@jbrowse/core 1.5.2 → 1.5.6

package/util/io/RemoteFileWithRangeCache.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -8,25 +8,27 @@ Object.defineProperty(exports, "__esModule", {
 exports.RemoteFileWithRangeCache = void 0;
 exports.clearCache = clearCache;
 
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+var _index = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _createForOfIteratorHelper2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createForOfIteratorHelper.js"));
 
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+var _objectSpread2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _slicedToArray2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
 
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+var _classCallCheck2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
 
-var _get2 = _interopRequireDefault(require("@babel/runtime/helpers/get"));
+var _createClass2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createClass.js"));
 
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+var _get2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/get.js"));
 
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+var _getPrototypeOf2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/getPrototypeOf.js"));
 
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+var _inherits2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/inherits.js"));
+
+var _createSuper2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
 
 var _httpRangeFetcher = require("http-range-fetcher");
 
@@ -34,20 +36,6 @@ var _buffer = require("buffer");
 
 var _genericFilehandle = require("generic-filehandle");
 
-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; }
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (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 = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { 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 fetchers = {};
 
 function binaryRangeFetch(url, start, end) {
@@ -78,22 +66,22 @@ function clearCache() {
 }
 
 var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
-  (0, _inherits2.default)(RemoteFileWithRangeCache, _RemoteFile);
+  (0, _inherits2["default"])(RemoteFileWithRangeCache, _RemoteFile);
 
-  var _super = _createSuper(RemoteFileWithRangeCache);
+  var _super = (0, _createSuper2["default"])(RemoteFileWithRangeCache);
 
   function RemoteFileWithRangeCache() {
-    (0, _classCallCheck2.default)(this, RemoteFileWithRangeCache);
+    (0, _classCallCheck2["default"])(this, RemoteFileWithRangeCache);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2.default)(RemoteFileWithRangeCache, [{
+  (0, _createClass2["default"])(RemoteFileWithRangeCache, [{
     key: "fetch",
     value: function () {
-      var _fetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(url, init) {
+      var _fetch = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(url, init) {
         var requestHeaders, range, _ref, _ref2, rangeParse, _rangeParse, _start, _end, s, e, response, headers;
 
-        return _regenerator.default.wrap(function _callee$(_context) {
+        return _index["default"].wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -110,12 +98,12 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
                   } else if (Array.isArray(requestHeaders)) {
                     ;
                     _ref = requestHeaders.find(function (_ref3) {
-                      var _ref4 = (0, _slicedToArray2.default)(_ref3, 1),
+                      var _ref4 = (0, _slicedToArray2["default"])(_ref3, 1),
                           key = _ref4[0];
 
                       return key === 'range';
                     }) || [undefined, undefined];
-                    _ref2 = (0, _slicedToArray2.default)(_ref, 2);
+                    _ref2 = (0, _slicedToArray2["default"])(_ref, 2);
                     range = _ref2[1];
                   } else {
                     range = requestHeaders.range;
@@ -134,7 +122,7 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
                   break;
                 }
 
-                _rangeParse = (0, _slicedToArray2.default)(rangeParse, 3), _start = _rangeParse[1], _end = _rangeParse[2];
+                _rangeParse = (0, _slicedToArray2["default"])(rangeParse, 3), _start = _rangeParse[1], _end = _rangeParse[2];
                 s = parseInt(_start, 10);
                 e = parseInt(_end, 10);
                 _context.next = 11;
@@ -151,7 +139,7 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
                 }));
 
               case 14:
-                return _context.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(RemoteFileWithRangeCache.prototype), "fetch", this).call(this, url, init));
+                return _context.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(RemoteFileWithRangeCache.prototype), "fetch", this).call(this, url, init));
 
               case 15:
               case "end":
@@ -170,7 +158,7 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
   }, {
     key: "fetchBinaryRange",
     value: function () {
-      var _fetchBinaryRange = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(url, start, end) {
+      var _fetchBinaryRange = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2(url, start, end) {
         var options,
             requestDate,
             requestHeaders,
@@ -187,17 +175,17 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
             arrayBuffer,
             _args2 = arguments;
 
