jbrowse-plugin-mafviewer 1.0.5 → 1.0.8
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +4 -0
- package/README.md +17 -2
- package/dist/BigMafAdapter/BigMafAdapter.d.ts +17 -0
- package/dist/BigMafAdapter/BigMafAdapter.js +92 -0
- package/dist/BigMafAdapter/BigMafAdapter.js.map +1 -0
- package/dist/BigMafAdapter/configSchema.d.ts +21 -0
- package/dist/BigMafAdapter/configSchema.js +28 -0
- package/dist/BigMafAdapter/configSchema.js.map +1 -0
- package/dist/BigMafAdapter/index.d.ts +2 -0
- package/dist/BigMafAdapter/index.js +11 -0
- package/dist/BigMafAdapter/index.js.map +1 -0
- package/dist/LinearMafDisplay/components/ColorLegend.d.ts +8 -0
- package/dist/LinearMafDisplay/components/ColorLegend.js +15 -0
- package/dist/LinearMafDisplay/components/ColorLegend.js.map +1 -0
- package/dist/LinearMafDisplay/components/ReactComponent.d.ts +6 -0
- package/dist/LinearMafDisplay/components/ReactComponent.js +15 -0
- package/dist/LinearMafDisplay/components/ReactComponent.js.map +1 -0
- package/dist/LinearMafDisplay/components/RectBg.d.ts +9 -0
- package/dist/LinearMafDisplay/components/RectBg.js +7 -0
- package/dist/LinearMafDisplay/components/RectBg.js.map +1 -0
- package/dist/LinearMafDisplay/components/SetRowHeight.d.ts +11 -0
- package/dist/LinearMafDisplay/components/SetRowHeight.js +36 -0
- package/dist/LinearMafDisplay/components/SetRowHeight.js.map +1 -0
- package/dist/LinearMafDisplay/components/YScaleBars.d.ts +9 -0
- package/dist/LinearMafDisplay/components/YScaleBars.js +41 -0
- package/dist/LinearMafDisplay/components/YScaleBars.js.map +1 -0
- package/dist/LinearMafDisplay/configSchema.d.ts +34 -0
- package/dist/LinearMafDisplay/configSchema.js +15 -0
- package/dist/LinearMafDisplay/configSchema.js.map +1 -0
- package/dist/LinearMafDisplay/index.d.ts +2 -0
- package/dist/LinearMafDisplay/index.js +20 -0
- package/dist/LinearMafDisplay/index.js.map +1 -0
- package/dist/LinearMafDisplay/renderSvg.d.ts +4 -0
- package/dist/LinearMafDisplay/renderSvg.js +17 -0
- package/dist/LinearMafDisplay/renderSvg.js.map +1 -0
- package/dist/LinearMafDisplay/stateModel.d.ts +364 -0
- package/dist/LinearMafDisplay/stateModel.js +176 -0
- package/dist/LinearMafDisplay/stateModel.js.map +1 -0
- package/dist/LinearMafRenderer/LinearMafRenderer.d.ts +45 -0
- package/dist/LinearMafRenderer/LinearMafRenderer.js +181 -0
- package/dist/LinearMafRenderer/LinearMafRenderer.js.map +1 -0
- package/dist/LinearMafRenderer/components/ReactComponent.d.ts +6 -0
- package/dist/LinearMafRenderer/components/ReactComponent.js +8 -0
- package/dist/LinearMafRenderer/components/ReactComponent.js.map +1 -0
- package/dist/LinearMafRenderer/configSchema.d.ts +2 -0
- package/dist/LinearMafRenderer/configSchema.js +13 -0
- package/dist/LinearMafRenderer/configSchema.js.map +1 -0
- package/dist/LinearMafRenderer/index.d.ts +2 -0
- package/dist/LinearMafRenderer/index.js +12 -0
- package/dist/LinearMafRenderer/index.js.map +1 -0
- package/dist/LinearMafRenderer/util.d.ts +10 -0
- package/dist/LinearMafRenderer/util.js +16 -0
- package/dist/LinearMafRenderer/util.js.map +1 -0
- package/dist/MafAddTrackWorkflow/AddTrackWorkflow.d.ts +5 -0
- package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js +111 -0
- package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map +1 -0
- package/dist/MafAddTrackWorkflow/index.d.ts +2 -0
- package/dist/MafAddTrackWorkflow/index.js +12 -0
- package/dist/MafAddTrackWorkflow/index.js.map +1 -0
- package/dist/MafTabixAdapter/MafTabixAdapter.d.ts +17 -0
- package/dist/MafTabixAdapter/MafTabixAdapter.js +96 -0
- package/dist/MafTabixAdapter/MafTabixAdapter.js.map +1 -0
- package/dist/MafTabixAdapter/configSchema.d.ts +33 -0
- package/dist/MafTabixAdapter/configSchema.js +40 -0
- package/dist/MafTabixAdapter/configSchema.js.map +1 -0
- package/dist/MafTabixAdapter/index.d.ts +2 -0
- package/dist/MafTabixAdapter/index.js +11 -0
- package/dist/MafTabixAdapter/index.js.map +1 -0
- package/dist/MafTrack/configSchema.d.ts +79 -0
- package/dist/MafTrack/configSchema.js +15 -0
- package/dist/MafTrack/configSchema.js.map +1 -0
- package/dist/MafTrack/index.d.ts +2 -0
- package/dist/MafTrack/index.js +14 -0
- package/dist/MafTrack/index.js.map +1 -0
- package/dist/TaffyAdapter/TaffyAdapter.d.ts +16 -0
- package/dist/TaffyAdapter/TaffyAdapter.js +89 -0
- package/dist/TaffyAdapter/TaffyAdapter.js.map +1 -0
- package/dist/TaffyAdapter/configSchema.d.ts +31 -0
- package/dist/TaffyAdapter/configSchema.js +38 -0
- package/dist/TaffyAdapter/configSchema.js.map +1 -0
- package/dist/TaffyAdapter/index.d.ts +2 -0
- package/dist/TaffyAdapter/index.js +11 -0
