@jbrowse/plugin-legacy-jbrowse 1.5.8 → 1.6.2

package/dist/plugin-legacy-jbrowse.cjs.development.js

@@ -189,14 +189,14 @@ 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);

package/dist/plugin-legacy-jbrowse.cjs.production.min.js

@@ -1,2 +1,2 @@
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pe={tracks:[],containerID:"GenomeBrowser",dataRoot:"data",show_tracklist:!0,show_nav:!0,show_menu:!0,show_overview:!0,show_fullviewlink:!0,update_browser_title:!0,updateBrowserURL:!0,refSeqs:"{dataRoot}/seq/refSeqs.json",include:["jbrowse.conf","jbrowse_conf.json"],nameUrl:"{dataRoot}/names/root.json",datasets:{_DEFAULT_EXAMPLES:!0,volvox:{url:"?data=sample_data/json/volvox",name:"Volvox Example"},modencode:{url:"?data=sample_data/json/modencode",name:"MODEncode Example"},yeast:{url:"?data=sample_data/json/yeast",name:"Yeast Example"}},highlightSearchedRegions:!1,highResolutionMode:"auto"};function he(e){if(e.tracks||(e.tracks=[]),!e.baseUrl)throw new Error("Must provide a `baseUrl` in configuration")}function de(e){return p.types.compose("JBrowse1Connection",f.BaseConnectionModelFactory(e),p.types.model({configuration:o.ConfigurationReference(V),type:p.types.literal("JBrowse1Connection")}).actions((function(e){return{connect:function(){var 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r=(e.features||[]).map((function(e){var t=JSON.parse(JSON.stringify(e));return t.refName=e.seq_id,t.uniqueId="".concat(e.seq_id,":").concat(e.start,"-").concat(e.end,":").concat(e.name||""),t}));return t.adapter={type:"FromConfigAdapter",features:r},t.type="FeatureTrack",t}(e,n)}var s=function(e){return new URL(e,"".concat(t,"/")).href.replace(/%7B/gi,"{").replace(/%7D/gi,"}")},f=s(e.urlTemplate);if(i){if("JBrowse/Store/SeqFeature/BAM"===i){var p={type:"BamAdapter",bamLocation:{uri:f,locationType:"UriLocation"}};return p.index=e.baiUrlTemplate?{location:{uri:s(e.baiUrlTemplate),locationType:"UriLocation"}}:e.csiUrlTemplate?{location:{uri:s(e.csiUrlTemplate),locationType:"UriLocation"},indexType:"CSI"}:{location:{uri:"".concat(f,".bai"),locationType:"UriLocation"}},x(x({},n),{},{type:"AlignmentsTrack",adapter:p})}if("JBrowse/Store/SeqFeature/CRAM"===i){var h={type:"CramAdapter",cramLocation:{uri:f,locationType:"UriLocation"},sequenceAdapter:r};return h.craiLocation=e.craiUrlTemplate?{uri:s(e.craiUrlTemplate),locationType:"UriLocation"}:{uri:"".concat(f,".crai"),locationType:"UriLocation"},x(x({},n),{},{type:"AlignmentsTrack",adapter:h})}if("JBrowse/Store/SeqFeature/NCList"===i)return x(x({},n),{},{type:"FeatureTrack",adapter:{type:"NCListAdapter",rootUrlTemplate:{uri:f,locationType:"UriLocation"}}});if("JBrowse/Store/SeqFeature/BigWig"===i||"JBrowse/Store/BigWig"===i)return e.type&&e.type.endsWith("XYPlot")?n.defaultRendering="xyplot":e.type&&e.type.endsWith("Density")&&(n.defaultRendering="density"),x(x({},n),{},{type:"QuantitativeTrack",adapter:{type:"BigWigAdapter",bigWigLocation:{uri:f,locationType:"UriLocation"}}});if("JBrowse/Store/SeqFeature/VCFTabix"===i){var d={type:"VcfTabixAdapter",vcfGzLocation:{uri:f,locationType:"UriLocation"}};return d.index=e.tbiUrlTemplate?{location:{uri:s(e.tbiUrlTemplate),locationType:"UriLocation"}}:e.csiUrlTemplate?{location:{uri:s(e.csiUrlTemplate),locationType:"UriLocation"},indexType:"CSI"}:{location:{uri:"".concat(f,".tbi"),locationType:"UriLocation"}},x(x({},n),{},{type:"VariantTrack",adapter:d})}if("JBrowse/Store/SeqFeature/VCFTribble"===i)return u.generateUnsupportedTrackConf(n.name,"VCFTribble (".concat(f,")"),n.category);if("JBrowse/Store/SeqFeature/GFF3"===i)return u.generateUnsupportedTrackConf(n.name,"GFF3 (".concat(f,")"),n.category);if("JBrowse/Store/SeqFeature/BigBed"===i)return x(x({},n),{},{type:"FeatureTrack",adapter:{type:"BigBedAdapter",bigBedLocation:{uri:f,locationType:"UriLocation"}}});if("JBrowse/Store/SeqFeature/GFF3Tabix"===i){var y={type:"Gff3TabixAdapter",gffGzLocation:{uri:f,locationType:"UriLocation"}};return 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b.faiLocation=e.faiUrlTemplate?{uri:s(e.faiUrlTemplate),locationType:"UriLocation"}:{uri:"".concat(f,".fai"),locationType:"UriLocation"},b.gziLocation=e.gziUrlTemplate?{uri:s(e.gziUrlTemplate),locationType:"UriLocation"}:{uri:"".concat(f,".gzi"),locationType:"UriLocation"},x(x({},n),{},{type:"ReferenceSequenceTrack",adapter:b})}if("JBrowse/Store/SeqFeature/TwoBit"===i)return x(x({},n),{},{type:"ReferenceSequenceTrack",adapter:{type:"TwoBitAdapter",twoBitLocation:{uri:f,locationType:"UriLocation"}}})}if(n.adapter=u.guessAdapter({uri:f,locationType:"UriLocation"},void 0,f),!n.adapter)throw new Error("Could not determine adapter");return 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pe={tracks:[],containerID:"GenomeBrowser",dataRoot:"data",show_tracklist:!0,show_nav:!0,show_menu:!0,show_overview:!0,show_fullviewlink:!0,update_browser_title:!0,updateBrowserURL:!0,refSeqs:"{dataRoot}/seq/refSeqs.json",include:["jbrowse.conf","jbrowse_conf.json"],nameUrl:"{dataRoot}/names/root.json",datasets:{_DEFAULT_EXAMPLES:!0,volvox:{url:"?data=sample_data/json/volvox",name:"Volvox Example"},modencode:{url:"?data=sample_data/json/modencode",name:"MODEncode Example"},yeast:{url:"?data=sample_data/json/yeast",name:"Yeast Example"}},highlightSearchedRegions:!1,highResolutionMode:"auto"};function he(e){if(e.tracks||(e.tracks=[]),!e.baseUrl)throw new Error("Must provide a `baseUrl` in configuration")}function de(e){return p.types.compose("JBrowse1Connection",f.BaseConnectionModelFactory(e),p.types.model({configuration:o.ConfigurationReference(V),type:p.types.literal("JBrowse1Connection")}).actions((function(e){return{connect:function(){var 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h.craiLocation=e.craiUrlTemplate?{uri:s(e.craiUrlTemplate),locationType:"UriLocation"}:{uri:"".concat(f,".crai"),locationType:"UriLocation"},x(x({},n),{},{type:"AlignmentsTrack",adapter:h})}if("JBrowse/Store/SeqFeature/NCList"===i)return x(x({},n),{},{type:"FeatureTrack",adapter:{type:"NCListAdapter",rootUrlTemplate:{uri:f,locationType:"UriLocation"}}});if("JBrowse/Store/SeqFeature/BigWig"===i||"JBrowse/Store/BigWig"===i)return e.type&&e.type.endsWith("XYPlot")?n.defaultRendering="xyplot":e.type&&e.type.endsWith("Density")&&(n.defaultRendering="density"),x(x({},n),{},{type:"QuantitativeTrack",adapter:{type:"BigWigAdapter",bigWigLocation:{uri:f,locationType:"UriLocation"}}});if("JBrowse/Store/SeqFeature/VCFTabix"===i){var d={type:"VcfTabixAdapter",vcfGzLocation:{uri:f,locationType:"UriLocation"}};return d.index=e.tbiUrlTemplate?{location:{uri:s(e.tbiUrlTemplate),locationType:"UriLocation"}}:e.csiUrlTemplate?{location:{uri:s(e.csiUrlTemplate),locationType:"UriLocation"},indexType:"CSI"}:{location:{uri:"".concat(f,".tbi"),locationType:"UriLocation"}},x(x({},n),{},{type:"VariantTrack",adapter:d})}if("JBrowse/Store/SeqFeature/VCFTribble"===i)return u.generateUnsupportedTrackConf(n.name,"VCFTribble (".concat(f,")"),n.category);if("JBrowse/Store/SeqFeature/GFF3"===i)return u.generateUnsupportedTrackConf(n.name,"GFF3 (".concat(f,")"),n.category);if("JBrowse/Store/SeqFeature/BigBed"===i)return x(x({},n),{},{type:"FeatureTrack",adapter:{type:"BigBedAdapter",bigBedLocation:{uri:f,locationType:"UriLocation"}}});if("JBrowse/Store/SeqFeature/GFF3Tabix"===i){var y={type:"Gff3TabixAdapter",gffGzLocation:{uri:f,locationType:"UriLocation"}};return y.index=e.tbiUrlTemplate?{location:{uri:s(e.tbiUrlTemplate),locationType:"UriLocation"}}:e.csiUrlTemplate?{location:{uri:s(e.csiUrlTemplate),locationType:"UriLocation"},indexType:"CSI"}:{location:{uri:"".concat(f,".tbi"),locationType:"UriLocation"}},x(x({},n),{},{type:"FeatureTrack",adapter:y})}if("JBrowse/Store/SeqFeature/BED"===i)return u.generateUnsupportedTrackConf(n.name,"BED (".concat(f,")"),n.category);if("JBrowse/Store/SeqFeature/BEDTabix"===i){var m={type:"BedTabixAdapter",bedGzLocation:{uri:f,locationType:"UriLocation"}};return m.index=e.tbiUrlTemplate?{location:{uri:s(e.tbiUrlTemplate),locationType:"UriLocation"}}:e.csiUrlTemplate?{location:{uri:s(e.csiUrlTemplate),locationType:"UriLocation"},indexType:"CSI"}:{location:{uri:"".concat(f,".tbi"),locationType:"UriLocation"}},x(x({},n),{},{type:"FeatureTrack",adapter:m})}if("JBrowse/Store/SeqFeature/GTF"===i)return u.generateUnsupportedTrackConf(n.name,"GTF (".concat(f,")"),n.category);if("JBrowse/Store/SeqFeature/StaticChunked"===i||"JBrowse/Store/Sequence/StaticChunked"===i)return u.generateUnsupportedTrackConf(n.name,"StaticChunked (".concat(f,")"),n.category);if("JBrowse/Store/SeqFeature/UnindexedFasta"===i)return u.generateUnsupportedTrackConf(n.name,"UnindexedFasta (".concat(f,")"),n.category);if("JBrowse/Store/SeqFeature/IndexedFasta"===i){var v={type:"IndexedFastaAdapter",fastaLocation:{uri:f,locationType:"UriLocation"}};return v.faiLocation=e.faiUrlTemplate?{uri:s(e.faiUrlTemplate),locationType:"UriLocation"}:{uri:"".concat(f,".fai"),locationType:"UriLocation"},x(x({},n),{},{type:"SequenceTrack",adapter:v})}if("JBrowse/Store/SeqFeature/BgzipIndexedFasta"===i){var b={type:"BgzipFastaAdapter",fastaLocation:{uri:f,locationType:"UriLocation"}};return b.faiLocation=e.faiUrlTemplate?{uri:s(e.faiUrlTemplate),locationType:"UriLocation"}:{uri:"".concat(f,".fai"),locationType:"UriLocation"},b.gziLocation=e.gziUrlTemplate?{uri:s(e.gziUrlTemplate),locationType:"UriLocation"}:{uri:"".concat(f,".gzi"),locationType:"UriLocation"},x(x({},n),{},{type:"ReferenceSequenceTrack",adapter:b})}if("JBrowse/Store/SeqFeature/TwoBit"===i)return x(x({},n),{},{type:"ReferenceSequenceTrack",adapter:{type:"TwoBitAdapter",twoBitLocation:{uri:f,locationType:"UriLocation"}}})}if(n.adapter=u.guessAdapter({uri:f,locationType:"UriLocation"},void 0,f),!n.adapter)throw new Error("Could not determine adapter");return n.adapter.type===u.UNSUPPORTED?u.generateUnsupportedTrackConf(n.name,f,n.category):n.adapter.type===u.UNKNOWN?u.generateUnknownTrackConf(n.name,f,n.category):(n.type=u.guessTrackType(n.adapter.type),"QuantitativeTrack"===n.type&&(e.type&&e.type.endsWith("XYPlot")?n.defaultRendering="xyplot":e.type&&e.type.endsWith("Density")&&(n.defaultRendering="density")),n)}(e,t.dataRoot,i);return r.assemblyNames=[n],r}));e.setTrackConfs(c)})).catch((function(t){console.error(t),r.notify('There was a problem connecting to the JBrowse 1 data directory "'.concat(e.name,'". Please make sure you have entered a valid location. The error that was thrown is: "').concat(t,'"'),"error"),r.breakConnection(e.configuration)}))}}})))}var ye=function(e){q(i,a);var o=O(i);function i(){var e;return L(this,i),(e=o.apply(this,arguments)).name="LegacyJBrowsePlugin",e}return B(i,[{key:"install",value:function(e){e.addAdapterType((function(){return new t({name:"NCListAdapter",configSchema:_,getAdapterClass:function(){return Promise.resolve().then((function(){return ge})).then((function(e){return e.default}))}})})),e.addToExtensionPoint("Core-guessAdapterForLocation",(function(e){return function(t,r,n){var a=u.getFileName(t);return/trackData.jsonz?$/i.test(a)||"NCListAdapter"===n?{type:"NCListAdapter",rootUrlTemplate:t}:e(t,r,n)}})),e.addTextSearchAdapterType((function(){return new r({name:"JBrowse1TextSearchAdapter",configSchema:M,AdapterClass:D,description:"A JBrowse 1 text search adapter"})})),e.addConnectionType((function(){return new n({name:"JBrowse1Connection",configSchema:V,stateModel:de(e),displayName:"JBrowse 1 Data",description:"A JBrowse 1 data directory",url:"//jbrowse.org/"})}))}}]),i}(),me={refName:"seq_id"},ve={seq_id:"refName"},be=function(){function e(t,r,n){L(this,e),this.ncFeature=t,this.uniqueId=n||t.id(),this.parentHandle=r}return B(e,[{key:"set",value:function(){throw new Error("not implemented")}},{key:"jb2TagToJb1Tag",value:function(e){return(me[e]||e).toLowerCase()}},{key:"jb1TagToJb2Tag",value:function(e){var t=e.toLowerCase();return ve[t]||t}},{key:"get",value:function(t){var r=this,n=this.ncFeature.get(this.jb2TagToJb1Tag(t));return n&&"subfeatures"===t?n.map((function(t){return new e(t,r)})):n}},{key:"tags",value:function(){var e=this;return this.ncFeature.tags().map((function(t){return e.jb1TagToJb2Tag(t)}))}},{key:"id",value:function(){return this.uniqueId}},{key:"parent",value:function(){return this.parentHandle}},{key:"children",value:function(){return this.get("subfeatures")}},{key:"toJSON",value:function(){var t=this,r={uniqueId:this.id()};return this.ncFeature.tags().forEach((function(n){var a=t.jb1TagToJb2Tag(n),o=t.ncFeature.get(n);"subfeatures"===a?r.subfeatures=(o||[]).map((function(r){return new e(r,t).toJSON()})):r[a]=o})),r}}]),e}(),ge={__proto__:null,default:function(e){q(n,i.BaseFeatureDataAdapter);var t,r=O(n);function n(e,t,a){var i;L(this,n),i=r.call(this,e,t,a);var c=o.readConfObject(e,"refNames"),s=o.readConfObject(e,"rootUrlTemplate");return i.configRefNames=c,i.nclist=new m({baseUrl:"",urlTemplate:s.uri,readFile:function(e){return new b.RemoteFile(String(s.baseUri?new URL(e,s.baseUri).toString():e)).readFile()}}),i}return B(n,[{key:"getFeatures",value:function(e){var t=this,r=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{};return v.ObservableCreate(function(){var n=U(N.mark((function n(a){var o,i,c,s,u,f,p;return N.wrap((function(n){for(;;)switch(n.prev=n.next){case 0:o=r.signal,i=!1,c=!1,n.prev=3,u=g(t.nclist.getFeatures(e,r));case 5:return n.next=7,u.next();case 7:if(!(i=!(f=n.sent).done)){n.next=14;break}p=f.value,l.checkAbortSignal(o),a.next(t.wrapFeature(p));case 11:i=!1,n.next=5;break;case 14:n.next=20;break;case 16:n.prev=16,n.t0=n.catch(3),c=!0,s=n.t0;case 20:if(n.prev=20,n.prev=21,!i||null==u.return){n.next=25;break}return n.next=25,u.return();case 25:if(n.prev=25,!c){n.next=28;break}throw s;case 28:return n.finish(25);case 29:return n.finish(20);case 30:a.complete();case 31:case"end":return n.stop()}}),n,null,[[3,16,20,30],[21,,25,29]])})));return function(e){return n.apply(this,arguments)}}())}},{key:"wrapFeature",value:function(e){return new be(e,void 0,"".concat(this.id,"-").concat(e.id()))}},{key:"hasDataForRefName",value:(t=U(N.mark((function e(t){var r;return N.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.nclist.getDataRoot(t);case 2:return e.abrupt("return",!!((r=e.sent)&&r.stats&&r.stats.featureCount));case 4:case"end":return e.stop()}}),e,this)}))),function(e){return t.apply(this,arguments)})},{key:"getRefNames",value:function(){return Promise.resolve(this.configRefNames||[])}},{key:"freeResources",value:function(){}}]),n}()};exports.default=ye;
 //# sourceMappingURL=plugin-legacy-jbrowse.cjs.production.min.js.map

package/dist/plugin-legacy-jbrowse.cjs.production.min.js.map

@@ -1 +1 @@
-{"version":3,"file":"plugin-legacy-jbrowse.cjs.production.min.js","sources":["../src/NCListAdapter/configSchema.ts","../../../node_modules/regenerator-runtime/runtime.js","../src/JBrowse1TextSeachAdapter/HttpMap.ts","../src/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.ts","../src/JBrowse1TextSeachAdapter/configSchema.ts","../src/JBrowse1Connection/configSchema.ts","../src/JBrowse1Connection/util.ts","../src/JBrowse1Connection/jb1ConfigParse.ts","../src/JBrowse1Connection/jb1ConfigLoad.ts","../src/JBrowse1Connection/model.js","../src/JBrowse1Connection/jb1ToJb2.ts","../src/index.ts","../src/NCListAdapter/NCListFeature.ts","../src/NCListAdapter/NCListAdapter.ts"],"sourcesContent":["import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'NCListAdapter',\n  {\n    rootUrlTemplate: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/my/{refseq}/trackData.json',\n        locationType: 'UriLocation',\n      },\n    },\n    refNames: {\n      type: 'stringArray',\n      defaultValue: [],\n      description: 'List of refNames used by the NCList used for aliasing',\n    },\n  },\n  { explicitlyTyped: true },\n)\n","/**\n * Copyright (c) 2014-present, Facebook, Inc.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\nvar runtime = (function (exports) {\n  \"use strict\";\n\n  var Op = Object.prototype;\n  var hasOwn = Op.hasOwnProperty;\n  var undefined; // More compressible than void 0.\n  var $Symbol = typeof Symbol === \"function\" ? Symbol : {};\n  var iteratorSymbol = $Symbol.iterator || \"@@iterator\";\n  var asyncIteratorSymbol = $Symbol.asyncIterator || \"@@asyncIterator\";\n  var toStringTagSymbol = $Symbol.toStringTag || \"@@toStringTag\";\n\n  function define(obj, key, value) {\n    Object.defineProperty(obj, key, {\n      value: value,\n      enumerable: true,\n      configurable: true,\n      writable: true\n    });\n    return obj[key];\n  }\n  try {\n    // IE 8 has a broken Object.defineProperty that only works on DOM objects.\n    define({}, \"\");\n  } catch (err) {\n    define = function(obj, key, value) {\n      return obj[key] = value;\n    };\n  }\n\n  function wrap(innerFn, outerFn, self, tryLocsList) {\n    // If outerFn provided and outerFn.prototype is a Generator, then outerFn.prototype instanceof Generator.\n    var protoGenerator = outerFn && outerFn.prototype instanceof Generator ? outerFn : Generator;\n    var generator = Object.create(protoGenerator.prototype);\n    var context = new Context(tryLocsList || []);\n\n    // The ._invoke method unifies the implementations of the .next,\n    // .throw, and .return methods.\n    generator._invoke = makeInvokeMethod(innerFn, self, context);\n\n    return generator;\n  }\n  exports.wrap = wrap;\n\n  // Try/catch helper to minimize deoptimizations. Returns a completion\n  // record like context.tryEntries[i].completion. This interface could\n  // have been (and was previously) designed to take a closure to be\n  // invoked without arguments, but in all the cases we care about we\n  // already have an existing method we want to call, so there's no need\n  // to create a new function object. We can even get away with assuming\n  // the method takes exactly one argument, since that happens to be true\n  // in every case, so we don't have to touch the arguments object. The\n  // only additional allocation required is the completion record, which\n  // has a stable shape and so hopefully should be cheap to allocate.\n  function tryCatch(fn, obj, arg) {\n    try {\n      return { type: \"normal\", arg: fn.call(obj, arg) };\n    } catch (err) {\n      return { type: \"throw\", arg: err };\n    }\n  }\n\n  var GenStateSuspendedStart = \"suspendedStart\";\n  var GenStateSuspendedYield = \"suspendedYield\";\n  var GenStateExecuting = \"executing\";\n  var GenStateCompleted = \"completed\";\n\n  // Returning this object from the innerFn has the same effect as\n  // breaking out of the dispatch switch statement.\n  var ContinueSentinel = {};\n\n  // Dummy constructor functions that we use as the .constructor and\n  // .constructor.prototype properties for functions that return Generator\n  // objects. For full spec compliance, you may wish to configure your\n  // minifier not to mangle the names of these two functions.\n  function Generator() {}\n  function GeneratorFunction() {}\n  function GeneratorFunctionPrototype() {}\n\n  // This is a polyfill for %IteratorPrototype% for environments that\n  // don't natively support it.\n  var IteratorPrototype = {};\n  define(IteratorPrototype, iteratorSymbol, function () {\n    return this;\n  });\n\n  var getProto = Object.getPrototypeOf;\n  var NativeIteratorPrototype = getProto && getProto(getProto(values([])));\n  if (NativeIteratorPrototype &&\n      NativeIteratorPrototype !== Op &&\n      hasOwn.call(NativeIteratorPrototype, iteratorSymbol)) {\n    // This environment has a native %IteratorPrototype%; use it instead\n    // of the polyfill.\n    IteratorPrototype = NativeIteratorPrototype;\n  }\n\n  var Gp = GeneratorFunctionPrototype.prototype =\n    Generator.prototype = Object.create(IteratorPrototype);\n  GeneratorFunction.prototype = GeneratorFunctionPrototype;\n  define(Gp, \"constructor\", GeneratorFunctionPrototype);\n  define(GeneratorFunctionPrototype, \"constructor\", GeneratorFunction);\n  GeneratorFunction.displayName = define(\n    GeneratorFunctionPrototype,\n    toStringTagSymbol,\n    \"GeneratorFunction\"\n  );\n\n  // Helper for defining the .next, .throw, and .return methods of the\n  // Iterator interface in terms of a single ._invoke method.\n  function defineIteratorMethods(prototype) {\n    [\"next\", \"throw\", \"return\"].forEach(function(method) {\n      define(prototype, method, function(arg) {\n        return this._invoke(method, arg);\n      });\n    });\n  }\n\n  exports.isGeneratorFunction = function(genFun) {\n    var ctor = typeof genFun === \"function\" && genFun.constructor;\n    return ctor\n      ? ctor === GeneratorFunction ||\n        // For the native GeneratorFunction constructor, the best we can\n        // do is to check its .name property.\n        (ctor.displayName || ctor.name) === \"GeneratorFunction\"\n      : false;\n  };\n\n  exports.mark = function(genFun) {\n    if (Object.setPrototypeOf) {\n      Object.setPrototypeOf(genFun, GeneratorFunctionPrototype);\n    } else {\n      genFun.__proto__ = GeneratorFunctionPrototype;\n      define(genFun, toStringTagSymbol, \"GeneratorFunction\");\n    }\n    genFun.prototype = Object.create(Gp);\n    return genFun;\n  };\n\n  // Within the body of any async function, `await x` is transformed to\n  // `yield regeneratorRuntime.awrap(x)`, so that the runtime can test\n  // `hasOwn.call(value, \"__await\")` to determine if the yielded value is\n  // meant to be awaited.\n  exports.awrap = function(arg) {\n    return { __await: arg };\n  };\n\n  function AsyncIterator(generator, PromiseImpl) {\n    function invoke(method, arg, resolve, reject) {\n      var record = tryCatch(generator[method], generator, arg);\n      if (record.type === \"throw\") {\n        reject(record.arg);\n      } else {\n        var result = record.arg;\n        var value = result.value;\n        if (value &&\n            typeof value === \"object\" &&\n            hasOwn.call(value, \"__await\")) {\n          return PromiseImpl.resolve(value.__await).then(function(value) {\n            invoke(\"next\", value, resolve, reject);\n          }, function(err) {\n            invoke(\"throw\", err, resolve, reject);\n          });\n        }\n\n        return PromiseImpl.resolve(value).then(function(unwrapped) {\n          // When a yielded Promise is resolved, its final value becomes\n          // the .value of the Promise<{value,done}> result for the\n          // current iteration.\n          result.value = unwrapped;\n          resolve(result);\n        }, function(error) {\n          // If a rejected Promise was yielded, throw the rejection back\n          // into the async generator function so it can be handled there.