@jbrowse/core 1.7.11 → 2.1.0

package/util/layouts/SceneGraph.js

@@ -1,92 +1,64 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-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("..");
-
-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; }
-
-var SceneGraph = /*#__PURE__*/function () {
-  /**
-   * note: all coordinates are inter-base or inter-pixel coordinates
-   */
-  function SceneGraph(name, left, top, width, height, // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  data) {
-    (0, _classCallCheck2.default)(this, SceneGraph);
-    this.name = name;
-    this.left = left;
-    this.top = top;
-    this.width = width;
-    this.height = height;
-    this.data = data;
-    (0, _defineProperty2.default)(this, "children", void 0);
-    (0, _defineProperty2.default)(this, "absoluteCache", void 0);
-    (0, _defineProperty2.default)(this, "parent", void 0);
-
-    if (_.inDevelopment && (typeof name !== 'string' || typeof left !== 'number' || Number.isNaN(left) || typeof top !== 'number' || Number.isNaN(top) || typeof width !== 'number' || Number.isNaN(width) || typeof height !== 'number' || Number.isNaN(height))) {
-      throw new TypeError('invalid SceneGraph arguments');
+Object.defineProperty(exports, "__esModule", { value: true });
+const __1 = require("..");
+class SceneGraph {
+    /**
+     * note: all coordinates are inter-base or inter-pixel coordinates
+     */
+    constructor(name, left, top, width, height, 
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    data) {
+        this.name = name;
+        this.left = left;
+        this.top = top;
+        this.width = width;
+        this.height = height;
+        this.data = data;
+        if (__1.inDevelopment &&
+            (typeof name !== 'string' ||
+                typeof left !== 'number' ||
+                Number.isNaN(left) ||
+                typeof top !== 'number' ||
+                Number.isNaN(top) ||
+                typeof width !== 'number' ||
+                Number.isNaN(width) ||
+                typeof height !== 'number' ||
+                Number.isNaN(height))) {
+            throw new TypeError('invalid SceneGraph arguments');
+        }
+        this.children = new Map();
+        this.absoluteCache = { dirty: true };
     }
-
-    this.children = new Map();
-    this.absoluteCache = {
-      dirty: true
-    };
-  }
-
-  (0, _createClass2.default)(SceneGraph, [{
-    key: "addChild",
-    value: function addChild(nameOrSceneGraph, left, top, width, height, // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    addChild(nameOrSceneGraph, left, top, width, height, 
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     data) {
-      var child;
-
-      if (nameOrSceneGraph instanceof SceneGraph) {
-        child = nameOrSceneGraph;
-      } else {
-        child = new SceneGraph(nameOrSceneGraph, left, top, width, height, data);
-      }
-
-      if (!(child instanceof SceneGraph)) {
-        throw new TypeError('argument to addChild must be an array or a SceneGraph');
-      }
-
-      if (this.children.has(child.name)) {
-        throw new Error("child named \"".concat(child.name, "\" already exists"));
-      } // update the bounds to match the child
-
-
-      child.parent = this;
-      var _child$absolute = child.absolute,
-          childLeft = _child$absolute.left,
-          childRight = _child$absolute.right,
-          childTop = _child$absolute.top,
-          childBottom = _child$absolute.bottom;
-
-      if (childLeft !== undefined && childRight !== undefined && childTop !== undefined && childBottom !== undefined) {
-        this.expand(childLeft, childRight, childTop, childBottom);
-        this.children.set(child.name, child);
-      }
-
-      return child;
+        let child;
+        if (nameOrSceneGraph instanceof SceneGraph) {
+            child = nameOrSceneGraph;
+        }
+        else {
+            child = new SceneGraph(nameOrSceneGraph, left, top, width, height, data);
+        }
+        if (!(child instanceof SceneGraph)) {
+            throw new TypeError('argument to addChild must be an array or a SceneGraph');
+        }
+        if (this.children.has(child.name)) {
+            throw new Error(`child named "${child.name}" already exists`);
+        }
+        // update the bounds to match the child
+        child.parent = this;
+        const { left: childLeft, right: childRight, top: childTop, bottom: childBottom, } = child.absolute;
+        if (childLeft !== undefined &&
+            childRight !== undefined &&
+            childTop !== undefined &&
+            childBottom !== undefined) {
+            this.expand(childLeft, childRight, childTop, childBottom);
