@jbrowse/core 1.7.11 → 2.1.0

package/pluggableElementTypes/renderers/BoxRendererType.js

@@ -1,313 +1,154 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = exports.LayoutSession = 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 _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
-
-var _get2 = _interopRequireDefault(require("@babel/runtime/helpers/get"));
-
-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 _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _fastDeepEqual = _interopRequireDefault(require("fast-deep-equal"));
-
-var _GranularRectLayout = _interopRequireDefault(require("../../util/layouts/GranularRectLayout"));
-
-var _MultiLayout = _interopRequireDefault(require("../../util/layouts/MultiLayout"));
-
-var _PrecomputedLayout = _interopRequireDefault(require("../../util/layouts/PrecomputedLayout"));
-
-var _FeatureRendererType2 = _interopRequireDefault(require("./FeatureRendererType"));
-
-var _util = require("../../util");
-
-var _configuration = require("../../configuration");
-
-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 LayoutSession = /*#__PURE__*/function () {
-  function LayoutSession(args) {
-    (0, _classCallCheck2.default)(this, LayoutSession);
-    (0, _defineProperty2.default)(this, "config", void 0);
-    (0, _defineProperty2.default)(this, "bpPerPx", void 0);
-    (0, _defineProperty2.default)(this, "filters", void 0);
-    (0, _defineProperty2.default)(this, "cachedLayout", void 0);
-    this.config = args.config;
-    this.bpPerPx = args.bpPerPx;
-    this.filters = args.filters;
-    this.update(args);
-  }
-
-  (0, _createClass2.default)(LayoutSession, [{
-    key: "update",
-    value: function update(props) {
-      Object.assign(this, props);
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.LayoutSession = void 0;
+const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
+const GranularRectLayout_1 = __importDefault(require("../../util/layouts/GranularRectLayout"));
+const MultiLayout_1 = __importDefault(require("../../util/layouts/MultiLayout"));
+const PrecomputedLayout_1 = __importDefault(require("../../util/layouts/PrecomputedLayout"));
+const FeatureRendererType_1 = __importDefault(require("./FeatureRendererType"));
+const util_1 = require("../../util");
+const configuration_1 = require("../../configuration");
+class LayoutSession {
+    constructor(args) {
+        this.config = args.config;
+        this.bpPerPx = args.bpPerPx;
+        this.filters = args.filters;
+        this.update(args);
     }
-  }, {
-    key: "makeLayout",
-    value: function makeLayout() {
-      return new _MultiLayout.default(_GranularRectLayout.default, {
-        maxHeight: (0, _configuration.readConfObject)(this.config, 'maxHeight'),
-        displayMode: (0, _configuration.readConfObject)(this.config, 'displayMode'),
-        pitchX: this.bpPerPx,
-        pitchY: (0, _configuration.readConfObject)(this.config, 'noSpacing') ? 1 : 3
-      });
+    update(props) {
+        Object.assign(this, props);
+    }
+    makeLayout() {
+        return new MultiLayout_1.default(GranularRectLayout_1.default, {
+            maxHeight: (0, configuration_1.readConfObject)(this.config, 'maxHeight'),
+            displayMode: (0, configuration_1.readConfObject)(this.config, 'displayMode'),
+            pitchX: this.bpPerPx,
+            pitchY: (0, configuration_1.readConfObject)(this.config, 'noSpacing') ? 1 : 3,
+        });
     }
     /**
      * @param layout -
      * @returns true if the given layout is a valid one to use for this session
      */
-
-  }, {
-    key: "cachedLayoutIsValid",
-    value: function cachedLayoutIsValid(cachedLayout) {
-      return cachedLayout && cachedLayout.layout.subLayoutConstructorArgs.pitchX === this.bpPerPx && (0, _fastDeepEqual.default)((0, _configuration.readConfObject)(this.config), cachedLayout.config) && (0, _fastDeepEqual.default)(this.filters, cachedLayout.filters);
+    cachedLayoutIsValid(cachedLayout) {
+        return (cachedLayout &&
+            cachedLayout.layout.subLayoutConstructorArgs.pitchX === this.bpPerPx &&
+            (0, fast_deep_equal_1.default)((0, configuration_1.readConfObject)(this.config), cachedLayout.config) &&
+            (0, fast_deep_equal_1.default)(this.filters, cachedLayout.filters));
     }
-  }, {
-    key: "layout",
-    get: function get() {
-      if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
-        this.cachedLayout = {
-          layout: this.makeLayout(),
-          config: (0, _configuration.readConfObject)(this.config),
-          filters: this.filters
-        };
-      }
-
-      return this.cachedLayout.layout;
+    get layout() {
+        if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
+            this.cachedLayout = {
+                layout: this.makeLayout(),
+                config: (0, configuration_1.readConfObject)(this.config),
+                filters: this.filters,
+            };
+        }
+        return this.cachedLayout.layout;
     }
-  }]);
-  return LayoutSession;
-}();
-
+}
 exports.LayoutSession = LayoutSession;
-
-var BoxRendererType = /*#__PURE__*/function (_FeatureRendererType) {
-  (0, _inherits2.default)(BoxRendererType, _FeatureRendererType);
-
-  var _super = _createSuper(BoxRendererType);
-
-  function BoxRendererType() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, BoxRendererType);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+class BoxRendererType extends FeatureRendererType_1.default {