\n          return invoke(\"throw\", error, resolve, reject);\n        });\n      }\n    }\n\n    var previousPromise;\n\n    function enqueue(method, arg) {\n      function callInvokeWithMethodAndArg() {\n        return new PromiseImpl(function(resolve, reject) {\n          invoke(method, arg, resolve, reject);\n        });\n      }\n\n      return previousPromise =\n        // If enqueue has been called before, then we want to wait until\n        // all previous Promises have been resolved before calling invoke,\n        // so that results are always delivered in the correct order. If\n        // enqueue has not been called before, then it is important to\n        // call invoke immediately, without waiting on a callback to fire,\n        // so that the async generator function has the opportunity to do\n        // any necessary setup in a predictable way. This predictability\n        // is why the Promise constructor synchronously invokes its\n        // executor callback, and why async functions synchronously\n        // execute code before the first await. Since we implement simple\n        // async functions in terms of async generators, it is especially\n        // important to get this right, even though it requires care.\n        previousPromise ? previousPromise.then(\n          callInvokeWithMethodAndArg,\n          // Avoid propagating failures to Promises returned by later\n          // invocations of the iterator.\n          callInvokeWithMethodAndArg\n        ) : callInvokeWithMethodAndArg();\n    }\n\n    // Define the unified helper method that is used to implement .next,\n    // .throw, and .return (see defineIteratorMethods).\n    this._invoke = enqueue;\n  }\n\n  defineIteratorMethods(AsyncIterator.prototype);\n  define(AsyncIterator.prototype, asyncIteratorSymbol, function () {\n    return this;\n  });\n  exports.AsyncIterator = AsyncIterator;\n\n  // Note that simple async functions are implemented on top of\n  // AsyncIterator objects; they just return a Promise for the value of\n  // the final result produced by the iterator.\n  exports.async = function(innerFn, outerFn, self, tryLocsList, PromiseImpl) {\n    if (PromiseImpl === void 0) PromiseImpl = Promise;\n\n    var iter = new AsyncIterator(\n      wrap(innerFn, outerFn, self, tryLocsList),\n      PromiseImpl\n    );\n\n    return exports.isGeneratorFunction(outerFn)\n      ? iter // If outerFn is a generator, return the full iterator.\n      : iter.next().then(function(result) {\n          return result.done ? result.value : iter.next();\n        });\n  };\n\n  function makeInvokeMethod(innerFn, self, context) {\n    var state = GenStateSuspendedStart;\n\n    return function invoke(method, arg) {\n      if (state === GenStateExecuting) {\n        throw new Error(\"Generator is already running\");\n      }\n\n      if (state === GenStateCompleted) {\n        if (method === \"throw\") {\n          throw arg;\n        }\n\n        // Be forgiving, per 25.3.3.3.3 of the spec:\n        // https://people.mozilla.org/~jorendorff/es6-draft.html#sec-generatorresume\n        return doneResult();\n      }\n\n      context.method = method;\n      context.arg = arg;\n\n      while (true) {\n        var delegate = context.delegate;\n        if (delegate) {\n          var delegateResult = maybeInvokeDelegate(delegate, context);\n          if (delegateResult) {\n            if (delegateResult === ContinueSentinel) continue;\n            return delegateResult;\n          }\n        }\n\n        if (context.method === \"next\") {\n          // Setting context._sent for legacy support of Babel's\n          // function.sent implementation.\n          context.sent = context._sent = context.arg;\n\n        } else if (context.method === \"throw\") {\n          if (state === GenStateSuspendedStart) {\n            state = GenStateCompleted;\n            throw context.arg;\n          }\n\n          context.dispatchException(context.arg);\n\n        } else if (context.method === \"return\") {\n          context.abrupt(\"return\", context.arg);\n        }\n\n        state = GenStateExecuting;\n\n        var record = tryCatch(innerFn, self, context);\n        if (record.type === \"normal\") {\n          // If an exception is thrown from innerFn, we leave state ===\n          // GenStateExecuting and loop back for another invocation.\n          state = context.done\n            ? GenStateCompleted\n            : GenStateSuspendedYield;\n\n          if (record.arg === ContinueSentinel) {\n            continue;\n          }\n\n          return {\n            value: record.arg,\n            done: context.done\n          };\n\n        } else if (record.type === \"throw\") {\n          state = GenStateCompleted;\n          // Dispatch the exception by looping back around to the\n          // context.dispatchException(context.arg) call above.\n          context.method = \"throw\";\n          context.arg = record.arg;\n        }\n      }\n    };\n  }\n\n  // Call delegate.iterator[context.method](context.arg) and handle the\n  // result, either by returning a { value, done } result from the\n  // delegate iterator, or by modifying context.method and context.arg,\n  // setting context.delegate to null, and returning the ContinueSentinel.\n  function maybeInvokeDelegate(delegate, context) {\n    var method = delegate.iterator[context.method];\n    if (method === undefined) {\n      // A .throw or .return when the delegate iterator has no .throw\n      // method always terminates the yield* loop.\n      context.delegate = null;\n\n      if (context.method === \"throw\") {\n        // Note: [\"return\"] must be used for ES3 parsing compatibility.\n        if (delegate.iterator[\"return\"]) {\n          // If the delegate iterator has a return method, give it a\n          // chance to clean up.\n          context.method = \"return\";\n          context.arg = undefined;\n          maybeInvokeDelegate(delegate, context);\n\n          if (context.method === \"throw\") {\n            // If maybeInvokeDelegate(context) changed context.method from\n            // \"return\" to \"throw\", let that override the TypeError below.\n            return ContinueSentinel;\n          }\n        }\n\n        context.method = \"throw\";\n        context.arg = new TypeError(\n          \"The iterator does not provide a 'throw' method\");\n      }\n\n      return ContinueSentinel;\n    }\n\n    var record = tryCatch(method, delegate.iterator, context.arg);\n\n    if (record.type === \"throw\") {\n      context.method = \"throw\";\n      context.arg = record.arg;\n      context.delegate = null;\n      return ContinueSentinel;\n    }\n\n    var info = record.arg;\n\n    if (! info) {\n      context.method = \"throw\";\n      context.arg = new TypeError(\"iterator result is not an object\");\n      context.delegate = null;\n      return ContinueSentinel;\n    }\n\n    if (info.done) {\n      // Assign the result of the finished delegate to the temporary\n      // variable specified by delegate.resultName (see delegateYield).\n      context[delegate.resultName] = info.value;\n\n      // Resume execution at the desired location (see delegateYield).\n      context.next = delegate.nextLoc;\n\n      // If context.method was \"throw\" but the delegate handled the\n      // exception, let the outer generator proceed normally. If\n      // context.method was \"next\", forget context.arg since it has been\n      // \"consumed\" by the delegate iterator. If context.method was\n      // \"return\", allow the original .return call to continue in the\n      // outer generator.\n      if (context.method !== \"return\") {\n        context.method = \"next\";\n        context.arg = undefined;\n      }\n\n    } else {\n      // Re-yield the result returned by the delegate method.\n      return info;\n    }\n\n    // The delegate iterator is finished, so forget it and continue with\n    // the outer generator.\n    context.delegate = null;\n    return ContinueSentinel;\n  }\n\n  // Define Generator.prototype.{next,throw,return} in terms of the\n  // unified ._invoke helper method.\n  defineIteratorMethods(Gp);\n\n  define(Gp, toStringTagSymbol, \"Generator\");\n\n  // A Generator should always return itself as the iterator object when the\n  // @@iterator function is called on it. Some browsers' implementations of the\n  // iterator prototype chain incorrectly implement this, causing the Generator\n  // object to not be returned from this call. This ensures that doesn't happen.\n  // See https://github.com/facebook/regenerator/issues/274 for more details.\n  define(Gp, iteratorSymbol, function() {\n    return this;\n  });\n\n  define(Gp, \"toString\", function() {\n    return \"[object Generator]\";\n  });\n\n  function pushTryEntry(locs) {\n    var entry = { tryLoc: locs[0] };\n\n    if (1 in locs) {\n      entry.catchLoc = locs[1];\n    }\n\n    if (2 in locs) {\n      entry.finallyLoc = locs[2];\n      entry.afterLoc = locs[3];\n    }\n\n    this.tryEntries.push(entry);\n  }\n\n  function resetTryEntry(entry) {\n    var record = entry.completion || {};\n    record.type = \"normal\";\n    delete record.arg;\n    entry.completion = record;\n  }\n\n  function Context(tryLocsList) {\n    // The root entry object (effectively a try statement without a catch\n    // or a finally block) gives us a place to store values thrown from\n    // locations where there is no enclosing try statement.\n    this.tryEntries = [{ tryLoc: \"root\" }];\n    tryLocsList.forEach(pushTryEntry, this);\n    this.reset(true);\n  }\n\n  exports.keys = function(object) {\n    var keys = [];\n    for (var key in object) {\n      keys.push(key);\n    }\n    keys.reverse();\n\n    // Rather than returning an object with a next method, we keep\n    // things simple and return the next function itself.\n    return function next() {\n      while (keys.length) {\n        var key = keys.pop();\n        if (key in object) {\n          next.value = key;\n          next.done = false;\n          return next;\n        }\n      }\n\n      // To avoid creating an additional object, we just hang the .value\n      // and .done properties off the next function object itself. This\n      // also ensures that the minifier will not anonymize the function.\n      next.done = true;\n      return next;\n    };\n  };\n\n  function values(iterable) {\n    if (iterable) {\n      var iteratorMethod = iterable[iteratorSymbol];\n      if (iteratorMethod) {\n        return iteratorMethod.call(iterable);\n      }\n\n      if (typeof iterable.next === \"function\") {\n        return iterable;\n      }\n\n      if (!isNaN(iterable.length)) {\n        var i = -1, next = function next() {\n          while (++i < iterable.length) {\n            if (hasOwn.call(iterable, i)) {\n              next.value = iterable[i];\n              next.done = false;\n              return next;\n            }\n          }\n\n          next.value = undefined;\n          next.done = true;\n\n          return next;\n        };\n\n        return next.next = next;\n      }\n    }\n\n    // Return an iterator with no values.\n    return { next: doneResult };\n  }\n  exports.values = values;\n\n  function doneResult() {\n    return { value: undefined, done: true };\n  }\n\n  Context.prototype = {\n    constructor: Context,\n\n    reset: function(skipTempReset) {\n      this.prev = 0;\n      this.next = 0;\n      // Resetting context._sent for legacy support of Babel's\n      // function.sent implementation.\n      this.sent = this._sent = undefined;\n      this.done = false;\n      this.delegate = null;\n\n      this.method = \"next\";\n      this.arg = undefined;\n\n      this.tryEntries.forEach(resetTryEntry);\n\n      if (!skipTempReset) {\n        for (var name in this) {\n          // Not sure about the optimal order of these conditions:\n          if (name.charAt(0) === \"t\" &&\n              hasOwn.call(this, name) &&\n              !isNaN(+name.slice(1))) {\n            this[name] = undefined;\n          }\n        }\n      }\n    },\n\n    stop: function() {\n      this.done = true;\n\n      var rootEntry = this.tryEntries[0];\n      var rootRecord = rootEntry.completion;\n      if (rootRecord.type === \"throw\") {\n        throw rootRecord.arg;\n      }\n\n      return this.rval;\n    },\n\n    dispatchException: function(exception) {\n      if (this.done) {\n        throw exception;\n      }\n\n      var context = this;\n      function handle(loc, caught) {\n        record.type = \"throw\";\n        record.arg = exception;\n        context.next = loc;\n\n        if (caught) {\n          // If the dispatched exception was caught by a catch block,\n          // then let that catch block handle the exception normally.\n          context.method = \"next\";\n          context.arg = undefined;\n        }\n\n        return !! caught;\n      }\n\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        var record = entry.completion;\n\n        if (entry.tryLoc === \"root\") {\n          // Exception thrown outside of any try block that could handle\n          // it, so set the completion value of the entire function to\n          // throw the exception.\n          return handle(\"end\");\n        }\n\n        if (entry.tryLoc <= this.prev) {\n          var hasCatch = hasOwn.call(entry, \"catchLoc\");\n          var hasFinally = hasOwn.call(entry, \"finallyLoc\");\n\n          if (hasCatch && hasFinally) {\n            if (this.prev < entry.catchLoc) {\n              return handle(entry.catchLoc, true);\n            } else if (this.prev < entry.finallyLoc) {\n              return handle(entry.finallyLoc);\n            }\n\n          } else if (hasCatch) {\n            if (this.prev < entry.catchLoc) {\n              return handle(entry.catchLoc, true);\n            }\n\n          } else if (hasFinally) {\n            if (this.prev < entry.finallyLoc) {\n              return handle(entry.finallyLoc);\n            }\n\n          } else {\n            throw new Error(\"try statement without catch or finally\");\n          }\n        }\n      }\n    },\n\n    abrupt: function(type, arg) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.tryLoc <= this.prev &&\n            hasOwn.call(entry, \"finallyLoc\") &&\n            this.prev < entry.finallyLoc) {\n          var finallyEntry = entry;\n          break;\n        }\n      }\n\n      if (finallyEntry &&\n          (type === \"break\" ||\n           type === \"continue\") &&\n          finallyEntry.tryLoc <= arg &&\n          arg <= finallyEntry.finallyLoc) {\n        // Ignore the finally entry if control is not jumping to a\n        // location outside the try/catch block.\n        finallyEntry = null;\n      }\n\n      var record = finallyEntry ? finallyEntry.completion : {};\n      record.type = type;\n      record.arg = arg;\n\n      if (finallyEntry) {\n        this.method = \"next\";\n        this.next = finallyEntry.finallyLoc;\n        return ContinueSentinel;\n      }\n\n      return this.complete(record);\n    },\n\n    complete: function(record, afterLoc) {\n      if (record.type === \"throw\") {\n        throw record.arg;\n      }\n\n      if (record.type === \"break\" ||\n          record.type === \"continue\") {\n        this.next = record.arg;\n      } else if (record.type === \"return\") {\n        this.rval = this.arg = record.arg;\n        this.method = \"return\";\n        this.next = \"end\";\n      } else if (record.type === \"normal\" && afterLoc) {\n        this.next = afterLoc;\n      }\n\n      return ContinueSentinel;\n    },\n\n    finish: function(finallyLoc) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.finallyLoc === finallyLoc) {\n          this.complete(entry.completion, entry.afterLoc);\n          resetTryEntry(entry);\n          return ContinueSentinel;\n        }\n      }\n    },\n\n    \"catch\": function(tryLoc) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.tryLoc === tryLoc) {\n          var record = entry.completion;\n          if (record.type === \"throw\") {\n            var thrown = record.arg;\n            resetTryEntry(entry);\n          }\n          return thrown;\n        }\n      }\n\n      // The context.catch method must only be called with a location\n      // argument that corresponds to a known catch block.\n      throw new Error(\"illegal catch attempt\");\n    },\n\n    delegateYield: function(iterable, resultName, nextLoc) {\n      this.delegate = {\n        iterator: values(iterable),\n        resultName: resultName,\n        nextLoc: nextLoc\n      };\n\n      if (this.method === \"next\") {\n        // Deliberately forget the last sent value so that we don't\n        // accidentally pass it on to the delegate.\n        this.arg = undefined;\n      }\n\n      return ContinueSentinel;\n    }\n  };\n\n  // Regardless of whether this script is executing as a CommonJS module\n  // or not, return the runtime object so that we can declare the variable\n  // regeneratorRuntime in the outer scope, which allows this module to be\n  // injected easily by `bin/regenerator --include-runtime script.js`.\n  return exports;\n\n}(\n  // If this script is executing as a CommonJS module, use module.exports\n  // as the regeneratorRuntime namespace. Otherwise create a new empty\n  // object. Either way, the resulting object will be used to initialize\n  // the regeneratorRuntime variable at the top of this file.\n  typeof module === \"object\" ? module.exports : {}\n));\n\ntry {\n  regeneratorRuntime = runtime;\n} catch (accidentalStrictMode) {\n  // This module should not be running in strict mode, so the above\n  // assignment should always work unless something is misconfigured. Just\n  // in case runtime.js accidentally runs in strict mode, in modern engines\n  // we can explicitly access globalThis. In older engines we can escape\n  // strict mode using a global Function call. This could conceivably fail\n  // if a Content Security Policy forbids using Function, but in that case\n  // the proper solution is to fix the accidental strict mode problem. If\n  // you've misconfigured your bundler to force strict mode and applied a\n  // CSP to forbid Function, and you're not willing to fix either of those\n  // problems, please detail your unique predicament in a GitHub issue.\n  if (typeof globalThis === \"object\") {\n    globalThis.regeneratorRuntime = runtime;\n  } else {\n    Function(\"r\", \"regeneratorRuntime = r\")(runtime);\n  }\n}\n","/*\n * Helper class allows reading names index generated in JBrowse1\n * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js\n */\nimport crc32 from 'buffer-crc32'\n\nexport default class HttpMap {\n  url: string\n\n  constructor(args: { url: string }) {\n    // make sure url has a trailing slash\n    this.url = /\\/$/.test(args.url) ? args.url : `${args.url}/`\n  }\n\n  /**\n   * loads meta.json file from names directory and reads number of hash_bits used\n   */\n  async readMeta() {\n    const meta = await this.loadFile('meta.json')\n    const { compress, track_names: tracks } = meta\n    const hashHexCharacters = Math.ceil(meta.hash_bits / 4)\n    return { hashHexCharacters, compress, tracks }\n  }\n\n  async getHashHexCharacters() {\n    const meta = await this.readMeta()\n    return meta.hashHexCharacters\n  }\n\n  async getCompress() {\n    const meta = await this.readMeta()\n    return meta.compress\n  }\n\n  async getTrackNames() {\n    const meta = await this.readMeta()\n    return meta.tracks\n  }\n\n  /**\n   * Returns contents of a bucket given a key\n   * @param key - string\n   */\n  async get(key: string) {\n    const bucket = await this.getBucket(key)\n    return bucket[key]\n  }\n\n  /**\n   * Returns a bucket given a key\n   * @param key - string\n   */\n  async getBucket(key: string) {\n    const bucketIdent = this.hash(key)\n    const hexToDirPath = await this.hexToDirPath(bucketIdent)\n    return this.loadFile(hexToDirPath)\n  }\n\n  /**\n   * Loads a file using the url and provided id.\n   * Returns response object with contents of the file\n   * @param id - string\n   */\n  async loadFile(id: string) {\n    const response = await fetch(`${this.url}${id}`)\n    if (!response.ok) {\n      throw new Error(`HTTP ${response.status} ${response.statusText}`)\n    }\n    return response.json()\n  }\n\n  /**\n   * Returns the corresponding path of the file given a hex string\n   * @param hex - hex string\n   */\n  async hexToDirPath(hex: string) {\n    // zero-pad the hex string to be 8 chars if necessary\n    const hashHexCharacters = await this.getHashHexCharacters()\n    if (hashHexCharacters) {\n      const compress = await this.getCompress()\n      while (hex.length < 8) {\n        hex = `0${hex}`\n      }\n      hex = hex.substr(8 - hashHexCharacters)\n      const dirpath = []\n      for (let i = 0; i < hex.length; i += 3) {\n        dirpath.push(hex.substring(i, i + 3))\n      }\n      return `${dirpath.join('/')}.json${compress ? 'z' : ''}`\n    }\n    return ''\n  }\n\n  hash(data: string) {\n    return crc32(Buffer.from(data))\n      .toString('hex')\n      .toLowerCase()\n      .replace('-', 'n')\n  }\n}\n","import {\n  BaseTextSearchAdapter,\n  BaseArgs,\n  BaseAdapter,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport BaseResult from '@jbrowse/core/TextSearch/BaseResults'\nimport { Instance } from 'mobx-state-tree'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport MyConfigSchema from './configSchema'\nimport HttpMap from './HttpMap'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\nexport interface TooManyHits {\n  name: string\n  hitLimit: number\n}\n\ninterface SearchResults {\n  prefix: ({ name: string } | string)[]\n  exact: [string, number, string, string, number, number][]\n}\n\nexport type NamesIndexRecord = string | Array<string | number>\n\n//  Jbrowse1 text search adapter\n// Uses index built by generate-names.pl\nexport default class JBrowse1TextSearchAdapter\n  extends BaseAdapter\n  implements BaseTextSearchAdapter\n{\n  httpMap: HttpMap\n\n  tracksNames?: string[]\n\n  constructor(\n    config: Instance<typeof MyConfigSchema>,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const namesIndexLocation = readConfObject(config, 'namesIndexLocation')\n    if (!namesIndexLocation) {\n      throw new Error('must provide namesIndexLocation')\n    }\n    this.httpMap = new HttpMap({\n      url: namesIndexLocation.baseUri\n        ? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href\n        : namesIndexLocation.uri,\n    })\n  }\n\n  /**\n   * Returns the contents of the file containing the query if it exists\n   * else it returns empty\n   * @param query - string query\n   */\n  async loadIndexFile(query: string): Promise<Record<string, SearchResults>> {\n    return this.httpMap.getBucket(query)\n  }\n\n  async searchIndex(args: BaseArgs) {\n    const { searchType, queryString } = args\n    const tracks = this.tracksNames || (await this.httpMap.getTrackNames())\n    const entries = await this.loadIndexFile(queryString.toLowerCase())\n    if (entries[queryString]) {\n      return this.formatResults(entries[queryString], tracks, searchType)\n    }\n    return []\n  }\n  formatResults(results: SearchResults, tracks: string[], searchType?: string) {\n    return [\n      ...