+            this.children.set(child.name, child);
+        }
+        return child;
     }
-  }, {
-    key: "getSubRecord",
-    value: function getSubRecord(name) {
-      return this.children.get(name);
+    getSubRecord(name) {
+        return this.children.get(name);
     }
     /**
      * if the record does not already cover the given
@@ -97,123 +69,81 @@ var SceneGraph = /*#__PURE__*/function () {
      * @param top -
      * @param bottom -
      */
-
-  }, {
-    key: "expand",
-    value: function expand(newLeft, newRight, newTop, newBottom) {
-      var _this$absolute = this.absolute,
-          left = _this$absolute.left,
-          right = _this$absolute.right,
-          top = _this$absolute.top,
-          bottom = _this$absolute.bottom;
-
-      if (left !== undefined && newLeft < left) {
-        var diff = left - newLeft;
-        this.width += diff;
-        this.left -= diff;
-      }
-
-      if (right !== undefined && newRight > right) {
-        this.width += newRight - right;
-      }
-
-      if (top !== undefined && newTop < top) {
-        var _diff = top - newTop;
-
-        this.height += _diff;
-        this.top -= _diff;
-      }
-
-      if (bottom !== undefined && newBottom > bottom) {
-        this.height += newBottom - bottom;
-      }
-
-      if (this.parent) {
-        this.parent.expand(newLeft, newRight, newTop, newBottom);
-      }
-
-      this.absoluteCache.dirty = true;
+    expand(newLeft, newRight, newTop, newBottom) {
+        const { left, right, top, bottom } = this.absolute;
+        if (left !== undefined && newLeft < left) {
+            const diff = left - newLeft;
+            this.width += diff;
+            this.left -= diff;
+        }
+        if (right !== undefined && newRight > right) {
+            this.width += newRight - right;
+        }
+        if (top !== undefined && newTop < top) {
+            const diff = top - newTop;
+            this.height += diff;
+            this.top -= diff;
+        }
+        if (bottom !== undefined && newBottom > bottom) {
+            this.height += newBottom - bottom;
+        }
+        if (this.parent) {
+            this.parent.expand(newLeft, newRight, newTop, newBottom);
+        }
+        this.absoluteCache.dirty = true;
     }
-  }, {
-    key: "bottom",
-    get: function get() {
-      return this.top + this.height;
+    get bottom() {
+        return this.top + this.height;
     }
-  }, {
-    key: "right",
-    get: function get() {
-      return this.left + this.width;
+    get right() {
+        return this.left + this.width;
     }
-  }, {
-    key: "walkParents",
-    value: function walkParents(callback) {
-      if (this.parent) {
-        callback(this.parent);
-        this.parent.walkParents(callback);
-      }
+    walkParents(callback) {
+        if (this.parent) {
+            callback(this.parent);
+            this.parent.walkParents(callback);
+        }
     }
-  }, {
-    key: "walkChildren",
-    value: function walkChildren(callback) {
-      var _iterator = _createForOfIteratorHelper(this.children.values()),
-          _step;
-
-      try {
-        for (_iterator.s(); !(_step = _iterator.n()).done;) {
-          var sub = _step.value;
-          callback(sub);
-          sub.walkChildren(callback);
+    walkChildren(callback) {
+        for (const sub of this.children.values()) {
+            callback(sub);
+            sub.walkChildren(callback);
         }
-      } catch (err) {
-        _iterator.e(err);
-      } finally {
-        _iterator.f();
-      }
     }
-  }, {
-    key: "absolute",
-    get: function get() {
-      if (this.absoluteCache.dirty) {
-        var xOffset = 0;
-        var yOffset = 0;
-        this.walkParents(function (node) {
-          xOffset += node.left;
-          yOffset += node.top;
-        });
-        this.absoluteCache = {
-          dirty: false,
-          left: this.left + xOffset,
-          right: this.right + xOffset,
-          top: this.top + yOffset,
-          bottom: this.bottom + yOffset,
-          width: this.width,
-          height: this.height
-        };
-      }
-
-      return this.absoluteCache;
+    get absolute() {
+        if (this.absoluteCache.dirty) {
+            let xOffset = 0;
+            let yOffset = 0;
+            this.walkParents((node) => {
+                xOffset += node.left;
+                yOffset += node.top;
+            });
+            this.absoluteCache = {
+                dirty: false,
+                left: this.left + xOffset,
+                right: this.right + xOffset,
+                top: this.top + yOffset,
+                bottom: this.bottom + yOffset,
+                width: this.width,
