@jbrowse/plugin-sequence 1.4.4 → 1.5.3

package/dist/plugin-sequence.esm.js

@@ -4,6 +4,7 @@ import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/F
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 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 { contrastingTextColor } from '@jbrowse/core/util/color';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
@@ -187,6 +188,8 @@ function _assertThisInitialized(self) {
 function _possibleConstructorReturn(self, call) {
   if (call && (typeof call === "object" || typeof call === "function")) {
     return call;
+  } else if (call !== void 0) {
+    throw new TypeError("Derived constructors may only return object or undefined");
   }
 
   return _assertThisInitialized(self);
@@ -290,19 +293,22 @@ var bgzipFastaAdapterConfigSchema = /*#__PURE__*/ConfigurationSchema('BgzipFasta
   fastaLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/seq.fa.gz'
+      uri: '/path/to/seq.fa.gz',
+      locationType: 'UriLocation'
     }
   },
   faiLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/seq.fa.gz.fai'
+      uri: '/path/to/seq.fa.gz.fai',
+      locationType: 'UriLocation'
     }
   },
   gziLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/seq.fa.gz.gzi'
+      uri: '/path/to/seq.fa.gz.gzi',
+      locationType: 'UriLocation'
     }
   }
 }, {
@@ -313,7 +319,8 @@ var chromSizesAdapterConfigSchema = /*#__PURE__*/ConfigurationSchema('ChromSizes
   chromSizesLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/species.chrom.sizes'
+      uri: '/path/to/species.chrom.sizes',
+      locationType: 'UriLocation'
     }
   }
 }, {
@@ -545,13 +552,15 @@ var indexedFastaAdapterConfigSchema = /*#__PURE__*/ConfigurationSchema('IndexedF
   fastaLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/seq.fa'
+      uri: '/path/to/seq.fa',
+      locationType: 'UriLocation'
     }
   },
   faiLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/seq.fa.fai'
+      uri: '/path/to/seq.fa.fai',
+      locationType: 'UriLocation'
     }
   }
 }, {
@@ -588,9 +597,7 @@ function modelFactory(configSchema) {
           showTranslation: showTranslation
         });
       },
-      regionCannotBeRendered: function regionCannotBeRendered()
-      /* region */
-      {
+      regionCannotBeRendered: function regionCannotBeRendered() {
         var view = getContainingView(self);
 
         if (view && view.bpPerPx >= 1) {
@@ -651,13 +658,15 @@ var twoBitAdapterConfigSchema = /*#__PURE__*/ConfigurationSchema('TwoBitAdapter'
   twoBitLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/my.2bit'
+      uri: '/path/to/my.2bit',
+      locationType: 'UriLocation'
     }
   },
   chromSizesLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/default.chrom.sizes'
+      uri: '/path/to/default.chrom.sizes',
+      locationType: 'UriLocation'
     },
     description: 'An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time'
   }
@@ -807,6 +816,12 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
         return new AdapterType({
           name: 'TwoBitAdapter',
           configSchema: twoBitAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return TwoBitAdapter$1; }).then(function (r) {
               return r["default"];
@@ -814,10 +829,41 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.2bit$/i;
+          var adapterName = 'TwoBitAdapter';
+          var fileName = getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              twoBitLocation: file
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'TwoBitAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'ChromSizesAdapter',
           configSchema: chromSizesAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return ChromSizesAdapter; }).then(function (r) {
               return r["default"];
@@ -829,6 +875,12 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
         return new AdapterType({
           name: 'IndexedFastaAdapter',
           configSchema: indexedFastaAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return IndexedFastaAdapter; }).then(function (r) {
               return r["default"];
@@ -836,10 +888,42 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i;
+          var adapterName = 'IndexedFastaAdapter';
+          var fileName = getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              fastaLocation: file,
+              faiLocation: index || makeIndex(file, '.fai')
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'IndexedFastaAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'BgzipFastaAdapter',
           configSchema: bgzipFastaAdapterConfigSchema,
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          },
           getAdapterClass: function getAdapterClass() {
             return Promise.resolve().then(function () { return BgzipFastaAdapter; }).then(function (r) {
               return r["default"];
@@ -847,9 +931,41 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i;
+          var adapterName = 'BgzipFastaAdapter';
+          var fileName = getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              faiLocation: makeIndex(file, '.fai'),
+              gziLocation: makeIndex(file, '.gzi')
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'BgzipFastaAdapter') {
+            return 'ReferenceSequenceTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType(_objectSpread2({
-          name: 'GCContentAdapter'
+          name: 'GCContentAdapter',
+          adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null
+          }
         }, pluginManager.load(GCContentAdapterF)));
       });
       pluginManager.addTrackType(function () {
@@ -982,11 +1098,9 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
 