(searchType === 'exact'\n        ? []\n        : results.prefix.map(result => {\n            return new BaseResult({\n              label: typeof result === 'object' ? result.name : result,\n              matchedAttribute: 'name',\n              matchedObject: { result: result },\n            })\n          })),\n      ...results.exact.map(result => {\n        const name = result[0] as string\n        const trackIndex = result[1] as number\n        const refName = result[3] as string\n        const start = result[4] as number\n        const end = result[5] as number\n        const locstring = `${refName || name}:${start}-${end}`\n        return new BaseResult({\n          locString: locstring,\n          label: name,\n          matchedAttribute: 'name',\n          matchedObject: result,\n          trackId: tracks[trackIndex],\n        })\n      }),\n    ].filter(result => result.getLabel() !== 'too many matches')\n  }\n\n  freeResources() {}\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'JBrowse1TextSearchAdapter',\n  {\n    // metadata about tracks and assemblies covered by text search adapter\n    namesIndexLocation: {\n      type: 'fileLocation',\n      defaultValue: { uri: '/volvox/names', locationType: 'UriLocation' },\n      description: 'the location of the JBrowse1 names index data directory',\n    },\n    tracks: {\n      type: 'stringArray',\n      defaultValue: [],\n      description: 'List of tracks covered by text search adapter',\n    },\n    assemblyNames: {\n      type: 'stringArray',\n      defaultValue: [],\n      description: 'List of assemblies covered by text search adapter',\n    },\n  },\n  { explicitlyTyped: true, explicitIdentifier: 'textSearchAdapterId' },\n)\n","import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'JBrowse1Connection',\n  {\n    dataDirLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: 'http://mysite.com/jbrowse/data/',\n        locationType: 'UriLocation',\n      },\n      description:\n        'the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/',\n    },\n    assemblyNames: {\n      description:\n        'name of the assembly the connection belongs to, should be a single entry',\n      type: 'stringArray',\n      defaultValue: [],\n    },\n  },\n  { baseConfiguration: baseConnectionConfig },\n)\n","import getValue from 'get-value'\nimport { Track, Source } from './types'\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nexport function isTrack(arg: any): arg is Track {\n  return arg && arg.label && typeof arg.label === 'string'\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nexport function isSource(arg: any): arg is Source {\n  return arg && arg.url && typeof arg.url === 'string'\n}\n\n/**\n * updates a with values from b, recursively\n */\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\ntype Obj = Record<string, any>\nexport function deepUpdate(a: Obj, b: Obj): Obj {\n  for (const prop of Object.keys(b)) {\n    if (\n      prop in a &&\n      typeof b[prop] === 'object' &&\n      typeof a[prop] === 'object'\n    ) {\n      deepUpdate(a[prop], b[prop])\n    } else if (\n      typeof a[prop] === 'undefined' ||\n      typeof b[prop] !== 'undefined'\n    ) {\n      a[prop] = b[prop]\n    }\n  }\n  return a\n}\n\n/**\n * replace variables in a template string with values\n * @param template - String with variable names in curly brackets\n * e.g., `http://foo/{bar}?arg={baz.foo}`\n * @param fillWith - object with attribute-value mappings\n * e.g., `{ 'bar': 'someurl', 'baz': { 'foo': 42 } }`\n * @returns the template string with variables in fillWith replaced\n * e.g., 'htp://foo/someurl?arg=valueforbaz'\n */\nexport function fillTemplate(template: string, fillWith: Obj): string {\n  return template.replace(\n    /\\{([\\w\\s.]+)\\}/g,\n    (match, varName: string): string => {\n      varName = varName.replace(/\\s+/g, '') // remove all whitespace\n      const fill = getValue(fillWith, varName)\n      if (fill !== undefined) {\n        if (typeof fill === 'function') {\n          return fill(varName)\n        }\n        return fill\n      }\n      if (fillWith.callback) {\n        // @ts-ignore\n        const v = fillWith.callback.call(this, varName)\n        if (v !== undefined) {\n          return v\n        }\n      }\n      return match\n    },\n  )\n}\n\n/**\n * Clones objects (including DOM nodes) and all children.\n * Warning: do not clone cyclic structures\n * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)\n * @param src - The object to clone\n */\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nexport function clone(src: any): any {\n  if (\n    !src ||\n    typeof src !== 'object' ||\n    Object.prototype.toString.call(src) === '[object Function]'\n  ) {\n    // null, undefined, any non-object, or function\n    return src // anything\n  }\n  if (src.nodeType && 'cloneNode' in src) {\n    // DOM Node\n    return src.cloneNode(true) // Node\n  }\n  if (src instanceof Date) {\n    // Date\n    return new Date(src.getTime()) // Date\n  }\n  if (src instanceof RegExp) {\n    // RegExp\n    return new RegExp(src) // RegExp\n  }\n  let r\n  let i\n  let l\n  if (Array.isArray(src)) {\n    // array\n    r = []\n    for (i = 0, l = src.length; i < l; ++i) {\n      if (i in src) {\n        r[i] = clone(src[i])\n      }\n    }\n    // we don't clone functions for performance reasons\n    //    }else if(d.isFunction(src)){\n    //      // function\n    //      r = function(){ return src.apply(this, arguments); };\n  } else {\n    // generic objects\n    r = src.constructor ? new src.constructor() : {}\n  }\n  return mixin(r, src, clone)\n}\n\n/**\n * Copies/adds all properties of source to dest; returns dest.\n * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)\n *\n * All properties, including functions (sometimes termed \"methods\"), excluding\n * any non-standard extensions found in Object.prototype, are copied/added to\n * dest. Copying/adding each particular property is delegated to copyFunc\n * (if any); copyFunc defaults to the Javascript assignment operator if not\n * provided. Notice that by default, mixin executes a so-called \"shallow copy\"\n * and aggregate types are copied/added by reference.\n * @param dest - The object to which to copy/add all properties contained in\n * source.\n * @param source - The object from which to draw all properties to copy into dest.\n * @param copyFunc - The process used to copy/add a property in source; defaults\n * to the Javascript assignment operator.\n * @returns dest, as modified\n */\nfunction mixin(dest: Obj, source: Obj, copyFunc: Function): Obj {\n  let name\n  let s\n  const empty = {}\n  for (name in source) {\n    // the (!(name in empty) || empty[name] !== s) condition avoids copying\n    // properties in \"source\" inherited from Object.prototype.\t For example,\n    // if dest has a custom toString() method, don't overwrite it with the\n    // toString() method that source inherited from Object.prototype\n    s = source[name]\n    if (\n      !(name in dest) ||\n      // @ts-ignore\n      (dest[name] !== s && (!(name in empty) || empty[name] !== s))\n    ) {\n      dest[name] = copyFunc ? copyFunc(s) : s\n    }\n  }\n\n  return dest // Object\n}\n","/* eslint no-cond-assign: [\"error\", \"except-parens\"] */\nimport getValue from 'get-value'\nimport setValue from 'set-value'\nimport { objectHash } from '@jbrowse/core/util'\nimport { isSource, isTrack } from './util'\nimport { Config, Track, Source, Store, Names } from './types'\n\nexport function parseJB1Json(config: Config | string, url: string): Config {\n  if (typeof config === 'string') {\n    let parsedConf\n    try {\n      parsedConf = JSON.parse(config)\n    } catch (error) {\n      throw new Error(`${error} when parsing configuration.`)\n    }\n    return regularizeConf(parsedConf, url)\n  }\n  return regularizeConf(config, url)\n}\n\nexport function parseJB1Conf(config: string, url: string): Config {\n  let parsedConf\n  try {\n    parsedConf = parse(config, url)\n  } catch (error) {\n    throw new Error(`${error} when parsing configuration.`)\n  }\n  return regularizeConf(parsedConf, url)\n}\n\nfunction isAlwaysArray(varName: string): boolean {\n  if (varName === 'include') {\n    return true\n  }\n  return false\n}\n\nfunction parse(text: string, url: string): Config {\n  let section: string[] = []\n  let keyPath: string[] | undefined\n  let operation: string\n  let value: string | undefined\n  const data: Config = { tracks: {} }\n  let lineNumber: number\n\n  function recordVal(): void {\n    if (value !== undefined) {\n      let parsedValue:\n        | string\n        | number\n        | boolean\n        | string[]\n        | number[]\n        | boolean[]\n      try {\n        // parse json\n        const match = value.match(/^json:(.+)/i)\n        if (match) {\n          parsedValue = JSON.parse(match[1])\n        }\n        // parse numbers if it looks numeric\n        else if (/^[+-]?[\\d.,]+([eE][-+]?\\d+)?$/.test(value)) {\n          parsedValue = parseFloat(value.replace(/,/g, ''))\n        } else {\n          parsedValue = value\n        }\n\n        if (!keyPath) {\n          throw new Error(`Error parsing in section ${section.join(' - ')}`)\n        }\n        const path = section.concat(keyPath).join('.')\n        if (operation === '+=') {\n          let existing = getValue(data, path)\n          if (existing) {\n            if (!Array.isArray(existing)) {\n              existing = [existing]\n            }\n          } else {\n            existing = []\n          }\n\n          existing.push(parsedValue)\n          parsedValue = existing\n        }\n        if (parsedValue === 'true') {\n          parsedValue = true\n        }\n        if (parsedValue === 'false') {\n          parsedValue = false\n        }\n        setValue(data, path, parsedValue)\n      } catch (e) {\n        throw new Error(\n          `syntax error${url ? ` in ${url}` : ''}${\n            lineNumber ? ` at line ${lineNumber - 1}` : ''\n          }`,\n        )\n      }\n    }\n  }\n\n  text.split('\\n').forEach((textLine, i): void => {\n    lineNumber = i + 1\n    const line = textLine.replace(/^\\s*#.+/, '')\n\n    // new section\n    let match: RegExpMatchArray | null\n    if ((match = line.match(/^\\s*\\[([^\\]]+)/))) {\n      // new section\n      recordVal()\n      keyPath = undefined\n      value = undefined\n      section = match[1].trim().split(/\\s*\\.\\s*/)\n      if (section.length === 1 && section[0].toLowerCase() === 'general') {\n        section = []\n      }\n    }\n    // new value\n    else if (\n      (match = line.match(\n        value === undefined ? /^([^+=]+)(\\+?=)(.*)/ : /^(\\S[^+=]+)(\\+?=)(.*)/,\n      ))\n    ) {\n      recordVal()\n      keyPath = match[1].trim().split(/\\s*\\.\\s*/)\n      ;[, , operation] = match\n      if (isAlwaysArray(section.concat(keyPath).join('.'))) {\n        operation = '+='\n      }\n      value = match[3].trim()\n    }\n    // add to existing array value\n    else if (\n      keyPath !== undefined &&\n      (match = line.match(/^\\s{0,4}\\+\\s*(.+)/))\n    ) {\n      recordVal()\n      operation = '+='\n      value = match[1].trim()\n    }\n    // add to existing value\n    else if (value !== undefined && (match = line.match(/^\\s+(\\S.*)/))) {\n      value += value.length ? ` ${match[1].trim()}` : match[1].trim()\n    }\n    // done with last value\n    else {\n      recordVal()\n      keyPath = undefined\n      value = undefined\n    }\n  })\n\n  recordVal()\n\n  return data\n}\n\n/**\n * Applies defaults and any other necessary tweaks to the loaded configuration.\n * @param conf - the object containing the configuration, which it modifies\n * in-place\n * @param url - URL of the config file\n * @returns the same object it was passed\n */\nexport function regularizeConf(conf: Config, url: string): Config {\n  // if tracks is not an array, convert it to one\n  if (conf.tracks && !Array.isArray(conf.tracks)) {\n    // if it's a single track config, wrap it in an arrayref\n    if (isTrack(conf.tracks)) {\n      conf.tracks = [conf.tracks]\n    }\n    // otherwise, coerce it to an array\n    else {\n      const tracks: Track[] = []\n      for (const label of Object.keys(conf.tracks)) {\n        const track = conf.tracks[label]\n        if (isTrack(track)) {\n          tracks.push(track)\n        } else {\n          tracks.push({ label, ...track })\n        }\n      }\n      conf.tracks = tracks\n    }\n  }\n\n  // regularize trackMetadata.sources\n  const meta = conf.trackMetadata\n  if (meta && meta.sources) {\n    // if it's a single source config, wrap it in an arrayref\n    if (typeof meta.sources === 'string') {\n      meta.sources = [meta.sources]\n    }\n    if (isSource(meta.sources)) {\n      meta.sources = [meta.sources]\n    }\n\n    if (!Array.isArray(meta.sources)) {\n      const sources: Source[] = []\n      for (const name of Object.keys(meta.sources)) {\n        const source = meta.sources[name]\n        if (!('name' in source)) {\n          source.name = name\n        }\n        sources.push(source)\n      }\n      meta.sources = sources\n    }\n\n    // coerce any string source defs to be URLs, and try to detect their types\n    meta.sources = meta.sources.map((sourceDef: string | Source): Source => {\n      if (typeof sourceDef === 'string') {\n        const newSourceDef: Source = { url: sourceDef }\n        const typeMatch = sourceDef.match(/\\.(\\w+)$/)\n        if (typeMatch) {\n          newSourceDef.type = typeMatch[1].toLowerCase()\n        }\n        return newSourceDef\n      }\n      return sourceDef\n    })\n  }\n\n  conf.sourceUrl = conf.sourceUrl || url\n  if (conf.sourceUrl.startsWith('/')) {\n    conf.sourceUrl = new URL(conf.sourceUrl, window.location.href).href\n  }\n  conf.baseUrl = conf.baseUrl || new URL('.', conf.sourceUrl).href\n  if (conf.baseUrl.length && !conf.baseUrl.endsWith('/')) {\n    conf.baseUrl += '/'\n  }\n\n  if (conf.sourceUrl) {\n    // set a default baseUrl in each of the track and store confs, and the names\n    // conf, if needed\n    const addBase: (Track | Store | Names)[] = []\n    if (conf.tracks) {\n      addBase.push(...conf.tracks)\n    }\n    if (conf.stores) {\n      addBase.push(...Object.values(conf.stores))\n    }\n    if (conf.names) {\n      addBase.push(conf.names)\n    }\n\n    addBase.forEach((t): void => {\n      if (!t.baseUrl) {\n        t.baseUrl = conf.baseUrl || '/'\n      }\n    })\n\n    // resolve the refSeqs and nameUrl if present\n    if (conf.refSeqs && typeof conf.refSeqs === 'string') {\n      conf.refSeqs = new URL(conf.refSeqs, conf.sourceUrl).href\n    }\n    if (conf.nameUrl) {\n      conf.nameUrl = new URL(conf.nameUrl, conf.sourceUrl).href\n    }\n  }\n\n  conf.stores = conf.stores || {}\n  ;(conf.tracks || []).forEach((trackConfig: Track): void => {\n    // if there is a `config` subpart, just copy its keys in to the top-level\n    // config\n    if (trackConfig.config) {\n      const c = trackConfig.config\n      delete trackConfig.config\n      trackConfig = { ...c, ...trackConfig }\n    }\n\n    // skip if it's a new-style track def\n    if (trackConfig.store) {\n      return\n    }\n\n    let trackClassName: string\n    if (trackConfig.type === 'FeatureTrack') {\n      trackClassName = 'JBrowse/View/Track/HTMLFeatures'\n    } else if (trackConfig.type === 'ImageTrack') {\n      trackClassName = 'JBrowse/View/Track/FixedImage'\n    } else if (trackConfig.type === 'ImageTrack.Wiggle') {\n      trackClassName = 'JBrowse/View/Track/FixedImage/Wiggle'\n    } else if (trackConfig.type === 'SequenceTrack') {\n      trackClassName = 'JBrowse/View/Track/Sequence'\n    } else {\n      trackClassName = regularizeClass('JBrowse/View/Track', trackConfig.type)\n    }\n\n    trackConfig.type = trackClassName\n\n    synthesizeTrackStoreConfig(conf, trackConfig)\n\n    if (trackConfig.histograms) {\n      if (!trackConfig.histograms.baseUrl) {\n        trackConfig.histograms.baseUrl = trackConfig.baseUrl\n      }\n      synthesizeTrackStoreConfig(conf, trackConfig.histograms)\n    }\n  })\n\n  return conf\n}\n\n/**\n * prefix class name with `root` if it contains no slashes\n * @param root - Prefix root\n * @param className - class name\n */\nfunction regularizeClass(root: string, className: string | undefined): string {\n  if (!className) {\n    return ''\n  }\n  if (!className.includes('/')) {\n    className = `${root}/${className}`\n  }\n  className = className.replace(/^\\//, '')\n  return className\n}\n\nfunction guessStoreClass(\n  trackConfig: Track | undefined,\n  urlTemplate: string,\n): string {\n  if (!trackConfig) {\n    return ''\n  }\n  if (trackConfig.type && trackConfig.type.includes('/FixedImage')) {\n    return `JBrowse/Store/TiledImage/Fixed${\n      trackConfig.backendVersion === 0 ? '_v0' : ''\n    }`\n  }\n  if (/\\.jsonz?$/i.test(urlTemplate)) {\n    return `JBrowse/Store/SeqFeature/NCList${\n      trackConfig.backendVersion === 0 ? '_v0' : ''\n    }`\n  }\n  if (/\\.bam$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BAM'\n  }\n  if (/\\.cram$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/CRAM'\n  }\n  if (/\\.gff3?$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/GFF3'\n  }\n  if (/\\.bed$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BED'\n  }\n  if (/\\.vcf.b?gz$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/VCFTabix'\n  }\n  if (/\\.gff3?.b?gz$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/GFF3Tabix'\n  }\n  if (/\\.bed.b?gz$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BEDTabix'\n  }\n  if (/\\.(bw|bigwig)$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BigWig'\n  }\n  if (/\\.(bb|bigbed)$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BigBed'\n  }\n  if (/\\.(fa|fasta)$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/IndexedFasta'\n  }\n  if (/\\.(fa|fasta)\\.b?gz$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BgzipIndexedFasta'\n  }\n  if (/\\.2bit$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/TwoBit'\n  }\n  if (trackConfig.type && trackConfig.type.endsWith('/Sequence')) {\n    return 'JBrowse/Store/Sequence/StaticChunked'\n  }\n  return ''\n}\n\nfunction synthesizeTrackStoreConfig(\n  mainConf: Config,\n  trackConfig: Track,\n): void {\n  // figure out what data store class to use with the track, applying some\n  // defaults if it is not explicit in the configuration\n  const { urlTemplate = '' } = trackConfig\n\n  let storeClass: string\n  if (trackConfig.storeClass) {\n    storeClass = regularizeClass('JBrowse/Store', trackConfig.storeClass)\n  } else {\n    storeClass = guessStoreClass(trackConfig, urlTemplate)\n  }\n\n  if (!storeClass) {\n    console.warn(\n      `Unable to determine an appropriate data store to use with track '${trackConfig.label}', please explicitly specify a storeClass in the configuration.`,\n    )\n    return\n  }\n\n  // synthesize a separate store conf\n  const storeConf: Store = { ...trackConfig, type: storeClass }\n\n  // if this is the first sequence store we see, and we have no refseqs store\n  // defined explicitly, make this the refseqs store.\n  if (\n    (storeClass === 'JBrowse/Store/Sequence/StaticChunked' ||\n      storeClass === 'JBrowse/Store/Sequence/IndexedFasta' ||\n      storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta' ||\n      storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta' ||\n      storeClass === 'JBrowse/Store/SeqFeature/TwoBit' ||\n      storeClass === 'JBrowse/Store/Sequence/TwoBit' ||\n      trackConfig.useAsRefSeqStore) &&\n    !(mainConf.stores && mainConf.stores.refseqs)\n  ) {\n    storeConf.name = 'refseqs'\n  } else {\n    storeConf.name = `store${objectHash(storeConf)}`\n  }\n  // record it\n  if (!mainConf.stores) {\n    mainConf.stores = {}\n  }\n  mainConf.stores[storeConf.name] = storeConf\n\n  // connect it to the track conf\n  trackConfig.store = storeConf.name\n}\n","import { openLocation } from '@jbrowse/core/util/io'\nimport { parseJB1Json, parseJB1Conf, regularizeConf } from './jb1ConfigParse'\nimport { clone, deepUpdate, fillTemplate } from './util'\nimport {\n  JBLocation,\n  UriLocation,\n  LocalPathLocation,\n  Config,\n  Track,\n  Include,\n} from './types'\n\nfunction isUriLocation(location: JBLocation): location is UriLocation {\n  return (location as UriLocation).uri !== undefined\n}\n\nfunction isLocalPathLocation(\n  location: JBLocation,\n): location is LocalPathLocation {\n  return (location as LocalPathLocation).localPath !== undefined\n}\n\nexport async function fetchJb1(\n  dataRoot: JBLocation = { uri: '', locationType: 'UriLocation' },\n  baseConfig: Config = {\n    include: ['{dataRoot}/trackList.json', '{dataRoot}/tracks.conf'],\n  },\n  baseConfigRoot: JBLocation = { uri: '', locationType: 'UriLocation' },\n): Promise<Config> {\n  const protocol = 'uri' in dataRoot ? 'uri' : 'localPath'\n  const dataRootReg = JSON.parse(JSON.stringify(dataRoot))\n  let dataRootLocation = ''\n  if (isUriLocation(dataRoot)) {\n    dataRootLocation = dataRoot.uri\n  }\n  if (isLocalPathLocation(dataRoot)) {\n    dataRootLocation = dataRoot.localPath\n  }\n  if (dataRootLocation.endsWith('/')) {\n    dataRootReg[protocol] = dataRootLocation.slice(\n      0,\n      dataRootLocation.length - 1,\n    )\n  }\n  if (\n    (isUriLocation(baseConfigRoot) && baseConfigRoot.uri) ||\n    (isLocalPathLocation(baseConfigRoot) && baseConfigRoot.localPath)\n  ) {\n    const baseProtocol = 'uri' in baseConfigRoot ? 'uri' : 'localPath'\n    let baseConfigLocation = ''\n    if (isUriLocation(baseConfigRoot)) {\n      baseConfigLocation = baseConfigRoot.uri\n    }\n    if (isLocalPathLocation(baseConfigRoot)) {\n      baseConfigLocation = baseConfigRoot.localPath\n    }\n    if (baseConfigLocation.endsWith('/')) {\n      baseConfigLocation = baseConfigLocation.slice(\n        0,\n        baseConfigLocation.length - 1,\n      )\n    }\n    let newConfig: Config = {}\n    for (const conf of ['jbrowse.conf', 'jbrowse_conf.json']) {\n      let fetchedConfig = null\n      try {\n        // @ts-ignore\n        fetchedConfig = await fetchConfigFile({\n          [baseProtocol]: `${baseConfigLocation}/${conf}`,\n        })\n      } catch (error) {\n        console.error(\n          `tried to access ${baseConfigLocation}/${conf}, but failed`,\n        )\n      }\n      newConfig = mergeConfigs(newConfig, fetchedConfig) || {}\n    }\n    if (dataRootReg[protocol]) {\n      newConfig.dataRoot = dataRootReg[protocol]\n    }\n    return createFinalConfig(newConfig)\n  }\n  const newConfig = regularizeConf(baseConfig, window.location.href)\n  if (dataRootReg[protocol]) {\n    newConfig.dataRoot = dataRootReg[protocol]\n  }\n  return createFinalConfig(newConfig)\n}\n\nexport async function createFinalConfig(\n  baseConfig: Config,\n  defaults = configDefaults,\n): Promise<Config> {\n  const configWithDefaults = deepUpdate(clone(defaults), baseConfig)\n  let finalConfig = await loadIncludes(configWithDefaults)\n  finalConfig = mergeConfigs(finalConfig, baseConfig) || finalConfig\n  fillTemplates(finalConfig, finalConfig)\n  validateConfig(finalConfig)\n  return finalConfig\n}\n\nexport async function fetchConfigFile(location: JBLocation): Promise<Config> {\n  const result = await openLocation(location).readFile('utf8')\n  if (isUriLocation(location)) {\n    return parseJb1(result, location.uri)\n  }\n  if (isLocalPathLocation(location)) {\n    return parseJb1(result, location.localPath)\n  }\n  return parseJb1(result)\n}\n\nexport function parseJb1(config: string, url = ''): Config {\n  if (config.trim().startsWith('{')) {\n    return parseJB1Json(config, url)\n  }\n  return parseJB1Conf(config, url)\n}\n\n/**\n * Merges config object b into a. Properties in b override those in a.