-        return _regenerator.default.wrap(function _callee2$(_context2) {
+        return _index["default"].wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
                 options = _args2.length > 3 && _args2[3] !== undefined ? _args2[3] : {};
                 requestDate = new Date();
-                requestHeaders = _objectSpread(_objectSpread({}, options.headers), {}, {
+                requestHeaders = (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, options.headers), {}, {
                   range: "bytes=".concat(start, "-").concat(end)
                 });
                 _context2.next = 5;
-                return (0, _get2.default)((0, _getPrototypeOf2.default)(RemoteFileWithRangeCache.prototype), "fetch", this).call(this, url, _objectSpread(_objectSpread({}, options), {}, {
+                return (0, _get2["default"])((0, _getPrototypeOf2["default"])(RemoteFileWithRangeCache.prototype), "fetch", this).call(this, url, (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, options), {}, {
                   headers: requestHeaders
                 }));
 
@@ -219,11 +207,11 @@ var RemoteFileWithRangeCache = /*#__PURE__*/function (_RemoteFile) {
                 // will miss duplicate headers of course
                 // eslint-disable-next-line @typescript-eslint/no-explicit-any
                 headers = {};
-                _iterator = _createForOfIteratorHelper(res.headers.entries());
+                _iterator = (0, _createForOfIteratorHelper2["default"])(res.headers.entries());
 
                 try {
                   for (_iterator.s(); !(_step = _iterator.n()).done;) {
-                    _step$value = (0, _slicedToArray2.default)(_step.value, 2), k = _step$value[0], v = _step$value[1];
+                    _step$value = (0, _slicedToArray2["default"])(_step.value, 2), k = _step$value[0], v = _step$value[1];
                     headers[k] = v;
                   } // return the response headers, and the data buffer
 

package/util/io/index.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -13,9 +13,9 @@ Object.defineProperty(exports, "RemoteFileWithRangeCache", {
 });
 exports.openLocation = openLocation;
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _index = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
 var _genericFilehandle = require("generic-filehandle");
 
@@ -41,9 +41,9 @@ function openLocation(location, pluginManager) {
   }
 
   function _checkAuthNeededFetch() {
-    _checkAuthNeededFetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(url, opts) {
+    _checkAuthNeededFetch = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(url, opts) {
       var response, authHeaders;
-      return _regenerator.default.wrap(function _callee$(_context) {
+      return _index["default"].wrap(function _callee$(_context) {
         while (1) {
           switch (_context.prev = _context.next) {
             case 0:
@@ -89,7 +89,7 @@ function openLocation(location, pluginManager) {
       throw new Error('No local path provided');
     }
 
-    if (_detectNode.default) {
+    if (_detectNode["default"]) {
       return new _genericFilehandle.LocalFile(location.localPath);
     } else {
       throw new Error("can't use local files in the browser");

package/util/jexl.js

@@ -1,24 +1,27 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = _default;
+exports["default"] = _default;
 
 var _jexl = _interopRequireDefault(require("jexl"));
 
 function
   /* config?: any*/
 _default() {
-  var j = new _jexl.default.Jexl(); // someday will make sure all of configs callbacks are added in, including
+  var j = new _jexl["default"].Jexl(); // someday will make sure all of configs callbacks are added in, including
   // ones passed in
   // below are core functions
 
   j.addFunction('get', function (feature, data) {
     return feature.get(data);
   });
+  j.addFunction('parent', function (feature) {
+    return feature.parent();
+  });
   j.addFunction('id', function (feature) {
     return feature.id();
   }); // let user cast a jexl type into a javascript type
@@ -46,8 +49,8 @@ _default() {
   j.addFunction('parseInt', Number.parseInt);
   j.addFunction('parseFloat', Number.parseFloat); // string
 
-  j.addFunction('split', function (str, char) {
-    return str.split(char);
+  j.addFunction('split', function (str, _char) {
+    return str.split(_char);
   });
   j.addFunction('charAt', function (str, index) {
     return str.charAt(index);

package/util/jexlStrings.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -32,7 +32,7 @@ jexl) {
     }
 
     var code = str.split('jexl:')[1];
-    var compiled = jexl ? jexl.compile("".concat(code)) : (0, _jexl.default)().compile("".concat(code));
+    var compiled = jexl ? jexl.compile("".concat(code)) : (0, _jexl["default"])().compile("".concat(code));
     compilationCache[cacheKey] = compiled;
   }
 

package/util/jexlStrings.test.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 var _jexlStrings = require("./jexlStrings");
 
