@jbrowse/core 1.7.11 → 2.1.0

package/util/simpleFeature.js

@@ -1,185 +1,121 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-exports.isFeature = isFeature;
-
-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 _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
-
-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; }
-
-/**
- * Abstract feature object
- */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isFeature = void 0;
 function isFeature(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && typeof thing.get === 'function' && typeof thing.id === 'function';
+    return (typeof thing === 'object' &&
+        thing !== null &&
+        typeof thing.get === 'function' &&
+        typeof thing.id === 'function');
 }
-
+exports.isFeature = isFeature;
 function isSimpleFeatureSerialized(args) {
-  return 'uniqueId' in args && (0, _typeof2.default)(args.data) !== 'object';
+    return 'uniqueId' in args && typeof args.data !== 'object';
 }
 /**
  * Simple implementation of a feature object.
  */
-
-
-var SimpleFeature = /*#__PURE__*/function () {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-  /**
-   * @param args - SimpleFeature args
-   *
-   * Note: args.data.subfeatures can be an array of these same args,
-   * which will be inflated to more instances of this class.
-   */
-  function SimpleFeature(args) {
-    var _this = this;
-
-    (0, _classCallCheck2.default)(this, SimpleFeature);
-    (0, _defineProperty2.default)(this, "data", void 0);
-    (0, _defineProperty2.default)(this, "subfeatures", void 0);
-    (0, _defineProperty2.default)(this, "parentHandle", void 0);
-    (0, _defineProperty2.default)(this, "uniqueId", void 0);
-
-    if (isSimpleFeatureSerialized(args)) {
-      this.data = args;
-    } else {
-      this.data = args.data || {}; // load handle from args.parent (not args.data.parent)
-      // this reason is because if args is an object, it likely isn't properly loaded with
-      // parent as a Feature reference (probably a raw parent ID or something instead)
-
-      this.parentHandle = args.parent;
-    } // the feature id comes from
-    // args.id, args.data.uniqueId, or args.uniqueId due to this initialization
-
-
-    var id = isSimpleFeatureSerialized(args) ? args.uniqueId : args.id;
-
-    if (id === undefined || id === null) {
-      throw new Error('SimpleFeature requires a unique `id` or `data.uniqueId` attribute');
-    }
-
-    this.uniqueId = String(id);
-
-    if (!(this.data.aliases || this.data.end - this.data.start >= 0)) {
-      throw new Error("invalid feature data, end less than start. end: ".concat(this.data.end, " start: ").concat(this.data.start));
-    }
-
-    if (this.data.subfeatures) {
-      var _this$data$subfeature;
-
-      this.subfeatures = (_this$data$subfeature = this.data.subfeatures) === null || _this$data$subfeature === void 0 ? void 0 : _this$data$subfeature.map( // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      function (f, i) {
-        return typeof f.get !== 'function' ? new SimpleFeature({
-          id: f.uniqueId || "".concat(id, "-").concat(i),
-          data: _objectSpread({
-            strand: _this.data.strand
-          }, f),
-          parent: _this
-        }) : f;
-      });
+class SimpleFeature {
+    /**
+     * @param args - SimpleFeature args
+     *
+     * Note: args.data.subfeatures can be an array of these same args,
+     * which will be inflated to more instances of this class.