\n */\nfunction mergeConfigs(a: Config | null, b: Config | null): Config | null {\n  if (b === null) {\n    return null\n  }\n\n  if (a === null) {\n    a = {}\n  }\n\n  for (const prop of Object.keys(b)) {\n    if (prop === 'tracks' && prop in a) {\n      const aTracks = a[prop] || []\n      const bTracks = b[prop] || []\n      if (Array.isArray(aTracks) && Array.isArray(bTracks)) {\n        a[prop] = mergeTrackConfigs(aTracks || [], bTracks || [])\n      } else {\n        throw new Error(\n          `Track config has not been properly regularized: ${aTracks} ${bTracks}`,\n        )\n      }\n    } else if (\n      !noRecursiveMerge(prop) &&\n      prop in a &&\n      // @ts-ignore\n      typeof b[prop] === 'object' &&\n      // @ts-ignore\n      typeof a[prop] === 'object'\n    ) {\n      // @ts-ignore\n      a[prop] = deepUpdate(a[prop], b[prop])\n    } else if (prop === 'dataRoot') {\n      if (\n        a[prop] === undefined ||\n        (a[prop] === 'data' && b[prop] !== undefined)\n      ) {\n        a[prop] = b[prop]\n      }\n      // @ts-ignore\n    } else if (a[prop] === undefined || b[prop] !== undefined) {\n      // @ts-ignore\n      a[prop] = b[prop]\n    }\n  }\n  return a\n}\n\n/**\n * Special-case merging of two `tracks` configuration arrays.\n */\nfunction mergeTrackConfigs(a: Track[], b: Track[]): Track[] {\n  if (!b.length) {\n    return a\n  }\n\n  // index the tracks in `a` by track label\n  const aTracks: Record<string, Track> = {}\n  a.forEach((t, i): void => {\n    t.index = i\n    aTracks[t.label] = t\n  })\n\n  b.forEach((bT): void => {\n    const aT = aTracks[bT.label]\n    if (aT) {\n      mergeConfigs(aT, bT)\n    } else {\n      a.push(bT)\n    }\n  })\n\n  return a\n}\n\n/**\n * Recursively fetch, parse, and merge all the includes in the given config\n * object.  Calls the callback with the resulting configuration when finished.\n * @param inputConfig - Config to load includes into\n */\nasync function loadIncludes(inputConfig: Config): Promise<Config> {\n  inputConfig = clone(inputConfig)\n\n  async function loadRecur(\n    config: Config,\n    upstreamConf: Config,\n  ): Promise<Config> {\n    const sourceUrl = config.sourceUrl || config.baseUrl\n    if (!sourceUrl) {\n      throw new Error(\n        `Could not determine source URL: ${JSON.stringify(config)}`,\n      )\n    }\n    const newUpstreamConf = mergeConfigs(clone(upstreamConf), config)\n    if (!newUpstreamConf) {\n      throw new Error('Problem merging configs')\n    }\n    const includes = fillTemplates(\n      regularizeIncludes(config.include || []),\n      newUpstreamConf,\n    )\n    delete config.include\n\n    const loads = includes.map(async (include): Promise<Config> => {\n      include.cacheBuster = inputConfig.cacheBuster\n      const includedData = await fetchConfigFile({\n        uri: new URL(include.url, sourceUrl).href,\n        locationType: 'UriLocation',\n      })\n      return loadRecur(includedData, newUpstreamConf)\n    })\n    const includedDataObjects = await Promise.all(loads)\n    includedDataObjects.forEach((includedData): void => {\n      config = mergeConfigs(config, includedData) || config\n    })\n    return config\n  }\n\n  return loadRecur(inputConfig, {})\n}\n\nfunction regularizeIncludes(\n  includes: Include | string | (Include | string)[] | null,\n): Include[] {\n  if (!includes) {\n    return []\n  }\n\n  // coerce include to an array\n  if (!Array.isArray(includes)) {\n    includes = [includes]\n  }\n\n  return includes.map((include): Include => {\n    // coerce bare strings in the includes to URLs\n    if (typeof include === 'string') {\n      include = { url: include }\n    }\n\n    // set defaults for format and version\n    if (!('format' in include)) {\n      include.format = include.url.endsWith('.conf') ? 'conf' : 'JB_json'\n    }\n    if (include.format === 'JB_json' && !('version' in include)) {\n      include.version = 1\n    }\n    return include\n  })\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction fillTemplates<T extends any>(subconfig: T, config: Config): T {\n  if (!subconfig) {\n    return subconfig\n  }\n  if (Array.isArray(subconfig)) {\n    for (let i = 0; i < subconfig.length; i += 1) {\n      subconfig[i] = fillTemplates(subconfig[i], config)\n    }\n  } else if (typeof subconfig === 'object') {\n    // eslint-disable-next-line @typescript-eslint/no-explicit-any\n    const sub = subconfig as Record<string, any>\n    for (const name of Object.keys(sub)) {\n      sub[name] = fillTemplates(sub[name], config)\n    }\n  } else if (typeof subconfig === 'string') {\n    // @ts-ignore\n    return fillTemplate(subconfig, config)\n  }\n\n  return subconfig\n}\n\n/**\n * list of config properties that should not be recursively merged\n * @param propName - name of config property\n */\nfunction noRecursiveMerge(propName: string): boolean {\n  return propName === 'datasets'\n}\n\nconst configDefaults = {\n  tracks: [],\n\n  containerID: 'GenomeBrowser',\n  dataRoot: 'data',\n  show_tracklist: true,\n  show_nav: true,\n  show_menu: true,\n  show_overview: true,\n  show_fullviewlink: true,\n  update_browser_title: true,\n  updateBrowserURL: true,\n\n  refSeqs: '{dataRoot}/seq/refSeqs.json',\n  include: ['jbrowse.conf', 'jbrowse_conf.json'],\n  nameUrl: '{dataRoot}/names/root.json',\n\n  datasets: {\n    _DEFAULT_EXAMPLES: true,\n    volvox: { url: '?data=sample_data/json/volvox', name: 'Volvox Example' },\n    modencode: {\n      url: '?data=sample_data/json/modencode',\n      name: 'MODEncode Example',\n    },\n    yeast: { url: '?data=sample_data/json/yeast', name: 'Yeast Example' },\n  },\n\n  highlightSearchedRegions: false,\n  highResolutionMode: 'auto',\n}\n\n/**\n * Examine the loaded and merged configuration for errors.  Throws\n * exceptions if it finds anything amiss.\n * @returns nothing meaningful\n */\nfunction validateConfig(config: Config): void {\n  if (!config.tracks) {\n    config.tracks = []\n  }\n  if (!config.baseUrl) {\n    throw new Error('Must provide a `baseUrl` in configuration')\n  }\n}\n","import {\n  ConfigurationReference,\n  readConfObject,\n} from '@jbrowse/core/configuration'\nimport { getSession } from '@jbrowse/core/util'\nimport { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'\nimport { types } from 'mobx-state-tree'\nimport configSchema from './configSchema'\n\nimport { fetchJb1 } from './jb1ConfigLoad'\nimport { convertTrackConfig } from './jb1ToJb2'\n\nexport default function (pluginManager) {\n  return types.compose(\n    'JBrowse1Connection',\n    BaseConnectionModelFactory(pluginManager),\n    types\n      .model({\n        configuration: ConfigurationReference(configSchema),\n        type: types.literal('JBrowse1Connection'),\n      })\n      .actions(self => ({\n        connect() {\n          const dataDirLocation = readConfObject(\n            self.configuration,\n            'dataDirLocation',\n          )\n          const session = getSession(self)\n          fetchJb1(dataDirLocation)\n            .then(config => {\n              const assemblyName = readConfObject(\n                self.configuration,\n                'assemblyNames',\n              )[0]\n              if (!assemblyName) {\n                throw new Error(\n                  'assembly name required for JBrowse 1 connection',\n                )\n              }\n              const assemblyConf = session.assemblies.find(\n                assembly => readConfObject(assembly, 'name') === assemblyName,\n              )\n              const sequenceAdapter = readConfObject(assemblyConf, [\n                'sequence',\n                'adapter',\n              ])\n              const jb2Tracks = config.tracks.map(jb1Track => {\n                const jb2Track = convertTrackConfig(\n                  jb1Track,\n                  config.dataRoot,\n                  sequenceAdapter,\n                )\n                jb2Track.assemblyNames = [assemblyName]\n                return jb2Track\n              })\n              self.setTrackConfs(jb2Tracks)\n            })\n            .catch(error => {\n              console.error(error)\n              session.notify(\n                `There was a problem connecting to the JBrowse 1 data directory \"${self.name}\". Please make sure you have entered a valid location. The error that was thrown is: \"${error}\"`,\n                'error',\n              )\n              session.breakConnection(self.configuration)\n            })\n        },\n      })),\n  )\n}\n","import { openLocation } from '@jbrowse/core/util/io'\nimport { objectHash } from '@jbrowse/core/util'\nimport {\n  generateUnknownTrackConf,\n  generateUnsupportedTrackConf,\n  guessAdapter,\n  guessTrackType,\n  UNKNOWN,\n  UNSUPPORTED,\n} from '@jbrowse/core/util/tracks'\nimport { Track, RefSeqs, RefSeq } from './types'\n\ninterface Jb2Track {\n  trackId: string\n  name: string\n  description?: string\n  category?: string[]\n  adapter?: Jb2Adapter\n  type?: string\n  defaultRendering?: string\n}\n\ninterface Jb2Adapter {\n  type: string\n  features?: Jb2Feature[]\n  bamLocation?: Jb2Location\n  cramLocation?: Jb2Location\n  craiLocation?: Jb2Location\n  fastaLocation?: Jb2Location\n  faiLocation?: Jb2Location\n  gziLocation?: Jb2Location\n  twoBitLocation?: Jb2Location\n  bigWigLocation?: Jb2Location\n  bigBedLocation?: Jb2Location\n  vcfGzLocation?: Jb2Location\n  gffGzLocation?: Jb2Location\n  bedGzLocation?: Jb2Location\n  index?: { location: Jb2Location; indexType?: string }\n  rootUrlTemplate?: Jb2Location\n  sequenceAdapter?: Jb2Adapter\n}\n\ninterface Jb2Feature {\n  refName: string\n  uniqueId: string\n  start: number\n  end: number\n}\n\ninterface Jb2Location {\n  uri?: string\n  localPath?: string\n  blobId?: string\n  locationType?: string\n}\n\nexport function convertTrackConfig(\n  jb1TrackConfig: Track,\n  dataRoot: string,\n  sequenceAdapter: Jb2Adapter,\n): Jb2Track {\n  const jb2TrackConfig: Jb2Track = {\n    trackId: objectHash(jb1TrackConfig),\n    name: jb1TrackConfig.key || jb1TrackConfig.label,\n  }\n\n  const description =\n    jb1TrackConfig.metadata &&\n    (jb1TrackConfig.metadata.description || jb1TrackConfig.metadata.Description)\n  if (description) {\n    jb2TrackConfig.description = description\n  }\n\n  const category =\n    jb1TrackConfig.category ||\n    (jb1TrackConfig.metadata && jb1TrackConfig.metadata.category)\n  jb2TrackConfig.category = category ? category.split(/\\s*\\/\\s*/) : []\n\n  const { storeClass } = jb1TrackConfig\n  if (!jb1TrackConfig.urlTemplate) {\n    if (!(storeClass && storeClass.endsWith('FromConfig'))) {\n      const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label\n      console.warn(\n        `Could not import JBrowse1 track \"${trackIdentifier}\" because it does not have a \"urlTemplate\" or is not a \"FromConfig\" track`,\n      )\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        trackIdentifier,\n        jb2TrackConfig.category,\n      )\n    }\n    return generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig)\n  }\n\n  const resolveUrlTemplate = (urlTemplate: string) => {\n    return new URL(urlTemplate, `${dataRoot}/`).href\n      .replace(/%7B/gi, '{')\n      .replace(/%7D/gi, '}')\n  }\n  const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate)\n\n  if (storeClass) {\n    if (storeClass === 'JBrowse/Store/SeqFeature/BAM') {\n      const adapter: Jb2Adapter = {\n        type: 'BamAdapter',\n        bamLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.baiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n        }\n      } else if (jb1TrackConfig.csiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n          indexType: 'CSI',\n        }\n      } else {\n        adapter.index = {\n          location: { uri: `${urlTemplate}.bai`, locationType: 'UriLocation' },\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'AlignmentsTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/CRAM') {\n      const adapter: Jb2Adapter = {\n        type: 'CramAdapter',\n        cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n        sequenceAdapter,\n      }\n      if (jb1TrackConfig.craiUrlTemplate) {\n        adapter.craiLocation = {\n          uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),\n          locationType: 'UriLocation',\n        }\n      } else {\n        adapter.craiLocation = {\n          uri: `${urlTemplate}.crai`,\n          locationType: 'UriLocation',\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'AlignmentsTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/NCList') {\n      return {\n        ...jb2TrackConfig,\n        type: 'FeatureTrack',\n        adapter: {\n          type: 'NCListAdapter',\n          rootUrlTemplate: { uri: urlTemplate, locationType: 'UriLocation' },\n        },\n      }\n    }\n    if (\n      storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||\n      storeClass === 'JBrowse/Store/BigWig'\n    ) {\n      if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {\n        jb2TrackConfig.defaultRendering = 'xyplot'\n      } else if (\n        jb1TrackConfig.type &&\n        jb1TrackConfig.type.endsWith('Density')\n      ) {\n        jb2TrackConfig.defaultRendering = 'density'\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'QuantitativeTrack',\n        adapter: {\n          type: 'BigWigAdapter',\n          bigWigLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n        },\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/VCFTabix') {\n      const adapter: Jb2Adapter = {\n        type: 'VcfTabixAdapter',\n        vcfGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.tbiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n        }\n      } else if (jb1TrackConfig.csiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n          indexType: 'CSI',\n        }\n      } else {\n        adapter.index = {\n          location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'VariantTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/VCFTribble') {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `VCFTribble (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `GFF3 (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {\n      return {\n        ...jb2TrackConfig,\n        type: 'FeatureTrack',\n        adapter: {\n          type: 'BigBedAdapter',\n          bigBedLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n        },\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/GFF3Tabix') {\n      const adapter: Jb2Adapter = {\n        type: 'Gff3TabixAdapter',\n        gffGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.tbiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n        }\n      } else if (jb1TrackConfig.csiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n          indexType: 'CSI',\n        }\n      } else {\n        adapter.index = {\n          location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'FeatureTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/BED') {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `BED (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/BEDTabix') {\n      const adapter: Jb2Adapter = {\n        type: 'BedTabixAdapter',\n        bedGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.tbiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n        }\n      } else if (jb1TrackConfig.csiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n          indexType: 'CSI',\n        }\n      } else {\n        adapter.index = {\n          location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'FeatureTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `GTF (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (\n      storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' ||\n      storeClass === 'JBrowse/Store/Sequence/StaticChunked'\n    ) {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `StaticChunked (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/UnindexedFasta') {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `UnindexedFasta (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta') {\n      const adapter: Jb2Adapter = {\n        type: 'IndexedFastaAdapter',\n        fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.faiUrlTemplate) {\n        adapter.faiLocation = {\n          uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),\n          locationType: 'UriLocation',\n        }\n      } else {\n        adapter.faiLocation = {\n          uri: `${urlTemplate}.fai`,\n          locationType: 'UriLocation',\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'SequenceTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta') {\n      const adapter: Jb2Adapter = {\n        type: 'BgzipFastaAdapter',\n        fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.faiUrlTemplate) {\n        adapter.faiLocation = {\n          uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),\n          locationType: 'UriLocation',\n        }\n      } else {\n        adapter.faiLocation = {\n          uri: `${urlTemplate}.fai`,\n          locationType: 'UriLocation',\n        }\n      }\n      if (jb1TrackConfig.gziUrlTemplate) {\n        adapter.gziLocation = {\n          uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),\n          locationType: 'UriLocation',\n        }\n      } else {\n        adapter.gziLocation = {\n          uri: `${urlTemplate}.gzi`,\n          locationType: 'UriLocation',\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'ReferenceSequenceTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/TwoBit') {\n      return {\n        ...jb2TrackConfig,\n        type: 'ReferenceSequenceTrack',\n        adapter: {\n          type: 'TwoBitAdapter',\n          twoBitLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n        },\n      }\n    }\n  }\n\n  // If we don't recogize the store class, make a best effort to guess by file type\n  jb2TrackConfig.adapter = guessAdapter(\n    { uri: urlTemplate, locationType: 'UriLocation' },\n    undefined,\n    urlTemplate,\n  )\n  if (!jb2TrackConfig.adapter) {\n    throw new Error('Could not determine adapter')\n  }\n\n  if (jb2TrackConfig.adapter.type === UNSUPPORTED) {\n    return generateUnsupportedTrackConf(\n      jb2TrackConfig.name,\n      urlTemplate,\n      jb2TrackConfig.category,\n    )\n  }\n  if (jb2TrackConfig.adapter.type === UNKNOWN) {\n    return generateUnknownTrackConf(\n      jb2TrackConfig.name,\n      urlTemplate,\n      jb2TrackConfig.category,\n    )\n  }\n\n  jb2TrackConfig.type = guessTrackType(jb2TrackConfig.adapter.type)\n\n  if (jb2TrackConfig.type === 'QuantitativeTrack') {\n    if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {\n      jb2TrackConfig.defaultRendering = 'xyplot'\n    } else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {\n      jb2TrackConfig.defaultRendering = 'density'\n    }\n  }\n\n  return jb2TrackConfig\n}\n\nfunction generateFromConfigTrackConfig(\n  jb1TrackConfig: Track,\n  jb2TrackConfig: Jb2Track,\n): Jb2Track {\n  const jb1Features = jb1TrackConfig.features || []\n  const jb2Features = jb1Features.map((feature): Jb2Feature => {\n    const jb2Feature: Jb2Feature = JSON.parse(JSON.stringify(feature))\n    jb2Feature.refName = feature.seq_id\n    jb2Feature.uniqueId = `${feature.seq_id}:${feature.start}-${feature.end}:${\n      feature.name || ''\n    }`\n    return jb2Feature\n  })\n  jb2TrackConfig.adapter = {\n    type: 'FromConfigAdapter',\n    features: jb2Features,\n  }\n  jb2TrackConfig.type = 'FeatureTrack'\n  return jb2TrackConfig\n}\n\nexport async function createRefSeqsAdapter(\n  refSeqs: string | RefSeqs,\n): Promise<Jb2Adapter> {\n  if (typeof refSeqs === 'string') {\n    // assume refSeqs is a url if it is string\n    refSeqs = {\n      url: refSeqs,\n    }\n  }\n\n  // check refseq urls\n  if (refSeqs.url) {\n    if (refSeqs.url.match(/.fai$/)) {\n      return {\n        type: 'IndexedFastaAdapter',\n        fastaLocation: {\n          uri: refSeqs.url.slice(0, -4),\n          locationType: 'UriLocation',\n        },\n        faiLocation: {\n          uri: refSeqs.url,\n          locationType: 'UriLocation',\n        },\n      }\n    }\n    if (refSeqs.url.match(/.2bit$/)) {\n      return {\n        type: 'TwoBitAdapter',\n        twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },\n      }\n    }\n    if (refSeqs.url.match(/.fa$/)) {\n      throw new Error('Unindexed FASTA adapter not available')\n    }\n    if (refSeqs.url.match(/.sizes/)) {\n      throw new Error('chromosome SIZES adapter not available')\n    }\n    const refSeqsJson = await openLocation({\n      uri: refSeqs.url,\n      locationType: 'UriLocation',\n    }).readFile('utf8')\n    const refSeqsData: RefSeq[] = JSON.parse(refSeqsJson)\n    return refSeqAdapterFromConfig(refSeqsData)\n  }\n  if ('data' in refSeqs) {\n    return refSeqAdapterFromConfig(refSeqs.data || [])\n  }\n  throw new Error(\n    `Could not determine adapter for JBrowse1 refSeqs: ${\n      refSeqs.url || JSON.stringify(refSeqs)\n    }`,\n  )\n}\n\nfunction refSeqAdapterFromConfig(refSeqsData: RefSeq[]): Jb2Adapter {\n  const features = refSeqsData.map(\n    (refSeq): Jb2Feature => ({\n      refName: refSeq.name,\n      uniqueId: refSeq.name,\n      start: refSeq.start,\n      end: refSeq.end,\n    }),\n  )\n  return {\n    type: 'FromConfigAdapter',\n    features,\n  }\n}\n","import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType'\nimport ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType'\nimport Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { FileLocation } from '@jbrowse/core/util/types'\nimport { configSchema as ncListAdapterConfigSchema } from './NCListAdapter'\nimport {\n  AdapterClass as JBrowse1TextSearchAdapterClass,\n  configSchema as jbrowse1AdapterConfigSchema,\n} from './JBrowse1TextSeachAdapter'\nimport { AdapterGuesser, getFileName } from '@jbrowse/core/util/tracks'\n\nimport {\n  configSchema as jbrowse1ConfigSchema,\n  modelFactory as jbrowse1ModelFactory,\n} from './JBrowse1Connection'\n\nexport default class LegacyJBrowsePlugin extends Plugin {\n  name = 'LegacyJBrowsePlugin'\n\n  install(pluginManager: PluginManager) {\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'NCListAdapter',\n          configSchema: ncListAdapterConfigSchema,\n          getAdapterClass: () =>\n            import('./NCListAdapter/NCListAdapter').then(r => r.default),\n        }),\n    )\n    pluginManager.addToExtensionPoint(\n      'Core-guessAdapterForLocation',\n      (adapterGuesser: AdapterGuesser) => {\n        return (\n          file: FileLocation,\n          index?: FileLocation,\n          adapterHint?: string,\n        ) => {\n          const regexGuess = /trackData.jsonz?