@jbrowse/plugin-wiggle 1.6.9 → 1.7.3

package/dist/plugin-wiggle.cjs.development.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"plugin-wiggle.cjs.development.js","sources":["../../../node_modules/regenerator-runtime/runtime.js","../src/WiggleBaseRenderer.tsx","../src/WiggleRendering.tsx","../src/BigWigAdapter/configSchema.ts","../src/util.ts","../src/configSchema.ts","../src/DensityRenderer/index.ts","../src/LinearWiggleDisplay/models/configSchema.ts","../src/LinearWiggleDisplay/components/Tooltip.tsx","../src/LinearWiggleDisplay/components/YScaleBar.tsx","../src/LinearWiggleDisplay/components/WiggleDisplayComponent.tsx","../src/LinearWiggleDisplay/models/model.tsx","../src/XYPlotRenderer/XYPlotRenderer.ts","../src/XYPlotRenderer/index.ts","../src/LinePlotRenderer/LinePlotRenderer.js","../src/LinePlotRenderer/index.js","../src/WiggleRPC/rpcMethods.ts","../src/index.ts","../src/LinearWiggleDisplay/components/SetMinMaxDialog.tsx","../src/LinearWiggleDisplay/components/SetColorDialog.tsx","../src/BigWigAdapter/BigWigAdapter.ts"],"sourcesContent":["/**\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","import { Feature } from '@jbrowse/core/util/simpleFeature'\nimport FeatureRendererType, {\n  RenderArgs as FeatureRenderArgs,\n  RenderArgsSerialized,\n  RenderArgsDeserialized as FeatureRenderArgsDeserialized,\n  RenderResults,\n  ResultsSerialized,\n  ResultsDeserialized,\n} from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'\nimport { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils'\nimport { ThemeOptions } from '@material-ui/core'\nimport { ScaleOpts } from './util'\n\nexport interface RenderArgs extends FeatureRenderArgs {\n  scaleOpts: ScaleOpts\n}\n\nexport interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {\n  bpPerPx: number\n  height: number\n  highResolutionScaling: number\n  scaleOpts: ScaleOpts\n  displayCrossHatches: boolean\n  ticks: { values: number[] }\n  theme: ThemeOptions\n}\n\nexport interface RenderArgsDeserializedWithFeatures\n  extends RenderArgsDeserialized {\n  features: Map<string, Feature>\n}\n\nexport type {\n  RenderArgsSerialized,\n  RenderResults,\n  ResultsSerialized,\n  ResultsDeserialized,\n}\n\nexport default abstract class WiggleBaseRenderer extends FeatureRendererType {\n  supportsSVG = true\n\n  async render(renderProps: RenderArgsDeserialized) {\n    const features = await this.getFeatures(renderProps)\n    const { height, regions, bpPerPx } = renderProps\n    const [region] = regions\n    const width = (region.end - region.start) / bpPerPx\n\n    const res = await renderToAbstractCanvas(\n      width,\n      height,\n      renderProps,\n      (ctx: CanvasRenderingContext2D) =>\n        this.draw(ctx, {\n          ...renderProps,\n          features,\n        }),\n    )\n\n    const results = await super.render({\n      ...renderProps,\n      ...res,\n      features,\n      height,\n      width,\n    })\n\n    return {\n      ...results,\n      ...res,\n      features,\n      height,\n      width,\n    }\n  }\n\n  /*\n   * draw features to context given props, to be used by derived renderer\n   * classes\n   */\n  abstract draw<T extends RenderArgsDeserializedWithFeatures>(\n    ctx: CanvasRenderingContext2D,\n    props: T,\n  ): void\n}\n","import { observer } from 'mobx-react'\nimport React, { useRef } from 'react'\n\nimport { Region } from '@jbrowse/core/util/types'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { PrerenderedCanvas } from '@jbrowse/core/ui'\n\nfunction WiggleRendering(props: {\n  regions: Region[]\n  features: Map<string, Feature>\n  bpPerPx: number\n  width: number\n  height: number\n  onMouseLeave: Function\n  onMouseMove: Function\n  onFeatureClick: Function\n  blockKey: string\n}) {\n  const {\n    regions,\n    features,\n    bpPerPx,\n    width,\n    height,\n    onMouseLeave = () => {},\n    onMouseMove = () => {},\n    onFeatureClick = () => {},\n  } = props\n  const [region] = regions\n  const ref = useRef<HTMLDivElement>(null)\n\n  function getFeatureUnderMouse(eventClientX: number) {\n    // calculates feature under mouse\n    let offset = 0\n    if (ref.current) {\n      offset = ref.current.getBoundingClientRect().left\n    }\n    const offsetX = eventClientX - offset\n    const px = region.reversed ? width - offsetX : offsetX\n    const clientBp = region.start + bpPerPx * px\n    let featureUnderMouse\n    for (const feature of features.values()) {\n      if (clientBp <= feature.get('end') && clientBp >= feature.get('start')) {\n        featureUnderMouse = feature\n        break\n      }\n    }\n    return featureUnderMouse\n  }\n  return (\n    <div\n      ref={ref}\n      data-testid=\"wiggle-rendering-test\"\n      onMouseMove={event => {\n        const featureUnderMouse = getFeatureUnderMouse(event.clientX)\n        onMouseMove(\n          event,\n          featureUnderMouse ? featureUnderMouse.id() : undefined,\n        )\n      }}\n      onClick={event => {\n        const featureUnderMouse = getFeatureUnderMouse(event.clientX)\n        onFeatureClick(\n          event,\n          featureUnderMouse ? featureUnderMouse.id() : undefined,\n        )\n      }}\n      onMouseLeave={event => onMouseLeave(event)}\n      role=\"presentation\"\n      className=\"WiggleRendering\"\n      style={{\n        overflow: 'visible',\n        position: 'relative',\n        height,\n      }}\n    >\n      <PrerenderedCanvas {...props} />\n    </div>\n  )\n}\n\nexport default observer(WiggleRendering)\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'BigWigAdapter',\n  {\n    bigWigLocation: {\n      type: 'fileLocation',\n      defaultValue: {\n        uri: '/path/to/my.bw',\n        locationType: 'UriLocation',\n      },\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import { scaleLinear, scaleLog, scaleQuantize } from 'd3-scale'\n\nexport interface ScaleOpts {\n  domain: number[]\n  range: number[]\n  scaleType: string\n  pivotValue?: number\n  inverted: boolean\n}\n/**\n * produces a d3-scale from arguments. applies a \"nice domain\" adjustment\n *\n * @param object - containing attributes\n *   - domain [min,max]\n *   - range [min,max]\n *   - bounds [min,max]\n *   - scaleType (linear or log)\n *   - pivotValue (number)\n *   - inverted (boolean)\n */\nexport function getScale({\n  domain = [],\n  range = [],\n  scaleType,\n  pivotValue,\n  inverted,\n}: ScaleOpts) {\n  let scale\n  const [min, max] = domain\n  if (min === undefined || max === undefined) {\n    throw new Error('invalid domain')\n  }\n  if (scaleType === 'linear') {\n    scale = scaleLinear()\n  } else if (scaleType === 'log') {\n    scale = scaleLog()\n    scale.base(2)\n  } else if (scaleType === 'quantize') {\n    scale = scaleQuantize()\n  } else {\n    throw new Error('undefined scaleType')\n  }\n  scale.domain(pivotValue !== undefined ? [min, pivotValue, max] : [min, max])\n  scale.nice()\n\n  const [rangeMin, rangeMax] = range\n  if (rangeMin === undefined || rangeMax === undefined) {\n    throw new Error('invalid range')\n  }\n  scale.range(inverted ? range.slice().reverse() : range)\n  return scale\n}\n/**\n * gets the origin for drawing the graph. for linear this is 0, for log this is arbitrarily set to log(1)==0\n *\n * @param scaleType -\n */\nexport function getOrigin(scaleType: string /* , pivot, stats */) {\n  // if (pivot) {\n  //   if (pivot === 'mean') {\n  //     return stats.scoreMean || 0\n  //   }\n  //   if (pivot === 'zero') {\n  //     return 0\n  //   }\n  //   return parseFloat()\n  // }\n  // if (scaleType === 'z_score') {\n  //   return stats.scoreMean || 0\n  // }\n  if (scaleType === 'log') {\n    return 1\n  }\n  return 0\n}\n\n/**\n * produces a \"nice\" domain that actually rounds down to 0 for the min\n * or 0 to the max depending on if all values are positive or negative\n *\n * @param object - containing attributes\n *   - domain [min,max]\n *   - bounds [min,max]\n *   - mean\n *   - stddev\n *   - scaleType (linear or log)\n */\nexport function getNiceDomain({\n  scaleType,\n  domain,\n  bounds,\n}: {\n  scaleType: string\n  domain: number[]\n  bounds: number[]\n}) {\n  const [minScore, maxScore] = bounds\n  let [min, max] = domain\n\n  if (scaleType === 'linear') {\n    if (max < 0) {\n      max = 0\n    }\n    if (min > 0) {\n      min = 0\n    }\n  }\n  if (scaleType === 'log') {\n    // if the min is 0, assume that it's just something\n    // with no read coverage and that we should ignore it in calculations\n    // if it's greater than 1 pin to 1 for the full range also\n    // otherwise, we may see bigwigs with fractional values\n    if (min === 0 || min > 1) {\n      min = 1\n    }\n  }\n  if (min === undefined || max === undefined) {\n    throw new Error('invalid domain supplied to stats function')\n  }\n  if (minScore !