@jbrowse/core 1.5.2 → 1.5.6

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -1,24 +1,24 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireWildcard = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireWildcard.js")["default"];
 
-var _typeof = require("@babel/runtime/helpers/typeof");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.SequencePanel = void 0;
-exports.default = SequenceFeatureDetails;
+exports["default"] = SequenceFeatureDetails;
 
-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 _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+var _slicedToArray2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
 
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+var _objectSpread2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
 
-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 _react = _interopRequireWildcard(require("react"));
 
@@ -34,14 +34,6 @@ var _configuration = require("../configuration");
 
 var _util2 = require("./util");
 
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
-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; }
-
 var useStyles = (0, _core.makeStyles)(function (theme) {
   return {
     button: {
@@ -60,7 +52,7 @@ var utrColor = 'rgb(200,240,240)';
 function GeneCDS(_ref) {
   var cds = _ref.cds,
       sequence = _ref.sequence;
-  return /*#__PURE__*/_react.default.createElement("span", {
+  return /*#__PURE__*/_react["default"].createElement("span", {
     style: {
       background: cdsColor
     }
@@ -79,7 +71,7 @@ function GeneProtein(_ref2) {
     protein += codonTable[str.slice(i, i + 3)] || '&';
   }
 
-  return /*#__PURE__*/_react.default.createElement("span", {
+  return /*#__PURE__*/_react["default"].createElement("span", {
     style: {
       background: proteinColor
     }
@@ -95,10 +87,10 @@ function GenecDNA(_ref3) {
       downstream = _ref3.downstream,
       includeIntrons = _ref3.includeIntrons,
       collapseIntron = _ref3.collapseIntron;
-  var chunks = cds.length ? [].concat((0, _toConsumableArray2.default)(cds), (0, _toConsumableArray2.default)(utr)).sort(function (a, b) {
+  var chunks = cds.length ? [].concat((0, _toConsumableArray2["default"])(cds), (0, _toConsumableArray2["default"])(utr)).sort(function (a, b) {
     return a.start - b.start;
   }) : exons;
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, upstream ? /*#__PURE__*/_react.default.createElement("span", {
+  return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, upstream ? /*#__PURE__*/_react["default"].createElement("span", {
     style: {
       background: updownstreamColor
     }
@@ -108,25 +100,25 @@ function GenecDNA(_ref3) {
     var _chunks;
 
     var intron = sequence.slice(chunk.end, (_chunks = chunks[index + 1]) === null || _chunks === void 0 ? void 0 : _chunks.start);
-    return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, {
+    return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, {
       key: JSON.stringify(chunk)
-    }, /*#__PURE__*/_react.default.createElement("span", {
+    }, /*#__PURE__*/_react["default"].createElement("span", {
       style: {
         background: chunk.type === 'CDS' ? cdsColor : utrColor
       }
-    }, sequence.slice(chunk.start, chunk.end)), includeIntrons && index < chunks.length - 1 ? /*#__PURE__*/_react.default.createElement("span", {
+    }, sequence.slice(chunk.start, chunk.end)), includeIntrons && index < chunks.length - 1 ? /*#__PURE__*/_react["default"].createElement("span", {
       style: {
         background: intronColor
       }
     }, collapseIntron && intron.length > 20 ? "".concat(intron.slice(0, 10), "...").concat(intron.slice(-10)) : intron) : null);
-  }), downstream ? /*#__PURE__*/_react.default.createElement("span", {
+  }), downstream ? /*#__PURE__*/_react["default"].createElement("span", {
     style: {
       background: updownstreamColor
     }
   }, downstream) : null);
 }
 
-var SequencePanel = /*#__PURE__*/_react.default.forwardRef(function (_ref4, ref) {
+var SequencePanel = /*#__PURE__*/_react["default"].forwardRef(function (_ref4, ref) {
   var feature = _ref4.feature,
       mode = _ref4.mode,
       _ref4$sequence = _ref4.sequence,
@@ -145,7 +137,7 @@ var SequencePanel = /*#__PURE__*/_react.default.forwardRef(function (_ref4, ref)
   var children = subfeatures.sort(function (a, b) {
     return a.start - b.start;
   }).map(function (sub) {
-    return _objectSpread(_objectSpread({}, sub), {}, {
+    return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, sub), {}, {
       start: sub.start - feature.start,
       end: sub.end - feature.start
     });
@@ -186,40 +178,41 @@ var SequencePanel = /*#__PURE__*/_react.default.forwardRef(function (_ref4, ref)
     utr = (0, _util2.revlist)(utr, sequence.length);
   }
 
