@jbrowse/core 1.7.11 → 2.1.0

package/util/layouts/MultiLayout.js

@@ -1,118 +1,50 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
-
-function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
-
-function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
-
-/* eslint-disable @typescript-eslint/no-explicit-any */
-var MultiLayout = /*#__PURE__*/function () {
-  /**
-   * layout class that just keeps a number of named sub-layouts.
-   * basically just a fancier
-   * `{ layout1: new GranularRectLayout(), layout2: new GranularRectLayout() ...}`
-   */
-  function MultiLayout(SubLayoutClass) {
-    var layoutArgs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-    (0, _classCallCheck2.default)(this, MultiLayout);
-    this.SubLayoutClass = SubLayoutClass;
-    (0, _defineProperty2.default)(this, "subLayouts", new Map());
-    (0, _defineProperty2.default)(this, "subLayoutConstructorArgs", {});
-    this.subLayouts = new Map();
-    this.subLayoutConstructorArgs = layoutArgs;
-  }
-
-  (0, _createClass2.default)(MultiLayout, [{
-    key: "getDataByID",
-    value: function getDataByID(id) {
-      var _iterator = _createForOfIteratorHelper(this.subLayouts.values()),
-          _step;
-
-      try {
-        for (_iterator.s(); !(_step = _iterator.n()).done;) {
-          var layout = _step.value;
-          // @ts-ignore
-          var r = layout.getDataByID(id);
-
-          if (r) {
-            return r;
-          }
+Object.defineProperty(exports, "__esModule", { value: true });
+class MultiLayout {
+    /**
+     * layout class that just keeps a number of named sub-layouts.
+     * basically just a fancier
+     * `{ layout1: new GranularRectLayout(), layout2: new GranularRectLayout() ...}`
+     */
+    constructor(SubLayoutClass, layoutArgs = {}) {
+        this.SubLayoutClass = SubLayoutClass;
+        this.subLayouts = new Map();
+        this.subLayoutConstructorArgs = {};
+        this.subLayouts = new Map();
+        this.subLayoutConstructorArgs = layoutArgs;
+    }
+    getDataByID(id) {
+        for (const layout of this.subLayouts.values()) {
+            // @ts-ignore
+            const r = layout.getDataByID(id);
+            if (r) {
+                return r;
+            }
         }
-      } catch (err) {
-        _iterator.e(err);
-      } finally {
-        _iterator.f();
-      }
-
-      return undefined;
+        return undefined;
     }
-  }, {
-    key: "getSublayout",
-    value: function getSublayout(layoutName) {
-      var subLayout = this.subLayouts.get(layoutName);
-
-      if (subLayout === undefined) {
-        subLayout = new this.SubLayoutClass(this.subLayoutConstructorArgs);
-        this.subLayouts.set(layoutName, subLayout);
+    getSublayout(layoutName) {
+        let subLayout = this.subLayouts.get(layoutName);
+        if (subLayout === undefined) {
+            subLayout = new this.SubLayoutClass(this.subLayoutConstructorArgs);
+            this.subLayouts.set(layoutName, subLayout);
+            return subLayout;
+        }
         return subLayout;
-      }
-
-      return subLayout;
     }
-  }, {
-    key: "addRect",
-    value: function addRect(layoutName, id, left, right, height) {
-      var data = arguments.length > 5 && arguments[5] !== undefined ? arguments[5] : {};
-      return this.getSublayout(layoutName).addRect(id, left, right, height, data);
+    addRect(layoutName, id, left, right, height, data = {}) {
+        return this.getSublayout(layoutName).addRect(id, left, right, height, data);
     }
-  }, {
-    key: "discardRange",
-    value: function discardRange(layoutName, left, right) {
-      var layout = this.subLayouts.get(layoutName);
-      return layout && layout.discardRange(left, right);
+    discardRange(layoutName, left, right) {
+        const layout = this.subLayouts.get(layoutName);
+        return layout && layout.discardRange(left, right);
     }
-  }, {
-    key: "toJSON",
-    value: function toJSON() {
-      var data = {};
-
-      var _iterator2 = _createForOfIteratorHelper(this.subLayouts.entries()),
-          _step2;
-
-      try {
-        for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
-          var _step2$value = (0, _slicedToArray2.default)(_step2.value, 2),
-              layoutName = _step2$value[0],
-              sublayout = _step2$value[1];
-
-          data[layoutName] = sublayout.toJSON();
+    toJSON() {
+        const data = {};
+        for (const [layoutName, sublayout] of this.subLayouts.entries()) {
+            data[layoutName] = sublayout.toJSON();
         }
-      } catch (err) {
-        _iterator2.e(err);
-      } finally {
-        _iterator2.f();
-      }
-
-      return data;
+        return data;
     }
-  }]);
-  return MultiLayout;
-}();
-
-exports.default = MultiLayout;
+}
+exports.default = MultiLayout;