== undefined && minScore !== Number.MIN_VALUE) {\n    min = minScore\n  }\n  if (maxScore !== undefined && maxScore !== Number.MAX_VALUE) {\n    max = maxScore\n  }\n  const getScaleType = (type: string) => {\n    if (type === 'linear') {\n      return scaleLinear()\n    }\n    if (type === 'log') {\n      const scale = scaleLog()\n      scale.base(2)\n      return scale\n    }\n    if (type === 'quantize') {\n      return scaleQuantize()\n    }\n    throw new Error(`undefined scaleType ${type}`)\n  }\n  const scale = getScaleType(scaleType)\n\n  scale.domain([min, max])\n  scale.nice()\n  return scale.domain() as [number, number]\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default ConfigurationSchema(\n  'WiggleRenderer',\n  {\n    color: {\n      type: 'color',\n      description: 'the color of track, overrides posColor and negColor',\n      defaultValue: '#f0f',\n    },\n    posColor: {\n      type: 'color',\n      description: 'the color to use when the score is positive',\n      defaultValue: 'blue',\n    },\n    negColor: {\n      type: 'color',\n      description: 'the color to use when the score is negative',\n      defaultValue: 'red',\n    },\n    highlightColor: {\n      type: 'color',\n      description: 'the color of highlights over the wiggle track',\n      defaultValue: 'rgba(255,255,0,0.5)',\n    },\n    clipColor: {\n      type: 'color',\n      description: 'the color of the clipping marker',\n      defaultValue: 'red',\n    },\n    renderType: {\n      type: 'stringEnum',\n      model: types.enumeration('Rendering type', ['xyplot', 'density', 'line']),\n      description: 'The type of rendering for wiggle data to use',\n      defaultValue: 'xyplot',\n    },\n    filled: {\n      type: 'boolean',\n      description: 'fill in histogram',\n      defaultValue: true,\n    },\n    bicolorPivot: {\n      type: 'stringEnum',\n      model: types.enumeration('Scale type', [\n        'numeric',\n        'mean',\n        'z_score',\n        'none',\n      ]),\n      description: 'type of bicolor pivot',\n      defaultValue: 'numeric',\n    },\n    bicolorPivotValue: {\n      type: 'number',\n      defaultValue: 0,\n      description: 'value to use for bicolor pivot',\n    },\n    summaryScoreMode: {\n      type: 'stringEnum',\n      model: types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),\n      description:\n        'choose whether to use max/min/average or whiskers which combines all three into the same rendering',\n      defaultValue: 'whiskers',\n    },\n    displayCrossHatches: {\n      type: 'boolean',\n      description: 'choose to draw cross hatches (sideways lines)',\n      defaultValue: false,\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import {\n  readConfObject,\n  ConfigurationSchema,\n} from '@jbrowse/core/configuration'\nimport { featureSpanPx } from '@jbrowse/core/util'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { getScale } from '../util'\n\nimport ConfigSchema from '../configSchema'\nimport WiggleBaseRenderer, {\n  RenderArgsDeserializedWithFeatures,\n} from '../WiggleBaseRenderer'\n\nexport { default as ReactComponent } from '../WiggleRendering'\n\nexport default class DensityRenderer extends WiggleBaseRenderer {\n  draw(\n    ctx: CanvasRenderingContext2D,\n    props: RenderArgsDeserializedWithFeatures,\n  ) {\n    const { features, regions, bpPerPx, scaleOpts, height, config } = props\n    const [region] = regions\n    const pivot = readConfObject(config, 'bicolorPivot')\n    const pivotValue = readConfObject(config, 'bicolorPivotValue')\n    const negColor = readConfObject(config, 'negColor')\n    const posColor = readConfObject(config, 'posColor')\n    const color = readConfObject(config, 'color')\n    let colorCallback\n    if (color === '#f0f') {\n      const colorScale =\n        pivot !== 'none'\n          ? getScale({\n              ...scaleOpts,\n              pivotValue,\n              range: [negColor, 'white', posColor],\n            })\n          : getScale({ ...scaleOpts, range: ['white', posColor] })\n      colorCallback = (feature: Feature) => colorScale(feature.get('score'))\n    } else {\n      colorCallback = (feature: Feature) =>\n        readConfObject(config, 'color', { feature })\n    }\n\n    for (const feature of features.values()) {\n      const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)\n      const w = rightPx - leftPx + 0.3 // fudge factor for subpixel rendering\n      ctx.fillStyle = colorCallback(feature)\n      ctx.fillRect(leftPx, 0, w, height)\n    }\n  }\n}\nexport const configSchema = ConfigurationSchema(\n  'DensityRenderer',\n  {},\n  { baseConfiguration: ConfigSchema, explicitlyTyped: true },\n)\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'\nimport { types } from 'mobx-state-tree'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function WiggleConfigFactory(pluginManager: PluginManager) {\n  const XYPlotRendererConfigSchema =\n    pluginManager.getRendererType('XYPlotRenderer').configSchema\n  const DensityRendererConfigSchema =\n    pluginManager.getRendererType('DensityRenderer').configSchema\n  const LinePlotRendererConfigSchema =\n    pluginManager.getRendererType('LinePlotRenderer').configSchema\n\n  return ConfigurationSchema(\n    'LinearWiggleDisplay',\n    {\n      autoscale: {\n        type: 'stringEnum',\n        defaultValue: 'local',\n        model: types.enumeration('Autoscale type', [\n          'global',\n          'local',\n          'globalsd',\n          'localsd',\n          'zscore',\n        ]),\n        description:\n          'global/local using their min/max values or w/ standard deviations (globalsd/localsd)',\n      },\n      minimalTicks: {\n        type: 'boolean',\n        defaultValue: false,\n        description: 'use the minimal amount of ticks',\n      },\n\n      minScore: {\n        type: 'number',\n        defaultValue: Number.MIN_VALUE,\n        description: 'minimum value for the y-scale',\n      },\n      maxScore: {\n        type: 'number',\n        description: 'maximum value for the y-scale',\n        defaultValue: Number.MAX_VALUE,\n      },\n      numStdDev: {\n        type: 'number',\n        description:\n          'number of standard deviations to use for autoscale types globalsd or localsd',\n        defaultValue: 3,\n      },\n      scaleType: {\n        type: 'stringEnum',\n        model: types.enumeration('Scale type', ['linear', 'log']), // todo zscale\n        description: 'The type of scale to use',\n        defaultValue: 'linear',\n      },\n      inverted: {\n        type: 'boolean',\n        description: 'draw upside down',\n        defaultValue: false,\n      },\n\n      defaultRendering: {\n        type: 'stringEnum',\n        model: types.enumeration('Rendering', ['density', 'xyplot', 'line']),\n        defaultValue: 'xyplot',\n      },\n\n      renderers: ConfigurationSchema('RenderersConfiguration', {\n        DensityRenderer: DensityRendererConfigSchema,\n        XYPlotRenderer: XYPlotRendererConfigSchema,\n        LinePlotRenderer: LinePlotRendererConfigSchema,\n      }),\n    },\n    { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n  )\n}\n","import React, { useMemo, useState } from 'react'\nimport { observer } from 'mobx-react'\nimport { makeStyles, alpha, Portal } from '@material-ui/core'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\n\n// locals\nimport { YSCALEBAR_LABEL_OFFSET } from '../models/model'\nimport { usePopper } from 'react-popper'\n\n// convert to number, apply shortened precision, and render\nfunction toP(s = 0) {\n  return +(+s).toPrecision(6)\n}\n\nfunction round(value: number) {\n  return Math.round(value * 1e5) / 1e5\n}\n\nconst en = (n: number) => n.toLocaleString('en-US')\n\nconst useStyles = makeStyles(theme => ({\n  // these styles come from\n  // https://github.com/mui-org/material-ui/blob/master/packages/material-ui/src/Tooltip/Tooltip.js\n  tooltip: {\n    position: 'absolute',\n    pointerEvents: 'none',\n    backgroundColor: alpha(theme.palette.grey[700], 0.9),\n    borderRadius: theme.shape.borderRadius,\n    color: theme.palette.common.white,\n    fontFamily: theme.typography.fontFamily,\n    padding: '4px 8px',\n    fontSize: theme.typography.pxToRem(12),\n    lineHeight: `${round(14 / 10)}em`,\n    maxWidth: 300,\n    wordWrap: 'break-word',\n  },\n\n  hoverVertical: {\n    background: '#333',\n    border: 'none',\n    width: 1,\n    height: '100%',\n    top: YSCALEBAR_LABEL_OFFSET,\n    cursor: 'default',\n    position: 'absolute',\n    pointerEvents: 'none',\n  },\n}))\n\nconst TooltipContents = React.forwardRef<HTMLDivElement, { feature: Feature }>(\n  ({ feature }: { feature: Feature }, ref) => {\n    const start = feature.get('start')\n    const end = feature.get('end')\n    const name = feature.get('refName')\n    const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]\n      .filter(f => !!f)\n      .join(':')\n\n    return feature.get('summary') !