$/i\n          const adapterName = 'NCListAdapter'\n          const fileName = getFileName(file)\n          if (regexGuess.test(fileName) || adapterHint === adapterName) {\n            return {\n              type: adapterName,\n              rootUrlTemplate: file,\n            }\n          }\n          return adapterGuesser(file, index, adapterHint)\n        }\n      },\n    )\n\n    pluginManager.addTextSearchAdapterType(\n      () =>\n        new TextSearchAdapterType({\n          name: 'JBrowse1TextSearchAdapter',\n          configSchema: jbrowse1AdapterConfigSchema,\n          AdapterClass: JBrowse1TextSearchAdapterClass,\n          description: 'A JBrowse 1 text search adapter',\n        }),\n    )\n\n    pluginManager.addConnectionType(\n      () =>\n        new ConnectionType({\n          name: 'JBrowse1Connection',\n          configSchema: jbrowse1ConfigSchema,\n          stateModel: jbrowse1ModelFactory(pluginManager),\n          displayName: 'JBrowse 1 Data',\n          description: 'A JBrowse 1 data directory',\n          url: '//jbrowse.org/',\n        }),\n    )\n  }\n}\n","import {\n  Feature,\n  SimpleFeatureSerialized,\n} from '@jbrowse/core/util/simpleFeature'\n\nconst jb2ToJb1 = { refName: 'seq_id' }\n\nconst jb1ToJb2 = { seq_id: 'refName' }\n\n/**\n * wrapper to adapt nclist features to act like jbrowse 2 features\n */\nexport default class NCListFeature implements Feature {\n  private parentHandle?: Feature\n\n  private uniqueId: string\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  constructor(private ncFeature: any, parent?: Feature, id?: string) {\n    this.uniqueId = id || ncFeature.id()\n    this.parentHandle = parent\n  }\n\n  set(): void {\n    throw new Error('not implemented')\n  }\n\n  jb2TagToJb1Tag(tag: string): string {\n    // @ts-ignore\n    const mapped = jb2ToJb1[tag] || tag\n    return mapped.toLowerCase()\n  }\n\n  jb1TagToJb2Tag(tag: string): string {\n    const t = tag.toLowerCase()\n    // @ts-ignore\n    const mapped = jb1ToJb2[t] || t\n    return mapped\n  }\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  get(attrName: string): any {\n    const attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName))\n    if (attr && attrName === 'subfeatures') {\n      // eslint-disable-next-line @typescript-eslint/no-explicit-any\n      return attr.map((subfeature: any) => new NCListFeature(subfeature, this))\n    }\n    return attr\n  }\n\n  /**\n   * Get an array listing which data keys are present in this feature.\n   */\n  tags(): string[] {\n    return this.ncFeature.tags().map((t: string) => this.jb1TagToJb2Tag(t))\n  }\n\n  /**\n   * Get the unique ID of this feature.\n   */\n  id(): string {\n    return this.uniqueId\n  }\n\n  /**\n   * Get this feature's parent feature, or undefined if none.\n   */\n  parent(): Feature | undefined {\n    return this.parentHandle\n  }\n\n  /**\n   * Get an array of child features, or undefined if none.\n   */\n  children(): Feature[] | undefined {\n    return this.get('subfeatures')\n  }\n\n  toJSON(): SimpleFeatureSerialized {\n    const data: SimpleFeatureSerialized = { uniqueId: this.id() }\n    this.ncFeature.tags().forEach((tag: string) => {\n      const mappedTag = this.jb1TagToJb2Tag(tag)\n      const value = this.ncFeature.get(tag)\n      if (mappedTag === 'subfeatures') {\n        data.subfeatures = (value || []).map((f: Feature) => {\n          // note: was new NCListFeature(f, `${this.id()}-${i}`, this).toJSON()\n          return new NCListFeature(f, this).toJSON()\n        })\n      } else {\n        data[mappedTag] = value\n      }\n    })\n    return data\n  }\n}\n","import NCListStore from '@gmod/nclist'\nimport { Region } from '@jbrowse/core/util/types'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { checkAbortSignal } from '@jbrowse/core/util'\nimport { RemoteFile } from 'generic-filehandle'\nimport { Instance } from 'mobx-state-tree'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport NCListFeature from './NCListFeature'\nimport MyConfigSchema from './configSchema'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\nexport default class NCListAdapter extends BaseFeatureDataAdapter {\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  private nclist: any\n\n  private configRefNames?: string[]\n\n  constructor(\n    config: Instance<typeof MyConfigSchema>,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const refNames = readConfObject(config, 'refNames')\n    const rootUrlTemplate = readConfObject(config, 'rootUrlTemplate')\n    this.configRefNames = refNames\n\n    this.nclist = new NCListStore({\n      baseUrl: '',\n      urlTemplate: rootUrlTemplate.uri,\n      readFile: (url: string) =>\n        new RemoteFile(\n          String(\n            rootUrlTemplate.baseUri\n              ? new URL(url, rootUrlTemplate.baseUri).toString()\n              : url,\n          ),\n        ).readFile(),\n    })\n  }\n\n  /**\n   * Fetch features for a certain region. Use getFeaturesInRegion() if you also\n   * want to verify that the store has features for the given reference sequence\n   * before fetching.\n   * @param region -\n   * @param opts - [signal] optional signalling object for aborting the fetch\n   * @returns Observable of Feature objects in the region\n   */\n  getFeatures(region: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const { signal } = opts\n      for await (const feature of this.nclist.getFeatures(region, opts)) {\n        checkAbortSignal(signal)\n        observer.next(this.wrapFeature(feature))\n      }\n      observer.complete()\n    })\n  }\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  wrapFeature(ncFeature: any): NCListFeature {\n    return new NCListFeature(\n      ncFeature,\n      undefined,\n      `${this.id}-${ncFeature.id()}`,\n    )\n  }\n\n  async hasDataForRefName(refName: string) {\n    const root = await 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+{"version":3,"file":"plugin-legacy-jbrowse.cjs.production.min.js","sources":["../src/NCListAdapter/configSchema.ts","../../../node_modules/regenerator-runtime/runtime.js","../src/JBrowse1TextSeachAdapter/HttpMap.ts","../src/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.ts","../src/JBrowse1TextSeachAdapter/configSchema.ts","../src/JBrowse1Connection/configSchema.ts","../src/JBrowse1Connection/util.ts","../src/JBrowse1Connection/jb1ConfigParse.ts","../src/JBrowse1Connection/jb1ConfigLoad.ts","../src/JBrowse1Connection/model.js","../src/JBrowse1Connection/jb1ToJb2.ts","../src/index.ts","../src/NCListAdapter/NCListFeature.ts","../src/NCListAdapter/NCListAdapter.ts"],"sourcesContent":["import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'NCListAdapter',\n  {\n    rootUrlTemplate: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/my/{refseq}/trackData.json',\n        locationType: 'UriLocation',\n      },\n    },\n    refNames: {\n      type: 'stringArray',\n      defaultValue: [],\n      description: 'List of refNames used by the NCList used for aliasing',\n    },\n  },\n  { explicitlyTyped: true },\n)\n","/**\n * Copyright (c) 2014-present, Facebook, Inc.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\nvar runtime = (function (exports) {\n  \"use strict\";\n\n  var Op = Object.prototype;\n  var hasOwn = Op.hasOwnProperty;\n  var undefined; // More compressible than void 0.\n  var $Symbol = typeof Symbol === \"function\" ? Symbol : {};\n  var iteratorSymbol = $Symbol.iterator || \"@@iterator\";\n  var asyncIteratorSymbol = $Symbol.asyncIterator || \"@@asyncIterator\";\n  var toStringTagSymbol = $Symbol.toStringTag || \"@@toStringTag\";\n\n  function define(obj, key, value) {\n    Object.defineProperty(obj, key, {\n      value: value,\n      enumerable: true,\n      configurable: true,\n      writable: true\n    });\n    return obj[key];\n  }\n  try {\n    // IE 8 has a broken Object.defineProperty that only works on DOM objects.\n    define({}, \"\");\n  } catch (err) {\n    define = function(obj, key, value) {\n      return obj[key] = value;\n    };\n  }\n\n  function wrap(innerFn, outerFn, self, tryLocsList) {\n    // If outerFn provided and outerFn.prototype is a Generator, then outerFn.prototype instanceof Generator.\n    var protoGenerator = outerFn && outerFn.prototype instanceof Generator ? outerFn : Generator;\n    var generator = Object.create(protoGenerator.prototype);\n    var context = new Context(tryLocsList || []);\n\n    // The ._invoke method unifies the implementations of the .next,\n    // .throw, and .return methods.\n    generator._invoke = makeInvokeMethod(innerFn, self, context);\n\n    return generator;\n  }\n  exports.wrap = wrap;\n\n  // Try/catch helper to minimize deoptimizations. Returns a completion\n  // record like context.tryEntries[i].completion. This interface could\n  // have been (and was previously) designed to take a closure to be\n  // invoked without arguments, but in all the cases we care about we\n  // already have an existing method we want to call, so there's no need\n  // to create a new function object. We can even get away with assuming\n  // the method takes exactly one argument, since that happens to be true\n  // in every case, so we don't have to touch the arguments object. The\n  // only additional allocation required is the completion record, which\n  // has a stable shape and so hopefully should be cheap to allocate.\n  function tryCatch(fn, obj, arg) {\n    try {\n      return { type: \"normal\", arg: fn.call(obj, arg) };\n    } catch (err) {\n      return { type: \"throw\", arg: err };\n    }\n  }\n\n  var GenStateSuspendedStart = \"suspendedStart\";\n  var GenStateSuspendedYield = \"suspendedYield\";\n  var GenStateExecuting = \"executing\";\n  var GenStateCompleted = \"completed\";\n\n  // Returning this object from the innerFn has the same effect as\n  // breaking out of the dispatch switch statement.\n  var ContinueSentinel = {};\n\n  // Dummy constructor functions that we use as the .constructor and\n  // .constructor.prototype properties for functions that return Generator\n  // objects. For full spec compliance, you may wish to configure your\n  // minifier not to mangle the names of these two functions.\n  function Generator() {}\n  function GeneratorFunction() {}\n  function GeneratorFunctionPrototype() {}\n\n  // This is a polyfill for %IteratorPrototype% for environments that\n  // don't natively support it.\n  var IteratorPrototype = {};\n  define(IteratorPrototype, iteratorSymbol, function () {\n    return this;\n  });\n\n  var getProto = Object.getPrototypeOf;\n  var NativeIteratorPrototype = getProto && getProto(getProto(values([])));\n  if (NativeIteratorPrototype &&\n      NativeIteratorPrototype !== Op &&\n      hasOwn.call(NativeIteratorPrototype, iteratorSymbol)) {\n    // This environment has a native %IteratorPrototype%; use it instead\n    // of the polyfill.\n    IteratorPrototype = NativeIteratorPrototype;\n  }\n\n  var Gp = GeneratorFunctionPrototype.prototype =\n    Generator.prototype = Object.create(IteratorPrototype);\n  GeneratorFunction.prototype = GeneratorFunctionPrototype;\n  define(Gp, \"constructor\", GeneratorFunctionPrototype);\n  define(GeneratorFunctionPrototype, \"constructor\", GeneratorFunction);\n  GeneratorFunction.displayName = define(\n    GeneratorFunctionPrototype,\n    toStringTagSymbol,\n    \"GeneratorFunction\"\n  );\n\n  // Helper for defining the .next, .throw, and .return methods of the\n  // Iterator interface in terms of a single ._invoke method.\n  function defineIteratorMethods(prototype) {\n    [\"next\", \"throw\", \"return\"].forEach(function(method) {\n      define(prototype, method, function(arg) {\n        return this._invoke(method, arg);\n      });\n    });\n  }\n\n  exports.isGeneratorFunction = function(genFun) {\n    var ctor = typeof genFun === \"function\" && genFun.constructor;\n    return ctor\n      ? ctor === GeneratorFunction ||\n        // For the native GeneratorFunction constructor, the best we can\n        // do is to check its .name property.\n        (ctor.displayName || ctor.name) === \"GeneratorFunction\"\n      : false;\n  };\n\n  exports.mark = function(genFun) {\n    if (Object.setPrototypeOf) {\n      Object.setPrototypeOf(genFun, GeneratorFunctionPrototype);\n    } else {\n      genFun.__proto__ = GeneratorFunctionPrototype;\n      define(genFun, toStringTagSymbol, \"GeneratorFunction\");\n    }\n    genFun.prototype = Object.create(Gp);\n    return genFun;\n  };\n\n  // Within the body of any async function, `await x` is transformed to\n  // `yield regeneratorRuntime.awrap(x)`, so that the runtime can test\n  // `hasOwn.call(value, \"__await\")` to determine if the yielded value is\n  // meant to be awaited.\n  exports.awrap = function(arg) {\n    return { __await: arg };\n  };\n\n  function AsyncIterator(generator, PromiseImpl) {\n    function invoke(method, arg, resolve, reject) {\n      var record = tryCatch(generator[method], generator, arg);\n      if (record.type === \"throw\") {\n        reject(record.arg);\n      } else {\n        var result = record.arg;\n        var value = result.value;\n        if (value &&\n            typeof value === \"object\" &&\n            hasOwn.call(value, \"__await\")) {\n          return PromiseImpl.resolve(value.__await).then(function(value) {\n            invoke(\"next\", value, resolve, reject);\n          }, function(err) {\n            invoke(\"throw\", err, resolve, reject);\n          });\n        }\n\n        return PromiseImpl.resolve(value).then(function(unwrapped) {\n          // When a yielded Promise is resolved, its final value becomes\n          // the .value of the Promise<{value,done}> result for the\n          // current iteration.\n          result.value = unwrapped;\n          resolve(result);\n        }, function(error) {\n          // If a rejected Promise was yielded, throw the rejection back\n          // into the async generator function so it can be handled there.\n          return invoke(\"throw\", error, resolve, reject);\n        });\n      }\n    }\n\n    var previousPromise;\n\n    function enqueue(method, arg) {\n      function callInvokeWithMethodAndArg() {\n        return new PromiseImpl(function(resolve, reject) {\n          invoke(method, arg, resolve, reject);\n        });\n      }\n\n      return previousPromise =\n        // If enqueue has been called before, then we want to wait until\n        // all previous Promises have been resolved before calling invoke,\n        // so that results are always delivered in the correct order. If\n        // enqueue has not been called before, then it is important to\n        // call invoke immediately, without waiting on a callback to fire,\n        // so that the async generator function has the opportunity to do\n        // any necessary setup in a predictable way. This predictability\n        // is why the Promise constructor synchronously invokes its\n        // executor callback, and why async functions synchronously\n        // execute code before the first await. Since we implement simple\n        // async functions in terms of async generators, it is especially\n        // important to get this right, even though it requires care.\n        previousPromise ? previousPromise.then(\n          callInvokeWithMethodAndArg,\n          // Avoid propagating failures to Promises returned by later\n          // invocations of the iterator.\n          callInvokeWithMethodAndArg\n        ) : callInvokeWithMethodAndArg();\n    }\n\n    // Define the unified helper method that is used to implement .next,\n    // .throw, and .return (see defineIteratorMethods).\n    this._invoke = enqueue;\n  }\n\n  defineIteratorMethods(AsyncIterator.prototype);\n  define(AsyncIterator.prototype, asyncIteratorSymbol, function () {\n    return this;\n  });\n  exports.AsyncIterator = AsyncIterator;\n\n  // Note that simple async functions are implemented on top of\n  // AsyncIterator objects; they just return a Promise for the value of\n  // the final result produced by the iterator.\n  exports.async = function(innerFn, outerFn, self, tryLocsList, PromiseImpl) {\n    if (PromiseImpl === void 0) PromiseImpl = Promise;\n\n    var iter = new AsyncIterator(\n      wrap(innerFn, outerFn, self, tryLocsList),\n      PromiseImpl\n    );\n\n    return exports.isGeneratorFunction(outerFn)\n      ? iter // If outerFn is a generator, return the full iterator.\n      : iter.next().then(function(result) {\n          return result.done ? result.value : iter.next();\n        });\n  };\n\n  function makeInvokeMethod(innerFn, self, context) {\n    var state = GenStateSuspendedStart;\n\n    return function invoke(method, arg) {\n      if (state === GenStateExecuting) {\n        throw new Error(\"Generator is already running\");\n      }\n\n      if (state === GenStateCompleted) {\n        if (method === \"throw\") {\n          throw arg;\n        }\n\n        // Be forgiving, per 25.3.3.3.3 of the spec:\n        // https://people.mozilla.org/~jorendorff/es6-draft.html#sec-generatorresume\n        return doneResult();\n      }\n\n      context.method = method;\n      context.arg = arg;\n\n      while (true) {\n        var delegate = context.delegate;\n        if (delegate) {\n          var delegateResult = maybeInvokeDelegate(delegate, context);\n          if (delegateResult) {\n            if (delegateResult === ContinueSentinel) continue;\n            return delegateResult;\n          }\n        }\n\n        if (context.method === \"next\") {\n          // Setting context._sent for legacy support of Babel's\n          // function.sent implementation.\n          context.sent = context._sent = context.arg;\n\n        } else if (context.method === \"throw\") {\n          if (state === GenStateSuspendedStart) {\n            state = GenStateCompleted;\n            throw context.arg;\n          }\n\n          context.dispatchException(context.arg);\n\n        } else if (context.method === \"return\") {\n          context.abrupt(\"return\", context.arg);\n        }\n\n        state = GenStateExecuting;\n\n        var record = tryCatch(innerFn, self, context);\n        if (record.type === \"normal\") {\n          // If an exception is thrown from innerFn, we leave state ===\n          // GenStateExecuting and loop back for another invocation.\n          state = context.done\n            ? GenStateCompleted\n            : GenStateSuspendedYield;\n\n          if (record.arg === ContinueSentinel) {\n            continue;\n          }\n\n          return {\n            value: record.arg,\n            done: context.done\n          };\n\n        } else if (record.type === \"throw\") {\n          state = GenStateCompleted;\n          // Dispatch the exception by looping back around to the\n          // context.dispatchException(context.arg) call above.\n          context.method = \"throw\";\n          context.arg = record.arg;\n        }\n      }\n    };\n  }\n\n  // Call delegate.iterator[context.method](context.arg) and handle the\n  // result, either by returning a { value, done } result from the\n  // delegate iterator, or by modifying context.method and context.arg,\n  // setting context.delegate to null, and returning the ContinueSentinel.\n  function maybeInvokeDelegate(delegate, context) {\n    var method = delegate.iterator[context.method];\n    if (method === undefined) {\n      // A .throw or .return when the delegate iterator has no .throw\n      // method always terminates the yield* loop.\n      context.delegate = null;\n\n      if (context.method === \"throw\") {\n        // Note: [\"return\"] must be used for ES3 parsing compatibility.\n        if (delegate.iterator[\"return\"]) {\n          // If the delegate iterator has a return method, give it a\n          // chance to clean up.\n          context.method = \"return\";\n          context.arg = undefined;\n          maybeInvokeDelegate(delegate, context);\n\n          if (context.method === \"throw\") {\n            // If maybeInvokeDelegate(context) changed context.method from\n            // \"return\" to \"throw\", let that override the TypeError below.\n            return ContinueSentinel;\n          }\n        }\n\n        context.method = \"throw\";\n        context.arg = new TypeError(\n          \"The iterator does not provide a 'throw' method\");\n      }\n\n      return ContinueSentinel;\n    }\n\n    var record = tryCatch(method, delegate.iterator, context.arg);\n\n    if (record.type === \"throw\") {\n      context.method = \"throw\";\n      context.arg = record.arg;\n      context.delegate = null;\n      return ContinueSentinel;\n    }\n\n    var info = record.arg;\n\n    if (! info) {\n      context.method = \"throw\";\n      context.arg = new TypeError(\"iterator result is not an object\");\n      context.delegate = null;\n      return ContinueSentinel;\n    }\n\n    if (info.done) {\n      // Assign the result of the finished delegate to the temporary\n      // variable specified by delegate.resultName (see delegateYield).\n      context[delegate.resultName] = info.value;\n\n      // Resume execution at the desired location (see delegateYield).\n      context.next = delegate.nextLoc;\n\n      // If context.method was \"throw\" but the delegate handled the\n      // exception, let the outer generator proceed normally. If\n      // context.method was \"next\", forget context.arg since it has been\n      // \"consumed\" by the delegate iterator. If context.method was\n      // \"return\", allow the original .return call to continue in the\n      // outer generator.\n      if (context.method !== \"return\") {\n        context.method = \"next\";\n        context.arg = undefined;\n      }\n\n    } else {\n      // Re-yield the result returned by the delegate method.\n      return info;\n    }\n\n    // The delegate iterator is finished, so forget it and continue with\n    // the outer generator.