@jbrowse/core 2.0.1 → 2.1.0

package/util/when.js

@@ -1,115 +1,68 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.when = when;
-exports.whenPresent = whenPresent;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _mobx = require("mobx");
-
-var _aborting = require("./aborting");
-
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.whenPresent = exports.when = void 0;
+const mobx_1 = require("mobx");
+const aborting_1 = require("./aborting");
 /**
  * Wrapper for mobx `when` that adds timeout and aborting support.
  */
-function when(getter) {
-  var _ref = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {},
-      timeout = _ref.timeout,
-      signal = _ref.signal,
-      name = _ref.name;
-
-  return new Promise(function (resolve, reject) {
-    var finished = false;
-    var whenPromise = (0, _mobx.when)(getter); // set up timeout
-
-    var timeoutId;
-
-    var finishTimeout = function finishTimeout() {};
-
-    if (timeout) {
-      timeoutId = setTimeout(function () {
-        if (!finished) {
-          finished = true;
-          whenPromise.cancel();
-          reject(new Error("timed out waiting for ".concat(name || 'whenPresent')));
+function when(getter, { timeout, signal, name } = {}) {
+    return new Promise((resolve, reject) => {
+        let finished = false;
+        const whenPromise = (0, mobx_1.when)(getter);
+        // set up timeout
+        let timeoutId;
+        let finishTimeout = () => { };
+        if (timeout) {
+            timeoutId = setTimeout(() => {
+                if (!finished) {
+                    finished = true;
+                    whenPromise.cancel();
+                    reject(new Error(`timed out waiting for ${name || 'whenPresent'}`));
+                }
+            }, timeout);
+            finishTimeout = () => timeoutId && clearTimeout(timeoutId);
         }
-      }, timeout);
-
-      finishTimeout = function finishTimeout() {
-        return timeoutId && clearTimeout(timeoutId);
-      };
-    } // set up aborting
-
-
-    if (signal) {
-      signal.addEventListener('abort', function () {
-        if (!finished) {
-          finished = true; // mobx when supports a cancel method
-
-          whenPromise.cancel();
-          finishTimeout();
-          reject((0, _aborting.makeAbortError)());
+        // set up aborting
+        if (signal) {
+            signal.addEventListener('abort', () => {
+                if (!finished) {
+                    finished = true;
+                    // mobx when supports a cancel method
+                    whenPromise.cancel();
+                    finishTimeout();
+                    reject((0, aborting_1.makeAbortError)());
+                }
+            });
         }
-      });
-    }
-
-    whenPromise.then(function () {
-      if (!finished) {
-        finished = true;
-        finishTimeout();
-        resolve(true);
-      }
-    }).catch(function (err) {
-      if (!finished) {
-        finished = true;
-        finishTimeout();
-        reject(err);
-      }
+        whenPromise
+            .then(() => {
+            if (!finished) {
+                finished = true;
+                finishTimeout();