== undefined ? (\n      <div ref={ref}>\n        {loc}\n        <br />\n        Max: {toP(feature.get('maxScore'))}\n        <br />\n        Avg: {toP(feature.get('score'))}\n        <br />\n        Min: {toP(feature.get('minScore'))}\n      </div>\n    ) : (\n      <div ref={ref}>\n        {loc}\n        <br />\n        {`${toP(feature.get('score'))}`}\n      </div>\n    )\n  },\n)\n\ntype Coord = [number, number]\n\nconst Tooltip = observer(\n  ({\n    model,\n    height,\n    clientMouseCoord,\n    offsetMouseCoord,\n    clientRect,\n    TooltipContents,\n  }: {\n    model: { featureUnderMouse: Feature }\n    height: number\n    clientMouseCoord: Coord\n    offsetMouseCoord: Coord\n    clientRect?: DOMRect\n\n    // eslint-disable-next-line @typescript-eslint/no-explicit-any\n    TooltipContents: React.FC<any>\n  }) => {\n    const { featureUnderMouse } = model\n    const [width, setWidth] = useState(0)\n    const [anchorEl, setAnchorEl] = useState<HTMLDivElement | null>(null)\n    const classes = useStyles()\n\n    // must be memoized a la https://github.com/popperjs/react-popper/issues/391\n    const virtElement = useMemo(\n      () => ({\n        getBoundingClientRect: () => {\n          const x = clientMouseCoord[0] + width / 2 + 20\n          const y = clientRect?.top || 0\n          return {\n            top: y,\n            left: x,\n            bottom: y,\n            right: x,\n            width: 0,\n            height: 0,\n            x,\n            y,\n            toJSON() {},\n          }\n        },\n      }),\n      [clientRect?.top, clientMouseCoord, width],\n    )\n    const { styles, attributes } = usePopper(virtElement, anchorEl)\n\n    return featureUnderMouse ? (\n      <>\n        <Portal>\n          <div\n            ref={setAnchorEl}\n            className={classes.tooltip}\n            // zIndex needed to go over widget drawer\n            style={{ ...styles.popper, zIndex: 100000 }}\n            {...attributes.popper}\n          >\n            <TooltipContents\n              ref={(elt: HTMLDivElement) => {\n                setWidth(elt?.getBoundingClientRect().width || 0)\n              }}\n              feature={featureUnderMouse}\n            />\n          </div>\n        </Portal>\n\n        <div\n          className={classes.hoverVertical}\n          style={{\n            left: offsetMouseCoord[0],\n            height: height - YSCALEBAR_LABEL_OFFSET * 2,\n          }}\n        />\n      </>\n    ) : null\n  },\n)\n\nconst WiggleTooltip = observer(\n  (props: {\n    model: { featureUnderMouse: Feature }\n    height: number\n    offsetMouseCoord: Coord\n    clientMouseCoord: Coord\n    clientRect?: DOMRect\n  }) => {\n    return <Tooltip TooltipContents={TooltipContents} {...props} />\n  },\n)\nexport default WiggleTooltip\nexport { Tooltip }\n","import React from 'react'\nimport { observer } from 'mobx-react'\nimport { Axis, LEFT, RIGHT } from 'react-d3-axis-mod'\nimport { WiggleDisplayModel } from '../models/model'\n\nconst YScaleBar = observer(\n  ({\n    model,\n    orientation,\n  }: {\n    model: WiggleDisplayModel\n    orientation?: string\n  }) => {\n    const { ticks } = model\n\n    return ticks ? (\n      <Axis\n        {...ticks}\n        shadow={2}\n        format={(n: number) => n}\n        style={{ orient: orientation === 'left' ? LEFT : RIGHT }}\n      />\n    ) : null\n  },\n)\nexport default YScaleBar\n","import React from 'react'\nimport {\n  measureText,\n  getContainingView,\n  getContainingTrack,\n} from '@jbrowse/core/util'\nimport { getConf } from '@jbrowse/core/configuration'\nimport { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'\nimport { observer } from 'mobx-react'\nimport { WiggleDisplayModel } from '../models/model'\nimport YScaleBar from './YScaleBar'\n\nconst LinearWiggleDisplay = observer((props: { model: WiggleDisplayModel }) => {\n  const { model } = props\n  const { stats, height, needsScalebar } = model\n\n  // @ts-ignore\n  const { trackLabels } = getContainingView(model)\n  const left =\n    trackLabels === 'overlapping'\n      ? measureText(getConf(getContainingTrack(model), 'name'), 12.8) + 100\n      : 50\n  return (\n    <div>\n      <BaseLinearDisplayComponent {...props} />\n      {stats && needsScalebar ? (\n        <svg\n          style={{\n            position: 'absolute',\n            top: 0,\n            left,\n            pointerEvents: 'none',\n            height,\n            width: 50,\n          }}\n        >\n          <YScaleBar model={model} />\n        </svg>\n      ) : null}\n    </div>\n  )\n})\n\nexport default LinearWiggleDisplay\n\nexport { YScaleBar }\n","import React, { lazy } from 'react'\nimport {\n  ConfigurationReference,\n  AnyConfigurationSchemaType,\n  getConf,\n  readConfObject,\n} from '@jbrowse/core/configuration'\nimport {\n  isAbortException,\n  getSession,\n  getContainingView,\n  isSelectionContainer,\n} from '@jbrowse/core/util'\nimport { getRpcSessionId } from '@jbrowse/core/util/tracks'\nimport {\n  BaseLinearDisplay,\n  LinearGenomeViewModel,\n} from '@jbrowse/plugin-linear-genome-view'\nimport { autorun, when } from 'mobx'\nimport { addDisposer, isAlive, types, getEnv, Instance } from 'mobx-state-tree'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nimport { FeatureStats } from '@jbrowse/core/util/stats'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { axisPropsFromTickScale } from 'react-d3-axis-mod'\nimport { getNiceDomain, getScale } from '../../util'\n\nimport Tooltip from '../components/Tooltip'\nimport { YScaleBar } from '../components/WiggleDisplayComponent'\n\nconst SetMinMaxDlg = lazy(() => import('../components/SetMinMaxDialog'))\nconst SetColorDlg = lazy(() => import('../components/SetColorDialog'))\n\n// fudge factor for making all labels on the YScalebar visible\nexport const YSCALEBAR_LABEL_OFFSET = 5\n\n// using a map because it preserves order\nconst rendererTypes = new Map([\n  ['xyplot', 'XYPlotRenderer'],\n  ['density', 'DensityRenderer'],\n  ['line', 'LinePlotRenderer'],\n])\n\ntype LGV = LinearGenomeViewModel\n\nconst stateModelFactory = (\n  pluginManager: PluginManager,\n  configSchema: AnyConfigurationSchemaType,\n) =>\n  types\n    .compose(\n      'LinearWiggleDisplay',\n      BaseLinearDisplay,\n      types.model({\n        type: types.literal('LinearWiggleDisplay'),\n        configuration: ConfigurationReference(configSchema),\n        selectedRendering: types.optional(types.string, ''),\n        resolution: types.optional(types.number, 1),\n        fill: types.maybe(types.boolean),\n        color: types.maybe(types.string),\n        posColor: types.maybe(types.string),\n        negColor: types.maybe(types.string),\n        summaryScoreMode: types.maybe(types.string),\n        rendererTypeNameState: types.maybe(types.string),\n        scale: types.maybe(types.string),\n        autoscale: types.maybe(types.string),\n        displayCrossHatches: types.maybe(types.boolean),\n        constraints: types.optional(\n          types.model({\n            max: types.maybe(types.number),\n            min: types.maybe(types.number),\n          }),\n          {},\n        ),\n      }),\n    )\n    .volatile(() => ({\n      statsReady: false,\n      message: undefined as undefined | string,\n      stats: { scoreMin: 0, scoreMax: 50 },\n      statsFetchInProgress: undefined as undefined | AbortController,\n    }))\n    .actions(self => ({\n      updateStats({\n        scoreMin,\n        scoreMax,\n      }: {\n        scoreMin: number\n        scoreMax: number\n      }) {\n        if (\n          self.stats.scoreMin !== scoreMin ||\n          self.stats.scoreMax !== scoreMax\n        ) {\n          self.stats = { scoreMin, scoreMax }\n        }\n        self.statsReady = true\n      },\n      setColor(color: string) {\n        self.color = color\n      },\n      setPosColor(color: string) {\n        self.posColor = color\n      },\n      setNegColor(color: string) {\n        self.negColor = color\n      },\n\n      setLoading(aborter: AbortController) {\n        const { statsFetchInProgress: statsFetch } = self\n        if (statsFetch !