@@ -29,7 +29,7 @@ describe('function string parsing', function () {
     expect(result).toEqual(35);
   });
   it('can use the loaded core helper functions to access feature info', function () {
-    var feature = new _simpleFeature.default({
+    var feature = new _simpleFeature["default"]({
       uniqueId: 'jexlFeature',
       score: 10,
       start: 1,

package/util/layouts/BaseLayout.js

@@ -1 +1,5 @@
-"use strict";
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});

package/util/layouts/GranularRectLayout.js

@@ -1,28 +1,22 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = void 0;
+exports["default"] = void 0;
 
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+var _createForOfIteratorHelper2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createForOfIteratorHelper.js"));
 
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+var _slicedToArray2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
 
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+var _classCallCheck2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
 
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+var _createClass2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createClass.js"));
 
 var _index = require("../index");
 
-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; }
-
 /**
  * Rectangle-layout manager that lays out rectangles using bitmaps at
  * resolution that, for efficiency, may be somewhat lower than that of
@@ -41,11 +35,11 @@ function segmentsIntersect(x1, x2, y1, y2) {
 // a single row in the layout
 var LayoutRow = /*#__PURE__*/function () {
   function LayoutRow() {
-    (0, _classCallCheck2.default)(this, LayoutRow);
-    (0, _defineProperty2.default)(this, "padding", void 0);
-    (0, _defineProperty2.default)(this, "allFilled", void 0);
-    (0, _defineProperty2.default)(this, "widthLimit", void 0);
-    (0, _defineProperty2.default)(this, "rowState", void 0);
+    (0, _classCallCheck2["default"])(this, LayoutRow);
+    this.padding = void 0;
+    this.allFilled = void 0;
+    this.widthLimit = void 0;
+    this.rowState = void 0;
     this.padding = 1;
     this.widthLimit = 1000000; // this.rowState.offset is the offset of the bits array relative to the genomic coordinates
     //      (modified by pitchX, but we don't know that in this class)
@@ -59,7 +53,7 @@ var LayoutRow = /*#__PURE__*/function () {
   // }
 
 
-  (0, _createClass2.default)(LayoutRow, [{
+  (0, _createClass2["default"])(LayoutRow, [{
     key: "setAllFilled",
     value: function setAllFilled(data) {
       this.allFilled = data;
@@ -307,16 +301,16 @@ var GranularRectLayout = /*#__PURE__*/function () {
         _ref$displayMode = _ref.displayMode,
         displayMode = _ref$displayMode === void 0 ? 'normal' : _ref$displayMode;
 
-    (0, _classCallCheck2.default)(this, GranularRectLayout);
-    (0, _defineProperty2.default)(this, "pitchX", void 0);
-    (0, _defineProperty2.default)(this, "pitchY", void 0);
-    (0, _defineProperty2.default)(this, "hardRowLimit", void 0);
-    (0, _defineProperty2.default)(this, "bitmap", void 0);
-    (0, _defineProperty2.default)(this, "rectangles", void 0);
-    (0, _defineProperty2.default)(this, "maxHeightReached", void 0);
-    (0, _defineProperty2.default)(this, "maxHeight", void 0);
-    (0, _defineProperty2.default)(this, "displayMode", void 0);
-    (0, _defineProperty2.default)(this, "pTotalHeight", void 0);
+    (0, _classCallCheck2["default"])(this, GranularRectLayout);
+    this.pitchX = void 0;
+    this.pitchY = void 0;
+    this.hardRowLimit = void 0;
+    this.bitmap = void 0;
+    this.rectangles = void 0;
+    this.maxHeightReached = void 0;
+    this.maxHeight = void 0;
+    this.displayMode = void 0;
+    this.pTotalHeight = void 0;
     this.pitchX = pitchX;
     this.pitchY = pitchY;
     this.hardRowLimit = hardRowLimit;
@@ -339,7 +333,7 @@ var GranularRectLayout = /*#__PURE__*/function () {
    */
 
 
-  (0, _createClass2.default)(GranularRectLayout, [{
+  (0, _createClass2["default"])(GranularRectLayout, [{
     key: "addRect",
     value: function addRect(id, left, right, height, data) {
       // if we have already laid it out, return its layout
@@ -499,7 +493,7 @@ var GranularRectLayout = /*#__PURE__*/function () {
       var r = this.rectangles.get(id);
 
       if (r) {
-        var t = r.top * this.pitchX;
+        var t = r.top * this.pitchY;
         return [r.l * this.pitchX, t, r.r * this.pitchX, t + r.originalHeight];
       }
 