-  return /*#__PURE__*/_react.default.createElement("div", {
+  return /*#__PURE__*/_react["default"].createElement("div", {
     ref: ref,
     "data-testid": "sequence_panel"
-  }, /*#__PURE__*/_react.default.createElement("div", {
+  }, /*#__PURE__*/_react["default"].createElement("div", {
     style: {
       fontFamily: 'monospace',
-      wordWrap: 'break-word'
+      wordWrap: 'break-word',
+      maxWidth: 600
     }
-  }, ">".concat(feature.name || feature.id || 'unknown', "-").concat(mode, "\n"), mode === 'cds' ? /*#__PURE__*/_react.default.createElement(GeneCDS, {
+  }, ">".concat(feature.name || feature.id || 'unknown', "-").concat(mode, "\n"), mode === 'cds' ? /*#__PURE__*/_react["default"].createElement(GeneCDS, {
     cds: cds,
     sequence: sequence
-  }) : mode === 'cdna' ? /*#__PURE__*/_react.default.createElement(GenecDNA, {
+  }) : mode === 'cdna' ? /*#__PURE__*/_react["default"].createElement(GenecDNA, {
     exons: exons,
     cds: cds,
     utr: utr,
     sequence: sequence
-  }) : mode === 'protein' ? /*#__PURE__*/_react.default.createElement(GeneProtein, {
+  }) : mode === 'protein' ? /*#__PURE__*/_react["default"].createElement(GeneProtein, {
     cds: cds,
     codonTable: codonTable,
     sequence: sequence
-  }) : mode === 'gene' ? /*#__PURE__*/_react.default.createElement(GenecDNA, {
+  }) : mode === 'gene' ? /*#__PURE__*/_react["default"].createElement(GenecDNA, {
     exons: exons,
     cds: cds,
     utr: utr,
     sequence: sequence,
     includeIntrons: true
-  }) : mode === 'gene_collapsed_intron' ? /*#__PURE__*/_react.default.createElement(GenecDNA, {
+  }) : mode === 'gene_collapsed_intron' ? /*#__PURE__*/_react["default"].createElement(GenecDNA, {
     exons: exons,
     cds: cds,
     sequence: sequence,
     utr: utr,
     includeIntrons: true,
     collapseIntron: true
-  }) : mode === 'gene_updownstream' ? /*#__PURE__*/_react.default.createElement(GenecDNA, {
+  }) : mode === 'gene_updownstream' ? /*#__PURE__*/_react["default"].createElement(GenecDNA, {
     exons: exons,
     cds: cds,
     sequence: sequence,
@@ -227,7 +220,7 @@ var SequencePanel = /*#__PURE__*/_react.default.forwardRef(function (_ref4, ref)
     upstream: upstream,
     downstream: downstream,
     includeIntrons: true
-  }) : mode === 'gene_updownstream_collapsed_intron' ? /*#__PURE__*/_react.default.createElement(GenecDNA, {
+  }) : mode === 'gene_updownstream_collapsed_intron' ? /*#__PURE__*/_react["default"].createElement(GenecDNA, {
     exons: exons,
     cds: cds,
     sequence: sequence,
@@ -236,7 +229,7 @@ var SequencePanel = /*#__PURE__*/_react.default.forwardRef(function (_ref4, ref)
     downstream: downstream,
     includeIntrons: true,
     collapseIntron: true
-  }) : /*#__PURE__*/_react.default.createElement("div", null, "Unknown type")));
+  }) : /*#__PURE__*/_react["default"].createElement("div", null, "Unknown type")));
 }); // display the stitched-together sequence of a gene's CDS, cDNA, or protein
 // sequence. this is a best effort and weird genomic phenomena could lead these
 // to not be 100% accurate
@@ -261,27 +254,27 @@ function SequenceFeatureDetails(_ref6) {
       inView = _useInView.inView;
 
   var _useState = (0, _react.useState)(),
-      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
+      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
       sequence = _useState2[0],
       setSequence = _useState2[1];
 