+                height: this.height,
+            };
+        }
+        return this.absoluteCache;
     }
-  }, {
-    key: "move",
-    value: function move(x, y) {
-      this.left += x;
-      this.top += y;
-      this.absoluteCache.dirty = true;
-      this.walkChildren(function (c) {
-        c.absoluteCache.dirty = true;
-      });
-      var _this$absolute2 = this.absolute,
-          left = _this$absolute2.left,
-          right = _this$absolute2.right,
-          top = _this$absolute2.top,
-          bottom = _this$absolute2.bottom;
-
-      if (left !== undefined && right !== undefined && top !== undefined && bottom !== undefined) {
-        this.expand(left, right, top, bottom);
-      }
+    move(x, y) {
+        this.left += x;
+        this.top += y;
+        this.absoluteCache.dirty = true;
+        this.walkChildren((c) => {
+            c.absoluteCache.dirty = true;
+        });
+        const { left, right, top, bottom } = this.absolute;
+        if (left !== undefined &&
+            right !== undefined &&
+            top !== undefined &&
+            bottom !== undefined) {
+            this.expand(left, right, top, bottom);
+        }
     }
-  }]);
-  return SceneGraph;
-}();
-
-exports.default = SceneGraph;
+}
+exports.default = SceneGraph;

package/util/layouts/index.js

@@ -1,68 +1,31 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-var _exportNames = {
-  GranularRectLayout: true,
-  MultiLayout: true,
-  PrecomputedLayout: true,
-  PrecomputedMultiLayout: true,
-  SceneGraph: true
-};
-Object.defineProperty(exports, "GranularRectLayout", {
-  enumerable: true,
-  get: function get() {
-    return _GranularRectLayout.default;
-  }
-});
-Object.defineProperty(exports, "MultiLayout", {
-  enumerable: true,
-  get: function get() {
-    return _MultiLayout.default;
-  }
-});
-Object.defineProperty(exports, "PrecomputedLayout", {
-  enumerable: true,
-  get: function get() {
-    return _PrecomputedLayout.default;
-  }
-});
-Object.defineProperty(exports, "PrecomputedMultiLayout", {
-  enumerable: true,
-  get: function get() {
-    return _PrecomputedMultiLayout.default;
-  }
-});
-Object.defineProperty(exports, "SceneGraph", {
-  enumerable: true,
-  get: function get() {
-    return _SceneGraph.default;
-  }
-});
-
-var _BaseLayout = require("./BaseLayout");
-
-Object.keys(_BaseLayout).forEach(function (key) {
-  if (key === "default" || key === "__esModule") return;
-  if (Object.prototype.hasOwnProperty.call(_exportNames, key)) return;
-  if (key in exports && exports[key] === _BaseLayout[key]) return;
-  Object.defineProperty(exports, key, {
-    enumerable: true,
-    get: function get() {
-      return _BaseLayout[key];
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
     }
-  });
-});
-
-var _GranularRectLayout = _interopRequireDefault(require("./GranularRectLayout"));
-
-var _MultiLayout = _interopRequireDefault(require("./MultiLayout"));
-
-var _PrecomputedLayout = _interopRequireDefault(require("./PrecomputedLayout"));
-
-var _PrecomputedMultiLayout = _interopRequireDefault(require("./PrecomputedMultiLayout"));
-
-var _SceneGraph = _interopRequireDefault(require("./SceneGraph"));
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SceneGraph = exports.PrecomputedMultiLayout = exports.PrecomputedLayout = exports.MultiLayout = exports.GranularRectLayout = void 0;
+__exportStar(require("./BaseLayout"), exports);
+var GranularRectLayout_1 = require("./GranularRectLayout");
+Object.defineProperty(exports, "GranularRectLayout", { enumerable: true, get: function () { return __importDefault(GranularRectLayout_1).default; } });
+var MultiLayout_1 = require("./MultiLayout");
+Object.defineProperty(exports, "MultiLayout", { enumerable: true, get: function () { return __importDefault(MultiLayout_1).default; } });
+var PrecomputedLayout_1 = require("./PrecomputedLayout");
+Object.defineProperty(exports, "PrecomputedLayout", { enumerable: true, get: function () { return __importDefault(PrecomputedLayout_1).default; } });
+var PrecomputedMultiLayout_1 = require("./PrecomputedMultiLayout");
+Object.defineProperty(exports, "PrecomputedMultiLayout", { enumerable: true, get: function () { return __importDefault(PrecomputedMultiLayout_1).default; } });
+var SceneGraph_1 = require("./SceneGraph");
+Object.defineProperty(exports, "SceneGraph", { enumerable: true, get: function () { return __importDefault(SceneGraph_1).default; } });

package/util/mst-reflection.js

@@ -1,19 +1,8 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.getDefaultValue = getDefaultValue;
-exports.getEnumerationValues = getEnumerationValues;
-exports.getPropertyType = getPropertyType;
-exports.getSubType = getSubType;