== undefined && !statsFetch.signal.aborted) {\n          statsFetch.abort()\n        }\n        self.statsFetchInProgress = aborter\n      },\n\n      // this overrides the BaseLinearDisplayModel to avoid popping up a\n      // feature detail display, but still sets the feature selection on the\n      // model so listeners can detect a click\n      selectFeature(feature: Feature) {\n        const session = getSession(self)\n        if (isSelectionContainer(session)) {\n          session.setSelection(feature)\n        }\n      },\n      setResolution(res: number) {\n        self.resolution = res\n      },\n\n      setFill(fill: boolean) {\n        self.fill = fill\n      },\n\n      toggleLogScale() {\n        if (self.scale !== 'log') {\n          self.scale = 'log'\n        } else {\n          self.scale = 'linear'\n        }\n      },\n\n      setScaleType(scale?: string) {\n        self.scale = scale\n      },\n\n      setSummaryScoreMode(val: string) {\n        self.summaryScoreMode = val\n      },\n\n      setAutoscale(val: string) {\n        self.autoscale = val\n      },\n\n      setMaxScore(val?: number) {\n        self.constraints.max = val\n      },\n\n      setRendererType(val: string) {\n        self.rendererTypeNameState = val\n      },\n\n      setMinScore(val?: number) {\n        self.constraints.min = val\n      },\n\n      toggleCrossHatches() {\n        self.displayCrossHatches = !self.displayCrossHatches\n      },\n\n      setCrossHatches(cross: boolean) {\n        self.displayCrossHatches = cross\n      },\n    }))\n    .views(self => ({\n      get TooltipComponent() {\n        return Tooltip as unknown as React.FC\n      },\n\n      get adapterTypeName() {\n        return self.adapterConfig.type\n      },\n\n      get rendererTypeName() {\n        const viewName =\n          self.rendererTypeNameState || getConf(self, 'defaultRendering')\n        const rendererType = rendererTypes.get(viewName)\n        if (!rendererType) {\n          throw new Error(`unknown alignments view name ${viewName}`)\n        }\n        return rendererType\n      },\n\n      // subclasses can define these, as snpcoverage track does\n      get filters() {\n        return undefined\n      },\n\n      get scaleType() {\n        return self.scale || getConf(self, 'scaleType')\n      },\n\n      get maxScore() {\n        const { max } = self.constraints\n        return max !== undefined ? max : getConf(self, 'maxScore')\n      },\n\n      get minScore() {\n        const { min } = self.constraints\n        return min !== undefined ? min : getConf(self, 'minScore')\n      },\n    }))\n    .views(self => ({\n      get rendererConfig() {\n        const configBlob =\n          getConf(self, ['renderers', self.rendererTypeName]) || {}\n\n        return self.rendererType.configSchema.create(\n          {\n            ...configBlob,\n            filled: self.fill,\n            scaleType: self.scaleType,\n            displayCrossHatches: self.displayCrossHatches,\n            summaryScoreMode: self.summaryScoreMode,\n            ...(self.color ? { color: self.color } : {}),\n            ...(self.negColor ? { negColor: self.negColor } : {}),\n            ...(self.posColor ? { posColor: self.posColor } : {}),\n          },\n          getEnv(self),\n        )\n      },\n    }))\n    .views(self => {\n      let oldDomain: [number, number] = [0, 0]\n      return {\n        get filled() {\n          return typeof self.fill !== 'undefined'\n            ? self.fill\n            : readConfObject(self.rendererConfig, 'filled')\n        },\n        get summaryScoreModeSetting() {\n          return (\n            self.summaryScoreMode ||\n            readConfObject(self.rendererConfig, 'summaryScoreMode')\n          )\n        },\n        get domain() {\n          const { stats, scaleType, minScore, maxScore } = self\n          const { scoreMin, scoreMax } = stats\n\n          const ret = getNiceDomain({\n            domain: [scoreMin, scoreMax],\n            bounds: [minScore, maxScore],\n            scaleType,\n          })\n\n          // avoid weird scalebar if log value and empty region displayed\n          if (scaleType === 'log' && ret[1] === Number.MIN_VALUE) {\n            return [0, Number.MIN_VALUE]\n          }\n\n          // avoid returning a new object if it matches the old value\n          if (JSON.stringify(oldDomain) !== JSON.stringify(ret)) {\n            oldDomain = ret\n          }\n\n          return oldDomain\n        },\n\n        get needsScalebar() {\n          return (\n            self.rendererTypeName === 'XYPlotRenderer' ||\n            self.rendererTypeName === 'LinePlotRenderer'\n          )\n        },\n        get scaleOpts() {\n          return {\n            domain: this.domain,\n            stats: self.stats,\n            autoscaleType: this.autoscaleType,\n            scaleType: self.scaleType,\n            inverted: getConf(self, 'inverted'),\n          }\n        },\n\n        get canHaveFill() {\n          return self.rendererTypeName === 'XYPlotRenderer'\n        },\n\n        get autoscaleType() {\n          return self.autoscale || getConf(self, 'autoscale')\n        },\n\n        get displayCrossHatchesSetting() {\n          return (\n            self.displayCrossHatches ||\n            readConfObject(self.rendererConfig, 'displayCrossHatches')\n          )\n        },\n      }\n    })\n    .views(self => ({\n      get ticks() {\n        const { scaleType, domain, height } = self\n        const minimalTicks = getConf(self, 'minimalTicks')\n        const range = [height - YSCALEBAR_LABEL_OFFSET, YSCALEBAR_LABEL_OFFSET]\n        const scale = getScale({\n          scaleType,\n          domain,\n          range,\n          inverted: getConf(self, 'inverted'),\n        })\n        const ticks = axisPropsFromTickScale(scale, 4)\n        return height < 100 || minimalTicks\n          ? { ...ticks, values: domain }\n          : ticks\n      },\n    }))\n    .views(self => {\n      const { renderProps: superRenderProps } = self\n      return {\n        renderProps() {\n          const superProps = superRenderProps()\n          return {\n            ...superProps,\n            notReady: superProps.notReady || !self.statsReady,\n            rpcDriverName: self.rpcDriverName,\n            displayModel: self,\n            config: self.rendererConfig,\n            scaleOpts: self.scaleOpts,\n            resolution: self.resolution,\n            height: self.height,\n            ticks: self.ticks,\n            displayCrossHatches: self.displayCrossHatches,\n            filters: self.filters,\n          }\n        },\n\n        get adapterCapabilities() {\n          return pluginManager.getAdapterType(self.adapterTypeName)\n            .adapterCapabilities\n        },\n\n        get hasResolution() {\n          return this.adapterCapabilities.includes('hasResolution')\n        },\n\n        get hasGlobalStats() {\n          return this.adapterCapabilities.includes('hasGlobalStats')\n        },\n      }\n    })\n    .views(self => {\n      const { trackMenuItems: superTrackMenuItems } = self\n      return {\n        trackMenuItems() {\n          return [\n            ...superTrackMenuItems(),\n            ...(self.hasResolution\n              ? [\n                  {\n                    label: 'Resolution',\n                    subMenu: [\n                      {\n                        label: 'Finer resolution',\n                        onClick: () => {\n                          self.setResolution(self.resolution * 5)\n                        },\n                      },\n                      {\n                        label: 'Coarser resolution',\n                        onClick: () => {\n                          self.setResolution(self.resolution / 5)\n                        },\n                      },\n                    ],\n                  },\n                  {\n                    label: 'Summary score mode',\n                    subMenu: ['min', 'max', 'avg', 'whiskers'].map(elt => {\n                      return {\n                        label: elt,\n                        onClick: () => self.setSummaryScoreMode(elt),\n                      }\n                    }),\n                  },\n                ]\n              : []),\n            ...(self.canHaveFill\n              ? [\n                  {\n                    label: self.filled\n                      ? 