   var _useState3 = (0, _react.useState)(),
-      _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
+      _useState4 = (0, _slicedToArray2["default"])(_useState3, 2),
       error = _useState4[0],
       setError = _useState4[1];
 
   var _useState5 = (0, _react.useState)(hasCDS ? 'cds' : 'cdna'),
-      _useState6 = (0, _slicedToArray2.default)(_useState5, 2),
+      _useState6 = (0, _slicedToArray2["default"])(_useState5, 2),
       mode = _useState6[0],
       setMode = _useState6[1];
 
   var _useState7 = (0, _react.useState)(false),
-      _useState8 = (0, _slicedToArray2.default)(_useState7, 2),
+      _useState8 = (0, _slicedToArray2["default"])(_useState7, 2),
       copied = _useState8[0],
       setCopied = _useState8[1];
 
   var _useState9 = (0, _react.useState)(false),
-      _useState10 = (0, _slicedToArray2.default)(_useState9, 2),
+      _useState10 = (0, _slicedToArray2["default"])(_useState9, 2),
       copiedHtml = _useState10[0],
       setCopiedHtml = _useState10[1];
 
@@ -299,7 +292,7 @@ function SequenceFeatureDetails(_ref6) {
         rpcManager = _getSession.rpcManager;
 
     var _ref7 = ((_model$view = model.view) === null || _model$view === void 0 ? void 0 : _model$view.assemblyNames) || [],
-        _ref8 = (0, _slicedToArray2.default)(_ref7, 1),
+        _ref8 = (0, _slicedToArray2["default"])(_ref7, 1),
         assemblyName = _ref8[0];
 
     function fetchSeq(_x, _x2, _x3) {
@@ -307,10 +300,10 @@ function SequenceFeatureDetails(_ref6) {
     }
 
     function _fetchSeq() {
-      _fetchSeq = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(start, end, refName) {
+      _fetchSeq = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2(start, end, refName) {
         var assembly, sessionId, feats, _ref11, _ref12, feat;
 
-        return _regenerator.default.wrap(function _callee2$(_context2) {
+        return _index["default"].wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -342,7 +335,7 @@ function SequenceFeatureDetails(_ref6) {
 
               case 8:
                 feats = _context2.sent;
-                _ref11 = feats, _ref12 = (0, _slicedToArray2.default)(_ref11, 1), feat = _ref12[0];
+                _ref11 = feats, _ref12 = (0, _slicedToArray2["default"])(_ref11, 1), feat = _ref12[0];
 
                 if (feat) {
                   _context2.next = 12;
@@ -365,10 +358,10 @@ function SequenceFeatureDetails(_ref6) {
     }
 
     ;
-    (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
+    (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee() {
       var _ref10, start, end, refName, seq, up, down;
 
-      return _regenerator.default.wrap(function _callee$(_context) {
+      return _index["default"].wrap(function _callee$(_context) {
         while (1) {
           switch (_context.prev = _context.next) {
             case 0:
@@ -418,28 +411,28 @@ function SequenceFeatureDetails(_ref6) {
     };
   }, [feature, inView, model]);
   var loading = !sequence;
-  return /*#__PURE__*/_react.default.createElement("div", {
+  return /*#__PURE__*/_react["default"].createElement("div", {
     ref: ref
-  }, /*#__PURE__*/_react.default.createElement(_core.Select, {
+  }, /*#__PURE__*/_react["default"].createElement(_core.Select, {
     value: mode,
     onChange: function onChange(event) {
       return setMode(event.target.value);
     }
-  }, hasCDS ? /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
+  }, hasCDS ? /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
     value: "cds"
-  }, "CDS") : null, hasCDS ? /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
+  }, "CDS") : null, hasCDS ? /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
     value: "protein"
-  }, "Protein") : null, /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
+  }, "Protein") : null, /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
     value: "gene"
-  }, "Gene w/ introns"), /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
+  }, "Gene w/ introns"), /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
     value: "gene_collapsed_intron"
-  }, "Gene w/ 10bp of intron"), /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
+  }, "Gene w/ 10bp of intron"), /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
     value: "gene_updownstream"
-  }, "Gene w/ 500bp up+down stream"), /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
+  }, "Gene w/ 500bp up+down stream"), /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
     value: "gene_updownstream_collapsed_intron"
-  }, "Gene w/ 500bp up+down stream w/ 10bp intron"), /*#__PURE__*/_react.default.createElement(_core.MenuItem, {
+  }, "Gene w/ 500bp up+down stream w/ 10bp intron"), /*#__PURE__*/_react["default"].createElement(_core.MenuItem, {
     value: "cdna"
-  }, "cDNA")), /*#__PURE__*/_react.default.createElement(_core.Button, {
+  }, "cDNA")), /*#__PURE__*/_react["default"].createElement(_core.Button, {
     className: classes.button,
     type: "button",
     variant: "contained",
@@ -447,7 +440,7 @@ function SequenceFeatureDetails(_ref6) {
       var ref = seqPanelRef.current;
 