+                resolve(true);
+            }
+        })
+            .catch(err => {
+            if (!finished) {
+                finished = true;
+                finishTimeout();
+                reject(err);
+            }
+        });
     });
-  });
 }
+exports.when = when;
 /**
  * Wrapper for mobx `when` that makes a promise for the return value
  * of the given function at the point in time when it becomes not
  * undefined and not null.
  */
-
-
-function whenPresent(_x) {
-  return _whenPresent.apply(this, arguments);
+async function whenPresent(getter, opts = {}) {
+    await when(() => {
+        const val = getter();
+        return val !== undefined && val !== null;
+    }, opts);
+    return getter();
 }
-
-function _whenPresent() {
-  _whenPresent = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(getter) {
-    var opts,
-        _args = arguments;
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            opts = _args.length > 1 && _args[1] !== undefined ? _args[1] : {};
-            _context.next = 3;
-            return when(function () {
-              var val = getter();
-              return val !== undefined && val !== null;
-            }, opts);
-
-          case 3:
-            return _context.abrupt("return", getter());
-
-          case 4:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  }));
-  return _whenPresent.apply(this, arguments);
-}
+exports.whenPresent = whenPresent;

package/BaseFeatureWidget/SequenceFeatureDetails.test.js

@@ -1,122 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-var _fs = _interopRequireDefault(require("fs"));
-
-var _SequenceFeatureDetails = require("./SequenceFeatureDetails");
-
-var _DLGAP = _interopRequireDefault(require("./test_data/DLGAP3.json"));
-
-var _NCDN = _interopRequireDefault(require("./test_data/NCDN.json"));
-
-test('test using the sequence feature panel', function () {
-  // produced from uniprot
-  // https://www.uniprot.org/uniprot/O95886.fasta
-  var pep = readFasta('./test_data/DLGAP3_pep.fa'); // produced with samtools faidx
-  // 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz'
-  // 1:35331037..35395251
-
-  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 _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_SequenceFeatureDetails.SequencePanel, {
-    sequence: {
-      seq: dna
-    },
-    mode: "protein",
-    feature: feature.subfeatures[0]
-  })),
-      getByTestId = _render.getByTestId;
-
-  var element = getByTestId('sequence_panel'); // http://m.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000116544;r=1:34865436-34929650
-  // with stop codon on the end
-
-  expect(element.textContent).toEqual(">NM_001080418.3-protein\n".concat(pep, "*"));
-});
-
-var readFasta = function readFasta(filename) {
-  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 _render2 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_SequenceFeatureDetails.SequencePanel, {
-    sequence: {
-      seq: dna
-    },
-    mode: "gene_collapsed_intron",
-    feature: feature.subfeatures[0]
-  })),
-      getByTestId = _render2.getByTestId;
-
-  var element = getByTestId('sequence_panel'); // UTR
-