'Turn off histogram fill'\n                      : 'Turn on histogram fill',\n                    onClick: () => {\n                      self.setFill(!self.filled)\n                    },\n                  },\n                ]\n              : []),\n            {\n              label:\n                self.scaleType === 'log' ? 'Set linear scale' : 'Set log scale',\n              onClick: () => {\n                self.toggleLogScale()\n              },\n            },\n            {\n              type: 'checkbox',\n              label: 'Draw cross hatches',\n              checked: self.displayCrossHatchesSetting,\n              onClick: () => {\n                self.toggleCrossHatches()\n              },\n            },\n\n            ...(Object.keys(getConf(self, 'renderers') || {}).length > 1\n              ? [\n                  {\n                    label: 'Renderer type',\n                    subMenu: [...rendererTypes.keys()].map(key => ({\n                      label: key,\n                      onClick: () => self.setRendererType(key),\n                    })),\n                  },\n                ]\n              : []),\n            {\n              label: 'Autoscale type',\n              subMenu: [\n                ['local', 'Local'],\n                ...(self.hasGlobalStats\n                  ? [\n                      ['global', 'Global'],\n                      ['globalsd', 'Global ± 3σ'],\n                    ]\n                  : []),\n                ['localsd', 'Local ± 3σ'],\n              ].map(([val, label]) => {\n                return {\n                  label,\n                  onClick() {\n                    self.setAutoscale(val)\n                  },\n                }\n              }),\n            },\n            {\n              label: 'Set min/max score',\n              onClick: () => {\n                getSession(self).queueDialog(doneCallback => [\n                  SetMinMaxDlg,\n                  { model: self, handleClose: doneCallback },\n                ])\n              },\n            },\n            {\n              label: 'Set color',\n              onClick: () => {\n                getSession(self).queueDialog(doneCallback => [\n                  SetColorDlg,\n                  { model: self, handleClose: doneCallback },\n                ])\n              },\n            },\n          ]\n        },\n      }\n    })\n    .actions(self => {\n      const { reload: superReload, renderSvg: superRenderSvg } = self\n\n      type ExportSvgOpts = Parameters<typeof superRenderSvg>[0]\n\n      async function getStats(opts: {\n        headers?: Record<string, string>\n        signal?: AbortSignal\n        filters?: string[]\n      }): Promise<FeatureStats> {\n        const { rpcManager } = getSession(self)\n        const nd = getConf(self, 'numStdDev') || 3\n        const { adapterConfig, autoscaleType } = self\n        const sessionId = getRpcSessionId(self)\n        const params = {\n          sessionId,\n          adapterConfig,\n          statusCallback: (message: string) => {\n            if (isAlive(self)) {\n              self.setMessage(message)\n            }\n          },\n          ...opts,\n        }\n\n        if (autoscaleType === 'global' || autoscaleType === 'globalsd') {\n          const results: FeatureStats = (await rpcManager.call(\n            sessionId,\n            'WiggleGetGlobalStats',\n            params,\n          )) as FeatureStats\n          const { scoreMin, scoreMean, scoreStdDev } = results\n          // globalsd uses heuristic to avoid unnecessary scoreMin<0\n          // if the scoreMin is never less than 0\n          // helps with most coverage bigwigs just being >0\n          return autoscaleType === 'globalsd'\n            ? {\n                ...results,\n                scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev,\n                scoreMax: scoreMean + nd * scoreStdDev,\n              }\n            : results\n        }\n        if (autoscaleType === 'local' || autoscaleType === 'localsd') {\n          const { dynamicBlocks, bpPerPx } = getContainingView(self) as LGV\n          const results = (await rpcManager.call(\n            sessionId,\n            'WiggleGetMultiRegionStats',\n            {\n              ...params,\n              regions: dynamicBlocks.contentBlocks.map(region => {\n                const { start, end } = region\n                return {\n                  ...JSON.parse(JSON.stringify(region)),\n                  start: Math.floor(start),\n                  end: Math.ceil(end),\n                }\n              }),\n              bpPerPx,\n            },\n          )) as FeatureStats\n          const { scoreMin, scoreMean, scoreStdDev } = results\n\n          // localsd uses heuristic to avoid unnecessary scoreMin<0 if the\n          // scoreMin is never less than 0 helps with most coverage bigwigs\n          // just being >0\n          return autoscaleType === 'localsd'\n            ? {\n                ...results,\n                scoreMin: scoreMin >= 0 ? 0 : scoreMean - nd * scoreStdDev,\n                scoreMax: scoreMean + nd * scoreStdDev,\n              }\n            : results\n        }\n        if (autoscaleType === 'zscale') {\n          return rpcManager.call(\n            sessionId,\n            'WiggleGetGlobalStats',\n            params,\n          ) as Promise<FeatureStats>\n        }\n        throw new Error(`invalid autoscaleType '${autoscaleType}'`)\n      }\n      return {\n        // re-runs stats and refresh whole display on reload\n        async reload() {\n          self.setError()\n          const aborter = new AbortController()\n          let stats\n          try {\n            stats = await getStats({\n              signal: aborter.signal,\n              filters: self.filters,\n            })\n            if (isAlive(self)) {\n              self.updateStats(stats)\n              superReload()\n            }\n          } catch (e) {\n            self.setError(e)\n          }\n        },\n        afterAttach() {\n          addDisposer(\n            self,\n            autorun(\n              async () => {\n                try {\n                  const aborter = new AbortController()\n                  const view = getContainingView(self) as LGV\n                  self.setLoading(aborter)\n\n                  if (!view.initialized) {\n                    return\n                  }\n\n                  if (!self.estimatedStatsReady) {\n                    return\n                  }\n                  if (self.regionTooLarge) {\n                    return\n                  }\n\n                  const wiggleStats = await getStats({\n                    signal: aborter.signal,\n                    filters: self.filters,\n                  })\n\n                  if (isAlive(self)) {\n                    self.updateStats(wiggleStats)\n                  }\n                } catch (e) {\n                  if (!isAbortException(e) && isAlive(self)) {\n                    console.error(e)\n                    self.setError(e)\n                  }\n                }\n              },\n              { delay: 1000 },\n            ),\n          )\n        },\n        async renderSvg(opts: ExportSvgOpts) {\n          await when(() => self.statsReady && !!self.regionCannotBeRenderedText)\n          const { needsScalebar, stats } = self\n          const { offsetPx } = getContainingView(self) as LGV\n          return (\n            <>\n              <g id=\"snpcov\">{await superRenderSvg(opts)}</g>\n              {needsScalebar && stats ? (\n                <g transform={`translate(${Math.max(-offsetPx, 0)})`}>\n                  <YScaleBar\n                    model={self as WiggleDisplayModel}\n                    orientation=\"left\"\n                  />\n                </g>\n              ) : null}\n            </>\n          )\n        },\n      }\n    })\n\nexport type WiggleDisplayStateModel = ReturnType<typeof stateModelFactory>\nexport type WiggleDisplayModel = Instance<WiggleDisplayStateModel>\n\nexport default stateModelFactory\n","import { readConfObject } from '@jbrowse/core/configuration'\nimport { featureSpanPx } from '@jbrowse/core/util'\nimport Color from 'color'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { getOrigin, getScale } from '../util'\nimport WiggleBaseRenderer, {\n  RenderArgsDeserializedWithFeatures,\n} from '../WiggleBaseRenderer'\nimport { YSCALEBAR_LABEL_OFFSET } from '../LinearWiggleDisplay/models/model'\n\nexport default class