       if (ref) {
-        (0, _copyToClipboard.default)(ref.textContent || '', {
+        (0, _copyToClipboard["default"])(ref.textContent || '', {
           format: 'text/plain'
         });
         setCopied(true);
@@ -456,9 +449,9 @@ function SequenceFeatureDetails(_ref6) {
         }, 1000);
       }
     }
-  }, copied ? 'Copied to clipboard!' : 'Copy as plaintext'), /*#__PURE__*/_react.default.createElement(_core.Tooltip, {
+  }, copied ? 'Copied to clipboard!' : 'Copy as plaintext'), /*#__PURE__*/_react["default"].createElement(_core.Tooltip, {
     title: "Note that 'Copy as HTML' can retain the colors but cannot be pasted into some programs like notepad that only expect plain text"
-  }, /*#__PURE__*/_react.default.createElement(_core.Button, {
+  }, /*#__PURE__*/_react["default"].createElement(_core.Button, {
     className: classes.button,
     type: "button",
     variant: "contained",
@@ -466,7 +459,7 @@ function SequenceFeatureDetails(_ref6) {
       var ref = seqPanelRef.current;
 
       if (ref) {
-        (0, _copyToClipboard.default)(ref.innerHTML, {
+        (0, _copyToClipboard["default"])(ref.innerHTML, {
           format: 'text/html'
         });
         setCopiedHtml(true);
@@ -475,14 +468,14 @@ function SequenceFeatureDetails(_ref6) {
         }, 1000);
       }
     }
-  }, copiedHtml ? 'Copied to clipboard!' : 'Copy as HTML')), /*#__PURE__*/_react.default.createElement("div", {
+  }, copiedHtml ? 'Copied to clipboard!' : 'Copy as HTML')), /*#__PURE__*/_react["default"].createElement("div", {
     "data-testid": "feature_sequence"
-  }, error ? /*#__PURE__*/_react.default.createElement(_core.Typography, {
+  }, error ? /*#__PURE__*/_react["default"].createElement(_core.Typography, {
     color: "error"
-  }, "".concat(error)) : loading ? /*#__PURE__*/_react.default.createElement("div", null, "Loading gene sequence...") : sequence ? /*#__PURE__*/_react.default.createElement(SequencePanel, {
+  }, "".concat(error)) : loading ? /*#__PURE__*/_react["default"].createElement("div", null, "Loading gene sequence...") : sequence ? /*#__PURE__*/_react["default"].createElement(SequencePanel, {
     ref: seqPanelRef,
     feature: parentFeature,
     mode: mode,
     sequence: sequence
-  }) : /*#__PURE__*/_react.default.createElement("div", null, "No sequence found")));
+  }) : /*#__PURE__*/_react["default"].createElement("div", null, "No sequence found")));
 }

package/BaseFeatureWidget/SequenceFeatureDetails.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 _react = _interopRequireDefault(require("react"));
 
@@ -23,9 +23,9 @@ test('test using the sequence feature panel', function () {
 
   var dna = readFasta('./test_data/DLGAP3_dna.fa'); // http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=share-zMPjiv36k0&password=ddxCy
 
-  var feature = _DLGAP.default;
+  var feature = _DLGAP["default"];
 