+     */
+    constructor(args) {
+        var _a;
+        if (isSimpleFeatureSerialized(args)) {
+            this.data = args;
+        }
+        else {
+            this.data = args.data || {};
+            // load handle from args.parent (not args.data.parent)
+            // this reason is because if args is an object, it likely isn't properly loaded with
+            // parent as a Feature reference (probably a raw parent ID or something instead)
+            this.parentHandle = args.parent;
+        }
+        // the feature id comes from
+        // args.id, args.data.uniqueId, or args.uniqueId due to this initialization
+        const id = isSimpleFeatureSerialized(args) ? args.uniqueId : args.id;
+        if (id === undefined || id === null) {
+            throw new Error('SimpleFeature requires a unique `id` or `data.uniqueId` attribute');
+        }
+        this.uniqueId = String(id);
+        if (!(this.data.aliases || this.data.end - this.data.start >= 0)) {
+            throw new Error(`invalid feature data, end less than start. end: ${this.data.end} start: ${this.data.start}`);
+        }
+        if (this.data.subfeatures) {
+            this.subfeatures = (_a = this.data.subfeatures) === null || _a === void 0 ? void 0 : _a.map(
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            (f, i) => typeof f.get !== 'function'
+                ? new SimpleFeature({
+                    id: f.uniqueId || `${id}-${i}`,
+                    data: {
+                        strand: this.data.strand,
+                        ...f,
+                        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+                    },
+                    parent: this,
+                })
+                : f);
+        }
     }
-  }
-  /**
-   * Get a piece of data about the feature.  All features must have
-   * 'start' and 'end', but everything else is optional.
-   */
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-
-  (0, _createClass2.default)(SimpleFeature, [{
-    key: "get",
-    value: function get(name) {
-      return name === 'subfeatures' ? this.subfeatures : name === 'parent' ? this.parent() : this.data[name];
+    /**
+     * Get a piece of data about the feature.  All features must have
+     * 'start' and 'end', but everything else is optional.
+     */
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    get(name) {
+        return name === 'subfeatures'
+            ? this.subfeatures
+            : name === 'parent'
+                ? this.parent()
+                : this.data[name];
     }
     /**
      * Set an item of data.
      */
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-  }, {
-    key: "set",
-    value: function set(name, val) {
-      this.data[name] = val;
+    set(name, val) {
+        this.data[name] = val;
     }
     /**
      * Get an array listing which data keys are present in this feature.
      */
-
-  }, {
-    key: "tags",
-    value: function tags() {
-      return Object.keys(this.data);
+    tags() {
+        return Object.keys(this.data);
     }
     /**
      * Get the unique ID of this feature.
      */
-
-  }, {
-    key: "id",
-    value: function id() {
-      return this.uniqueId;
+    id() {
+        return this.uniqueId;
     }
     /**
      * Get this feature's parent feature, or undefined if none.
      */
-
-  }, {
-    key: "parent",
-    value: function parent() {
-      return this.parentHandle;
+    parent() {
+        return this.parentHandle;
     }
     /**
      * Get an array of child features, or undefined if none.
      */
-
-  }, {
-    key: "children",
-    value: function children() {
-      return this.get('subfeatures');
+    children() {
+        return this.get('subfeatures');
     }
-  }, {
-    key: "toJSON",
-    value: function toJSON() {
-      var d = _objectSpread(_objectSpread({}, this.data), {}, {
-        uniqueId: this.id()
-      });
-
-      var p = this.parent();
-
-      if (p) {
-        d.parentId = p.id();
-      }
-
-      var c = this.children();
-
-      if (c) {
-        d.subfeatures = c.map(function (child) {
-          return child.toJSON();
-        });
-      }
-
-      return d;
+    toJSON() {
+        const d = { ...this.data, uniqueId: this.id() };
+        const p = this.parent();
+        if (p) {
+            d.parentId = p.id();