package/util/layouts/PrecomputedLayout.js

@@ -1,129 +1,71 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-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 _ = require("..");
-
-var _rbush = _interopRequireDefault(require("rbush"));
-
-var PrecomputedLayout = /*#__PURE__*/function () {
-  function PrecomputedLayout(_ref) {
-    var rectangles = _ref.rectangles,
-        totalHeight = _ref.totalHeight,
-        maxHeightReached = _ref.maxHeightReached;
-    (0, _classCallCheck2.default)(this, PrecomputedLayout);
-    (0, _defineProperty2.default)(this, "rectangles", void 0);
-    (0, _defineProperty2.default)(this, "totalHeight", void 0);
-    (0, _defineProperty2.default)(this, "maxHeightReached", void 0);
-    (0, _defineProperty2.default)(this, "rbush", void 0);
-    this.rectangles = new Map(Object.entries(rectangles)); // rectangles is of the form "featureId": [leftPx, topPx, rightPx, bottomPx]
-
-    this.totalHeight = totalHeight;
-    this.maxHeightReached = maxHeightReached;
-    this.rbush = new _rbush.default();
-
-    for (var _i = 0, _Object$entries = Object.entries(rectangles); _i < _Object$entries.length; _i++) {
-      var _Object$entries$_i = (0, _slicedToArray2.default)(_Object$entries[_i], 2),
-          key = _Object$entries$_i[0],
-          layout = _Object$entries$_i[1];
-
-      this.rbush.insert({
-        minX: layout[0],
-        minY: layout[1],
-        maxX: layout[2],
-        maxY: layout[3],
-        name: key
-      });
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const rbush_1 = __importDefault(require("rbush"));
+class PrecomputedLayout {
+    constructor({ rectangles, totalHeight, maxHeightReached }) {
+        this.rectangles = new Map(Object.entries(rectangles));
+        // rectangles is of the form "featureId": [leftPx, topPx, rightPx, bottomPx]
+        this.totalHeight = totalHeight;
+        this.maxHeightReached = maxHeightReached;
+        this.rbush = new rbush_1.default();
+        for (const [key, layout] of Object.entries(rectangles)) {
+            this.rbush.insert({
+                minX: layout[0],
+                minY: layout[1],
+                maxX: layout[2],
+                maxY: layout[3],
+                name: key,
+            });
+        }
     }
-  }
-
-  (0, _createClass2.default)(PrecomputedLayout, [{
-    key: "addRect",
-    value: function addRect(id) {
-      var rect = this.rectangles.get(id);
-
-      if (!rect) {
-        throw new Error("id ".concat(id, " not found in precomputed feature layout"));
-      } // left, top, right, bottom
-
-
-      return rect[1];
+    addRect(id) {
+        const rect = this.rectangles.get(id);
+        if (!rect) {
+            throw new Error(`id ${id} not found in precomputed feature layout`);
+        }
+        // left, top, right, bottom
+        return rect[1];
     }
     /**
      * returns a Map of `feature id -> rectangle`
      */
-
-  }, {
-    key: "getRectangles",
-    value: function getRectangles() {
-      return this.rectangles;
+    getRectangles() {
+        return this.rectangles;
     }
-  }, {
-    key: "getTotalHeight",
-    value: function getTotalHeight() {
-      return this.totalHeight;
+    getTotalHeight() {
+        return this.totalHeight;
     }
-  }, {
-    key: "collides",
-    value: function collides(_rect, _top) {
-      throw new Error('Method not implemented.');
+    collides(_rect, _top) {
+        throw new Error('Method not implemented.');
     }
-  }, {
-    key: "getByCoord",
-    value: function getByCoord(x, y) {
-      var rect = {
-        minX: x,
-        minY: y,
-        maxX: x + 1,
-        maxY: y + 1
-      };
-      return this.rbush.collides(rect) ? this.rbush.search(rect)[0].name : undefined;
+    getByCoord(x, y) {
+        const rect = { minX: x, minY: y, maxX: x + 1, maxY: y + 1 };
+        return this.rbush.collides(rect)
+            ? this.rbush.search(rect)[0].name
+            : undefined;
     }
-  }, {
-    key: "getByID",
-    value: function getByID(id) {
-      return this.rectangles.get(id);
+    getByID(id) {
+        return this.rectangles.get(id);
     }
-  }, {
-    key: "addRectToBitmap",
-    value: function addRectToBitmap(_rect, _data) {
-      throw new Error('Method not implemented.');
+    addRectToBitmap(_rect, _data) {
+        throw new Error('Method not implemented.');
     }
-  }, {
-    key: "discardRange",
-    value: function discardRange(_left, _right) {
-      throw new Error('Method not implemented.');
+    discardRange(_left, _right) {
+        throw new Error('Method not implemented.');
     }
-  }, {
-    key: "serializeRegion",
-    value: function serializeRegion(_region) {
-      throw new Error('Method not implemented.');
+    serializeRegion(_region) {
+        throw new Error('Method not implemented.');
     }
-  }, {
-    key: "toJSON",
-    value: function toJSON() {
-      return {
-        rectangles: (0, _.objectFromEntries)(this.rectangles),
-        totalHeight: this.totalHeight,
-        maxHeightReached: false,
-        containsNoTransferables: true
-      };
+    toJSON() {
+        return {
+            rectangles: Object.fromEntries(this.rectangles),
+            totalHeight: this.totalHeight,
+            maxHeightReached: false,
+            containsNoTransferables: true,
+        };
     }
-  }]);
-  return PrecomputedLayout;
-}();
-
-exports.default = PrecomputedLayout;
+}
+exports.default = PrecomputedLayout;