-  expect(element.children[0].textContent).toEqual('>NM_014284.3-gene_collapsed_intron\nAGTGGGCAACGCGGCGTGAGCAGCGGCCCGAGGCTCCCGGAGCATCGCGCTGGGAGAAGACTTCGCCGCTCGGGGCCGCAGCCTGGTGAGCTCAGCCCCCTTCGGGCCCTCCCCTGCATCCCAGCCGGGGCCTCTCCGAGCCGGCGCTGATCGATGCCGACACACCCCGGGGACCCTATCGCGACTCCATCGCGCCATATCGCGACACCATCGTGCCCTGTCGAGACTCCATTTTGTCACAGCCCTTTTCAATATATATCTTTTTTTTTTTTAATTTGCCCTGTCATCTTTGGGGGCTGTCTCCCATGTCGTGATTTTGACGTGATCTCTCCGTGACATCACCGCGCCATCGTGAAGTGTGATCTCATCGCCGCCCTGTCGTGACTTCATCAATGTCGTGTTGTGACCTGGCTGCGGCGGGACAGGTGGTGACCG...GTGTTCACAGTTGGGCAAGGCGAGCATCATGGCCTCGGATTGCGAGCCAGCTCTGAACCAGGCAGAGGGCCGAAACCCCACCCTGGAGCGCTACCTGGGAGCCCTCCGTGAGGCCAAGAATGACAGCGAGCAGTTTGCAGCCCTGCTGCTAGTAAGGAACT...CCCCCTATAGGTGACCAAGGCAGTCAAAGCAGGTGACATAGATGCCAAAACTCGGCGGCGGATCTTCGATGCTGTCGGCTTCACCTTCCCCAATCGTCTCCTGACCACCAAGGAGGCGCCGGATGGCTGCCCTGACCATGTTCTGCGGGCTTTGGGTGTGGCCCTGCTGGCCTGCTTCTGCAGTGACCCTGAACTGGCCGCCCATCCCCAAGTCCTGAACAAGATTCCCATTCTTAGCACCTTCCTCACAGCCCGGGGGGACCCGGACGATGCTGCCCGCCGCTCCATGATTGATGACACCTACCAGTGCCTGACGGCTGTAGCAGGCACACCCAGAGGGCCTCGGCACCTCATTGCTGGTGGCACCGTGTCTGCCCTATGCCAGGCATACCTGGGGCACGGCTATGGCTTTGACCAGGCCCTGGCACTCCTGGTGGGGCTGCTGGCTGCTGCCGAGACACAGTGCTGGAAGGAGGCGGAGCCCGACCTGCTGGCCGTGTTGCGGGGCCTCAGTGAGGATTTCCAGAAAGCTGAGGATGCCAGCAAGTTTGAGCTCTGCCAGCTGCTGCCCCTCTTTTTGCCCCCGACAACCGTGCCCCCTGAATGCTACCGGGATCTGCAGGCCGGGCTGGCACGCATCCTGGGAAGCAAGCTGAGCTCCTGGCAGCGCAACCCTGCACTGAAGCTGGCAGCCCGCCTGGCACACGCCTGCGGCTCCGACTGGATCCCGGCGGGCAGCTCCGGGAGCAAGTTCCTGGCCCTGCTGGTGAATCTGGCGTGCGTGGAAGTGCGGCTGGCACTGGAGGAGACGGGCACGGAGGTGAAAGAGGATGTGGTGACCGCCTGCTATGCCCTCATGGAGTTGGGGATCCAGGAATGCACTCGCTGTGAGCAGTCACTGCTTAAGGAGCCACAGAAGGTGCAGCTCGTGAGCGTCATGAAGGAGGCCATAGGGGCTGTTATCCACTACCTGCTGCAGGTGAGGGTGC...GTGGCAACAGGTGGGGTCAGAGAAGCAGAAGGAGCCCTTTGTGTTTGCCTCGGTGCGGATCCTGGGTGCCTGGCTGGCCGAGGAGACCTCATCCTTGCGTAAGGAGGTGTGCCAGCTGCTGCCCTTCCTCGTCCGCTATGCCAAGACCCTCTACGAGGAGGCCGAGGAGGCCAATGACCTTTCCCAGCAGGTGGCCAACCTGGCCATCTCCCCCACCACCCCAGGGCCCACCTGGCCAGGAGACGCTCTCCGGTGAGTCTGT...ACATCCCCAGGCTCCTCCTGCCTGGCTGGTGCCACCTGACCGTTGAAGATGGGCCCCGGGAGATCCTGATCAAGGAAGGGGCCCCCTCGCTTCTGTGCAAGTATTTCCTGCAGCAGTGGGAACTCACATCCCCTGGCCACGACACCTCGGTGCTGCCTGACAGCGTGGAGATTGGCCTGCAGACCTGCTGCCACATCTTCCTCAACCTCGTGGTCACCGCACCGGGGCTGATCAAGTGAGGGGCT...TCTTTTCCAGGCGTGACGCCTGCTTCACATCTCTAATGAACACCCTCATGACGTCGCTACCAGCACTAGTGCAGCAACAGGGAAGGCTGCTTCTGGCTGCTAATGTGGCCACCCTGGGGCTCCTCATGGCCCGGCTCCTTAGCACCTCTCCAGGTAAGAACTG...TACCTTGCAGCTCTTCAGGGAACACCAGCATCCCGAGGGTTCTTCGCAGCTGCCATCCTCTTCCTATCACAGTCCCACGTGGCGCGGGCCACCCCGGGCTCAGACCAGGCAGTGCTAGCCCTGTCCCCTGAGTATGAGGGCATCTGGGCCGACCTGCAGGAGCTCTGGTTCCTGGGCATGCAGGCCTTCACCGGCTGTGTGCCTCTGCTGCCCTGGCTGGCCCCCGCTGCCCTGCGCTCCCGCTGGCCGCAGGAGCTGCTCCAGCTGCTAGGCAGTGTCAGCCCCAACTCTGTCAAGCCCGAGATGGTGGCCGCCTATCAGGGTGTCCTGGTGGAGCTGGCGCGGGCCAACCGGCTGTGCCGGGAGGCCATGAGGCTGCAGGCGGGCGAGGAGACGGCCAGCCACTACCGCATGGCTGCCTTGGAGCAGTGCCTGTCAGAGCCCTGAGGGGTGTCCACCGGGGACAGACCCAGGGGCGGGCAGAGAGGGAAGGAGGGAGGAGGCATCTTCCCTGAAGCCCCCAATCTGGCCCCCCCCTCCCCAGACTTCCTCCCCAAAACACCCCAGCTTTCTGGCTTTTCTGAGGGCAAGGGCATGGTGCCCACCCCTCAAGTGTAAGGAACTGCGTTCCGCCCCTCAGGCCCCCATGGGGGCAGGGATCGGCTTGGAAATCAACGTGGTTGTCCCCGCCAGGCCGGGGAAGGTTGGAGCAGCCCCCAGGGAGGGGGGCACTAGGTGTCATTGTGCCCGATGTCTGGCTCCCCTGCAGGAGGGAGGCTCCAGGGTAAGACAGGGCTGGCAGGAGCAGACTGCCTCAGCCCATGTGCCCTGCCGGCCAGGGCGTGGGCTCCCCTCGGCTGTGGTGCCTCCTCTGGCCCCCCAGGTCCACGTCCTTTAAATTGGCCCTTTGGCTCTTGCCCTTGGCTCCCTTGGGCAGACAGCAGGCTTAGGCCATTGATATCGCAGTTCTTCCTATCAGCTTCAGTGACCCAGGGTCTGAACTGCCTCCATCCTAGGGCAACCTGGGGCAGACAGGCCTGGTGGGGGGTGGGGAAACCTCCTTCCACCTGAGCTTGCTTGAAGGGACCCAGAGTCTTTGGGCCCAGATCTTTAAACCTTTGTGTCGTGTTGCAGCAGAGTGACGATGGGGGTTGGGGGGTTATTTATTTTGCCTGTCCTTATCCCTGCTTGGACACCTGAGCATCTGATTCCTGTCCCCCTGGTGCCATCTGGCCTGGCTGGAGCCAGGAACAGGAGGGACACTTCCCCAGAATCCGCATGTTTCCCCAGTGATTACACTCCACTGCCACCGTGGTGCCTGGCTTTAACTCCCACCCCTGCTATGACTCCTCTCTGCAGAGACGCGACTGGCGGCTCCAGCAGGGACTACCTTTCTTATAAACCCAGGGGGACcacacacacacacacacacacacacacacacacacacacacacacacacacTCTTGATCCCTTGCTTCCCTCCCCCAGTGCGTTCTGTGATCGCCAAGTTCAAAGCTGTGCACATGTGGACACTCAATAAATGTTCATTGGTGACGAGAA');
-});
-test('NCDN updownstream', function () {
-  // produced from uniprot
-  // https://www.uniprot.org/uniprot/O95886.fasta
-  var upstream = readFasta('./test_data/NCDN_upstream_dna.fa'); // samtools faidx 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz' 1:36,023,400-36,032,380 > out.fa
-
-  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 _render3 = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_SequenceFeatureDetails.SequencePanel, {
-    sequence: {
-      seq: seq,
-      upstream: upstream
-    },
-    mode: "gene_updownstream",
-    feature: feature.subfeatures[0]
-  })),
-      getByTestId = _render3.getByTestId;
-
-  var element = getByTestId('sequence_panel');
-  expect(element.children[0].textContent).toEqual('>NM_014284.3-gene_updownstream\nCTCACCCGGAGGAGGAGGAGGAAGAGGAAGAAGGTAGTGCGGGCTCCCCACCCGGACAGCTACCTCTCGCCTCAGCCTCCCTGGACAGCGACGGCGGCCGGAAACACCGCCTCCTCCCACCTCCCCGGGACCGACCCGGAAACACACTCTCCATGCTAACCAAGCCCTCCCGCCCCTCCCCCGGGAAGGGCAATGCCGGCCGCGAGACCAAGGGGGAGGAGGGGCAGTGCTGGGCGGGTAAAACTACGCACAAGCGAAGGAATCTGGGCCCCCAGCCTCTCGCCGCCCGCTCTCCAGAGGCAGTCTGCACCTTGCCTCCTTCGCTCGAGCCCCAGCCCCCAGACTCGGGCAATACCCACAAGCAAGATGGCGGCAACGGCGGCACCCCCTACTGCTTAGCACCCTGACTTGCCATTGGCCAGAGCCCGGAGTGAAGCAGCCGCGGATTCGTCAAGAGCGGTGCGGGGGTGGGGGTGGAGCTGCAGCAGCCTGGAGCCAGGAGTGGGCAACGCGGCGTGAGCAGCGGCCCGAGGCTCCCGGAGCATCGCGCTGGGAGAAGACTTCGCCGCTCGGGGCCGCAGCCTGGTGAGCTCAGCCCCCTTCGGGCCCTCCCCTGCATCCCAGCCGGGGCCTCTCCGAGCCGGCGCTGATCGATGCCGACACACCCCGGGGACCCTATCGCGACTCCATCGCGCCATATCGCGACACCATCGTGCCCTGTCGAGACTCCATTTTGTCACAGCCCTTTTCAATATATATCTTTTTTTTTTTTAATTTGCCCTGTCATCTTTGGGGGCTGTCTCCCATGTCGTGATTTTGACGTGATCTCTCCGTGACATCACCGCGCCATCGTGAAGTGTGATCTCATCGCCGCCCTGTCGTGACTTCATCAATGTCGTGTTGTGACCTGGCTGCGGCGGGACAGGTGGTGACCGCCAGGAACCCTCCTCCCCTTCTCATCTCCCCATCTCAGCAGCCCTGCTTCGATTATCCGGCTTTTGGATTCTCCGTTGTCCTGGGAACTATCCGGGACCCCCTCTTGCTTCTCCAGCCCCTGCCGGCATCCACAGGCTGGTAGCGGGACGGGGAGGGCGAGAAGAGGGAGCGCAAGGGGTTAATTctgctgctgccgccgccgctgctgctgctgctgcAGCCTCTACCCGAGGGAGGGAAAGGAGAGGAGGCAAGGAGCCTGCGGGGGCGACTGAGAGCCCTGGCTGGAGGGGTGGGGTCCCCAAAGGGGCCTCCAAGCCTTCCCTGTTGAGCGTCTTGTATTCTCACTTCTGAAGCGTATCTCTGCCTCTGAAGAAGGGAGGGGAAAGGAAGCCTGGGGTGTCCTTTTCTCCCATGTCAGCCTGAGTCCGGATAATCGAACTTCACCCATGTATGTCTCCATTTCTCCCTGTCTGTCCTCACCACTCACTCCCTCTGTGTCCCTGTGGAGGGAGATAAAACCCAGCCTCCGGTGCCAGGGGGACAGCTGAGCAGTGGGGCCAGCTCCCGCCCACCCCCAGGAGACTGGTGAGGAGAGCTGTCCGGCTGAGCAGCAGCATGCATGGTCCTTCTTTCCCGCTTTCTGGAGGTGACCTTGGACCAGGGTCCCTTCTTTATCCCTAAGGATTTGCAGATCCAGCCCCTTAAAGGGGCTTCTGGGGGGAGGTCAGTCCTGAGGAGTCCACCCCTCCAGATtctctcctcccctccctctgtgctaatccctccctccctccatcctccactctcacccccaccccacccccgtccctccTCTGCAGAGGGATGCTCAGTCCCTCTTGTGTTCACAGTTGGGCAAGGCGAGCATCATGGCCTCGGATTGCGAGCCAGCTCTGAACCAGGCAGAGGGCCGAAACCCCACCCTGGAGCGCTACCTGGGAGCCCTCCGTGAGGCCAAGAATGACAGCGAGCAGTTTGCAGCCCTGCTGCTAGTAAGGAACTGGCTGAAAATTGGGAGGTGGGAAGGGCTGGGTGGTTGGGCCCCCAAGGAATGGGGTCAGTGAGTCCCCAAGGATATGTACGTAGTGCTAGCAACCCTGGAGGCACCAACGAAGGCCCAAGACCCCTACCTTTGTGCTCTTTTTTGCTCCCCCTGAGAATGGGGGCAAAGAGGAGAATGGGACTGAATAAGGCTGTGGCACTAGGGGCTGCCTGGGTCTGTTTTCTGGGGCGTCCCAGAGCAGATGGAAGCTGACTCATAGGGTAACAGCAGCAGGTAGTAACTAGTGCAGAGTACTTGAGGGCTGGGGATGGTTGTTCTGGGCCTGGAGAGAGTAGCAGGGCTGGAAGTGGCTGGGGAGGGGTCCTAGGGGAAGGCCAGGATGGCAGTAGGTAGGTTAAGGAATGGGAGCTAGTTTGGGGCTTAGCCTTTTTGGAGGAACCCAAGCTGGGGACAGCAGAGCAGAAGCTGCAGTGCTAGGAAGGGGGGGTTGTGTGTGGGGGGTGAAGGGAGGAGGGAGTACAGCCGCTGCTTGTTTGCCATGGCAACAAGGAGAAGGCTCTGGAGTCAAgggctcacactgcagcagaggaggtgtttaggtgaaatgtaaggggaaatgttttgacaggcggagcggcgagacacaggagccatttcccctgagaaggtggcagaaatggatcagggacttctctggagggAGCAATTAAGGAAGGACTTTAAATCCTTGGGAGATCTTAAAACATTGAGTTCTAAGCCCCTTCCATCCCAGGTTGTGGGCATttagacatcaggaagaacttctcaactggccaggtgttgaaatgctcaaatgaatggttgaggaagactAGACCTCACTTCCATGGGACAGTCACAGATGAGAGGGATCCCAGAGGTCACATTTATCTGCCTCTAAGGAGAAAAAAGGAGCTGGATGAAATGACCTCAGATGAGTCCTGTTGCATAACCTCATCTTGCTAGTCCTCAGTGCCCCAGGATGCAGGAGAGGGACAGTCTTTCCCACTTCTTCCTTTCATCCTGATGATAGCACATACCCCCTATAGGTGACCAAGGCAGTCAAAGCAGGTGACATAGATGCCAAAACTCGGCGGCGGATCTTCGATGCTGTCGGCTTCACCTTCCCCAATCGTCTCCTGACCACCAAGGAGGCGCCGGATGGCTGCCCTGACCATGTTCTGCGGGCTTTGGGTGTGGCCCTGCTGGCCTGCTTCTGCAGTGACCCTGAACTGGCCGCCCATCCCCAAGTCCTGAACAAGATTCCCATTCTTAGCACCTTCCTCACAGCCCGGGGGGACCCGGACGATGCTGCCCGCCGCTCCATGATTGATGACACCTACCAGTGCCTGACGGCTGTAGCAGGCACACCCAGAGGGCCTCGGCACCTCATTGCTGGTGGCACCGTGTCTGCCCTATGCCAGGCATACCTGGGGCACGGCTATGGCTTTGACCAGGCCCTGGCACTCCTGGTGGGGCTGCTGGCTGCTGCCGAGACACAGTGCTGGAAGGAGGCGGAGCCCGACCTGCTGGCCGTGTTGCGGGGCCTCAGTGAGGATTTCCAGAAAGCTGAGGATGCCAGCAAGTTTGAGCTCTGCCAGCTGCTGCCCCTCTTTTTGCCCCCGACAACCGTGCCCCCTGAATGCTACCGGGATCTGCAGGCCGGGCTGGCACGCATCCTGGGAAGCAAGCTGAGCTCCTGGCAGCGCAACCCTGCACTGAAGCTGGCAGCCCGCCTGGCACACGCCTGCGGCTCCGACTGGATCCCGGCGGGCAGCTCCGGGAGCAAGTTCCTGGCCCTGCTGGTGAATCTGGCGTGCGTGGAAGTGCGGCTGGCACTGGAGGAGACGGGCACGGAGGTGAAAGAGGATGTGGTGACCGCCTGCTATGCCCTCATGGAGTTGGGGATCCAGGAATGCACTCGCTGTGAGCAGTCACTGCTTAAGGAGCCACAGAAGGTGCAGCTCGTGAGCGTCATGAAGGAGGCCATAGGGGCTGTTATCCACTACCTGCTGCAGGTGAGGGTGCAGTGACCCACAGAGGGGGCCCAGTATGGGGGGAGCCAGTGCTGGAGCTGGGAGGCAAGGGGGAGGAGAATAATGGGGAGACAGCGAAGCTGCATGTCCACACAAGCTGATACTGTAGCCAGCACTCCAGGGAGTAGTGTGCGGCCCAACCTCCCTCTCTCTCCCTCCCTCCACACAAGCACCATACCACACACCATATGTGCACTCACATCACAGTacacacacacgcacacacacacaacacaGTAACCTCCCACTCAAACGCTCCCCCCAATACACACACACTACACGCCACACACCTCTCCCCAACACATGCACACAAGATTGAAGCAGTCTGTTCTGCTCACTCCATAGCATTGTTTTATACACGCACACACCCGAACTTCTAATGGTGCAGGGAAGAGAAGCAGGGCTGCCTGGTTCCTGGCCTCTATAGAGGTCTGGCTAGATCAATTCGCCTGCCTCCCCTACATCCCCTCCTGCCTCCCCGCCTGAGAGGCCAGCTGTCCTGTCCCACAGGGATTCAGTCATGACTCTGGTCTCTTTAATGGCCTGCTCCAGCCACCGAGCTCACCAGCCATATATTCCATGCACCACGCTAAGCTCATGTCTTTTTTCTGACTTAGCACAAAAGAGAGCATCCCCTCACTCCCACCATTGGGAGCAGTTACACAGTAGCCAGGAACCTGCCCTCCCACCCCAGGTCAGAGCTGCTGTAAAGGGTGTTTAACTTAGCTTTTGACCTATGAATTTCCTTCTAGCCTTGAGACACTCCAGAGGTAGGGAGTTAGGGAGATGTGACTGGAGCCTCAGCGAGTACGGGGGCATGTCACTCAATTCACTCAGGCCCAGTTCACTCAGCAGACGTGTGTGGAGGGCCTGGCTCACTCTGTGCCAGTCCCTTGTGTGCGTCcctaccacatgctaggtgctgggttcatgggacagaataaaggttggggcctgcctttgaaaggctcacaggccagAATTTCCTTCTAGTTGTATTATTTCTAGCTGGCTGGCCTCTGGCAAGGCAGGGAGGGTCCCTGGTCCTGCTCCATCTCAAGGGGGTCCTGTGGCAACAGGTGGGGTCAGAGAAGCAGAAGGAGCCCTTTGTGTTTGCCTCGGTGCGGATCCTGGGTGCCTGGCTGGCCGAGGAGACCTCATCCTTGCGTAAGGAGGTGTGCCAGCTGCTGCCCTTCCTCGTCCGCTATGCCAAGACCCTCTACGAGGAGGCCGAGGAGGCCAATGACCTTTCCCAGCAGGTGGCCAACCTGGCCATCTCCCCCACCACCCCAGGGCCCACCTGGCCAGGAGACGCTCTCCGGTGAGTCTGTAGTTACAGTCTGTCCAGCTAGATCATTCTACCGAAAAGCGTTAACACAAGGACACCCCTCCCCACAAACTGAGCTGTGCCAGGCTTCCTGATTGGGCCATGAGATATCCCTTAGGGTTATTTCTGTTTTGGGGGGCTTGTTCCCACAGGACTCCTCGGCTGCCAGGTGTCACTTGCCAACCCCAGATTTCTCAGTTAAaagagaacttatacttattgagcacctactacgagccaggtattttgctataccctttaccaaaatgatctcatttggtccacgtggtaaatataacagaagtctcattcacatatgaaagattaggaaactgaggctcatagagattaaagtcacttgcccacagtcacactttgtggcagagcccaagtttggtcctgggttgtgcgactctgaagcttgtactttttctgtggtaccTGCGAGGATGTGTCCTTCTCCCCTACTTCCATTTCTCTTAGGCAAGGTGCCCTAAAAAGGGAATCTATGTGCCTTCATCTCTCCCAATCCCACACACGTCTGTCCCTTCCACATCCCCAGGCTCCTCCTGCCTGGCTGGTGCCACCTGACCGTTGAAGATGGGCCCCGGGAGATCCTGATCAAGGAAGGGGCCCCCTCGCTTCTGTGCAAGTATTTCCTGCAGCAGTGGGAACTCACATCCCCTGGCCACGACACCTCGGTGCTGCCTGACAGCGTGGAGATTGGCCTGCAGACCTGCTGCCACATCTTCCTCAACCTCGTGGTCACCGCACCGGGGCTGATCAAGTGAGGGGCTCGGGAGAGGTGGGGGAGGAGGCCGGAGGAGGCAAAGGAGGCTGCCCAGTTGCCTCAATTCTCAGTCTCCTACTTTGCCCCCCATGCCCATGGATTTGTTAGTGGTAGCATGGGGGTCTCAGAGTAGACATAGCCAGCCCCGCACAAGGATTCGGCATGCTGGAACCCCCAGGTACTGTCTCAGCATGTCTGCTTGTTCCAATCTCTGCCCCCCAGATGCTATGTTTGGGGCCCAAAGTTAATCACCCTACTGCCTAATTTCTTGCCAAGGGCTTGATTTGGCTGTACTAGACCCCCACCTACCTCCATCCTTCCCCCCTTTCTTTTCCAGGCGTGACGCCTGCTTCACATCTCTAATGAACACCCTCATGACGTCGCTACCAGCACTAGTGCAGCAACAGGGAAGGCTGCTTCTGGCTGCTAATGTGGCCACCCTGGGGCTCCTCATGGCCCGGCTCCTTAGCACCTCTCCAGGTAAGAACTGGGGATCCAGTCCTGATGGGTGAGGACAGAAGACCTGGGTGGACCTCCTGTGTTTGGGGCAAAAGTCACCATTTTTAGAAGATGGTTTTGCAGCATTTTCTAAGCAAGAGGAAATCTTTGCAGTGTATCTCCATCCCCTACCCCCACCGTTCTTCCCAAAATGCTAACATTCTCTTTCTTCTGAAGACTTTTAAGGCAAAGTCTGGTGGGTGTTAAGTACAGACCTGCTCACAGGCACAGGCATAGGCACCTGGAATCCCTGGCAGCCAGAGGAATCTGAATCCAGTGTTTTCAAGGTGGAGCCGCCCCCACCCAGGCCTTGAGTCAGAAACCTGACTTCCTTCCATTGATGTTTTTCTCTGCTCTGCTCGGTACCTCACCCCCATCAGTGACAGCCTTCAGCACTTGGTGTCCCTCTATGCACACCTTCTCCCTAGCTCTGCCTCACTCTGGCTGTTTGCAGGGGGAGGGACGTCCCCTCCAGCCCCTGGCAGCCCTCCGTGTCTCCCTCTTTGGCTGTGGGTGTCTGCTTGGGTCCCTCTGTCCCTGCCTGTTCCCTGTGCCCCATCTGTCAGGTTGGAGGAGCTGAGCAGATGCCTGGGAACAGGGCGTAACATGCCCGTACCTTCCACTGCCTCTGTGTTCCTTTTGAGGGGTTCCCAGCAGGGTACCCCGTCATGGGAAGGGGTGCACATCCCTGTACACCAGGAGCCCACTCTGCACTCTCAGTCCCAGGCTGCATCTCTGCAGCCCCCAATTTCATGGTCCCAGTTCTGGCTCACCCTCAAATACCACCAGGTTAGGTTGACAGCTTCCTGGAGAGCACCTGCAGTGTGAGGGTCACCCCTTGAACAGCCAGTAAGCAAAGCAGGGTCACTTGCTTATGTTCCTCTCTGGCGCCCTCTTCTGGCCCAAGGATCAAATGGTGCAACTCCCTTAACCTGTGTCTGAGCTCTGTGTCCAGAACCCTGAGGGGTTCTCTCTCCCATCTGACCCTGTGACTCACCCCCACCTCCAGTGCCGGTAGAGGTCTTGGTGGTTGAGTGTACCAAGATGATCAcatttaattctcacaacaaatttctaagatgagcactattggcccattttacaagtaaagaaacagacccagaaaagttaattacccaaggtcacacagtgagcatctaaggcagggtttcaacgcaggcagtctgattccaggctgtgccctGGCTCCTGCATGTGTCTACACAGAGGACTAGGGAAGGGTCTGACACAGCAGCTGGCCTGTCCGATTCATGCCCCACTCCTTCCGTTACCTTGCAGCTCTTCAGGGAACACCAGCATCCCGAGGGTTCTTCGCAGCTGCCATCCTCTTCCTATCACAGTCCCACGTGGCGCGGGCCACCCCGGGCTCAGACCAGGCAGTGCTAGCCCTGTCCCCTGAGTATGAGGGCATCTGGGCCGACCTGCAGGAGCTCTGGTTCCTGGGCATGCAGGCCTTCACCGGCTGTGTGCCTCTGCTGCCCTGGCTGGCCCCCGCTGCCCTGCGCTCCCGCTGGCCGCAGGAGCTGCTCCAGCTGCTAGGCAGTGTCAGCCCCAACTCTGTCAAGCCCGAGATGGTGGCCGCCTATCAGGGTGTCCTGGTGGAGCTGGCGCGGGCCAACCGGCTGTGCCGGGAGGCCATGAGGCTGCAGGCGGGCGAGGAGACGGCCAGCCACTACCGCATGGCTGCCTTGGAGCAGTGCCTGTCAGAGCCCTGAGGGGTGTCCACCGGGGACAGACCCAGGGGCGGGCAGAGAGGGAAGGAGGGAGGAGGCATCTTCCCTGAAGCCCCCAATCTGGCCCCCCCCTCCCCAGACTTCCTCCCCAAAACACCCCAGCTTTCTGGCTTTTCTGAGGGCAAGGGCATGGTGCCCACCCCTCAAGTGTAAGGAACTGCGTTCCGCCCCTCAGGCCCCCATGGGGGCAGGGATCGGCTTGGAAATCAACGTGGTTGTCCCCGCCAGGCCGGGGAAGGTTGGAGCAGCCCCCAGGGAGGGGGGCACTAGGTGTCATTGTGCCCGATGTCTGGCTCCCCTGCAGGAGGGAGGCTCCAGGGTAAGACAGGGCTGGCAGGAGCAGACTGCCTCAGCCCATGTGCCCTGCCGGCCAGGGCGTGGGCTCCCCTCGGCTGTGGTGCCTCCTCTGGCCCCCCAGGTCCACGTCCTTTAAATTGGCCCTTTGGCTCTTGCCCTTGGCTCCCTTGGGCAGACAGCAGGCTTAGGCCATTGATATCGCAGTTCTTCCTATCAGCTTCAGTGACCCAGGGTCTGAACTGCCTCCATCCTAGGGCAACCTGGGGCAGACAGGCCTGGTGGGGGGTGGGGAAACCTCCTTCCACCTGAGCTTGCTTGAAGGGACCCAGAGTCTTTGGGCCCAGATCTTTAAACCTTTGTGTCGTGTTGCAGCAGAGTGACGATGGGGGTTGGGGGGTTATTTATTTTGCCTGTCCTTATCCCTGCTTGGACACCTGAGCATCTGATTCCTGTCCCCCTGGTGCCATCTGGCCTGGCTGGAGCCAGGAACAGGAGGGACACTTCCCCAGAATCCGCATGTTTCCCCAGTGATTACACTCCACTGCCACCGTGGTGCCTGGCTTTAACTCCCACCCCTGCTATGACTCCTCTCTGCAGAGACGCGACTGGCGGCTCCAGCAGGGACTACCTTTCTTATAAACCCAGGGGGACcacacacacacacacacacacacacacacacacacacacacacacacacacTCTTGATCCCTTGCTTCCCTCCCCCAGTGCGTTCTGTGATCGCCAAGTTCAAAGCTGTGCACATGTGGACACTCAATAAATGTTCATTGGTGACGAGAA'); // expect(element.children[1].textContent).toEqual(
-  //   'AGTGGGCAACGCGGCGTGAGCAGCGGCCCGAGGCTCCCGGAGCATCGCGCTGGGAGAAGACTTCGCCGCTCGGGGCCGCAGCCTGGTGAGCTCAGCCCCCTTCGGGCCCTCCCCTGCATCCCAGCCGGGGCCTCTCCGAGCCGGCGCTGATCGATGCCGACACACCCCGGGGACCCTATCGCGACTCCATCGCGCCATATCGCGACACCATCGTGCCCTGTCGAGACTCCATTTTGTCACAGCCCTTTTCAATATATATCTTTTTTTTTTTTAATTTGCCCTGTCATCTTTGGGGGCTGTCTCCCATGTCGTGATTTTGACGTGATCTCTCCGTGACATCACCGCGCCATCGTGAAGTGTGATCTCATCGCCGCCCTGTCGTGACTTCATCA',
-  // )
-  // 3rd is a blank element, so go to 4th, not strictly needed for 3rd to be
-  // blank but helps test
-  // expect(element.children[3].textContent).toEqual(
-  //   'ATGTCGTGTTGTGACCTGGCTGCGGCGGGACAG',
-  // )
-});
-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, {
-    sequence: {
-      seq: seq
-    },
-    mode: "cdna",
-    feature: {
-      start: 1200,
-      end: 1500,
-      type: 'mRNA',
-      subfeatures: [{
-        start: 1200,
-        end: 1500,
-        type: 'exon'
-      }, {
-        start: 1200,
-        end: 1500,
-        type: 'CDS'
-      }]
-    }
-  })),
-      getByTestId = _render4.getByTestId;
-
-  var element = getByTestId('sequence_panel');
-  expect(element.children[0].textContent).toEqual('>unknown-cdna\natgtcacctcgggtactgcctctattacagaggtatcttaatggcgcatccagccttgtggctgggtctacgtacgcgtgggcaccatacgtatgttggcaggaaaggtcaatcatgcttgtttcctcgtcgcagaaacgttcacactattggctcgcgggatcgaacgggcctgattatttttccagctcctgcgttcctatcacgccaactgtcgctaataaaatgttatatagagataacccattgctatgcaaggatggagaaaccgcttcacaacaccctagaattacttcagca');
-});

package/BaseFeatureWidget/index.test.js

@@ -1,69 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _react = _interopRequireDefault(require("react"));
-
-var _react2 = require("@testing-library/react");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configuration = require("../configuration");