\n    context.delegate = null;\n    return ContinueSentinel;\n  }\n\n  // Define Generator.prototype.{next,throw,return} in terms of the\n  // unified ._invoke helper method.\n  defineIteratorMethods(Gp);\n\n  define(Gp, toStringTagSymbol, \"Generator\");\n\n  // A Generator should always return itself as the iterator object when the\n  // @@iterator function is called on it. Some browsers' implementations of the\n  // iterator prototype chain incorrectly implement this, causing the Generator\n  // object to not be returned from this call. This ensures that doesn't happen.\n  // See https://github.com/facebook/regenerator/issues/274 for more details.\n  define(Gp, iteratorSymbol, function() {\n    return this;\n  });\n\n  define(Gp, \"toString\", function() {\n    return \"[object Generator]\";\n  });\n\n  function pushTryEntry(locs) {\n    var entry = { tryLoc: locs[0] };\n\n    if (1 in locs) {\n      entry.catchLoc = locs[1];\n    }\n\n    if (2 in locs) {\n      entry.finallyLoc = locs[2];\n      entry.afterLoc = locs[3];\n    }\n\n    this.tryEntries.push(entry);\n  }\n\n  function resetTryEntry(entry) {\n    var record = entry.completion || {};\n    record.type = \"normal\";\n    delete record.arg;\n    entry.completion = record;\n  }\n\n  function Context(tryLocsList) {\n    // The root entry object (effectively a try statement without a catch\n    // or a finally block) gives us a place to store values thrown from\n    // locations where there is no enclosing try statement.\n    this.tryEntries = [{ tryLoc: \"root\" }];\n    tryLocsList.forEach(pushTryEntry, this);\n    this.reset(true);\n  }\n\n  exports.keys = function(object) {\n    var keys = [];\n    for (var key in object) {\n      keys.push(key);\n    }\n    keys.reverse();\n\n    // Rather than returning an object with a next method, we keep\n    // things simple and return the next function itself.\n    return function next() {\n      while (keys.length) {\n        var key = keys.pop();\n        if (key in object) {\n          next.value = key;\n          next.done = false;\n          return next;\n        }\n      }\n\n      // To avoid creating an additional object, we just hang the .value\n      // and .done properties off the next function object itself. This\n      // also ensures that the minifier will not anonymize the function.\n      next.done = true;\n      return next;\n    };\n  };\n\n  function values(iterable) {\n    if (iterable) {\n      var iteratorMethod = iterable[iteratorSymbol];\n      if (iteratorMethod) {\n        return iteratorMethod.call(iterable);\n      }\n\n      if (typeof iterable.next === \"function\") {\n        return iterable;\n      }\n\n      if (!isNaN(iterable.length)) {\n        var i = -1, next = function next() {\n          while (++i < iterable.length) {\n            if (hasOwn.call(iterable, i)) {\n              next.value = iterable[i];\n              next.done = false;\n              return next;\n            }\n          }\n\n          next.value = undefined;\n          next.done = true;\n\n          return next;\n        };\n\n        return next.next = next;\n      }\n    }\n\n    // Return an iterator with no values.\n    return { next: doneResult };\n  }\n  exports.values = values;\n\n  function doneResult() {\n    return { value: undefined, done: true };\n  }\n\n  Context.prototype = {\n    constructor: Context,\n\n    reset: function(skipTempReset) {\n      this.prev = 0;\n      this.next = 0;\n      // Resetting context._sent for legacy support of Babel's\n      // function.sent implementation.\n      this.sent = this._sent = undefined;\n      this.done = false;\n      this.delegate = null;\n\n      this.method = \"next\";\n      this.arg = undefined;\n\n      this.tryEntries.forEach(resetTryEntry);\n\n      if (!skipTempReset) {\n        for (var name in this) {\n          // Not sure about the optimal order of these conditions:\n          if (name.charAt(0) === \"t\" &&\n              hasOwn.call(this, name) &&\n              !isNaN(+name.slice(1))) {\n            this[name] = undefined;\n          }\n        }\n      }\n    },\n\n    stop: function() {\n      this.done = true;\n\n      var rootEntry = this.tryEntries[0];\n      var rootRecord = rootEntry.completion;\n      if (rootRecord.type === \"throw\") {\n        throw rootRecord.arg;\n      }\n\n      return this.rval;\n    },\n\n    dispatchException: function(exception) {\n      if (this.done) {\n        throw exception;\n      }\n\n      var context = this;\n      function handle(loc, caught) {\n        record.type = \"throw\";\n        record.arg = exception;\n        context.next = loc;\n\n        if (caught) {\n          // If the dispatched exception was caught by a catch block,\n          // then let that catch block handle the exception normally.\n          context.method = \"next\";\n          context.arg = undefined;\n        }\n\n        return !! caught;\n      }\n\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        var record = entry.completion;\n\n        if (entry.tryLoc === \"root\") {\n          // Exception thrown outside of any try block that could handle\n          // it, so set the completion value of the entire function to\n          // throw the exception.\n          return handle(\"end\");\n        }\n\n        if (entry.tryLoc <= this.prev) {\n          var hasCatch = hasOwn.call(entry, \"catchLoc\");\n          var hasFinally = hasOwn.call(entry, \"finallyLoc\");\n\n          if (hasCatch && hasFinally) {\n            if (this.prev < entry.catchLoc) {\n              return handle(entry.catchLoc, true);\n            } else if (this.prev < entry.finallyLoc) {\n              return handle(entry.finallyLoc);\n            }\n\n          } else if (hasCatch) {\n            if (this.prev < entry.catchLoc) {\n              return handle(entry.catchLoc, true);\n            }\n\n          } else if (hasFinally) {\n            if (this.prev < entry.finallyLoc) {\n              return handle(entry.finallyLoc);\n            }\n\n          } else {\n            throw new Error(\"try statement without catch or finally\");\n          }\n        }\n      }\n    },\n\n    abrupt: function(type, arg) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.tryLoc <= this.prev &&\n            hasOwn.call(entry, \"finallyLoc\") &&\n            this.prev < entry.finallyLoc) {\n          var finallyEntry = entry;\n          break;\n        }\n      }\n\n      if (finallyEntry &&\n          (type === \"break\" ||\n           type === \"continue\") &&\n          finallyEntry.tryLoc <= arg &&\n          arg <= finallyEntry.finallyLoc) {\n        // Ignore the finally entry if control is not jumping to a\n        // location outside the try/catch block.\n        finallyEntry = null;\n      }\n\n      var record = finallyEntry ? finallyEntry.completion : {};\n      record.type = type;\n      record.arg = arg;\n\n      if (finallyEntry) {\n        this.method = \"next\";\n        this.next = finallyEntry.finallyLoc;\n        return ContinueSentinel;\n      }\n\n      return this.complete(record);\n    },\n\n    complete: function(record, afterLoc) {\n      if (record.type === \"throw\") {\n        throw record.arg;\n      }\n\n      if (record.type === \"break\" ||\n          record.type === \"continue\") {\n        this.next = record.arg;\n      } else if (record.type === \"return\") {\n        this.rval = this.arg = record.arg;\n        this.method = \"return\";\n        this.next = \"end\";\n      } else if (record.type === \"normal\" && afterLoc) {\n        this.next = afterLoc;\n      }\n\n      return ContinueSentinel;\n    },\n\n    finish: function(finallyLoc) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.finallyLoc === finallyLoc) {\n          this.complete(entry.completion, entry.afterLoc);\n          resetTryEntry(entry);\n          return ContinueSentinel;\n        }\n      }\n    },\n\n    \"catch\": function(tryLoc) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.tryLoc === tryLoc) {\n          var record = entry.completion;\n          if (record.type === \"throw\") {\n            var thrown = record.arg;\n            resetTryEntry(entry);\n          }\n          return thrown;\n        }\n      }\n\n      // The context.catch method must only be called with a location\n      // argument that corresponds to a known catch block.\n      throw new Error(\"illegal catch attempt\");\n    },\n\n    delegateYield: function(iterable, resultName, nextLoc) {\n      this.delegate = {\n        iterator: values(iterable),\n        resultName: resultName,\n        nextLoc: nextLoc\n      };\n\n      if (this.method === \"next\") {\n        // Deliberately forget the last sent value so that we don't\n        // accidentally pass it on to the delegate.\n        this.arg = undefined;\n      }\n\n      return ContinueSentinel;\n    }\n  };\n\n  // Regardless of whether this script is executing as a CommonJS module\n  // or not, return the runtime object so that we can declare the variable\n  // regeneratorRuntime in the outer scope, which allows this module to be\n  // injected easily by `bin/regenerator --include-runtime script.js`.\n  return exports;\n\n}(\n  // If this script is executing as a CommonJS module, use module.exports\n  // as the regeneratorRuntime namespace. Otherwise create a new empty\n  // object. Either way, the resulting object will be used to initialize\n  // the regeneratorRuntime variable at the top of this file.\n  typeof module === \"object\" ? module.exports : {}\n));\n\ntry {\n  regeneratorRuntime = runtime;\n} catch (accidentalStrictMode) {\n  // This module should not be running in strict mode, so the above\n  // assignment should always work unless something is misconfigured. Just\n  // in case runtime.js accidentally runs in strict mode, in modern engines\n  // we can explicitly access globalThis. In older engines we can escape\n  // strict mode using a global Function call. This could conceivably fail\n  // if a Content Security Policy forbids using Function, but in that case\n  // the proper solution is to fix the accidental strict mode problem. If\n  // you've misconfigured your bundler to force strict mode and applied a\n  // CSP to forbid Function, and you're not willing to fix either of those\n  // problems, please detail your unique predicament in a GitHub issue.\n  if (typeof globalThis === \"object\") {\n    globalThis.regeneratorRuntime = runtime;\n  } else {\n    Function(\"r\", \"regeneratorRuntime = r\")(runtime);\n  }\n}\n","/*\n * Helper class allows reading names index generated in JBrowse1\n * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js\n */\nimport crc32 from 'buffer-crc32'\n\nexport default class HttpMap {\n  url: string\n\n  constructor(args: { url: string }) {\n    // make sure url has a trailing slash\n    this.url = /\\/$/.test(args.url) ? args.url : `${args.url}/`\n  }\n\n  /**\n   * loads meta.json file from names directory and reads number of hash_bits used\n   */\n  async readMeta() {\n    const meta = await this.loadFile('meta.json')\n    const { compress, track_names: tracks } = meta\n    const hashHexCharacters = Math.ceil(meta.hash_bits / 4)\n    return { hashHexCharacters, compress, tracks }\n  }\n\n  async getHashHexCharacters() {\n    const meta = await this.readMeta()\n    return meta.hashHexCharacters\n  }\n\n  async getCompress() {\n    const meta = await this.readMeta()\n    return meta.compress\n  }\n\n  async getTrackNames() {\n    const meta = await this.readMeta()\n    return meta.tracks\n  }\n\n  /**\n   * Returns contents of a bucket given a key\n   * @param key - string\n   */\n  async get(key: string) {\n    const bucket = await this.getBucket(key)\n    return bucket[key]\n  }\n\n  /**\n   * Returns a bucket given a key\n   * @param key - string\n   */\n  async getBucket(key: string) {\n    const bucketIdent = this.hash(key)\n    const hexToDirPath = await this.hexToDirPath(bucketIdent)\n    return this.loadFile(hexToDirPath)\n  }\n\n  /**\n   * Loads a file using the url and provided id.\n   * Returns response object with contents of the file\n   * @param id - string\n   */\n  async loadFile(id: string) {\n    const response = await fetch(`${this.url}${id}`)\n    if (!response.ok) {\n      throw new Error(`HTTP ${response.status} ${response.statusText}`)\n    }\n    return response.json()\n  }\n\n  /**\n   * Returns the corresponding path of the file given a hex string\n   * @param hex - hex string\n   */\n  async hexToDirPath(hex: string) {\n    // zero-pad the hex string to be 8 chars if necessary\n    const hashHexCharacters = await this.getHashHexCharacters()\n    if (hashHexCharacters) {\n      const compress = await this.getCompress()\n      while (hex.length < 8) {\n        hex = `0${hex}`\n      }\n      hex = hex.substr(8 - hashHexCharacters)\n      const dirpath = []\n      for (let i = 0; i < hex.length; i += 3) {\n        dirpath.push(hex.substring(i, i + 3))\n      }\n      return `${dirpath.join('/')}.json${compress ? 'z' : ''}`\n    }\n    return ''\n  }\n\n  hash(data: string) {\n    return crc32(Buffer.from(data))\n      .toString('hex')\n      .toLowerCase()\n      .replace('-', 'n')\n  }\n}\n","import {\n  BaseTextSearchAdapter,\n  BaseArgs,\n  BaseAdapter,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport BaseResult from '@jbrowse/core/TextSearch/BaseResults'\nimport { Instance } from 'mobx-state-tree'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport MyConfigSchema from './configSchema'\nimport HttpMap from './HttpMap'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\nexport interface TooManyHits {\n  name: string\n  hitLimit: number\n}\n\ninterface SearchResults {\n  prefix: ({ name: string } | string)[]\n  exact: [string, number, string, string, number, number][]\n}\n\nexport type NamesIndexRecord = string | Array<string | number>\n\n//  Jbrowse1 text search adapter\n// Uses index built by generate-names.pl\nexport default class JBrowse1TextSearchAdapter\n  extends BaseAdapter\n  implements BaseTextSearchAdapter\n{\n  httpMap: HttpMap\n\n  tracksNames?: string[]\n\n  constructor(\n    config: Instance<typeof MyConfigSchema>,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const namesIndexLocation = readConfObject(config, 'namesIndexLocation')\n    if (!namesIndexLocation) {\n      throw new Error('must provide namesIndexLocation')\n    }\n    this.httpMap = new HttpMap({\n      url: namesIndexLocation.baseUri\n        ? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href\n        : namesIndexLocation.uri,\n    })\n  }\n\n  /**\n   * Returns the contents of the file containing the query if it exists\n   * else it returns empty\n   * @param query - string query\n   */\n  async loadIndexFile(query: string): Promise<Record<string, SearchResults>> {\n    return this.httpMap.getBucket(query)\n  }\n\n  async searchIndex(args: BaseArgs) {\n    const { searchType, queryString } = args\n    const tracks = this.tracksNames || (await this.httpMap.getTrackNames())\n    const entries = await this.loadIndexFile(queryString.toLowerCase())\n    if (entries[queryString]) {\n      return this.formatResults(entries[queryString], tracks, searchType)\n    }\n    return []\n  }\n  formatResults(results: SearchResults, tracks: string[], searchType?: string) {\n    return [\n      ...(searchType === 'exact'\n        ? []\n        : results.prefix.map(result => {\n            return new BaseResult({\n              label: typeof result === 'object' ? result.name : result,\n              matchedAttribute: 'name',\n              matchedObject: { result: result },\n            })\n          })),\n      ...results.exact.map(result => {\n        const name = result[0] as string\n        const trackIndex = result[1] as number\n        const refName = result[3] as string\n        const start = result[4] as number\n        const end = result[5] as number\n        const locstring = `${refName || name}:${start}-${end}`\n        return new BaseResult({\n          locString: locstring,\n          label: name,\n          matchedAttribute: 'name',\n          matchedObject: result,\n          trackId: tracks[trackIndex],\n        })\n      }),\n    ].filter(result => result.getLabel() !== 'too many matches')\n  }\n\n  freeResources() {}\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'JBrowse1TextSearchAdapter',\n  {\n    // metadata about tracks and assemblies covered by text search adapter\n    namesIndexLocation: {\n      type: 'fileLocation',\n      defaultValue: { uri: '/volvox/names', locationType: 'UriLocation' },\n      description: 'the location of the JBrowse1 names index data directory',\n    },\n    tracks: {\n      type: 'stringArray',\n      defaultValue: [],\n      description: 'List of tracks covered by text search adapter',\n    },\n    assemblyNames: {\n      type: 'stringArray',\n      defaultValue: [],\n      description: 'List of assemblies covered by text search adapter',\n    },\n  },\n  { explicitlyTyped: true, explicitIdentifier: 'textSearchAdapterId' },\n)\n","import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'JBrowse1Connection',\n  {\n    dataDirLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: 'http://mysite.com/jbrowse/data/',\n        locationType: 'UriLocation',\n      },\n      description:\n        'the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/',\n    },\n    assemblyNames: {\n      description:\n        'name of the assembly the connection belongs to, should be a single entry',\n      type: 'stringArray',\n      defaultValue: [],\n    },\n  },\n  { baseConfiguration: baseConnectionConfig },\n)\n","import getValue from 'get-value'\nimport { Track, Source } from './types'\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nexport function isTrack(arg: any): arg is Track {\n  return arg && arg.label && typeof arg.label === 'string'\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nexport function isSource(arg: any): arg is Source {\n  return arg && arg.url && typeof arg.url === 'string'\n}\n\n/**\n * updates a with values from b, recursively\n */\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\ntype Obj = Record<string, any>\nexport function deepUpdate(a: Obj, b: Obj): Obj {\n  for (const prop of Object.keys(b)) {\n    if (\n      prop in a &&\n      typeof b[prop] === 'object' &&\n      typeof a[prop] === 'object'\n    ) {\n      deepUpdate(a[prop], b[prop])\n    } else if (\n      typeof a[prop] === 'undefined' ||\n      typeof b[prop] !== 'undefined'\n    ) {\n      a[prop] = b[prop]\n    }\n  }\n  return a\n}\n\n/**\n * replace variables in a template string with values\n * @param template - String with variable names in curly brackets\n * e.g., `http://foo/{bar}?arg={baz.foo}`\n * @param fillWith - object with attribute-value mappings\n * e.g., `{ 'bar': 'someurl', 'baz': { 'foo': 42 } }`\n * @returns the template string with variables in fillWith replaced\n * e.g., 'htp://foo/someurl?arg=valueforbaz'\n */\nexport function fillTemplate(template: string, fillWith: Obj): string {\n  return template.replace(\n    /\\{([\\w\\s.]+)\\}/g,\n    (match, varName: string): string => {\n      varName = varName.replace(/\\s+/g, '') // remove all whitespace\n      const fill = getValue(fillWith, varName)\n      if (fill !== undefined) {\n        if (typeof fill === 'function') {\n          return fill(varName)\n        }\n        return fill\n      }\n      if (fillWith.callback) {\n        // @ts-ignore\n        const v = fillWith.callback.call(this, varName)\n        if (v !== undefined) {\n          return v\n        }\n      }\n      return match\n    },\n  )\n}\n\n/**\n * Clones objects (including DOM nodes) and all children.\n * Warning: do not clone cyclic structures\n * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)\n * @param src - The object to clone\n */\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nexport function clone(src: any): any {\n  if (\n    !src ||\n    typeof src !== 'object' ||\n    Object.prototype.toString.call(src) === '[object Function]'\n  ) {\n    // null, undefined, any non-object, or function\n    return src // anything\n  }\n  if (src.nodeType && 'cloneNode' in src) {\n    // DOM Node\n    return src.cloneNode(true) // Node\n  }\n  if (src instanceof Date) {\n    // Date\n    return new Date(src.getTime()) // Date\n  }\n  if (src instanceof RegExp) {\n    // RegExp\n    return new RegExp(src) // RegExp\n  }\n  let r\n  let i\n  let l\n  if (Array.isArray(src)) {\n    // array\n    r = []\n    for (i = 0, l = src.length; i < l; ++i) {\n      if (i in src) {\n        r[i] = clone(src[i])\n      }\n    }\n    // we don't clone functions for performance reasons\n    //    }else if(d.isFunction(src)){\n    //      // function\n    //      r = function(){ return src.apply(this, arguments); };\n  } else {\n    // generic objects\n    r = src.constructor ? new src.constructor() : {}\n  }\n  return mixin(r, src, clone)\n}\n\n/**\n * Copies/adds all properties of source to dest; returns dest.\n * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)\n *\n * All properties, including functions (sometimes termed \"methods\"), excluding\n * any non-standard extensions found in Object.prototype, are copied/added to\n * dest. Copying/adding each particular property is delegated to copyFunc\n * (if any); copyFunc defaults to the Javascript assignment operator if not\n * provided. Notice that by default, mixin executes a so-called \"shallow copy\"\n * and aggregate types are copied/added by reference.\n * @param dest - The object to which to copy/add all properties contained in\n * source.\n * @param source - The object from which to draw all properties to copy into dest.\n * @param copyFunc - The process used to copy/add a property in source; defaults\n * to the Javascript assignment operator.\n * @returns dest, as modified\n */\nfunction mixin(dest: Obj, source: Obj, copyFunc: Function): Obj {\n  let name\n  let s\n  const empty = {}\n  for (name in source) {\n    // the (!(name in empty) || empty[name] !== s) condition avoids copying\n    // properties in \"source\" inherited from Object.prototype.\t For example,\n    // if dest has a custom toString() method, don't overwrite it with the\n    // toString() method that source inherited from Object.prototype\n    s = source[name]\n    if (\n      !(name in dest) ||\n      // @ts-ignore\n      (dest[name] !== s && (!(name in empty) || empty[name] !== s))\n    ) {\n      dest[name] = copyFunc ? copyFunc(s) : s\n    }\n  }\n\n  return dest // Object\n}\n","/* eslint no-cond-assign: [\"error\", \"except-parens\"] */\nimport getValue from 'get-value'\nimport setValue from 'set-value'\nimport { objectHash } from '@jbrowse/core/util'\nimport { isSource, isTrack } from './util'\nimport { Config, Track, Source, Store, Names } from './types'\n\nexport function parseJB1Json(config: Config | string, url: string): Config {\n  if (typeof config === 'string') {\n    let parsedConf\n    try {\n      parsedConf = JSON.parse(config)\n    } catch (error) {\n      throw new Error(`${error} when parsing configuration.