-exports.getUnionSubTypes = getUnionSubTypes;
-exports.resolveLateType = resolveLateType;
-
-var _mobxStateTree = require("mobx-state-tree");
-
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.resolveLateType = exports.getEnumerationValues = exports.getDefaultValue = exports.getPropertyType = exports.getUnionSubTypes = exports.getSubType = void 0;
 /* eslint-disable no-underscore-dangle */
-
+const mobx_state_tree_1 = require("mobx-state-tree");
 /**
  * get the inner type of an MST optional, array, or late type object
  *
@@ -21,46 +10,46 @@ var _mobxStateTree = require("mobx-state-tree");
  * @returns {IModelType}
  */
 function getSubType(type) {
-  var t;
-
-  if ((0, _mobxStateTree.isOptionalType)(type)) {
-    t = type._subtype || type.type;
-  } else if ((0, _mobxStateTree.isArrayType)(type) || (0, _mobxStateTree.isMapType)(type)) {
-    t = type._subtype || type._subType || type.subType;
-  } else if (typeof type.getSubType === 'function') {
-    return type.getSubType();
-  } else {
-    throw new TypeError('unsupported mst type');
-  }
-
-  if (!t) {
-    // debugger
-    throw new Error('failed to get subtype');
-  }
-
-  return t;
+    let t;
+    if ((0, mobx_state_tree_1.isOptionalType)(type)) {
+        t = type._subtype || type.type;
+    }
+    else if ((0, mobx_state_tree_1.isArrayType)(type) || (0, mobx_state_tree_1.isMapType)(type)) {
+        t = type._subtype || type._subType || type.subType;
+    }
+    else if (typeof type.getSubType === 'function') {
+        return type.getSubType();
+    }
+    else {
+        throw new TypeError('unsupported mst type');
+    }
+    if (!t) {
+        // debugger
+        throw new Error('failed to get subtype');
+    }
+    return t;
 }
+exports.getSubType = getSubType;
 /**
  * get the array of
  * @param {MST Union Type obj} unionType
  * @returns {Array<IModelType>}
  */
-
-
 function getUnionSubTypes(unionType) {
-  if (!(0, _mobxStateTree.isUnionType)(unionType)) {
-    throw new TypeError('not an MST union type');
-  }
-
-  var t = unionType._types || unionType.types || getSubType(unionType)._types || getSubType(unionType).types;
-
-  if (!t) {
-    // debugger
-    throw new Error('failed to extract subtypes from mst union');
-  }
-
-  return t;
+    if (!(0, mobx_state_tree_1.isUnionType)(unionType)) {
+        throw new TypeError('not an MST union type');
+    }
+    const t = unionType._types ||
+        unionType.types ||
+        getSubType(unionType)._types ||
+        getSubType(unionType).types;
+    if (!t) {
+        // debugger
+        throw new Error('failed to extract subtypes from mst union');
+    }
+    return t;
 }
+exports.getUnionSubTypes = getUnionSubTypes;
 /**
  * get the type of one of the properties of the given MST model type
  *
@@ -68,40 +57,35 @@ function getUnionSubTypes(unionType) {
  * @param {string} propertyName
  * @returns {IModelType}
  */
-
-
 function getPropertyType(type, propertyName) {
-  var propertyType = type.properties[propertyName];
-  return propertyType;
+    const propertyType = type.properties[propertyName];
+    return propertyType;
 }
+exports.getPropertyType = getPropertyType;
 /**
  * get the base type from inside an MST optional type
  * @param {*} type
  */
-
-
 function getDefaultValue(type) {
-  if (!(0, _mobxStateTree.isOptionalType)(type)) {
-    throw new TypeError('type must be an optional type');
-  }
-
-  return type._defaultValue || type.defaultValue;
+    if (!(0, mobx_state_tree_1.isOptionalType)(type)) {
+        throw new TypeError('type must be an optional type');
+    }
+    return type._defaultValue || type.defaultValue;
 }
+exports.getDefaultValue = getDefaultValue;
 /** get the string values of an MST enumeration type */
-
-
 function getEnumerationValues(type) {
-  var subtypes = getUnionSubTypes(type); // the subtypes should all be literals with a value member
-
-  return subtypes.map(function (t) {
-    return t.value;
-  });
+    const subtypes = getUnionSubTypes(type);
+    // the subtypes should all be literals with a value member
+    return subtypes.map(t => t.value);
 }
-
+exports.getEnumerationValues = getEnumerationValues;
 function resolveLateType(maybeLate) {
-  if (!(0, _mobxStateTree.isUnionType)(maybeLate) && !(0, _mobxStateTree.isArrayType)(maybeLate) && (0, _mobxStateTree.isLateType)(maybeLate)) {
-    return maybeLate.getSubType();
-  }
-
-  return maybeLate;
-}
+    if (!(0, mobx_state_tree_1.isUnionType)(maybeLate) &&
+        !(0, mobx_state_tree_1.isArrayType)(maybeLate) &&
+        (0, mobx_state_tree_1.isLateType)(maybeLate)) {
+        return maybeLate.getSubType();
+    }
+    return maybeLate;
+}
+exports.resolveLateType = resolveLateType;