XYPlotRenderer extends WiggleBaseRenderer {\n  draw(\n    ctx: CanvasRenderingContext2D,\n    props: RenderArgsDeserializedWithFeatures,\n  ) {\n    const {\n      features,\n      bpPerPx,\n      regions,\n      scaleOpts,\n      height: unadjustedHeight,\n      config,\n      ticks,\n      displayCrossHatches,\n    } = props\n    const [region] = regions\n    const width = (region.end - region.start) / bpPerPx\n\n    // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the\n    // wiggle display, and makes the height of the actual drawn area add\n    // \"padding\" to the top and bottom of the display\n    const offset = YSCALEBAR_LABEL_OFFSET\n    const height = unadjustedHeight - offset * 2\n\n    const pivotValue = readConfObject(config, 'bicolorPivotValue')\n    const negColor = readConfObject(config, 'negColor')\n    const posColor = readConfObject(config, 'posColor')\n    const filled = readConfObject(config, 'filled')\n    const clipColor = readConfObject(config, 'clipColor')\n    const highlightColor = readConfObject(config, 'highlightColor')\n    const summaryScoreMode = readConfObject(config, 'summaryScoreMode')\n\n    const scale = getScale({ ...scaleOpts, range: [0, height] })\n    const originY = getOrigin(scaleOpts.scaleType)\n    const [niceMin, niceMax] = scale.domain()\n\n    const toY = (n: number) => height - (scale(n) || 0) + offset\n    const toHeight = (n: number) => toY(originY) - toY(n)\n\n    const colorCallback =\n      readConfObject(config, 'color') === '#f0f'\n        ? (_: Feature, score: number) =>\n            score < pivotValue ? negColor : posColor\n        : (feature: Feature, _score: number) =>\n            readConfObject(config, 'color', { feature })\n\n    const crossingOrigin = niceMin < pivotValue && niceMax > pivotValue\n    for (const feature of features.values()) {\n      const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)\n      let score = feature.get('score')\n      const maxr = feature.get('maxScore')\n      const minr = feature.get('minScore')\n\n      const lowClipping = score < niceMin\n      const highClipping = score > niceMax\n      const w = rightPx - leftPx + 0.4 // fudge factor for subpixel rendering\n\n      const summary = feature.get('summary')\n\n      if (summaryScoreMode === 'max') {\n        score = summary ? maxr : score\n        ctx.fillStyle = colorCallback(feature, score)\n        ctx.fillRect(leftPx, toY(score), w, filled ? toHeight(score) : 1)\n      } else if (summaryScoreMode === 'min') {\n        score = summary ? minr : score\n        ctx.fillStyle = colorCallback(feature, score)\n        ctx.fillRect(leftPx, toY(score), w, filled ? toHeight(score) : 1)\n      } else if (summaryScoreMode === 'whiskers') {\n        const c = colorCallback(feature, score)\n        if (summary) {\n          ctx.fillStyle = crossingOrigin\n            ? colorCallback(feature, maxr)\n            : Color(c).lighten(0.6).toString()\n          ctx.fillRect(\n            leftPx,\n            toY(maxr),\n            w,\n            filled ? toHeight(maxr) - toHeight(score) : 1,\n          )\n        }\n\n        // normal\n        ctx.fillStyle =\n          crossingOrigin && summary\n            ? Color(colorCallback(feature, maxr)).mix(\n                Color(colorCallback(feature, minr)),\n              )\n            : c\n        ctx.fillRect(\n          leftPx,\n          toY(score),\n          w,\n          filled ? toHeight(score) - (summary ? toHeight(minr) : 0) : 1,\n        )\n\n        // min\n        if (summary) {\n          ctx.fillStyle = crossingOrigin\n            ? colorCallback(feature, minr)\n            : Color(c).darken(0.6).toString()\n          ctx.fillRect(leftPx, toY(minr), w, filled ? toHeight(minr) : 1)\n        }\n      } else {\n        ctx.fillStyle = colorCallback(feature, score)\n        ctx.fillRect(leftPx, toY(score), w, filled ? toHeight(score) : 1)\n      }\n\n      if (highClipping) {\n        ctx.fillStyle = clipColor\n        ctx.fillRect(leftPx, 0, w, 4)\n      } else if (lowClipping && scaleOpts.scaleType !== 'log') {\n        ctx.fillStyle = clipColor\n        ctx.fillRect(leftPx, unadjustedHeight - 4, w, 4)\n      }\n      if (feature.get('highlighted')) {\n        ctx.fillStyle = highlightColor\n        ctx.fillRect(leftPx, 0, w, height)\n      }\n    }\n\n    if (displayCrossHatches) {\n      ctx.lineWidth = 1\n      ctx.strokeStyle = 'rgba(200,200,200,0.8)'\n      ticks.values.forEach(tick => {\n        ctx.beginPath()\n        ctx.moveTo(0, Math.round(toY(tick)))\n        ctx.lineTo(width, Math.round(toY(tick)))\n        ctx.stroke()\n      })\n    }\n  }\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport ConfigSchema from '../configSchema'\n\nexport { default as ReactComponent } from '../WiggleRendering'\nexport { default } from './XYPlotRenderer'\n\nexport const configSchema = ConfigurationSchema(\n  'XYPlotRenderer',\n  {},\n  { baseConfiguration: ConfigSchema, explicitlyTyped: true },\n)\n","import { readConfObject } from '@jbrowse/core/configuration'\nimport { featureSpanPx } from '@jbrowse/core/util'\nimport { getScale } from '../util'\nimport WiggleBaseRenderer from '../WiggleBaseRenderer'\nimport { YSCALEBAR_LABEL_OFFSET } from '../LinearWiggleDisplay/models/model'\n\nexport default class LinePlotRenderer extends WiggleBaseRenderer {\n  draw(ctx, props) {\n    const {\n      features,\n      regions,\n      bpPerPx,\n      scaleOpts,\n      height: unadjustedHeight,\n      ticks: { values },\n      displayCrossHatches,\n      config,\n    } = props\n    const [region] = regions\n    const width = (region.end - region.start) / bpPerPx\n    const offset = YSCALEBAR_LABEL_OFFSET\n\n    // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the\n    // wiggle display, and makes the height of the actual drawn area add\n    // \"padding\" to the top and bottom of the display\n    const height = unadjustedHeight - offset * 2\n    const clipColor = readConfObject(config, 'clipColor')\n    const highlightColor = readConfObject(config, 'highlightColor')\n    const scale = getScale({ ...scaleOpts, range: [0, height] })\n    const [niceMin, niceMax] = scale.domain()\n    const toY = rawscore => height - scale(rawscore) + offset\n    const colorCallback =\n      readConfObject(config, 'color') === '#f0f'\n        ? () => 'grey'\n        : feature => readConfObject(config, 'color', { feature })\n\n    let lastVal\n    for (const feature of features.values()) {\n      const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)\n      const score = feature.get('score')\n      const lowClipping = score < niceMin\n      const highClipping = score > niceMax\n      const w = rightPx - leftPx + 0.3 // fudge factor for subpixel rendering\n\n      const c = colorCallback(feature)\n\n      ctx.strokeStyle = c\n      ctx.beginPath()\n      if (!region.reversed) {\n        ctx.moveTo(\n          leftPx,\n          toY(typeof lastVal !== 'undefined' ? lastVal : score),\n        )\n        ctx.lineTo(leftPx, toY(score))\n        ctx.lineTo(rightPx, toY(score))\n      } else {\n        ctx.moveTo(\n          rightPx,\n          toY(typeof lastVal !== 'undefined' ? lastVal : score),\n        )\n        ctx.lineTo(rightPx, toY(score))\n        ctx.lineTo(leftPx, toY(score))\n      }\n      ctx.stroke()\n      lastVal = score\n\n      if (highClipping) {\n        ctx.fillStyle = clipColor\n        ctx.fillRect(leftPx, 0, w, 4)\n      } else if (lowClipping && scaleOpts.scaleType !