`)\n    }\n    return regularizeConf(parsedConf, url)\n  }\n  return regularizeConf(config, url)\n}\n\nexport function parseJB1Conf(config: string, url: string): Config {\n  let parsedConf\n  try {\n    parsedConf = parse(config, url)\n  } catch (error) {\n    throw new Error(`${error} when parsing configuration.`)\n  }\n  return regularizeConf(parsedConf, url)\n}\n\nfunction isAlwaysArray(varName: string): boolean {\n  if (varName === 'include') {\n    return true\n  }\n  return false\n}\n\nfunction parse(text: string, url: string): Config {\n  let section: string[] = []\n  let keyPath: string[] | undefined\n  let operation: string\n  let value: string | undefined\n  const data: Config = { tracks: {} }\n  let lineNumber: number\n\n  function recordVal(): void {\n    if (value !== undefined) {\n      let parsedValue:\n        | string\n        | number\n        | boolean\n        | string[]\n        | number[]\n        | boolean[]\n      try {\n        // parse json\n        const match = value.match(/^json:(.+)/i)\n        if (match) {\n          parsedValue = JSON.parse(match[1])\n        }\n        // parse numbers if it looks numeric\n        else if (/^[+-]?[\\d.,]+([eE][-+]?\\d+)?$/.test(value)) {\n          parsedValue = parseFloat(value.replace(/,/g, ''))\n        } else {\n          parsedValue = value\n        }\n\n        if (!keyPath) {\n          throw new Error(`Error parsing in section ${section.join(' - ')}`)\n        }\n        const path = section.concat(keyPath).join('.')\n        if (operation === '+=') {\n          let existing = getValue(data, path)\n          if (existing) {\n            if (!Array.isArray(existing)) {\n              existing = [existing]\n            }\n          } else {\n            existing = []\n          }\n\n          existing.push(parsedValue)\n          parsedValue = existing\n        }\n        if (parsedValue === 'true') {\n          parsedValue = true\n        }\n        if (parsedValue === 'false') {\n          parsedValue = false\n        }\n        setValue(data, path, parsedValue)\n      } catch (e) {\n        throw new Error(\n          `syntax error${url ? ` in ${url}` : ''}${\n            lineNumber ? ` at line ${lineNumber - 1}` : ''\n          }`,\n        )\n      }\n    }\n  }\n\n  text.split('\\n').forEach((textLine, i): void => {\n    lineNumber = i + 1\n    const line = textLine.replace(/^\\s*#.+/, '')\n\n    // new section\n    let match: RegExpMatchArray | null\n    if ((match = line.match(/^\\s*\\[([^\\]]+)/))) {\n      // new section\n      recordVal()\n      keyPath = undefined\n      value = undefined\n      section = match[1].trim().split(/\\s*\\.\\s*/)\n      if (section.length === 1 && section[0].toLowerCase() === 'general') {\n        section = []\n      }\n    }\n    // new value\n    else if (\n      (match = line.match(\n        value === undefined ? /^([^+=]+)(\\+?=)(.*)/ : /^(\\S[^+=]+)(\\+?=)(.*)/,\n      ))\n    ) {\n      recordVal()\n      keyPath = match[1].trim().split(/\\s*\\.\\s*/)\n      ;[, , operation] = match\n      if (isAlwaysArray(section.concat(keyPath).join('.'))) {\n        operation = '+='\n      }\n      value = match[3].trim()\n    }\n    // add to existing array value\n    else if (\n      keyPath !== undefined &&\n      (match = line.match(/^\\s{0,4}\\+\\s*(.+)/))\n    ) {\n      recordVal()\n      operation = '+='\n      value = match[1].trim()\n    }\n    // add to existing value\n    else if (value !== undefined && (match = line.match(/^\\s+(\\S.*)/))) {\n      value += value.length ? ` ${match[1].trim()}` : match[1].trim()\n    }\n    // done with last value\n    else {\n      recordVal()\n      keyPath = undefined\n      value = undefined\n    }\n  })\n\n  recordVal()\n\n  return data\n}\n\n/**\n * Applies defaults and any other necessary tweaks to the loaded configuration.\n * @param conf - the object containing the configuration, which it modifies\n * in-place\n * @param url - URL of the config file\n * @returns the same object it was passed\n */\nexport function regularizeConf(conf: Config, url: string): Config {\n  // if tracks is not an array, convert it to one\n  if (conf.tracks && !Array.isArray(conf.tracks)) {\n    // if it's a single track config, wrap it in an arrayref\n    if (isTrack(conf.tracks)) {\n      conf.tracks = [conf.tracks]\n    }\n    // otherwise, coerce it to an array\n    else {\n      const tracks: Track[] = []\n      for (const label of Object.keys(conf.tracks)) {\n        const track = conf.tracks[label]\n        if (isTrack(track)) {\n          tracks.push(track)\n        } else {\n          tracks.push({ label, ...track })\n        }\n      }\n      conf.tracks = tracks\n    }\n  }\n\n  // regularize trackMetadata.sources\n  const meta = conf.trackMetadata\n  if (meta && meta.sources) {\n    // if it's a single source config, wrap it in an arrayref\n    if (typeof meta.sources === 'string') {\n      meta.sources = [meta.sources]\n    }\n    if (isSource(meta.sources)) {\n      meta.sources = [meta.sources]\n    }\n\n    if (!Array.isArray(meta.sources)) {\n      const sources: Source[] = []\n      for (const name of Object.keys(meta.sources)) {\n        const source = meta.sources[name]\n        if (!('name' in source)) {\n          source.name = name\n        }\n        sources.push(source)\n      }\n      meta.sources = sources\n    }\n\n    // coerce any string source defs to be URLs, and try to detect their types\n    meta.sources = meta.sources.map((sourceDef: string | Source): Source => {\n      if (typeof sourceDef === 'string') {\n        const newSourceDef: Source = { url: sourceDef }\n        const typeMatch = sourceDef.match(/\\.(\\w+)$/)\n        if (typeMatch) {\n          newSourceDef.type = typeMatch[1].toLowerCase()\n        }\n        return newSourceDef\n      }\n      return sourceDef\n    })\n  }\n\n  conf.sourceUrl = conf.sourceUrl || url\n  if (conf.sourceUrl.startsWith('/')) {\n    conf.sourceUrl = new URL(conf.sourceUrl, window.location.href).href\n  }\n  conf.baseUrl = conf.baseUrl || new URL('.', conf.sourceUrl).href\n  if (conf.baseUrl.length && !conf.baseUrl.endsWith('/')) {\n    conf.baseUrl += '/'\n  }\n\n  if (conf.sourceUrl) {\n    // set a default baseUrl in each of the track and store confs, and the names\n    // conf, if needed\n    const addBase: (Track | Store | Names)[] = []\n    if (conf.tracks) {\n      addBase.push(...conf.tracks)\n    }\n    if (conf.stores) {\n      addBase.push(...Object.values(conf.stores))\n    }\n    if (conf.names) {\n      addBase.push(conf.names)\n    }\n\n    addBase.forEach((t): void => {\n      if (!t.baseUrl) {\n        t.baseUrl = conf.baseUrl || '/'\n      }\n    })\n\n    // resolve the refSeqs and nameUrl if present\n    if (conf.refSeqs && typeof conf.refSeqs === 'string') {\n      conf.refSeqs = new URL(conf.refSeqs, conf.sourceUrl).href\n    }\n    if (conf.nameUrl) {\n      conf.nameUrl = new URL(conf.nameUrl, conf.sourceUrl).href\n    }\n  }\n\n  conf.stores = conf.stores || {}\n  ;(conf.tracks || []).forEach((trackConfig: Track): void => {\n    // if there is a `config` subpart, just copy its keys in to the top-level\n    // config\n    if (trackConfig.config) {\n      const c = trackConfig.config\n      delete trackConfig.config\n      trackConfig = { ...c, ...trackConfig }\n    }\n\n    // skip if it's a new-style track def\n    if (trackConfig.store) {\n      return\n    }\n\n    let trackClassName: string\n    if (trackConfig.type === 'FeatureTrack') {\n      trackClassName = 'JBrowse/View/Track/HTMLFeatures'\n    } else if (trackConfig.type === 'ImageTrack') {\n      trackClassName = 'JBrowse/View/Track/FixedImage'\n    } else if (trackConfig.type === 'ImageTrack.Wiggle') {\n      trackClassName = 'JBrowse/View/Track/FixedImage/Wiggle'\n    } else if (trackConfig.type === 'SequenceTrack') {\n      trackClassName = 'JBrowse/View/Track/Sequence'\n    } else {\n      trackClassName = regularizeClass('JBrowse/View/Track', trackConfig.type)\n    }\n\n    trackConfig.type = trackClassName\n\n    synthesizeTrackStoreConfig(conf, trackConfig)\n\n    if (trackConfig.histograms) {\n      if (!trackConfig.histograms.baseUrl) {\n        trackConfig.histograms.baseUrl = trackConfig.baseUrl\n      }\n      synthesizeTrackStoreConfig(conf, trackConfig.histograms)\n    }\n  })\n\n  return conf\n}\n\n/**\n * prefix class name with `root` if it contains no slashes\n * @param root - Prefix root\n * @param className - class name\n */\nfunction regularizeClass(root: string, className: string | undefined): string {\n  if (!className) {\n    return ''\n  }\n  if (!className.includes('/')) {\n    className = `${root}/${className}`\n  }\n  className = className.replace(/^\\//, '')\n  return className\n}\n\nfunction guessStoreClass(\n  trackConfig: Track | undefined,\n  urlTemplate: string,\n): string {\n  if (!trackConfig) {\n    return ''\n  }\n  if (trackConfig.type && trackConfig.type.includes('/FixedImage')) {\n    return `JBrowse/Store/TiledImage/Fixed${\n      trackConfig.backendVersion === 0 ? '_v0' : ''\n    }`\n  }\n  if (/\\.jsonz?$/i.test(urlTemplate)) {\n    return `JBrowse/Store/SeqFeature/NCList${\n      trackConfig.backendVersion === 0 ? '_v0' : ''\n    }`\n  }\n  if (/\\.bam$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BAM'\n  }\n  if (/\\.cram$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/CRAM'\n  }\n  if (/\\.gff3?$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/GFF3'\n  }\n  if (/\\.bed$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BED'\n  }\n  if (/\\.vcf.b?gz$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/VCFTabix'\n  }\n  if (/\\.gff3?.b?gz$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/GFF3Tabix'\n  }\n  if (/\\.bed.b?gz$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BEDTabix'\n  }\n  if (/\\.(bw|bigwig)$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BigWig'\n  }\n  if (/\\.(bb|bigbed)$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BigBed'\n  }\n  if (/\\.(fa|fasta)$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/IndexedFasta'\n  }\n  if (/\\.(fa|fasta)\\.b?gz$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/BgzipIndexedFasta'\n  }\n  if (/\\.2bit$/i.test(urlTemplate)) {\n    return 'JBrowse/Store/SeqFeature/TwoBit'\n  }\n  if (trackConfig.type && trackConfig.type.endsWith('/Sequence')) {\n    return 'JBrowse/Store/Sequence/StaticChunked'\n  }\n  return ''\n}\n\nfunction synthesizeTrackStoreConfig(\n  mainConf: Config,\n  trackConfig: Track,\n): void {\n  // figure out what data store class to use with the track, applying some\n  // defaults if it is not explicit in the configuration\n  const { urlTemplate = '' } = trackConfig\n\n  let storeClass: string\n  if (trackConfig.storeClass) {\n    storeClass = regularizeClass('JBrowse/Store', trackConfig.storeClass)\n  } else {\n    storeClass = guessStoreClass(trackConfig, urlTemplate)\n  }\n\n  if (!storeClass) {\n    console.warn(\n      `Unable to determine an appropriate data store to use with track '${trackConfig.label}', please explicitly specify a storeClass in the configuration.`,\n    )\n    return\n  }\n\n  // synthesize a separate store conf\n  const storeConf: Store = { ...trackConfig, type: storeClass }\n\n  // if this is the first sequence store we see, and we have no refseqs store\n  // defined explicitly, make this the refseqs store.\n  if (\n    (storeClass === 'JBrowse/Store/Sequence/StaticChunked' ||\n      storeClass === 'JBrowse/Store/Sequence/IndexedFasta' ||\n      storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta' ||\n      storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta' ||\n      storeClass === 'JBrowse/Store/SeqFeature/TwoBit' ||\n      storeClass === 'JBrowse/Store/Sequence/TwoBit' ||\n      trackConfig.useAsRefSeqStore) &&\n    !(mainConf.stores && mainConf.stores.refseqs)\n  ) {\n    storeConf.name = 'refseqs'\n  } else {\n    storeConf.name = `store${objectHash(storeConf)}`\n  }\n  // record it\n  if (!mainConf.stores) {\n    mainConf.stores = {}\n  }\n  mainConf.stores[storeConf.name] = storeConf\n\n  // connect it to the track conf\n  trackConfig.store = storeConf.name\n}\n","import { openLocation } from '@jbrowse/core/util/io'\nimport { parseJB1Json, parseJB1Conf, regularizeConf } from './jb1ConfigParse'\nimport { clone, deepUpdate, fillTemplate } from './util'\nimport {\n  JBLocation,\n  UriLocation,\n  LocalPathLocation,\n  Config,\n  Track,\n  Include,\n} from './types'\n\nfunction isUriLocation(location: JBLocation): location is UriLocation {\n  return (location as UriLocation).uri !== undefined\n}\n\nfunction isLocalPathLocation(\n  location: JBLocation,\n): location is LocalPathLocation {\n  return (location as LocalPathLocation).localPath !== undefined\n}\n\nexport async function fetchJb1(\n  dataRoot: JBLocation = { uri: '', locationType: 'UriLocation' },\n  baseConfig: Config = {\n    include: ['{dataRoot}/trackList.json', '{dataRoot}/tracks.conf'],\n  },\n  baseConfigRoot: JBLocation = { uri: '', locationType: 'UriLocation' },\n): Promise<Config> {\n  const protocol = 'uri' in dataRoot ? 'uri' : 'localPath'\n  const dataRootReg = JSON.parse(JSON.stringify(dataRoot))\n  let dataRootLocation = ''\n  if (isUriLocation(dataRoot)) {\n    dataRootLocation = dataRoot.uri\n  }\n  if (isLocalPathLocation(dataRoot)) {\n    dataRootLocation = dataRoot.localPath\n  }\n  if (dataRootLocation.endsWith('/')) {\n    dataRootReg[protocol] = dataRootLocation.slice(\n      0,\n      dataRootLocation.length - 1,\n    )\n  }\n  if (\n    (isUriLocation(baseConfigRoot) && baseConfigRoot.uri) ||\n    (isLocalPathLocation(baseConfigRoot) && baseConfigRoot.localPath)\n  ) {\n    const baseProtocol = 'uri' in baseConfigRoot ? 'uri' : 'localPath'\n    let baseConfigLocation = ''\n    if (isUriLocation(baseConfigRoot)) {\n      baseConfigLocation = baseConfigRoot.uri\n    }\n    if (isLocalPathLocation(baseConfigRoot)) {\n      baseConfigLocation = baseConfigRoot.localPath\n    }\n    if (baseConfigLocation.endsWith('/')) {\n      baseConfigLocation = baseConfigLocation.slice(\n        0,\n        baseConfigLocation.length - 1,\n      )\n    }\n    let newConfig: Config = {}\n    for (const conf of ['jbrowse.conf', 'jbrowse_conf.json']) {\n      let fetchedConfig = null\n      try {\n        // @ts-ignore\n        fetchedConfig = await fetchConfigFile({\n          [baseProtocol]: `${baseConfigLocation}/${conf}`,\n        })\n      } catch (error) {\n        console.error(\n          `tried to access ${baseConfigLocation}/${conf}, but failed`,\n        )\n      }\n      newConfig = mergeConfigs(newConfig, fetchedConfig) || {}\n    }\n    if (dataRootReg[protocol]) {\n      newConfig.dataRoot = dataRootReg[protocol]\n    }\n    return createFinalConfig(newConfig)\n  }\n  const newConfig = regularizeConf(baseConfig, window.location.href)\n  if (dataRootReg[protocol]) {\n    newConfig.dataRoot = dataRootReg[protocol]\n  }\n  return createFinalConfig(newConfig)\n}\n\nexport async function createFinalConfig(\n  baseConfig: Config,\n  defaults = configDefaults,\n): Promise<Config> {\n  const configWithDefaults = deepUpdate(clone(defaults), baseConfig)\n  let finalConfig = await loadIncludes(configWithDefaults)\n  finalConfig = mergeConfigs(finalConfig, baseConfig) || finalConfig\n  fillTemplates(finalConfig, finalConfig)\n  validateConfig(finalConfig)\n  return finalConfig\n}\n\nexport async function fetchConfigFile(location: JBLocation): Promise<Config> {\n  const result = await openLocation(location).readFile('utf8')\n  if (isUriLocation(location)) {\n    return parseJb1(result, location.uri)\n  }\n  if (isLocalPathLocation(location)) {\n    return parseJb1(result, location.localPath)\n  }\n  return parseJb1(result)\n}\n\nexport function parseJb1(config: string, url = ''): Config {\n  if (config.trim().startsWith('{')) {\n    return parseJB1Json(config, url)\n  }\n  return parseJB1Conf(config, url)\n}\n\n/**\n * Merges config object b into a. Properties in b override those in a.\n */\nfunction mergeConfigs(a: Config | null, b: Config | null): Config | null {\n  if (b === null) {\n    return null\n  }\n\n  if (a === null) {\n    a = {}\n  }\n\n  for (const prop of Object.keys(b)) {\n    if (prop === 'tracks' && prop in a) {\n      const aTracks = a[prop] || []\n      const bTracks = b[prop] || []\n      if (Array.isArray(aTracks) && Array.isArray(bTracks)) {\n        a[prop] = mergeTrackConfigs(aTracks || [], bTracks || [])\n      } else {\n        throw new Error(\n          `Track config has not been properly regularized: ${aTracks} ${bTracks}`,\n        )\n      }\n    } else if (\n      !noRecursiveMerge(prop) &&\n      prop in a &&\n      // @ts-ignore\n      typeof b[prop] === 'object' &&\n      // @ts-ignore\n      typeof a[prop] === 'object'\n    ) {\n      // @ts-ignore\n      a[prop] = deepUpdate(a[prop], b[prop])\n    } else if (prop === 'dataRoot') {\n      if (\n        a[prop] === undefined ||\n        (a[prop] === 'data' && b[prop] !== undefined)\n      ) {\n        a[prop] = b[prop]\n      }\n      // @ts-ignore\n    } else if (a[prop] === undefined || b[prop] !== undefined) {\n      // @ts-ignore\n      a[prop] = b[prop]\n    }\n  }\n  return a\n}\n\n/**\n * Special-case merging of two `tracks` configuration arrays.\n */\nfunction mergeTrackConfigs(a: Track[], b: Track[]): Track[] {\n  if (!b.length) {\n    return a\n  }\n\n  // index the tracks in `a` by track label\n  const aTracks: Record<string, Track> = {}\n  a.forEach((t, i): void => {\n    t.index = i\n    aTracks[t.label] = t\n  })\n\n  b.forEach((bT): void => {\n    const aT = aTracks[bT.label]\n    if (aT) {\n      mergeConfigs(aT, bT)\n    } else {\n      a.push(bT)\n    }\n  })\n\n  return a\n}\n\n/**\n * Recursively fetch, parse, and merge all the includes in the given config\n * object.  Calls the callback with the resulting configuration when finished.\n * @param inputConfig - Config to load includes into\n */\nasync function loadIncludes(inputConfig: Config): Promise<Config> {\n  inputConfig = clone(inputConfig)\n\n  async function loadRecur(\n    config: Config,\n    upstreamConf: Config,\n  ): Promise<Config> {\n    const sourceUrl = config.sourceUrl || config.baseUrl\n    if (!sourceUrl) {\n      throw new Error(\n        `Could not determine source URL: ${JSON.stringify(config)}`,\n      )\n    }\n    const newUpstreamConf = mergeConfigs(clone(upstreamConf), config)\n    if (!newUpstreamConf) {\n      throw new Error('Problem merging configs')\n    }\n    const includes = fillTemplates(\n      regularizeIncludes(config.include || []),\n      newUpstreamConf,\n    )\n    delete config.include\n\n    const loads = includes.map(async (include): Promise<Config> => {\n      include.cacheBuster = inputConfig.cacheBuster\n      const includedData = await fetchConfigFile({\n        uri: new URL(include.url, sourceUrl).href,\n        locationType: 'UriLocation',\n      })\n      return loadRecur(includedData, newUpstreamConf)\n    })\n    const includedDataObjects = await Promise.all(loads)\n    includedDataObjects.forEach((includedData): void => {\n      config = mergeConfigs(config, includedData) || config\n    })\n    return config\n  }\n\n  return loadRecur(inputConfig, {})\n}\n\nfunction regularizeIncludes(\n  includes: Include | string | (Include | string)[] | null,\n): Include[] {\n  if (!includes) {\n    return []\n  }\n\n  // coerce include to an array\n  if (!Array.isArray(includes)) {\n    includes = [includes]\n  }\n\n  return includes.map((include): Include => {\n    // coerce bare strings in the includes to URLs\n    if (typeof include === 'string') {\n      include = { url: include }\n    }\n\n    // set defaults for format and version\n    if (!('format' in include)) {\n      include.format = include.url.endsWith('.conf') ? 'conf' : 'JB_json'\n    }\n    if (include.format === 'JB_json' && !('version' in include)) {\n      include.version = 1\n    }\n    return include\n  })\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction fillTemplates<T extends any>(subconfig: T, config: Config): T {\n  if (!subconfig) {\n    return subconfig\n  }\n  if (Array.isArray(subconfig)) {\n    for (let i = 0; i < subconfig.length; i += 1) {\n      subconfig[i] = fillTemplates(subconfig[i], config)\n    }\n  } else if (typeof subconfig === 'object') {\n    // eslint-disable-next-line @typescript-eslint/no-explicit-any\n    const sub = subconfig as Record<string, any>\n    for (const name of Object.keys(sub)) {\n      sub[name] = fillTemplates(sub[name], config)\n    }\n  } else if (typeof subconfig === 'string') {\n    // @ts-ignore\n    return fillTemplate(subconfig, config)\n  }\n\n  return subconfig\n}\n\n/**\n * list of config properties that should not be recursively merged\n * @param propName - name of config property\n */\nfunction noRecursiveMerge(propName: string): boolean {\n  return propName === 'datasets'\n}\n\nconst configDefaults = {\n  tracks: [],\n\n  containerID: 'GenomeBrowser',\n  dataRoot: 'data',\n  show_tracklist: true,\n  show_nav: true,\n  show_menu: true,\n  show_overview: true,\n  show_fullviewlink: true,\n  update_browser_title: true,\n  updateBrowserURL: true,\n\n  refSeqs: '{dataRoot}/seq/refSeqs.json',\n  include: ['jbrowse.conf', 'jbrowse_conf.json'],\n  nameUrl: '{dataRoot}/names/root.json',\n\n  datasets: {\n    _DEFAULT_EXAMPLES: true,\n    volvox: { url: '?data=sample_data/json/volvox', name: 'Volvox Example' },\n    modencode: {\n      url: '?data=sample_data/json/modencode',\n      name: 'MODEncode Example',\n    },\n    yeast: { url: '?data=sample_data/json/yeast', name: 'Yeast Example' },\n  },\n\n  highlightSearchedRegions: false,\n  highResolutionMode: 'auto',\n}\n\n/**\n * Examine the loaded and merged configuration for errors.  Throws\n * exceptions if it finds anything amiss.