+        }
+        const c = this.children();
+        if (c) {
+            d.subfeatures = c.map(child => child.toJSON());
+        }
+        return d;
     }
-  }], [{
-    key: "fromJSON",
-    value: function fromJSON(json) {
-      return new SimpleFeature(_objectSpread({}, json));
+    static fromJSON(json) {
+        return new SimpleFeature({ ...json });
     }
-  }]);
-  return SimpleFeature;
-}();
-
-exports.default = SimpleFeature;
+}
+exports.default = SimpleFeature;

package/util/stats.js

@@ -1,28 +1,7 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.blankStats = blankStats;
-exports.calcPerBaseStats = calcPerBaseStats;
-exports.calcStdFromSums = calcStdFromSums;
-exports.rectifyStats = rectifyStats;
-exports.scoresToStats = scoresToStats;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _operators = require("rxjs/operators");
-
-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; }
-
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.blankStats = exports.scoresToStats = exports.calcPerBaseStats = exports.rectifyStats = exports.calcStdFromSums = void 0;
+const operators_1 = require("rxjs/operators");
 /*
  * calculate standard deviation using the 'shortcut method' that accepts
  * the sum and the sum squares of the elements
@@ -33,155 +12,116 @@ function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { va
  * @param population - boolean: use population instead of sample correction
  * @return the estimated std deviation
  */
-function calcStdFromSums(sum, sumSquares, n) {
-  var population = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : false;
-
-  if (n === 0) {
-    return 0;
-  }
-
-  var variance;
-
-  if (population) {
-    variance = sumSquares / n - sum * sum / (n * n);
-  } else {
-    // sample correction is n-1
-    variance = sumSquares - sum * sum / n;
-
-    if (n > 1) {
-      variance /= n - 1;
+function calcStdFromSums(sum, sumSquares, n, population = false) {
+    if (n === 0) {
+        return 0;
+    }
+    let variance;
+    if (population) {
+        variance = sumSquares / n - (sum * sum) / (n * n);
     }
-  }
-
-  return variance < 0 ? 0 : Math.sqrt(variance);
+    else {
+        // sample correction is n-1
+        variance = sumSquares - (sum * sum) / n;
+        if (n > 1) {
+            variance /= n - 1;
+        }
+    }
+    return variance < 0 ? 0 : Math.sqrt(variance);
 }
+exports.calcStdFromSums = calcStdFromSums;
 /*
  * @param stats - a summary stats object with scoreSum, featureCount, scoreSumSquares, and basesCovered
  * @return - a summary stats object with scoreMean, scoreStdDev, and featureDensity added
  */
-
-
 function rectifyStats(s) {
-  return _objectSpread(_objectSpread({}, s), {}, {
-    scoreMean: (s.scoreSum || 0) / (s.featureCount || s.basesCovered || 1),
-    scoreStdDev: calcStdFromSums(s.scoreSum, s.scoreSumSquares, s.featureCount || s.basesCovered),
-    featureDensity: (s.featureCount || 1) / s.basesCovered
-  });
+    return {
+        ...s,
+        scoreMean: (s.scoreSum || 0) / (s.featureCount || s.basesCovered || 1),
+        scoreStdDev: calcStdFromSums(s.scoreSum, s.scoreSumSquares, s.featureCount || s.basesCovered),
+        featureDensity: (s.featureCount || 1) / s.basesCovered,
+    };
 }
+exports.rectifyStats = rectifyStats;
 /*
  * calculates per-base scores for variable width features over a region
  * @param region - object contains start, end
  * @param features - list of features with start, end, score
  * @return array of numeric scores
  */
-
-
 function calcPerBaseStats(region, features) {
-  var start = region.start,
-      end = region.end;
-  var scores = [];
-  var feats = features.sort(function (a, b) {
-    return a.get('start') - b.get('start');
-  });
-  var pos = start;
-  var currentFeat = 0;
-  var i = 0;
-
-  while (pos < end) {
-    while (currentFeat < feats.length && pos >= feats[currentFeat].get('end')) {
-      currentFeat += 1;
-    }
-
-    var f = feats[currentFeat];
-
-    if (!f) {
-      scores[i] = 0;
-    } else if (pos >= f.get('start') && pos < f.get('end')) {
-      scores[i] = f.get('score');
-    } else {
-      scores[i] = 0;
+    const { start, end } = region;
+    const scores = [];
+    const feats = features.sort((a, b) => a.get('start') - b.get('start'));
+    let pos = start;
+    let currentFeat = 0;
+    let i = 0;