+    constructor() {
+        super(...arguments);
+        this.sessions = {};
+    }
+    getWorkerSession(props) {
+        const key = (0, util_1.getLayoutId)(props);
+        if (!this.sessions[key]) {
+            this.sessions[key] = this.createSession(props);
+        }
+        const session = this.sessions[key];
+        session.update(props);
+        return session;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "sessions", {});
-    return _this;
-  }
-
-  (0, _createClass2.default)(BoxRendererType, [{
-    key: "getWorkerSession",
-    value: function getWorkerSession(props) {
-      var key = (0, _util.getLayoutId)(props);
-
-      if (!this.sessions[key]) {
-        this.sessions[key] = this.createSession(props);
-      }
-
-      var session = this.sessions[key];
-      session.update(props);
-      return session;
-    } // expands region for glyphs to use
-
-  }, {
-    key: "getExpandedRegion",
-    value: function getExpandedRegion(region, renderArgs) {
-      if (!region) {
-        return region;
-      }
-
-      var bpPerPx = renderArgs.bpPerPx,
-          config = renderArgs.config;
-      var maxFeatureGlyphExpansion = config === undefined ? 0 : (0, _configuration.readConfObject)(config, 'maxFeatureGlyphExpansion');
-
-      if (!maxFeatureGlyphExpansion) {
-        return region;
-      }
-
-      var bpExpansion = Math.round(maxFeatureGlyphExpansion * bpPerPx);
-      return _objectSpread(_objectSpread({}, region), {}, {
-        start: Math.floor(Math.max(region.start - bpExpansion, 0)),
-        end: Math.ceil(region.end + bpExpansion)
-      });
+    // expands region for glyphs to use
+    getExpandedRegion(region, renderArgs) {
+        if (!region) {
+            return region;
+        }
+        const { bpPerPx, config } = renderArgs;
+        const maxFeatureGlyphExpansion = config === undefined
+            ? 0
+            : (0, configuration_1.readConfObject)(config, 'maxFeatureGlyphExpansion');
+        if (!maxFeatureGlyphExpansion) {
+            return region;
+        }
+        const bpExpansion = Math.round(maxFeatureGlyphExpansion * bpPerPx);
+        return {
+            ...region,
+            start: Math.floor(Math.max(region.start - bpExpansion, 0)),
+            end: Math.ceil(region.end + bpExpansion),
+        };
     }
-  }, {
-    key: "createSession",
-    value: function createSession(props) {
-      return new LayoutSession(props);
+    createSession(props) {
+        return new LayoutSession(props);
     }
-  }, {
-    key: "freeResourcesInClient",
-    value: function () {
-      var _freeResourcesInClient = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(rpcManager, args) {
-        var regions, key, freed, session;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                regions = args.regions;
-                key = (0, _util.getLayoutId)(args);
-                freed = 0;
-                session = this.sessions[key];
-
-                if (!regions && session) {
-                  delete this.sessions[key];
-                  freed = 1;
-                }
-
-                if (session && regions) {
-                  session.layout.discardRange(regions[0].refName, regions[0].start, regions[0].end);
-                }
-
-                _context.t0 = freed;
-                _context.next = 9;
-                return (0, _get2.default)((0, _getPrototypeOf2.default)(BoxRendererType.prototype), "freeResourcesInClient", this).call(this, rpcManager, args);
-
-              case 9:
-                _context.t1 = _context.sent;
-                return _context.abrupt("return", _context.t0 + _context.t1);
-
-              case 11:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function freeResourcesInClient(_x, _x2) {
-        return _freeResourcesInClient.apply(this, arguments);
-      }
-
-      return freeResourcesInClient;
-    }()
-  }, {
-    key: "deserializeLayoutInClient",
-    value: function deserializeLayoutInClient(json) {
-      return new _PrecomputedLayout.default(json);
+    async freeResourcesInClient(rpcManager, args) {
+        const { regions } = args;
+        const key = (0, util_1.getLayoutId)(args);
+        let freed = 0;
+        const session = this.sessions[key];
+        if (!regions && session) {
+            delete this.sessions[key];
+            freed = 1;
+        }
+        if (session && regions) {
+            session.layout.discardRange(regions[0].refName, regions[0].start, regions[0].end);
+        }
+        return freed + (await super.freeResourcesInClient(rpcManager, args));
     }
-  }, {
-    key: "deserializeResultsInClient",
-    value: function deserializeResultsInClient(result, args) {
-      var layout = this.deserializeLayoutInClient(result.layout);
-      var deserialized = (0, _get2.default)((0, _getPrototypeOf2.default)(BoxRendererType.prototype), "deserializeResultsInClient", this).call(this, _objectSpread(_objectSpread({}, result), {}, {
-        layout: layout
-      }), args); // // debugging aid: check if there are features in `features` that are not in the layout
-      // const featureIds1 = iterMap(deserialized.features.values(), f =>
-      //   f.id(),
-      // ).sort()
-      // const featureIds2 = Object.keys(
-      //   deserialized.layout.toJSON().rectangles,
-      // ).sort()
-      // if (