-  var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_SequenceFeatureDetails.SequencePanel, {
+  var _render = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_SequenceFeatureDetails.SequencePanel, {
     sequence: {
       seq: dna
     },
@@ -41,16 +41,16 @@ test('test using the sequence feature panel', function () {
 });
 
 var readFasta = function readFasta(filename) {
-  return _fs.default.readFileSync(require.resolve(filename), 'utf8').split('\n').slice(1).join('');
+  return _fs["default"].readFileSync(require.resolve(filename), 'utf8').split('\n').slice(1).join('');
 };
 
 test('NCDN collapsed intron', function () {
   // samtools faidx 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz' 1:36,023,400-36,032,380 > out.fa
   var dna = readFasta('./test_data/NCDN_dna.fa'); // http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=share-zMPjiv36k0&password=ddxCy
 
-  var feature = _NCDN.default;
+  var feature = _NCDN["default"];
 
-  var _render2 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_SequenceFeatureDetails.SequencePanel, {
+  var _render2 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_SequenceFeatureDetails.SequencePanel, {
     sequence: {
       seq: dna
     },
@@ -70,9 +70,9 @@ test('NCDN updownstream', function () {
 
   var seq = readFasta('./test_data/NCDN_dna.fa'); // http://localhost:3000/?config=test_data%2Fconfig_demo.json&session=share-zMPjiv36k0&password=ddxCy
 
-  var feature = _NCDN.default;
+  var feature = _NCDN["default"];
 
-  var _render3 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_SequenceFeatureDetails.SequencePanel, {
+  var _render3 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_SequenceFeatureDetails.SequencePanel, {
     sequence: {
       seq: seq,
       upstream: upstream
@@ -95,7 +95,7 @@ test('NCDN updownstream', function () {
 test('single exon cDNA should not have duplicate sequences', function () {
   var seq = readFasta('./test_data/volvox.fa');
 
-  var _render4 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_SequenceFeatureDetails.SequencePanel, {
+  var _render4 = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_SequenceFeatureDetails.SequencePanel, {
     sequence: {
       seq: seq
     },

package/BaseFeatureWidget/index.js

@@ -4,7 +4,7 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.configSchema = void 0;
-exports.stateModelFactory = exports.default = stateModelFactory;
+exports.stateModelFactory = exports["default"] = stateModelFactory;
 
 var _mobxStateTree = require("mobx-state-tree");
 

package/BaseFeatureWidget/index.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 _react = _interopRequireDefault(require("react"));
 
@@ -18,7 +18,7 @@ var _BaseFeatureDetail = _interopRequireDefault(require("./BaseFeatureDetail"));
 
 test('open up a widget', function () {
   console.warn = jest.fn();
-  var pluginManager = new _PluginManager.default([]);
+  var pluginManager = new _PluginManager["default"]([]);
 
   var Session = _mobxStateTree.types.model({
     pluginManager: _mobxStateTree.types.optional(_mobxStateTree.types.frozen(), {}),
@@ -33,7 +33,7 @@ test('open up a widget', function () {
     }
   });
 
-  var _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_BaseFeatureDetail.default, {
+  var _render = (0, _react2.render)( /*#__PURE__*/_react["default"].createElement(_BaseFeatureDetail["default"], {
     model: model.widget
   })),
       container = _render.container,

package/BaseFeatureWidget/types.js

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

package/BaseFeatureWidget/util.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
@@ -11,13 +11,9 @@ exports.ellipses = ellipses;
 exports.revlist = revlist;
 exports.stitch = stitch;
 
-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 _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-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; }
+var _objectSpread2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
 
 function stitch(subfeats, sequence) {
   return subfeats.map(function (sub) {
@@ -39,7 +35,7 @@ function dedupe(list) {
 