+    while (pos < end) {
+        while (currentFeat < feats.length && pos >= feats[currentFeat].get('end')) {
+            currentFeat += 1;
+        }
+        const f = feats[currentFeat];
+        if (!f) {
+            scores[i] = 0;
+        }
+        else if (pos >= f.get('start') && pos < f.get('end')) {
+            scores[i] = f.get('score');
+        }
+        else {
+            scores[i] = 0;
+        }
+        i += 1;
+        pos += 1;
     }
-
-    i += 1;
-    pos += 1;
-  }
-
-  return scores;
+    return scores;
 }
+exports.calcPerBaseStats = calcPerBaseStats;
 /*
  * transform a list of scores to summary statistics
  * @param region - object with start, end
  * @param feats - array of features which are possibly summary features
  * @return - object with scoreMax, scoreMin, scoreSum, scoreSumSquares, etc
  */
-
-
-function scoresToStats(_x, _x2) {
-  return _scoresToStats.apply(this, arguments);
+async function scoresToStats(region, features) {
+    const { start, end } = region;
+    const { scoreMin, scoreMax, scoreSum, scoreSumSquares, featureCount } = await features
+        .pipe((0, operators_1.reduce)((seed, f) => {
+        const score = f.get('score');
+        seed.scoreMax = Math.max(seed.scoreMax, f.get('summary') ? f.get('maxScore') : score);
+        seed.scoreMin = Math.min(seed.scoreMin, f.get('summary') ? f.get('minScore') : score);
+        seed.scoreSum += score;
+        seed.scoreSumSquares += score * score;
+        seed.featureCount += 1;
+        return seed;
+    }, {
+        scoreMin: Number.MAX_VALUE,
+        scoreMax: Number.MIN_VALUE,
+        scoreSum: 0,
+        scoreSumSquares: 0,
+        featureCount: 0,
+    }))
+        .toPromise();
+    return rectifyStats({
+        scoreMax,
+        scoreMin,
+        scoreSum,
+        scoreSumSquares,
+        featureCount,
+        basesCovered: end - start + 1,
+    });
 }
-
-function _scoresToStats() {
-  _scoresToStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(region, features) {
-    var start, end, _yield$features$pipe$, scoreMin, scoreMax, scoreSum, scoreSumSquares, featureCount;
-
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            start = region.start, end = region.end;
-            _context.next = 3;
-            return features.pipe((0, _operators.reduce)(function (seed, f) {
-              var score = f.get('score');
-              seed.scoreMax = Math.max(seed.scoreMax, f.get('summary') ? f.get('maxScore') : score);
-              seed.scoreMin = Math.min(seed.scoreMin, f.get('summary') ? f.get('minScore') : score);
-              seed.scoreSum += score;
-              seed.scoreSumSquares += score * score;
-              seed.featureCount += 1;
-              return seed;
-            }, {
-              scoreMin: Number.MAX_VALUE,
-              scoreMax: Number.MIN_VALUE,
-              scoreSum: 0,
-              scoreSumSquares: 0,
-              featureCount: 0
-            })).toPromise();
-
-          case 3:
-            _yield$features$pipe$ = _context.sent;
-            scoreMin = _yield$features$pipe$.scoreMin;
-            scoreMax = _yield$features$pipe$.scoreMax;
-            scoreSum = _yield$features$pipe$.scoreSum;
-            scoreSumSquares = _yield$features$pipe$.scoreSumSquares;
-            featureCount = _yield$features$pipe$.featureCount;
-            return _context.abrupt("return", rectifyStats({
-              scoreMax: scoreMax,
-              scoreMin: scoreMin,
-              scoreSum: scoreSum,
-              scoreSumSquares: scoreSumSquares,
-              featureCount: featureCount,
-              basesCovered: end - start + 1
-            }));
-
-          case 10:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  }));
-  return _scoresToStats.apply(this, arguments);
-}
-
+exports.scoresToStats = scoresToStats;
 function blankStats() {
-  return {
-    scoreMin: 0,
-    scoreMax: 0,
-    scoreMean: 0,
-    scoreStdDev: 0,
-    scoreSum: 0,
-    scoreSumSquares: 0,
-    featureCount: 0,
-    featureDensity: 0,
-    basesCovered: 0
-  };
-}
+    return {
+        scoreMin: 0,
+        scoreMax: 0,
+        scoreMean: 0,
+        scoreStdDev: 0,
+        scoreSum: 0,
+        scoreSumSquares: 0,
+        featureCount: 0,
+        featureDensity: 0,
+        basesCovered: 0,
+    };
+}
+exports.blankStats = blankStats;