-      //   featureIds1.length > featureIds2.length &&
-      //   !deserialized.layout.maxHeightReached
-      // )
-      //   debugger
-
-      return deserialized;
+    deserializeLayoutInClient(json) {
+        return new PrecomputedLayout_1.default(json);
     }
-  }, {
-    key: "createLayoutInWorker",
-    value: function createLayoutInWorker(args) {
-      var regions = args.regions;
-      var session = this.getWorkerSession(args);
-      var subLayout = session.layout.getSublayout(regions[0].refName);
-      return subLayout;
+    deserializeResultsInClient(result, args) {
+        const layout = this.deserializeLayoutInClient(result.layout);
+        const deserialized = super.deserializeResultsInClient({ ...result, layout }, args);
+        // // debugging aid: check if there are features in `features` that are not in the layout
+        // const featureIds1 = iterMap(deserialized.features.values(), f =>
+        //   f.id(),
+        // ).sort()
+        // const featureIds2 = Object.keys(
+        //   deserialized.layout.toJSON().rectangles,
+        // ).sort()
+        // if (
+        //   featureIds1.length > featureIds2.length &&
+        //   !deserialized.layout.maxHeightReached
+        // )
+        //   debugger
+        return deserialized;
     }
-  }, {
-    key: "serializeResultsInWorker",
-    value: function serializeResultsInWorker(results, args) {
-      var serialized = (0, _get2.default)((0, _getPrototypeOf2.default)(BoxRendererType.prototype), "serializeResultsInWorker", this).call(this, results, args);
-
-      var _args$regions = (0, _slicedToArray2.default)(args.regions, 1),
-          region = _args$regions[0];
-
-      serialized.layout = results.layout.serializeRegion(this.getExpandedRegion(region, args));
-
-      if (serialized.layout.rectangles) {
-        serialized.features = serialized.features.filter(function (f) {
-          return Boolean(serialized.layout.rectangles[f.uniqueId]);
-        });
-      }
-
-      serialized.maxHeightReached = serialized.layout.maxHeightReached;
-      return serialized;
+    createLayoutInWorker(args) {
+        const { regions } = args;
+        const session = this.getWorkerSession(args);
+        const subLayout = session.layout.getSublayout(regions[0].refName);
+        return subLayout;
+    }
+    serializeResultsInWorker(results, args) {
+        const serialized = super.serializeResultsInWorker(results, args);
+        const [region] = args.regions;
+        serialized.layout = results.layout.serializeRegion(this.getExpandedRegion(region, args));
+        if (serialized.layout.rectangles) {
+            serialized.features = serialized.features.filter(f => {
+                return Boolean(serialized.layout.rectangles[f.uniqueId]);
+            });
+        }
+        serialized.maxHeightReached = serialized.layout.maxHeightReached;
+        return serialized;
     }
     /**
      * gets layout and renders
      *
      * @param props - render args
      */
-
-  }, {
-    key: "render",
-    value: function () {
-      var _render = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(props) {
-        var layout, result;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                layout = props.layout || this.createLayoutInWorker(props);
-                _context2.next = 3;
-                return (0, _get2.default)((0, _getPrototypeOf2.default)(BoxRendererType.prototype), "render", this).call(this, _objectSpread(_objectSpread({}, props), {}, {
-                  layout: layout
-                }));
-
-              case 3:
-                result = _context2.sent;
-                return _context2.abrupt("return", _objectSpread(_objectSpread({}, result), {}, {
-                  layout: layout
-                }));
-
-              case 5:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function render(_x3) {
-        return _render.apply(this, arguments);
-      }
-
-      return render;
-    }()
-  }]);
-  return BoxRendererType;
-}(_FeatureRendererType2.default);
-
-exports.default = BoxRendererType;
+    async render(props) {
+        const layout = props.layout ||
+            this.createLayoutInWorker(props);
+        const result = await super.render({ ...props, layout });
+        return { ...result, layout };
+    }
+}
+exports.default = BoxRendererType;

package/pluggableElementTypes/renderers/CircularChordRendererType.js

@@ -1,39 +1,9 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-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 _FeatureRendererType = _interopRequireDefault(require("./FeatureRendererType"));
-
-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 CircularChordRendererType = /*#__PURE__*/function (_FeatureRenderer) {
-  (0, _inherits2.default)(CircularChordRendererType, _FeatureRenderer);
-
-  var _super = _createSuper(CircularChordRendererType);
-
-  function CircularChordRendererType() {
-    (0, _classCallCheck2.default)(this, CircularChordRendererType);
-    return _super.apply(this, arguments);
-  }
-
-  return (0, _createClass2.default)(CircularChordRendererType);
-}(_FeatureRendererType.default);
-
-exports.default = CircularChordRendererType;
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const FeatureRendererType_1 = __importDefault(require("./FeatureRendererType"));
+class CircularChordRendererType extends FeatureRendererType_1.default {
+}
+exports.default = CircularChordRendererType;