== 'log') {\n        ctx.fillStyle = clipColor\n        ctx.fillRect(leftPx, height - 4, w, height)\n      }\n      if (feature.get('highlighted')) {\n        ctx.fillStyle = highlightColor\n        ctx.fillRect(leftPx, 0, w, height)\n      }\n    }\n\n    if (displayCrossHatches) {\n      ctx.lineWidth = 1\n      ctx.strokeStyle = 'rgba(200,200,200,0.8)'\n      values.forEach(tick => {\n        ctx.beginPath()\n        ctx.moveTo(0, Math.round(toY(tick)))\n        ctx.lineTo(width, Math.round(toY(tick)))\n        ctx.stroke()\n      })\n    }\n  }\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport ConfigSchema from '../configSchema'\n\nexport { default as ReactComponent } from '../WiggleRendering'\nexport { default } from './LinePlotRenderer'\n\nexport const configSchema = ConfigurationSchema(\n  'LinePlotRenderer',\n  {},\n  { baseConfiguration: ConfigSchema, explicitlyTyped: true },\n)\n","import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'\nimport { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'\nimport { renameRegionsIfNeeded } from '@jbrowse/core/util'\nimport { Region } from '@jbrowse/core/util/types'\nimport { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'\nimport { FeatureStats } from '@jbrowse/core/util/stats'\n\nexport class WiggleGetGlobalStats extends RpcMethodType {\n  name = 'WiggleGetGlobalStats'\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  async deserializeArguments(args: any, rpcDriverClassName: string) {\n    const l = await super.deserializeArguments(args, rpcDriverClassName)\n    return {\n      ...l,\n      filters: args.filters\n        ? new SerializableFilterChain({\n            filters: args.filters,\n          })\n        : undefined,\n    }\n  }\n\n  async execute(\n    args: {\n      adapterConfig: {}\n      signal?: RemoteAbortSignal\n      headers?: Record<string, string>\n      sessionId: string\n    },\n    rpcDriverClassName: string,\n  ): Promise<FeatureStats> {\n    const deserializedArgs = await this.deserializeArguments(\n      args,\n      rpcDriverClassName,\n    )\n    const { adapterConfig, sessionId } = deserializedArgs\n    const { dataAdapter } = await getAdapter(\n      this.pluginManager,\n      sessionId,\n      adapterConfig,\n    )\n\n    // @ts-ignore\n    return dataAdapter.getGlobalStats(deserializedArgs)\n  }\n}\n\nexport class WiggleGetMultiRegionStats extends RpcMethodType {\n  name = 'WiggleGetMultiRegionStats'\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  async deserializeArguments(args: any, rpcDriverClassName: string) {\n    const l = await super.deserializeArguments(args, rpcDriverClassName)\n    return {\n      ...l,\n      filters: args.filters\n        ? new SerializableFilterChain({\n            filters: args.filters,\n          })\n        : undefined,\n    }\n  }\n\n  async serializeArguments(\n    args: RenderArgs & { signal?: AbortSignal; statusCallback?: Function },\n    rpcDriverClassName: string,\n  ) {\n    const assemblyManager =\n      this.pluginManager.rootModel?.session?.assemblyManager\n    if (!assemblyManager) {\n      return args\n    }\n\n    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {\n      ...args,\n      filters: args.filters && args.filters.toJSON().filters,\n    })\n\n    return super.serializeArguments(renamedArgs, rpcDriverClassName)\n  }\n\n  async execute(\n    args: {\n      adapterConfig: {}\n      signal?: RemoteAbortSignal\n      sessionId: string\n      headers?: Record<string, string>\n      regions: Region[]\n      bpPerPx: number\n    },\n    rpcDriverClassName: string,\n  ) {\n    const deserializedArgs = await this.deserializeArguments(\n      args,\n      rpcDriverClassName,\n    )\n    const { regions, adapterConfig, sessionId } = deserializedArgs\n    const { dataAdapter } = await getAdapter(\n      this.pluginManager,\n      sessionId,\n      adapterConfig,\n    )\n\n    if (dataAdapter instanceof BaseFeatureDataAdapter) {\n      return dataAdapter.getMultiRegionStats(regions, deserializedArgs)\n    }\n    throw new Error('Data adapter not found')\n  }\n}\n","import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'\nimport Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nimport {\n  createBaseTrackConfig,\n  createBaseTrackModel,\n} from '@jbrowse/core/pluggableElementTypes/models'\nimport DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\nimport { FileLocation } from '@jbrowse/core/util/types'\nimport WiggleBaseRenderer from './WiggleBaseRenderer'\nimport WiggleRendering from './WiggleRendering'\nimport { configSchema as bigWigAdapterConfigSchema } from './BigWigAdapter'\nimport DensityRenderer, {\n  configSchema as densityRendererConfigSchema,\n  ReactComponent as DensityRendererReactComponent,\n} from './DensityRenderer'\nimport * as utils from './util'\nimport {\n  configSchemaFactory as linearWiggleDisplayConfigSchemaFactory,\n  modelFactory as linearWiggleDisplayModelFactory,\n  ReactComponent as LinearWiggleDisplayReactComponent,\n  YSCALEBAR_LABEL_OFFSET,\n} from './LinearWiggleDisplay'\nimport XYPlotRenderer, {\n  configSchema as xyPlotRendererConfigSchema,\n  ReactComponent as XYPlotRendererReactComponent,\n} from './XYPlotRenderer'\nimport LinePlotRenderer, {\n  configSchema as linePlotRendererConfigSchema,\n  ReactComponent as LinePlotRendererReactComponent,\n} from './LinePlotRenderer'\nimport {\n  WiggleGetGlobalStats,\n  WiggleGetMultiRegionStats,\n} from './WiggleRPC/rpcMethods'\nimport {\n  AdapterGuesser,\n  getFileName,\n  TrackTypeGuesser,\n} from '@jbrowse/core/util/tracks'\n\nexport default class WigglePlugin extends Plugin {\n  name = 'WigglePlugin'\n\n  install(pluginManager: PluginManager) {\n    pluginManager.addTrackType(() => {\n      const configSchema = ConfigurationSchema(\n        'QuantitativeTrack',\n        {},\n        { baseConfiguration: createBaseTrackConfig(pluginManager) },\n      )\n      return new TrackType({\n        name: 'QuantitativeTrack',\n        configSchema,\n        stateModel: createBaseTrackModel(\n          pluginManager,\n          'QuantitativeTrack',\n          configSchema,\n        ),\n      })\n    })\n\n    pluginManager.addDisplayType(() => {\n      const configSchema = linearWiggleDisplayConfigSchemaFactory(pluginManager)\n      return new DisplayType({\n        name: 'LinearWiggleDisplay',\n        configSchema,\n        stateModel: linearWiggleDisplayModelFactory(\n          pluginManager,\n          configSchema,\n        ),\n        trackType: 'QuantitativeTrack',\n        viewType: 'LinearGenomeView',\n        ReactComponent: LinearWiggleDisplayReactComponent,\n      })\n    })\n\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'BigWigAdapter',\n          configSchema: bigWigAdapterConfigSchema,\n          adapterCapabilities: [\n            'hasResolution',\n            'hasLocalStats',\n            'hasGlobalStats',\n          ],\n          getAdapterClass: () =>\n            import('./BigWigAdapter/BigWigAdapter').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 = /\\.(bw|bigwig)$/i\n          const adapterName = 'BigWigAdapter'\n          const fileName = getFileName(file)\n          const obj = {\n            type: adapterName,\n            bigWigLocation: file,\n          }\n\n          if (regexGuess.test(fileName) && !adapterHint) {\n            return obj\n          } else if (adapterHint === adapterName) {\n            return obj\n          }\n\n          return adapterGuesser(file, index, adapterHint)\n        }\n      },\n    )\n    pluginManager.addToExtensionPoint(\n      'Core-guessTrackTypeForLocation',\n      (trackTypeGuesser: TrackTypeGuesser) => {\n        return (adapterName: string) => {\n          if (adapterName === 'BigWigAdapter') {\n            return 'QuantitativeTrack'\n          }\n          return trackTypeGuesser(adapterName)\n        }\n      },\n    )\n\n    pluginManager.addRendererType(\n      () =>\n        new DensityRenderer({\n          name: 'DensityRenderer',\n          ReactComponent: DensityRendererReactComponent,\n          configSchema: densityRendererConfigSchema,\n          pluginManager,\n        }),\n    )\n\n    pluginManager.addRendererType(\n      () =>\n        new LinePlotRenderer({\n          name: 'LinePlotRenderer',\n          ReactComponent: LinePlotRendererReactComponent,\n          configSchema: linePlotRendererConfigSchema,\n          pluginManager,\n        }),\n    )\n\n    pluginManager.addRendererType(\n      () =>\n        new XYPlotRenderer({\n          name: 'XYPlotRenderer',\n          ReactComponent: XYPlotRendererReactComponent,\n          configSchema: xyPlotRendererConfigSchema,\n          pluginManager,\n        }),\n    )\n\n    pluginManager.addRpcMethod(() => new WiggleGetGlobalStats(pluginManager))\n    pluginManager.addRpcMethod(\n      () => new WiggleGetMultiRegionStats(pluginManager),\n    )\n  }\n\n  exports = {\n    LinearWiggleDisplayReactComponent,\n    XYPlotRendererReactComponent,\n    XYPlotRenderer,\n    xyPlotRendererConfigSchema,\n    utils,\n    WiggleBaseRenderer,\n    linearWiggleDisplayModelFactory,\n  }\n}\n\nexport * from './util'\n\nexport { WiggleRendering }\nexport { WiggleBaseRenderer }\nexport { LinearWiggleDisplayReactComponent, linearWiggleDisplayModelFactory }\nexport { Tooltip } from './LinearWiggleDisplay/components/Tooltip'\nexport { YSCALEBAR_LABEL_OFFSET }\n","import React, { useState } from 'react'\nimport { makeStyles } from '@material-ui/core/styles'\nimport Button from '@material-ui/core/Button'\nimport TextField from '@material-ui/core/TextField'\nimport Typography from '@material-ui/core/Typography'\nimport Dialog from '@material-ui/core/Dialog'\nimport DialogContent from '@material-ui/core/DialogContent'\nimport DialogTitle from '@material-ui/core/DialogTitle'\nimport IconButton from '@material-ui/core/IconButton'\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {},\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n}))\n\nexport default function SetMinMaxDlg(props: {\n  model: {\n    minScore: number\n    maxScore: number\n    scaleType: string\n    setMinScore: Function\n    setMaxScore: Function\n  }\n  handleClose: () => void\n}) {\n  const classes = useStyles()\n  const { model, handleClose } = props\n  const { minScore, maxScore, scaleType } = model\n\n  const [min, setMin] = useState(\n    `${minScore !