 ? 0 : _opts$bpPerPx,
-          signal = opts.signal,
-          _opts$resolution = opts.resolution,
-          resolution = _opts$resolution === void 0 ? 1 : _opts$resolution,
-          _opts$statusCallback = opts.statusCallback,
-          statusCallback = _opts$statusCallback === void 0 ? function () {} : _opts$statusCallback;
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(observer) {
-          var ob;
-          return _regenerator.default.wrap(function _callee5$(_context5) {
-            while (1) {
-              switch (_context5.prev = _context5.next) {
-                case 0:
-                  statusCallback('Downloading bigwig data');
-                  _context5.next = 3;
-                  return _this3.bigwig.getFeatureStream(refName, start, end, _objectSpread(_objectSpread({}, opts), {}, {
-                    basesPerSpan: bpPerPx / resolution
-                  }));
-
-                case 3:
-                  ob = _context5.sent;
-                  ob.pipe((0, _operators.mergeAll)(), (0, _operators.map)(function (record) {
-                    return new _simpleFeature.default({
-                      id: "".concat(refName, ":").concat(record.start, "-").concat(record.end),
-                      data: _objectSpread(_objectSpread({}, record), {}, {
-                        refName: refName
-                      })
-                    });
-                  })).subscribe(observer);
-
-                case 5:
-                case "end":
-                  return _context5.stop();
-              }
-            }
-          }, _callee5);
-        }));
-
-        return function (_x5) {
-          return _ref2.apply(this, arguments);
-        };
-      }(), signal);
-    } // always render bigwig instead of calculating a feature density for it
-
-  }, {
-    key: "estimateRegionsStats",
-    value: function () {
-      var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(_regions) {
-        return _regenerator.default.wrap(function _callee6$(_context6) {
-          while (1) {
-            switch (_context6.prev = _context6.next) {
-              case 0:
-                return _context6.abrupt("return", {
-                  featureDensity: 0
-                });
-
-              case 1:
-              case "end":
-                return _context6.stop();
-            }
-          }
-        }, _callee6);
-      }));
-
-      function estimateRegionsStats(_x6) {
-        return _estimateRegionsStats.apply(this, arguments);
-      }
-
-      return estimateRegionsStats;
-    }()
-  }, {
-    key: "freeResources",
-    value: function freeResources() {}
-  }]);
-  return BigWigAdapter;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
+            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 });
+var bbi_1 = require("@gmod/bbi");
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var io_1 = require("@jbrowse/core/util/io");
+var util_1 = require("@jbrowse/core/util");
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+var operators_1 = require("rxjs/operators");
+var configuration_1 = require("@jbrowse/core/configuration");
+var stats_1 = require("@jbrowse/core/util/stats");
+var BigWigAdapter = /** @class */ (function (_super) {
+    __extends(BigWigAdapter, _super);
+    function BigWigAdapter(config, getSubAdapter, pluginManager) {
+        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
+        _this.bigwig = new bbi_1.BigWig({
+            filehandle: (0, io_1.openLocation)((0, configuration_1.readConfObject)(config, 'bigWigLocation'), _this.pluginManager),
+        });
+        return _this;
+    }
+    BigWigAdapter.prototype.setup = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, statusCallback;
+            var _this = this;
+            return __generator(this, function (_b) {
+                _a = (opts || {}).statusCallback, statusCallback = _a === void 0 ? function () { } : _a;
+                return [2 /*return*/, (0, util_1.updateStatus)('Downloading bigwig header', statusCallback, function () {
+                        return _this.bigwig.getHeader(opts);
+                    })];
+            });
+        });
+    };
+    BigWigAdapter.prototype.getRefNames = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var refsByName;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.setup(opts)];
+                    case 1:
+                        refsByName = (_a.sent()).refsByName;
+                        return [2 /*return*/, Object.keys(refsByName)];
+                }
+            });
+        });
+    };
+    BigWigAdapter.prototype.refIdToName = function (refId) {
+        var _a;
+        return __awaiter(this, void 0, void 0, function () {
+            var refsByNumber;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0: return [4 /*yield*/, this.setup()];
+                    case 1:
+                        refsByNumber = (_b.sent()).refsByNumber;
+                        return [2 /*return*/, (_a = refsByNumber[refId]) === null || _a === void 0 ? void 0 : _a.name];
+                }
+            });
+        });
+    };
+    BigWigAdapter.prototype.getGlobalStats = function (opts) {
+        return __awaiter(this, void 0, void 0, function () {
+            var totalSummary;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.setup(opts)];
+                    case 1:
+                        totalSummary = (_a.sent()).totalSummary;
+                        return [2 /*return*/, (0, stats_1.rectifyStats)(totalSummary)];
+                }
+            });
+        });
+    };
+    BigWigAdapter.prototype.getFeatures = function (region, opts) {
+        var _this = this;
+        if (opts === void 0) { opts = {}; }
+        var refName = region.refName, start = region.start, end = region.end;
+        var _a = opts.bpPerPx, bpPerPx = _a === void 0 ? 0 : _a, signal = opts.signal, _b = opts.resolution, resolution = _b === void 0 ? 1 : _b, _c = opts.statusCallback, statusCallback = _c === void 0 ? function () { } : _c;
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var ob;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        statusCallback('Downloading bigwig data');
+                        return [4 /*yield*/, this.bigwig.getFeatureStream(refName, start, end, __assign(__assign({}, opts), { basesPerSpan: bpPerPx / resolution }))];
+                    case 1:
+                        ob = _a.sent();
+                        ob.pipe((0, operators_1.mergeAll)(), (0, operators_1.map)(function (record) {
+                            return new simpleFeature_1.default({
+                                id: "".concat(refName, ":").concat(record.start, "-").concat(record.end),
+                                data: __assign(__assign({}, record), { refName: refName }),
+                            });
+                        })).subscribe(observer);
+                        return [2 /*return*/];
+                }
+            });
+        }); }, signal);
+    };
+    // always render bigwig instead of calculating a feature density for it
+    BigWigAdapter.prototype.estimateRegionsStats = function (_regions) {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                return [2 /*return*/, { featureDensity: 0 }];
+            });
+        });
+    };
+    BigWigAdapter.prototype.freeResources = function () { };
+    BigWigAdapter.capabilities = [
+        'hasResolution',
+        'hasLocalStats',
+        'hasGlobalStats',
+    ];
+    return BigWigAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
 exports.default = BigWigAdapter;
-(0, _defineProperty2.default)(BigWigAdapter, "capabilities", ['hasResolution', 'hasLocalStats', 'hasGlobalStats']);
+//# sourceMappingURL=BigWigAdapter.js.map

package/dist/BigWigAdapter/BigWigAdapter.js.map

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

@@ -1,22 +1,13 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('BigWigAdapter', {
-  bigWigLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/my.bw',
-      locationType: 'UriLocation'
-    }
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('BigWigAdapter', {
+    bigWigLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bw',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/BigWigAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BigWigAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,eAAe,EACf;IACE,cAAc,EAAE;QACd,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,gBAAgB;YACrB,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/BigWigAdapter/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/BigWigAdapter/index.js.map

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

package/dist/DensityRenderer/index.d.ts

@@ -1,6 +1,6 @@
 import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
 export { default as ReactComponent } from '../WiggleRendering';
 export default class DensityRenderer extends WiggleBaseRenderer {
-    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): void;
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;
 }
 export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;