\n * @returns nothing meaningful\n */\nfunction validateConfig(config: Config): void {\n  if (!config.tracks) {\n    config.tracks = []\n  }\n  if (!config.baseUrl) {\n    throw new Error('Must provide a `baseUrl` in configuration')\n  }\n}\n","import {\n  ConfigurationReference,\n  readConfObject,\n} from '@jbrowse/core/configuration'\nimport { getSession } from '@jbrowse/core/util'\nimport { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'\nimport { types } from 'mobx-state-tree'\nimport configSchema from './configSchema'\n\nimport { fetchJb1 } from './jb1ConfigLoad'\nimport { convertTrackConfig } from './jb1ToJb2'\n\nexport default function (pluginManager) {\n  return types.compose(\n    'JBrowse1Connection',\n    BaseConnectionModelFactory(pluginManager),\n    types\n      .model({\n        configuration: ConfigurationReference(configSchema),\n        type: types.literal('JBrowse1Connection'),\n      })\n      .actions(self => ({\n        connect() {\n          const dataDirLocation = readConfObject(\n            self.configuration,\n            'dataDirLocation',\n          )\n          const session = getSession(self)\n          fetchJb1(dataDirLocation)\n            .then(config => {\n              const assemblyName = readConfObject(\n                self.configuration,\n                'assemblyNames',\n              )[0]\n              if (!assemblyName) {\n                throw new Error(\n                  'assembly name required for JBrowse 1 connection',\n                )\n              }\n              const assemblyConf = session.assemblies.find(\n                assembly => readConfObject(assembly, 'name') === assemblyName,\n              )\n              const sequenceAdapter = readConfObject(assemblyConf, [\n                'sequence',\n                'adapter',\n              ])\n              const jb2Tracks = config.tracks.map(jb1Track => {\n                const jb2Track = convertTrackConfig(\n                  jb1Track,\n                  config.dataRoot,\n                  sequenceAdapter,\n                )\n                jb2Track.assemblyNames = [assemblyName]\n                return jb2Track\n              })\n              self.setTrackConfs(jb2Tracks)\n            })\n            .catch(error => {\n              console.error(error)\n              session.notify(\n                `There was a problem connecting to the JBrowse 1 data directory \"${self.name}\". Please make sure you have entered a valid location. The error that was thrown is: \"${error}\"`,\n                'error',\n              )\n              session.breakConnection(self.configuration)\n            })\n        },\n      })),\n  )\n}\n","import { openLocation } from '@jbrowse/core/util/io'\nimport { objectHash } from '@jbrowse/core/util'\nimport {\n  generateUnknownTrackConf,\n  generateUnsupportedTrackConf,\n  guessAdapter,\n  guessTrackType,\n  UNKNOWN,\n  UNSUPPORTED,\n} from '@jbrowse/core/util/tracks'\nimport { Track, RefSeqs, RefSeq } from './types'\n\ninterface Jb2Track {\n  trackId: string\n  name: string\n  description?: string\n  category?: string[]\n  adapter?: Jb2Adapter\n  type?: string\n  defaultRendering?: string\n}\n\ninterface Jb2Adapter {\n  type: string\n  features?: Jb2Feature[]\n  bamLocation?: Jb2Location\n  cramLocation?: Jb2Location\n  craiLocation?: Jb2Location\n  fastaLocation?: Jb2Location\n  faiLocation?: Jb2Location\n  gziLocation?: Jb2Location\n  twoBitLocation?: Jb2Location\n  bigWigLocation?: Jb2Location\n  bigBedLocation?: Jb2Location\n  vcfGzLocation?: Jb2Location\n  gffGzLocation?: Jb2Location\n  bedGzLocation?: Jb2Location\n  index?: { location: Jb2Location; indexType?: string }\n  rootUrlTemplate?: Jb2Location\n  sequenceAdapter?: Jb2Adapter\n}\n\ninterface Jb2Feature {\n  refName: string\n  uniqueId: string\n  start: number\n  end: number\n}\n\ninterface Jb2Location {\n  uri?: string\n  localPath?: string\n  blobId?: string\n  locationType?: string\n}\n\nexport function convertTrackConfig(\n  jb1TrackConfig: Track,\n  dataRoot: string,\n  sequenceAdapter: Jb2Adapter,\n): Jb2Track {\n  const jb2TrackConfig: Jb2Track = {\n    trackId: objectHash(jb1TrackConfig),\n    name: jb1TrackConfig.key || jb1TrackConfig.label,\n  }\n\n  const description =\n    jb1TrackConfig.metadata &&\n    (jb1TrackConfig.metadata.description || jb1TrackConfig.metadata.Description)\n  if (description) {\n    jb2TrackConfig.description = description\n  }\n\n  const category =\n    jb1TrackConfig.category ||\n    (jb1TrackConfig.metadata && jb1TrackConfig.metadata.category)\n  jb2TrackConfig.category = category ? category.split(/\\s*\\/\\s*/) : []\n\n  const { storeClass } = jb1TrackConfig\n  if (!jb1TrackConfig.urlTemplate) {\n    if (!(storeClass && storeClass.endsWith('FromConfig'))) {\n      const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label\n      console.warn(\n        `Could not import JBrowse1 track \"${trackIdentifier}\" because it does not have a \"urlTemplate\" or is not a \"FromConfig\" track`,\n      )\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        trackIdentifier,\n        jb2TrackConfig.category,\n      )\n    }\n    return generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig)\n  }\n\n  const resolveUrlTemplate = (urlTemplate: string) => {\n    return new URL(urlTemplate, `${dataRoot}/`).href\n      .replace(/%7B/gi, '{')\n      .replace(/%7D/gi, '}')\n  }\n  const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate)\n\n  if (storeClass) {\n    if (storeClass === 'JBrowse/Store/SeqFeature/BAM') {\n      const adapter: Jb2Adapter = {\n        type: 'BamAdapter',\n        bamLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.baiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n        }\n      } else if (jb1TrackConfig.csiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n          indexType: 'CSI',\n        }\n      } else {\n        adapter.index = {\n          location: { uri: `${urlTemplate}.bai`, locationType: 'UriLocation' },\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'AlignmentsTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/CRAM') {\n      const adapter: Jb2Adapter = {\n        type: 'CramAdapter',\n        cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n        sequenceAdapter,\n      }\n      if (jb1TrackConfig.craiUrlTemplate) {\n        adapter.craiLocation = {\n          uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),\n          locationType: 'UriLocation',\n        }\n      } else {\n        adapter.craiLocation = {\n          uri: `${urlTemplate}.crai`,\n          locationType: 'UriLocation',\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'AlignmentsTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/NCList') {\n      return {\n        ...jb2TrackConfig,\n        type: 'FeatureTrack',\n        adapter: {\n          type: 'NCListAdapter',\n          rootUrlTemplate: { uri: urlTemplate, locationType: 'UriLocation' },\n        },\n      }\n    }\n    if (\n      storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||\n      storeClass === 'JBrowse/Store/BigWig'\n    ) {\n      if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {\n        jb2TrackConfig.defaultRendering = 'xyplot'\n      } else if (\n        jb1TrackConfig.type &&\n        jb1TrackConfig.type.endsWith('Density')\n      ) {\n        jb2TrackConfig.defaultRendering = 'density'\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'QuantitativeTrack',\n        adapter: {\n          type: 'BigWigAdapter',\n          bigWigLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n        },\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/VCFTabix') {\n      const adapter: Jb2Adapter = {\n        type: 'VcfTabixAdapter',\n        vcfGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.tbiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n        }\n      } else if (jb1TrackConfig.csiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n          indexType: 'CSI',\n        }\n      } else {\n        adapter.index = {\n          location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'VariantTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/VCFTribble') {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `VCFTribble (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `GFF3 (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {\n      return {\n        ...jb2TrackConfig,\n        type: 'FeatureTrack',\n        adapter: {\n          type: 'BigBedAdapter',\n          bigBedLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n        },\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/GFF3Tabix') {\n      const adapter: Jb2Adapter = {\n        type: 'Gff3TabixAdapter',\n        gffGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.tbiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n        }\n      } else if (jb1TrackConfig.csiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n          indexType: 'CSI',\n        }\n      } else {\n        adapter.index = {\n          location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'FeatureTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/BED') {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `BED (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/BEDTabix') {\n      const adapter: Jb2Adapter = {\n        type: 'BedTabixAdapter',\n        bedGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.tbiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n        }\n      } else if (jb1TrackConfig.csiUrlTemplate) {\n        adapter.index = {\n          location: {\n            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),\n            locationType: 'UriLocation',\n          },\n          indexType: 'CSI',\n        }\n      } else {\n        adapter.index = {\n          location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'FeatureTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `GTF (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (\n      storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' ||\n      storeClass === 'JBrowse/Store/Sequence/StaticChunked'\n    ) {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `StaticChunked (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/UnindexedFasta') {\n      return generateUnsupportedTrackConf(\n        jb2TrackConfig.name,\n        `UnindexedFasta (${urlTemplate})`,\n        jb2TrackConfig.category,\n      )\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta') {\n      const adapter: Jb2Adapter = {\n        type: 'IndexedFastaAdapter',\n        fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.faiUrlTemplate) {\n        adapter.faiLocation = {\n          uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),\n          locationType: 'UriLocation',\n        }\n      } else {\n        adapter.faiLocation = {\n          uri: `${urlTemplate}.fai`,\n          locationType: 'UriLocation',\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'SequenceTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta') {\n      const adapter: Jb2Adapter = {\n        type: 'BgzipFastaAdapter',\n        fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n      }\n      if (jb1TrackConfig.faiUrlTemplate) {\n        adapter.faiLocation = {\n          uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),\n          locationType: 'UriLocation',\n        }\n      } else {\n        adapter.faiLocation = {\n          uri: `${urlTemplate}.fai`,\n          locationType: 'UriLocation',\n        }\n      }\n      if (jb1TrackConfig.gziUrlTemplate) {\n        adapter.gziLocation = {\n          uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),\n          locationType: 'UriLocation',\n        }\n      } else {\n        adapter.gziLocation = {\n          uri: `${urlTemplate}.gzi`,\n          locationType: 'UriLocation',\n        }\n      }\n      return {\n        ...jb2TrackConfig,\n        type: 'ReferenceSequenceTrack',\n        adapter,\n      }\n    }\n    if (storeClass === 'JBrowse/Store/SeqFeature/TwoBit') {\n      return {\n        ...jb2TrackConfig,\n        type: 'ReferenceSequenceTrack',\n        adapter: {\n          type: 'TwoBitAdapter',\n          twoBitLocation: { uri: urlTemplate, locationType: 'UriLocation' },\n        },\n      }\n    }\n  }\n\n  // If we don't recogize the store class, make a best effort to guess by file type\n  jb2TrackConfig.adapter = guessAdapter(\n    { uri: urlTemplate, locationType: 'UriLocation' },\n    undefined,\n    urlTemplate,\n  )\n  if (!jb2TrackConfig.adapter) {\n    throw new Error('Could not determine adapter')\n  }\n\n  if (jb2TrackConfig.adapter.type === UNSUPPORTED) {\n    return generateUnsupportedTrackConf(\n      jb2TrackConfig.name,\n      urlTemplate,\n      jb2TrackConfig.category,\n    )\n  }\n  if (jb2TrackConfig.adapter.type === UNKNOWN) {\n    return generateUnknownTrackConf(\n      jb2TrackConfig.name,\n      urlTemplate,\n      jb2TrackConfig.category,\n    )\n  }\n\n  jb2TrackConfig.type = guessTrackType(jb2TrackConfig.adapter.type)\n\n  if (jb2TrackConfig.type === 'QuantitativeTrack') {\n    if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {\n      jb2TrackConfig.defaultRendering = 'xyplot'\n    } else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {\n      jb2TrackConfig.defaultRendering = 'density'\n    }\n  }\n\n  return jb2TrackConfig\n}\n\nfunction generateFromConfigTrackConfig(\n  jb1TrackConfig: Track,\n  jb2TrackConfig: Jb2Track,\n): Jb2Track {\n  const jb1Features = jb1TrackConfig.features || []\n  const jb2Features = jb1Features.map((feature): Jb2Feature => {\n    const jb2Feature: Jb2Feature = JSON.parse(JSON.stringify(feature))\n    jb2Feature.refName = feature.seq_id\n    jb2Feature.uniqueId = `${feature.seq_id}:${feature.start}-${feature.end}:${\n      feature.name || ''\n    }`\n    return jb2Feature\n  })\n  jb2TrackConfig.adapter = {\n    type: 'FromConfigAdapter',\n    features: jb2Features,\n  }\n  jb2TrackConfig.type = 'FeatureTrack'\n  return jb2TrackConfig\n}\n\nexport async function createRefSeqsAdapter(\n  refSeqs: string | RefSeqs,\n): Promise<Jb2Adapter> {\n  if (typeof refSeqs === 'string') {\n    // assume refSeqs is a url if it is string\n    refSeqs = {\n      url: refSeqs,\n    }\n  }\n\n  // check refseq urls\n  if (refSeqs.url) {\n    if (refSeqs.url.match(/.fai$/)) {\n      return {\n        type: 'IndexedFastaAdapter',\n        fastaLocation: {\n          uri: refSeqs.url.slice(0, -4),\n          locationType: 'UriLocation',\n        },\n        faiLocation: {\n          uri: refSeqs.url,\n          locationType: 'UriLocation',\n        },\n      }\n    }\n    if (refSeqs.url.match(/.2bit$/)) {\n      return {\n        type: 'TwoBitAdapter',\n        twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },\n      }\n    }\n    if (refSeqs.url.match(/.fa$/)) {\n      throw new Error('Unindexed FASTA adapter not available')\n    }\n    if (refSeqs.url.match(/.sizes/)) {\n      throw new Error('chromosome SIZES adapter not available')\n    }\n    const refSeqsJson = await openLocation({\n      uri: refSeqs.url,\n      locationType: 'UriLocation',\n    }).readFile('utf8')\n    const refSeqsData: RefSeq[] = JSON.parse(refSeqsJson)\n    return refSeqAdapterFromConfig(refSeqsData)\n  }\n  if ('data' in refSeqs) {\n    return refSeqAdapterFromConfig(refSeqs.data || [])\n  }\n  throw new Error(\n    `Could not determine adapter for JBrowse1 refSeqs: ${\n      refSeqs.url || JSON.stringify(refSeqs)\n    }`,\n  )\n}\n\nfunction refSeqAdapterFromConfig(refSeqsData: RefSeq[]): Jb2Adapter {\n  const features = refSeqsData.map(\n    (refSeq): Jb2Feature => ({\n      refName: refSeq.name,\n      uniqueId: refSeq.name,\n      start: refSeq.start,\n      end: refSeq.end,\n    }),\n  )\n  return {\n    type: 'FromConfigAdapter',\n    features,\n  }\n}\n","import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType'\nimport ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType'\nimport Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { FileLocation } from '@jbrowse/core/util/types'\nimport { configSchema as ncListAdapterConfigSchema } from './NCListAdapter'\nimport {\n  AdapterClass as JBrowse1TextSearchAdapterClass,\n  configSchema as jbrowse1AdapterConfigSchema,\n} from './JBrowse1TextSeachAdapter'\nimport { AdapterGuesser, getFileName } from '@jbrowse/core/util/tracks'\n\nimport {\n  configSchema as jbrowse1ConfigSchema,\n  modelFactory as jbrowse1ModelFactory,\n} from './JBrowse1Connection'\n\nexport default class LegacyJBrowsePlugin extends Plugin {\n  name = 'LegacyJBrowsePlugin'\n\n  install(pluginManager: PluginManager) {\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'NCListAdapter',\n          configSchema: ncListAdapterConfigSchema,\n          getAdapterClass: () =>\n            import('./NCListAdapter/NCListAdapter').then(r => r.default),\n        }),\n    )\n    pluginManager.addToExtensionPoint(\n      'Core-guessAdapterForLocation',\n      (adapterGuesser: AdapterGuesser) => {\n        return (\n          file: FileLocation,\n          index?: FileLocation,\n          adapterHint?: string,\n        ) => {\n          const regexGuess = /trackData.jsonz?$/i\n          const adapterName = 'NCListAdapter'\n          const fileName = getFileName(file)\n          if (regexGuess.test(fileName) || adapterHint === adapterName) {\n            return {\n              type: adapterName,\n              rootUrlTemplate: file,\n            }\n          }\n          return adapterGuesser(file, index, adapterHint)\n        }\n      },\n    )\n\n    pluginManager.addTextSearchAdapterType(\n      () =>\n        new TextSearchAdapterType({\n          name: 'JBrowse1TextSearchAdapter',\n          configSchema: jbrowse1AdapterConfigSchema,\n          AdapterClass: JBrowse1TextSearchAdapterClass,\n          description: 'A JBrowse 1 text search adapter',\n        }),\n    )\n\n    pluginManager.addConnectionType(\n      () =>\n        new ConnectionType({\n          name: 'JBrowse1Connection',\n          configSchema: jbrowse1ConfigSchema,\n          stateModel: jbrowse1ModelFactory(pluginManager),\n          displayName: 'JBrowse 1 Data',\n          description: 'A JBrowse 1 data directory',\n          url: '//jbrowse.org/',\n        }),\n    )\n  }\n}\n","import {\n  Feature,\n  SimpleFeatureSerialized,\n} from '@jbrowse/core/util/simpleFeature'\n\nconst jb2ToJb1 = { refName: 'seq_id' }\n\nconst jb1ToJb2 = { seq_id: 'refName' }\n\n/**\n * wrapper to adapt nclist features to act like jbrowse 2 features\n */\nexport default class NCListFeature implements Feature {\n  private parentHandle?: Feature\n\n  private uniqueId: string\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  constructor(private ncFeature: any, parent?: Feature, id?: string) {\n    this.uniqueId = id || ncFeature.id()\n    this.parentHandle = parent\n  }\n\n  set(): void {\n    throw new Error('not implemented')\n  }\n\n  jb2TagToJb1Tag(tag: string): string {\n    // @ts-ignore\n    const mapped = jb2ToJb1[tag] || tag\n    return mapped.toLowerCase()\n  }\n\n  jb1TagToJb2Tag(tag: string): string {\n    const t = tag.toLowerCase()\n    // @ts-ignore\n    const mapped = jb1ToJb2[t] || t\n    return mapped\n  }\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  get(attrName: string): any {\n    const attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName))\n    if (attr && attrName === 'subfeatures') {\n      // eslint-disable-next-line @typescript-eslint/no-explicit-any\n      return attr.map((subfeature: any) => new NCListFeature(subfeature, this))\n    }\n    return attr\n  }\n\n  /**\n   * Get an array listing which data keys are present in this feature.\n   */\n  tags(): string[] {\n    return this.ncFeature.tags().map((t: string) => this.jb1TagToJb2Tag(t))\n  }\n\n  /**\n   * Get the unique ID of this feature.\n   */\n  id(): string {\n    return this.uniqueId\n  }\n\n  /**\n   * Get this feature's parent feature, or undefined if none.\n   */\n  parent(): Feature | undefined {\n    return this.parentHandle\n  }\n\n  /**\n   * Get an array of child features, or undefined if none.\n   */\n  children(): Feature[] | undefined {\n    return this.get('subfeatures')\n  }\n\n  toJSON(): SimpleFeatureSerialized {\n    const data: SimpleFeatureSerialized = { uniqueId: this.id() }\n    this.ncFeature.tags().forEach((tag: string) => {\n      const mappedTag = this.jb1TagToJb2Tag(tag)\n      const value = this.ncFeature.get(tag)\n      if (mappedTag === 'subfeatures') {\n        data.subfeatures = (value || []).map((f: Feature) => {\n          // note: was new NCListFeature(f, `${this.id()}-${i}`, this).toJSON()\n          return new NCListFeature(f, this).toJSON()\n        })\n      } else {\n        data[mappedTag] = value\n      }\n    })\n    return data\n  }\n}\n","import NCListStore from '@gmod/nclist'\nimport { Region } from '@jbrowse/core/util/types'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { checkAbortSignal } from '@jbrowse/core/util'\nimport { RemoteFile } from 'generic-filehandle'\nimport { Instance } from 'mobx-state-tree'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport NCListFeature from './NCListFeature'\nimport MyConfigSchema from './configSchema'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\nexport default class NCListAdapter extends BaseFeatureDataAdapter {\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  private nclist: any\n\n  private configRefNames?: string[]\n\n  constructor(\n    config: Instance<typeof MyConfigSchema>,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const refNames = readConfObject(config, 'refNames')\n    const rootUrlTemplate = readConfObject(config, 'rootUrlTemplate')\n    this.configRefNames = refNames\n\n    this.nclist = new NCListStore({\n      baseUrl: '',\n      urlTemplate: rootUrlTemplate.uri,\n      readFile: (url: string) =>\n        new RemoteFile(\n          String(\n            rootUrlTemplate.baseUri\n              ? new URL(url, rootUrlTemplate.baseUri).toString()\n              : url,\n          ),\n        ).readFile(),\n    })\n  }\n\n  /**\n   * Fetch features for a certain region. Use getFeaturesInRegion() if you also\n   * want to verify that the store has features for the given reference sequence\n   * before fetching.\n   * @param region -\n   * @param opts - [signal] optional signalling object for aborting the fetch\n   * @returns Observable of Feature objects in the region\n   */\n  getFeatures(region: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const { signal } = opts\n      for await (const feature of this.nclist.getFeatures(region, opts)) {\n        checkAbortSignal(signal)\n        observer.next(this.wrapFeature(feature))\n      }\n      observer.complete()\n    })\n  }\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  wrapFeature(ncFeature: any): NCListFeature {\n    return new NCListFeature(\n      ncFeature,\n      undefined,\n      `${this.id}-${ncFeature.id()}`,\n    )\n  }\n\n  async hasDataForRefName(refName: string) {\n    const root = await 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package/dist/plugin-legacy-jbrowse.esm.js

@@ -183,14 +183,14 @@ 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);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "1.5.8",
+  "version": "1.6.2",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -49,5 +49,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "f16afc382629a4a830f9040410a9ff1a3a328918"
+  "gitHead": "92455c6021abd69548496a450983d89f8837860d"
 }