package/util/layouts/PrecomputedMultiLayout.js

@@ -1,60 +1,23 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-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 _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _MultiLayout2 = _interopRequireDefault(require("./MultiLayout"));
-
-var _PrecomputedLayout = _interopRequireDefault(require("./PrecomputedLayout"));
-
-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 ThrowingLayout = /*#__PURE__*/(0, _createClass2.default)(function ThrowingLayout() {
-  (0, _classCallCheck2.default)(this, ThrowingLayout);
-  throw new Error('invalid layout name');
-});
-
-var PrecomputedMultiLayout = /*#__PURE__*/function (_MultiLayout) {
-  (0, _inherits2.default)(PrecomputedMultiLayout, _MultiLayout);
-
-  var _super = _createSuper(PrecomputedMultiLayout);
-
-  function PrecomputedMultiLayout(json) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, PrecomputedMultiLayout);
-    // use ThrowingLayout because there is not supposed to be any creation
-    // of new layouts in a precomputed layout
-    _this = _super.call(this, ThrowingLayout);
-    Object.entries(json).forEach(function (_ref) {
-      var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-          layoutName = _ref2[0],
-          sublayoutJson = _ref2[1];
-
-      _this.subLayouts.set(layoutName, new _PrecomputedLayout.default(sublayoutJson));
-    });
-    return _this;
-  }
-
-  return (0, _createClass2.default)(PrecomputedMultiLayout);
-}(_MultiLayout2.default);
-
-exports.default = PrecomputedMultiLayout;
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const MultiLayout_1 = __importDefault(require("./MultiLayout"));
+const PrecomputedLayout_1 = __importDefault(require("./PrecomputedLayout"));
+class ThrowingLayout {
+    constructor() {
+        throw new Error('invalid layout name');
+    }
+}
+class PrecomputedMultiLayout extends MultiLayout_1.default {
+    constructor(json) {
+        // use ThrowingLayout because there is not supposed to be any creation
+        // of new layouts in a precomputed layout
+        super(ThrowingLayout);
+        Object.entries(json).forEach(([layoutName, sublayoutJson]) => {
+            this.subLayouts.set(layoutName, new PrecomputedLayout_1.default(sublayoutJson));
+        });
+    }
+}
+exports.default = PrecomputedMultiLayout;