 
     var IteratorPrototype = {};
-
-    IteratorPrototype[iteratorSymbol] = function () {
+    define(IteratorPrototype, iteratorSymbol, function () {
       return this;
-    };
-
+    });
     var getProto = Object.getPrototypeOf;
     var NativeIteratorPrototype = getProto && getProto(getProto(values([])));
 
@@ -997,8 +1111,9 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
     }
 
     var Gp = GeneratorFunctionPrototype.prototype = Generator.prototype = Object.create(IteratorPrototype);
-    GeneratorFunction.prototype = Gp.constructor = GeneratorFunctionPrototype;
-    GeneratorFunctionPrototype.constructor = GeneratorFunction;
+    GeneratorFunction.prototype = GeneratorFunctionPrototype;
+    define(Gp, "constructor", GeneratorFunctionPrototype);
+    define(GeneratorFunctionPrototype, "constructor", GeneratorFunction);
     GeneratorFunction.displayName = define(GeneratorFunctionPrototype, toStringTagSymbol, "GeneratorFunction"); // Helper for defining the .next, .throw, and .return methods of the
     // Iterator interface in terms of a single ._invoke method.
 
@@ -1103,11 +1218,9 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
     }
 
     defineIteratorMethods(AsyncIterator.prototype);
-
-    AsyncIterator.prototype[asyncIteratorSymbol] = function () {
+    define(AsyncIterator.prototype, asyncIteratorSymbol, function () {
       return this;
-    };
-
+    });
     exports.AsyncIterator = AsyncIterator; // Note that simple async functions are implemented on top of
     // AsyncIterator objects; they just return a Promise for the value of
     // the final result produced by the iterator.
@@ -1284,13 +1397,12 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
     // object to not be returned from this call. This ensures that doesn't happen.
     // See https://github.com/facebook/regenerator/issues/274 for more details.
 
-    Gp[iteratorSymbol] = function () {
+    define(Gp, iteratorSymbol, function () {
       return this;
-    };
-
-    Gp.toString = function () {
+    });
+    define(Gp, "toString", function () {
       return "[object Generator]";
-    };
+    });
 
     function pushTryEntry(locs) {
       var entry = {
@@ -1602,14 +1714,19 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
   } catch (accidentalStrictMode) {
     // This module should not be running in strict mode, so the above
     // assignment should always work unless something is misconfigured. Just
-    // in case runtime.js accidentally runs in strict mode, we can escape
+    // in case runtime.js accidentally runs in strict mode, in modern engines
+    // we can explicitly access globalThis. In older engines we can escape
     // strict mode using a global Function call. This could conceivably fail
     // if a Content Security Policy forbids using Function, but in that case
     // the proper solution is to fix the accidental strict mode problem. If
     // you've misconfigured your bundler to force strict mode and applied a
     // CSP to forbid Function, and you're not willing to fix either of those
     // problems, please detail your unique predicament in a GitHub issue.
-    Function("r", "regeneratorRuntime = r")(runtime);
+    if (typeof globalThis === "object") {
+      globalThis.regeneratorRuntime = runtime;
+    } else {
+      Function("r", "regeneratorRuntime = r")(runtime);
+    }
   }
 });
 
@@ -1818,9 +1935,9 @@ var default_1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   }, {
     key: "freeResources",
-    value: function freeResources()
-    /* { region } */
-    {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return default_1;
@@ -1837,15 +1954,15 @@ var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   var _super = /*#__PURE__*/_createSuper(TwoBitAdapter);
 
-  function TwoBitAdapter(config) {
+  function TwoBitAdapter(config, getSubAdapter, pluginManager) {
     var _this;
 