@@ -524,7 +518,7 @@ var GranularRectLayout = /*#__PURE__*/function () {
       var _this = this;
 
       return new Map(Array.from(this.rectangles.entries()).map(function (_ref2) {
-        var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
+        var _ref3 = (0, _slicedToArray2["default"])(_ref2, 2),
             id = _ref3[0],
             rect = _ref3[1];
 
@@ -543,12 +537,12 @@ var GranularRectLayout = /*#__PURE__*/function () {
       var regionRectangles = {};
       var maxHeightReached = false;
 
-      var _iterator = _createForOfIteratorHelper(this.rectangles.entries()),
+      var _iterator = (0, _createForOfIteratorHelper2["default"])(this.rectangles.entries()),
           _step;
 
       try {
         for (_iterator.s(); !(_step = _iterator.n()).done;) {
-          var _step$value = (0, _slicedToArray2.default)(_step.value, 2),
+          var _step$value = (0, _slicedToArray2["default"])(_step.value, 2),
               id = _step$value[0],
               rect = _step$value[1];
 
@@ -598,4 +592,4 @@ var GranularRectLayout = /*#__PURE__*/function () {
   return GranularRectLayout;
 }();
 
-exports.default = GranularRectLayout;
+exports["default"] = GranularRectLayout;

package/util/layouts/GranularRectLayout.test.js

@@ -1,26 +1,26 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+var _toConsumableArray2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/toConsumableArray.js"));
 
 var _GranularRectLayout = _interopRequireDefault(require("./GranularRectLayout"));
 
 describe('GranularRectLayout', function () {
   it('lays out non-overlapping features end to end', function () {
-    var l = new _GranularRectLayout.default({
+    var l = new _GranularRectLayout["default"]({
       pitchX: 10,
       pitchY: 4
     });
     var testRects = [['1,0', 4133, 5923, 16], ['1,1', 11299, 12389, 16], ['1,2', 21050, 22778, 16], ['1,3', 41125, 47459, 16], ['1,4', 47926, 49272, 16], ['1,5', 50240, 52495, 16], ['1,6', 53329, 56283, 16], ['1,7', 59309, 79441, 16], ['1,8', 80359, 83196, 16], ['1,9', 92147, 94188, 16], ['1,10', 96241, 103626, 16], ['1,11', 104396, 108110, 16], ['1,12', 111878, 125251, 16], ['1,13', 125747, 128085, 16], ['1,14', 131492, 132641, 16], ['1,15', 133857, 134931, 16], ['1,16', 137023, 138220, 16], ['1,17', 140703, 145668, 16], ['1,18', 146045, 147059, 16], ['1,19', 162296, 165395, 16], ['1,20', 168531, 170795, 16], ['1,21', 174812, 180475, 16], ['1,22', 184302, 188826, 16], ['1,23', 189609, 191141, 16], ['1,24', 199799, 201389, 16], ['1,25', 203436, 211345, 16], ['1,26', 212100, 212379, 16], ['1,27', 213418, 214627, 16], ['1,28', 215115, 219344, 16], ['1,29', 220067, 222525, 16], ['1,30', 223308, 228141, 16], ['1,31', 234473, 236768, 16], ['1,32', 239691, 245015, 16]];
 
     for (var i = 0; i < testRects.length; i += 1) {
-      var top = l.addRect.apply(l, (0, _toConsumableArray2.default)(testRects[i]));
+      var top = l.addRect.apply(l, (0, _toConsumableArray2["default"])(testRects[i]));
       expect(top).toEqual(0);
     }
   });
   it('stacks up overlapping features', function () {
-    var l = new _GranularRectLayout.default({
+    var l = new _GranularRectLayout["default"]({
       pitchX: 10,
       pitchY: 4
     });
@@ -31,12 +31,12 @@ describe('GranularRectLayout', function () {
     }
 
     for (var _i = 0; _i < testRects.length; _i += 1) {
-      var top = l.addRect.apply(l, (0, _toConsumableArray2.default)(testRects[_i]));
+      var top = l.addRect.apply(l, (0, _toConsumableArray2["default"])(testRects[_i]));
       expect(top).toEqual(_i % 2 * 4);
     }
   });
   it('discards regions', function () {
-    var l = new _GranularRectLayout.default({
+    var l = new _GranularRectLayout["default"]({
       pitchX: 10,
       pitchY: 4
     });
@@ -59,7 +59,7 @@ describe('GranularRectLayout', function () {
   }); // see issue #486
 