 function revlist(list, seqlen) {
   return list.map(function (sub) {
-    return _objectSpread(_objectSpread({}, sub), {}, {
+    return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, sub), {}, {
       start: seqlen - sub.end,
       end: seqlen - sub.start
     });
@@ -60,23 +56,23 @@ function calculateUTRs(cds, exons) {
   });
   var lastCdsExon = exons[lastCdsIdx];
   var firstCdsExon = exons[firstCdsIdx];
-  var fiveUTRs = [].concat((0, _toConsumableArray2.default)(exons.slice(0, firstCdsIdx)), [{
+  var fiveUTRs = [].concat((0, _toConsumableArray2["default"])(exons.slice(0, firstCdsIdx)), [{
     start: firstCdsExon.start,
     end: firstCds.start
   }]).map(function (elt) {
-    return _objectSpread(_objectSpread({}, elt), {}, {
+    return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, elt), {}, {
       type: 'five_prime_UTR'
     });
   });
   var threeUTRs = [{
     start: lastCds.end,
     end: lastCdsExon.end
-  }].concat((0, _toConsumableArray2.default)(exons.slice(lastCdsIdx + 1))).map(function (elt) {
-    return _objectSpread(_objectSpread({}, elt), {}, {
+  }].concat((0, _toConsumableArray2["default"])(exons.slice(lastCdsIdx + 1))).map(function (elt) {
+    return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, elt), {}, {
       type: 'three_prime_UTR'
     });
   });
-  return [].concat((0, _toConsumableArray2.default)(fiveUTRs), (0, _toConsumableArray2.default)(threeUTRs));
+  return [].concat((0, _toConsumableArray2["default"])(fiveUTRs), (0, _toConsumableArray2["default"])(threeUTRs));
 }
 
 function ellipses(slug) {

package/CorePlugin.js

@@ -1,27 +1,23 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireWildcard3 = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireWildcard.js")["default"];
 
-var _typeof = require("@babel/runtime/helpers/typeof");
+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 _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+var _interopRequireWildcard2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/interopRequireWildcard.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 _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+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 _inherits2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/inherits.js"));
 
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+var _createSuper2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
 
 var _react = require("react");
 
@@ -31,42 +27,34 @@ var _Plugin2 = _interopRequireDefault(require("./Plugin"));
 
 var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 
-var coreRpcMethods = _interopRequireWildcard(require("./rpc/coreRpcMethods"));
+var coreRpcMethods = _interopRequireWildcard3(require("./rpc/coreRpcMethods"));
 
 var _WidgetType = _interopRequireDefault(require("./pluggableElementTypes/WidgetType"));
 
 var _CytobandAdapter = require("./data_adapters/CytobandAdapter");
 
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
-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; } }
-
 // the core plugin, which registers types that ALL JBrowse applications are
 // expected to need.
 var CorePlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(CorePlugin, _Plugin);
+  (0, _inherits2["default"])(CorePlugin, _Plugin);
 
-  var _super = _createSuper(CorePlugin);
+  var _super = (0, _createSuper2["default"])(CorePlugin);
 
   function CorePlugin() {
     var _this;
 
-    (0, _classCallCheck2.default)(this, CorePlugin);
+    (0, _classCallCheck2["default"])(this, CorePlugin);
 
     for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
       args[_key] = arguments[_key];
     }
 
     _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'CorePlugin');
+    _this.name = 'CorePlugin';
     return _this;
   }
 
-  (0, _createClass2.default)(CorePlugin, [{
+  (0, _createClass2["default"])(CorePlugin, [{
     key: "install",
     value: function install(pluginManager) {
       // register all our core rpc methods
@@ -76,21 +64,21 @@ var CorePlugin = /*#__PURE__*/function (_Plugin) {
         });
       });
       pluginManager.addAdapterType(function () {
-        return new _AdapterType.default({
+        return new _AdapterType["default"]({
           name: 'CytobandAdapter',
           configSchema: _CytobandAdapter.configSchema,
           AdapterClass: _CytobandAdapter.DataAdapter
         });
       });
       pluginManager.addWidgetType(function () {
-        return new _WidgetType.default({
+        return new _WidgetType["default"]({
           name: 'BaseFeatureWidget',
           heading: 'Feature details',
           configSchema: _BaseFeatureWidget.configSchema,
           stateModel: (0, _BaseFeatureWidget.stateModelFactory)(pluginManager),
           ReactComponent: /*#__PURE__*/(0, _react.lazy)(function () {
             return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('./BaseFeatureWidget/BaseFeatureDetail'));
+              return (0, _interopRequireWildcard2["default"])(require('./BaseFeatureWidget/BaseFeatureDetail'));
             });
           })
         });
@@ -98,6 +86,6 @@ var CorePlugin = /*#__PURE__*/function (_Plugin) {
     }
   }]);
   return CorePlugin;
-}(_Plugin2.default);
+}(_Plugin2["default"]);
 
-exports.default = CorePlugin;
+exports["default"] = CorePlugin;