== Number.MIN_VALUE ? minScore : ''}`,\n  )\n  const [max, setMax] = useState(\n    `${maxScore !== Number.MAX_VALUE ? maxScore : ''}`,\n  )\n\n  const ok =\n    min !== '' && max !== '' && !Number.isNaN(+min) && !Number.isNaN(+max)\n      ? +max > +min\n      : true\n\n  const logOk =\n    scaleType === 'log' && min !== '' && !Number.isNaN(+min) ? +min > 0 : true\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Set min/max score for track\n        <IconButton className={classes.closeButton} onClick={handleClose}>\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent style={{ overflowX: 'hidden' }}>\n        <div className={classes.root}>\n          <Typography>Enter min/max score: </Typography>\n          {!ok ? (\n            <Typography color=\"error\">\n              Max is greater than or equal to min\n            </Typography>\n          ) : null}\n\n          {!logOk ? (\n            <Typography color=\"error\">\n              Min score should be greater than 0 for log scale\n            </Typography>\n          ) : null}\n\n          <TextField\n            value={min}\n            onChange={event => {\n              setMin(event.target.value)\n            }}\n            placeholder=\"Enter min score\"\n          />\n          <TextField\n            value={max}\n            onChange={event => {\n              setMax(event.target.value)\n            }}\n            placeholder=\"Enter max score\"\n          />\n\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            type=\"submit\"\n            style={{ marginLeft: 20 }}\n            disabled={!ok}\n            onClick={() => {\n              model.setMinScore(\n                min !== '' && !Number.isNaN(+min) ? +min : undefined,\n              )\n              model.setMaxScore(\n                max !== '' && !Number.isNaN(+max) ? +max : undefined,\n              )\n              handleClose()\n            }}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n","import React, { useState } from 'react'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogActions,\n  DialogTitle,\n  IconButton,\n  Typography,\n  FormControlLabel,\n  Radio,\n  makeStyles,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\nimport { CompactPicker, Color, RGBColor } from 'react-color'\n\nconst useStyles = makeStyles(theme => ({\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n}))\n\n// this is needed because passing a entire color object into the react-color\n// for alpha, can't pass in an rgba string for example\nfunction serialize(color: Color) {\n  if (color instanceof Object) {\n    const { r, g, b } = color as RGBColor\n    return `rgb(${r},${g},${b})`\n  }\n  return color\n}\n\nexport default function SetColorDialog({\n  model,\n  handleClose,\n}: {\n  model: {\n    color: number\n    setColor: (arg?: string) => void\n    setPosColor: (arg?: string) => void\n    setNegColor: (arg?: string) => void\n  }\n  handleClose: () => void\n}) {\n  const classes = useStyles()\n  const [posneg, setPosNeg] = useState(false)\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Select either an overall color, or the positive/negative colors. Note\n        that density renderers only work properly with positive/negative colors\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <FormControlLabel\n          checked={!posneg}\n          onClick={() => setPosNeg(false)}\n          control={<Radio />}\n          label={'Overall color'}\n        />\n        <FormControlLabel\n          checked={posneg}\n          onClick={() => setPosNeg(true)}\n          control={<Radio />}\n          label={'Positive/negative color'}\n        />\n\n        {posneg ? (\n          <>\n            <Typography>Positive color</Typography>\n            <CompactPicker\n              onChange={event => {\n                model.setPosColor(serialize(event.rgb))\n                model.setColor(undefined)\n              }}\n            />\n            <Typography>Negative color</Typography>\n            <CompactPicker\n              onChange={event => {\n                model.setNegColor(serialize(event.rgb))\n                model.setColor(undefined)\n              }}\n            />\n          </>\n        ) : (\n          <>\n            <Typography>Overall color</Typography>\n            <CompactPicker\n              onChange={event => {\n                model.setColor(serialize(event.rgb))\n              }}\n            />\n          </>\n        )}\n      </DialogContent>\n      <DialogActions>\n        <Button\n          onClick={() => {\n            model.setPosColor(undefined)\n            model.setNegColor(undefined)\n            model.setColor(undefined)\n          }}\n          color=\"secondary\"\n          variant=\"contained\"\n        >\n          Restore default\n        </Button>\n\n        <Button\n          variant=\"contained\"\n          color=\"primary\"\n          type=\"submit\"\n          onClick={() => {\n            handleClose()\n          }}\n        >\n          Submit\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n}\n","import { BigWig } from '@gmod/bbi'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { AugmentedRegion as Region } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { map, mergeAll } from 'rxjs/operators'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'\nimport { rectifyStats, UnrectifiedFeatureStats } from '@jbrowse/core/util/stats'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\ninterface WiggleOptions extends BaseOptions {\n  resolution?: number\n}\n\nexport default class BigWigAdapter extends BaseFeatureDataAdapter {\n  private bigwig: BigWig\n\n  public static capabilities = [\n    'hasResolution',\n    'hasLocalStats',\n    'hasGlobalStats',\n  ]\n\n  public constructor(\n    config: AnyConfigurationModel,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    this.bigwig = new BigWig({\n      filehandle: openLocation(\n        readConfObject(config, 'bigWigLocation'),\n        this.pluginManager,\n      ),\n    })\n  }\n\n  private async setup(opts?: BaseOptions) {\n    const { statusCallback = () => {} } = opts || {}\n    return updateStatus('Downloading bigwig header', statusCallback, () =>\n      this.bigwig.getHeader(opts),\n    )\n  }\n\n  public async getRefNames(opts?: BaseOptions) {\n    const { refsByName } = await this.setup(opts)\n    return Object.keys(refsByName)\n  }\n\n  public async refIdToName(refId: number) {\n    const { refsByNumber } = await this.setup()\n    return refsByNumber[refId]?.name\n  }\n\n  public async getGlobalStats(opts?: BaseOptions) {\n    const { totalSummary } = await this.setup(opts)\n    return rectifyStats(totalSummary as UnrectifiedFeatureStats)\n  }\n\n  public getFeatures(region: Region, opts: WiggleOptions = {}) {\n    const { refName, start, end } = region\n    const {\n      bpPerPx = 0,\n      signal,\n      resolution = 1,\n      statusCallback = () => {},\n    } = opts\n    return ObservableCreate<Feature>(async observer => {\n      statusCallback('Downloading bigwig data')\n      const ob = await this.bigwig.getFeatureStream(refName, start, end, {\n        ...opts,\n        basesPerSpan: bpPerPx / resolution,\n      })\n      ob.pipe(\n        mergeAll(),\n        map(record => {\n          return new SimpleFeature({\n            id: `${refName}:${record.start}-${record.end}`,\n            data: { ...record, refName },\n          })\n        }),\n      ).subscribe(observer)\n    }, signal)\n  }\n\n  // always render bigwig instead of calculating a feature density for it\n  async estimateRegionsStats(_regions: Region[]) {\n    return { featureDensity: 0 }\n  }\n\n  public freeResources(): void 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package/dist/plugin-wiggle.cjs.production.min.js

@@ -1,2 +0,0 @@
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