-
-var _PluginManager = _interopRequireDefault(require("../PluginManager"));
-
-var _ = require(".");
-
-var _BaseFeatureDetail = _interopRequireDefault(require("./BaseFeatureDetail"));
-
-// locals
-test('open up a widget', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var pluginManager, Session, model, _render, container, findByText;
-
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          console.warn = jest.fn();
-          pluginManager = new _PluginManager.default([]);
-          Session = _mobxStateTree.types.model({
-            pluginManager: _mobxStateTree.types.optional(_mobxStateTree.types.frozen(), {}),
-            rpcManager: _mobxStateTree.types.optional(_mobxStateTree.types.frozen(), {}),
-            configuration: (0, _configuration.ConfigurationSchema)('test', {}),
-            widget: (0, _.stateModelFactory)(pluginManager)
-          });
-          model = Session.create({
-            widget: {
-              type: 'BaseFeatureWidget'
-            }
-          });
-          _render = (0, _react2.render)( /*#__PURE__*/_react.default.createElement(_BaseFeatureDetail.default, {
-            model: model.widget
-          })), container = _render.container, findByText = _render.findByText;
-          model.widget.setFeatureData({
-            start: 2,
-            end: 102,
-            strand: 1,
-            score: 37,
-            refName: 'ctgA'
-          });
-          _context.t0 = expect;
-          _context.next = 9;
-          return findByText('ctgA:3..102 (+)');
-
-        case 9:
-          _context.t1 = _context.sent;
-          (0, _context.t0)(_context.t1).toBeTruthy();
-          expect(container.firstChild).toMatchSnapshot();
-
-        case 12:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/TextSearch/BaseResults.test.js

@@ -1,42 +0,0 @@
-"use strict";
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-var _BaseResults = _interopRequireWildcard(require("./BaseResults"));
-
-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; }
-
-test('create BaseResult', function () {
-  var baseResult = new _BaseResults.default({
-    label: 'chr1'
-  });
-  expect(baseResult.getLabel()).toEqual('chr1');
-  expect(baseResult.getLocation()).toEqual('chr1');
-});
-test('create LocationResult', function () {
-  var locationResult = new _BaseResults.default({
-    label: 'location result',
-    locString: 'chr1:1-900'
-  });
-  expect(locationResult.getLabel()).toEqual('location result');
-  expect(locationResult.getLocation()).toEqual('chr1:1-900');
-});
-test('create RefSequenceResult', function () {
-  var refSeqResult = new _BaseResults.RefSequenceResult({
-    refName: 'chr1',
-    label: 'chromosome 1'
-  });
-  expect(refSeqResult.getLabel()).toEqual('chromosome 1');
-  expect(refSeqResult.getLocation()).toEqual('chr1');
-});
-test('can update score of result and throw appropriate errors', function () {
-  var refSeqResult = new _BaseResults.RefSequenceResult({
-    refName: 'chr1',
-    label: 'chromosome 1'
-  });
-  expect(refSeqResult.getScore()).toBe(1);
-  refSeqResult.updateScore(1000);
-  expect(refSeqResult.getScore()).toBe(1000);
-});