@jbrowse/plugin-sequence 1.5.8 → 1.6.2

package/dist/plugin-sequence.esm.js

@@ -6,13 +6,13 @@ import Plugin from '@jbrowse/core/Plugin';
 import { BaseLinearDisplay, BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import { getFileName, makeIndex } from '@jbrowse/core/util/tracks';
 import { ConfigurationSchema, ConfigurationReference, readConfObject } from '@jbrowse/core/configuration';
+import React from 'react';
 import { contrastingTextColor } from '@jbrowse/core/util/color';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
-import React from 'react';
 import { generateCodonTable, defaultCodonTable, complement, revcom, defaultStarts, defaultStops, bpSpanPx, getContainingView } from '@jbrowse/core/util';
 import { types } from 'mobx-state-tree';
-import { BaseFeatureDataAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseFeatureDataAdapter, BaseSequenceAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { toArray } from 'rxjs/operators';
@@ -129,14 +129,14 @@ function _inherits(subClass, superClass) {
     throw new TypeError("Super expression must either be null or a function");
   }
 
+  subClass.prototype = Object.create(superClass && superClass.prototype, {
+    constructor: {
+      value: subClass,
+      writable: true,
+      configurable: true
+    }
+  });
   Object.defineProperty(subClass, "prototype", {
-    value: Object.create(superClass && superClass.prototype, {
-      constructor: {
-        value: subClass,
-        writable: true,
-        configurable: true
-      }
-    }),
     writable: false
   });
   if (superClass) _setPrototypeOf(subClass, superClass);
@@ -506,6 +506,7 @@ var Wrapper = function Wrapper(_ref3) {
       totalHeight = _ref3.totalHeight,
       children = _ref3.children;
   return exportSVG ? React.createElement(React.Fragment, null, children) : React.createElement("svg", {
+    "data-testid": "sequence_track",
     width: width,
     height: totalHeight,
     style: {
@@ -828,12 +829,15 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           var regexGuess = /\.2bit$/i;
           var adapterName = 'TwoBitAdapter';
           var fileName = getFileName(file);
+          var obj = {
+            type: adapterName,
+            twoBitLocation: file
+          };
 
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              twoBitLocation: file
-            };
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
           }
 
           return adapterGuesser(file, index, adapterHint);
@@ -887,13 +891,16 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           var regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i;
           var adapterName = 'IndexedFastaAdapter';
           var fileName = getFileName(file);
+          var obj = {
+            type: adapterName,
+            fastaLocation: file,
+            faiLocation: index || makeIndex(file, '.fai')
+          };
 
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              fastaLocation: file,
-              faiLocation: index || makeIndex(file, '.fai')
-            };
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
           }
 
           return adapterGuesser(file, index, adapterHint);
@@ -930,13 +937,16 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           var regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i;
           var adapterName = 'BgzipFastaAdapter';
           var fileName = getFileName(file);
+          var obj = {
+            type: adapterName,
+            faiLocation: makeIndex(file, '.fai'),
+            gziLocation: makeIndex(file, '.gzi')
+          };
 
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              faiLocation: makeIndex(file, '.fai'),
-              gziLocation: makeIndex(file, '.gzi')
-            };
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
           }
 
           return adapterGuesser(file, index, adapterHint);
@@ -1830,8 +1840,9 @@ var default_1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
       this.gcMode = 'content';
       return ObservableCreate( /*#__PURE__*/function () {
         var _ref = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3(observer) {
-          var sequenceAdapter, hw, f, queryStart, queryEnd, ret, _yield$ret$pipe$toPro, _yield$ret$pipe$toPro2, feat, residues, i, r, nc, ng, len, j, pos, score;
+          var _feats$;
 
+          var sequenceAdapter, hw, f, queryStart, queryEnd, ret, feats, residues, i, r, nc, ng, len, j, pos, score;
           return runtime_1.wrap(function _callee3$(_context3) {
             while (1) {
               switch (_context3.prev = _context3.next) {
@@ -1860,15 +1871,13 @@ var default_1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   ret = sequenceAdapter.getFeatures(_objectSpread2(_objectSpread2({}, query), {}, {
                     start: queryStart,
                     end: queryEnd
-                  }), opts);
+                  }));
                   _context3.next = 14;
                   return ret.pipe(toArray()).toPromise();
 
                 case 14:
-                  _yield$ret$pipe$toPro = _context3.sent;
-                  _yield$ret$pipe$toPro2 = _slicedToArray(_yield$ret$pipe$toPro, 1);
-                  feat = _yield$ret$pipe$toPro2[0];
-                  residues = feat.get('seq');
+                  feats = _context3.sent;
+                  residues = ((_feats$ = feats[0]) === null || _feats$ === void 0 ? void 0 : _feats$.get('seq')) || '';
 
                   for (i = hw; i < residues.length - hw; i += _this2.windowDelta) {
                     r = f ? residues[i] : residues.slice(i - hw, i + hw);
@@ -1895,20 +1904,19 @@ var default_1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                       score = (ng + nc) / (len || 1);
                     } else if (_this2.gcMode === 'skew') {
                       score = (ng - nc) / (ng + nc || 1);
-                    } // if (r[Math.floor(r.length / 2)] !== 'N') {
-
+                    }
 
                     observer.next(new SimpleFeature({
                       uniqueId: "".concat(_this2.id, "_").concat(pos + i),
                       start: pos + i,
                       end: pos + i + _this2.windowDelta,
                       score: score
-                    })); // }
+                    }));
                   }
 
                   observer.complete();
 
-                case 20:
+                case 18:
                 case "end":
                   return _context3.stop();
               }
@@ -1943,8 +1951,8 @@ var GCContentAdapter = {
   'default': default_1
 };
 
-var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  _inherits(TwoBitAdapter, _BaseFeatureDataAdapt);
+var TwoBitAdapter = /*#__PURE__*/function (_BaseSequenceAdapter) {
+  _inherits(TwoBitAdapter, _BaseSequenceAdapter);
 
   var _super = /*#__PURE__*/_createSuper(TwoBitAdapter);
 
@@ -2182,7 +2190,7 @@ var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }]);
 
   return TwoBitAdapter;
-}(BaseFeatureDataAdapter);
+}(BaseSequenceAdapter);
 
 var TwoBitAdapter$1 = {
   __proto__: null,
@@ -2318,8 +2326,8 @@ var ChromSizesAdapter = {
   'default': _default
 };
 
-var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  _inherits(_default, _BaseFeatureDataAdapt);
+var _default$1 = /*#__PURE__*/function (_BaseSequenceAdapter) {
+  _inherits(_default, _BaseSequenceAdapter);
 
   var _super = /*#__PURE__*/_createSuper(_default);
 
@@ -2499,7 +2507,7 @@ var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }]);
 
   return _default;
-}(BaseFeatureDataAdapter);
+}(BaseSequenceAdapter);
 
 var IndexedFastaAdapter = {
   __proto__: null,