     _classCallCheck(this, TwoBitAdapter);
 
-    _this = _super.call(this, config);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
     _this.chromSizesData = _this.initChromSizes();
     _this.twobit = new TwoBitFile({
-      filehandle: openLocation(readConfObject(config, 'twoBitLocation'))
+      filehandle: openLocation(readConfObject(config, 'twoBitLocation'), _this.pluginManager)
     });
     return _this;
   }
@@ -1868,7 +1985,7 @@ var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   break;
                 }
 
-                file = openLocation(conf);
+                file = openLocation(conf, this.pluginManager);
                 _context.next = 5;
                 return file.readFile('utf8');
 
@@ -2065,9 +2182,9 @@ var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   }, {
     key: "freeResources",
-    value: function freeResources()
-    /* { region } */
-    {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return TwoBitAdapter;
@@ -2083,19 +2200,19 @@ var _default = /*#__PURE__*/function (_BaseAdapter) {
 
   var _super = /*#__PURE__*/_createSuper(_default);
 
-  function _default(config) {
+  function _default(config, getSubAdapter, pluginManager) {
     var _this;
 
     _classCallCheck(this, _default);
 
-    _this = _super.call(this, config);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
     var chromSizesLocation = readConfObject(config, 'chromSizesLocation');
 
     if (!chromSizesLocation) {
       throw new Error('must provide chromSizesLocation');
     }
 
-    var file = openLocation(chromSizesLocation);
+    var file = openLocation(chromSizesLocation, _this.pluginManager);
     _this.source = file.toString();
     _this.refSeqs = _this.init(file);
     return _this;
@@ -2194,9 +2311,9 @@ var _default = /*#__PURE__*/function (_BaseAdapter) {
     }
   }, {
     key: "freeResources",
-    value: function freeResources()
-    /* { region } */
-    {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return _default;
@@ -2212,12 +2329,12 @@ var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   var _super = /*#__PURE__*/_createSuper(_default);
 
-  function _default(config) {
+  function _default(config, getSubAdapter, pluginManager) {
     var _this;
 
     _classCallCheck(this, _default);
 
-    _this = _super.call(this, config);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
     _this.seqCache = new AbortablePromiseCache({
       cache: new LRU({
         maxSize: 200
@@ -2252,8 +2369,8 @@ var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     var fastaLocation = readConfObject(config, 'fastaLocation');
     var faiLocation = readConfObject(config, 'faiLocation');
     var fastaOpts = {
-      fasta: openLocation(fastaLocation),
-      fai: openLocation(faiLocation)
+      fasta: openLocation(fastaLocation, _this.pluginManager),
+      fai: openLocation(faiLocation, _this.pluginManager)
     };
     _this.fasta = new IndexedFasta(fastaOpts);
     return _this;
@@ -2382,9 +2499,9 @@ var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   }, {
     key: "freeResources",
-    value: function freeResources()
-    /* { region } */
-    {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return _default;
@@ -2400,12 +2517,12 @@ var _default$2 = /*#__PURE__*/function (_IndexedFasta) {
 
   var _super = /*#__PURE__*/_createSuper(_default);
 
-  function _default(config) {
+  function _default(config, getSubAdapter, pluginManager) {
     var _this;
 
     _classCallCheck(this, _default);
 
-    _this = _super.call(this, config);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
     var fastaLocation = readConfObject(config, 'fastaLocation');
     var faiLocation = readConfObject(config, 'faiLocation');
     var gziLocation = readConfObject(config, 'gziLocation');
@@ -2423,9 +2540,9 @@ var _default$2 = /*#__PURE__*/function (_IndexedFasta) {
     }
 
     var fastaOpts = {
-      fasta: openLocation(fastaLocation),
-      fai: openLocation(faiLocation),
-      gzi: openLocation(gziLocation)
+      fasta: openLocation(fastaLocation, _this.pluginManager),
+      fai: openLocation(faiLocation, _this.pluginManager),
+      gzi: openLocation(gziLocation, _this.pluginManager)
     };
     _this.fasta = new BgzipIndexedFasta(fastaOpts);
     return _this;