   it('tests that adding +/- pitchX fixes resolution causing errors', function () {
-    var l = new _GranularRectLayout.default({
+    var l = new _GranularRectLayout["default"]({
       pitchX: 91.21851599727707,
       pitchY: 3
     });
@@ -71,7 +71,7 @@ describe('GranularRectLayout', function () {
   });
   it('tests reinitializing layout due to throwing away old one', function () {
     var spy = jest.spyOn(console, 'warn').mockImplementation(function () {});
-    var l = new _GranularRectLayout.default({
+    var l = new _GranularRectLayout["default"]({
       pitchX: 1,
       pitchY: 1,
       maxHeight: 600
@@ -84,7 +84,7 @@ describe('GranularRectLayout', function () {
     spy.mockRestore();
   });
   it('tests adding a gigantic feature that fills entire row with another smaller added on top', function () {
-    var l = new _GranularRectLayout.default({
+    var l = new _GranularRectLayout["default"]({
       pitchX: 100,
       pitchY: 1,
       maxHeight: 600

package/util/layouts/MultiLayout.d.ts

@@ -1,7 +1,7 @@
 import { BaseLayout, SerializedLayout } from './BaseLayout';
 export default class MultiLayout<SUB_LAYOUT_CLASS extends BaseLayout<T>, T> {
-    subLayouts: Map<string, SUB_LAYOUT_CLASS>;
     SubLayoutClass: new (...args: any[]) => SUB_LAYOUT_CLASS;
+    subLayouts: Map<string, SUB_LAYOUT_CLASS>;
     subLayoutConstructorArgs: Record<string, any>;
     /**
      * layout class that just keeps a number of named sub-layouts.

package/util/layouts/MultiLayout.js

@@ -1,25 +1,19 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = void 0;
+exports["default"] = void 0;
 
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+var _slicedToArray2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
 
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+var _createForOfIteratorHelper2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createForOfIteratorHelper.js"));
 
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+var _classCallCheck2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
 
-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; }
+var _createClass2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createClass.js"));
 
 /* eslint-disable @typescript-eslint/no-explicit-any */
 var MultiLayout = /*#__PURE__*/function () {
@@ -30,16 +24,15 @@ var MultiLayout = /*#__PURE__*/function () {
    */
   function MultiLayout(SubLayoutClass) {
     var layoutArgs = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-    (0, _classCallCheck2.default)(this, MultiLayout);
-    (0, _defineProperty2.default)(this, "subLayouts", new Map());
-    (0, _defineProperty2.default)(this, "SubLayoutClass", void 0);
-    (0, _defineProperty2.default)(this, "subLayoutConstructorArgs", {});
-    this.subLayouts = new Map();
+    (0, _classCallCheck2["default"])(this, MultiLayout);
     this.SubLayoutClass = SubLayoutClass;
+    this.subLayouts = new Map();
+    this.subLayoutConstructorArgs = {};
+    this.subLayouts = new Map();
     this.subLayoutConstructorArgs = layoutArgs;
   }
 
-  (0, _createClass2.default)(MultiLayout, [{
+  (0, _createClass2["default"])(MultiLayout, [{
     key: "getSublayout",
     value: function getSublayout(layoutName) {
       var subLayout = this.subLayouts.get(layoutName);
@@ -69,12 +62,12 @@ var MultiLayout = /*#__PURE__*/function () {
     value: function toJSON() {
       var data = {};
 
-      var _iterator = _createForOfIteratorHelper(this.subLayouts.entries()),
+      var _iterator = (0, _createForOfIteratorHelper2["default"])(this.subLayouts.entries()),
           _step;
 
       try {
         for (_iterator.s(); !(_step = _iterator.n()).done;) {
-          var _step$value = (0, _slicedToArray2.default)(_step.value, 2),
+          var _step$value = (0, _slicedToArray2["default"])(_step.value, 2),
               layoutName = _step$value[0],
               sublayout = _step$value[1];
 
@@ -92,4 +85,4 @@ var MultiLayout = /*#__PURE__*/function () {
   return MultiLayout;
 }();
 
-exports.default = MultiLayout;
+exports["default"] = MultiLayout;