- package/dist/TaffyAdapter/index.js.map +1 -0
- package/dist/index.d.ts +8 -0
- package/dist/index.js +24 -0
- package/dist/index.js.map +1 -0
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +4 -1
- package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +7 -1
- package/package.json +22 -51
- package/src/BigMafAdapter/BigMafAdapter.ts +1 -2
- package/src/LinearMafDisplay/components/ColorLegend.tsx +2 -2
- package/src/LinearMafDisplay/components/SetRowHeight.tsx +9 -3
- package/src/LinearMafDisplay/components/YScaleBars.tsx +11 -3
- package/src/LinearMafDisplay/stateModel.ts +29 -1
- package/src/LinearMafRenderer/LinearMafRenderer.ts +38 -34
- package/src/LinearMafRenderer/util.ts +20 -0
- package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx +60 -22
- package/src/MafTabixAdapter/MafTabixAdapter.ts +27 -10
- package/src/TaffyAdapter/TaffyAdapter.ts +112 -0
- package/src/TaffyAdapter/configSchema.ts +44 -0
- package/src/TaffyAdapter/index.ts +15 -0
- package/src/index.ts +2 -0
- package/dist/jbrowse-plugin-mafviewer.umd.development.js +0 -1423
- package/dist/jbrowse-plugin-mafviewer.umd.development.js.map +0 -1
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SuppressedError : function (error, suppressed, message) {\n var e = new Error(message);\n return e.name = \"SuppressedError\", e.error = error, e.suppressed = suppressed, e;\n};\n\nexport function __disposeResources(env) {\n function fail(e) {\n env.error = env.hasError ? new _SuppressedError(e, env.error, \"An error was suppressed during disposal.\") : e;\n env.hasError = true;\n }\n function next() {\n while (env.stack.length) {\n var rec = env.stack.pop();\n try {\n var result = rec.dispose && rec.dispose.call(rec.value);\n if (rec.async) return Promise.resolve(result).then(next, function(e) { fail(e); return next(); });\n }\n catch (e) {\n fail(e);\n }\n }\n if (env.hasError) throw env.error;\n }\n return next();\n}\n\nexport default {\n __extends,\n __assign,\n __rest,\n __decorate,\n __param,\n __metadata,\n __awaiter,\n __generator,\n __createBinding,\n __exportStar,\n __values,\n __read,\n __spread,\n __spreadArrays,\n __spreadArray,\n __await,\n __asyncGenerator,\n __asyncDelegator,\n __asyncValues,\n __makeTemplateObject,\n __importStar,\n __importDefault,\n __classPrivateFieldGet,\n __classPrivateFieldSet,\n __classPrivateFieldIn,\n __addDisposableResource,\n __disposeResources,\n};\n","export function isFunction(value) {\n return typeof value === 'function';\n}\n//# sourceMappingURL=isFunction.js.map","export function createErrorClass(createImpl) {\n var _super = function (instance) {\n Error.call(instance);\n instance.stack = new Error().stack;\n };\n var ctorFunc = createImpl(_super);\n ctorFunc.prototype = Object.create(Error.prototype);\n ctorFunc.prototype.constructor = ctorFunc;\n return ctorFunc;\n}\n//# sourceMappingURL=createErrorClass.js.map","import { createErrorClass } from './createErrorClass';\nexport var UnsubscriptionError = createErrorClass(function (_super) {\n return function UnsubscriptionErrorImpl(errors) {\n _super(this);\n this.message = errors\n ? errors.length + \" errors occurred during unsubscription:\\n\" + errors.map(function (err, i) { return i + 1 + \") \" + err.toString(); }).join('\\n ')\n : '';\n this.name = 'UnsubscriptionError';\n this.errors = errors;\n };\n});\n//# sourceMappingURL=UnsubscriptionError.js.map","export function arrRemove(arr, item) {\n if (arr) {\n var index = arr.indexOf(item);\n 0 <= index && arr.splice(index, 1);\n }\n}\n//# sourceMappingURL=arrRemove.js.map","import { __read, __spreadArray, __values } from \"tslib\";\nimport { isFunction } from './util/isFunction';\nimport { UnsubscriptionError } from './util/UnsubscriptionError';\nimport { arrRemove } from './util/arrRemove';\nvar Subscription = (function () {\n function Subscription(initialTeardown) {\n this.initialTeardown = initialTeardown;\n this.closed = false;\n this._parentage = null;\n this._finalizers = null;\n }\n Subscription.prototype.unsubscribe = function () {\n var e_1, _a, e_2, _b;\n var errors;\n if (!this.closed) {\n this.closed = true;\n var _parentage = this._parentage;\n if (_parentage) {\n this._parentage = null;\n if (Array.isArray(_parentage)) {\n try {\n for (var _parentage_1 = __values(_parentage), _parentage_1_1 = _parentage_1.next(); !_parentage_1_1.done; _parentage_1_1 = _parentage_1.next()) {\n var parent_1 = _parentage_1_1.value;\n parent_1.remove(this);\n }\n }\n catch (e_1_1) { e_1 = { error: e_1_1 }; }\n finally {\n try {\n if (_parentage_1_1 && !_parentage_1_1.done && (_a = _parentage_1.return)) _a.call(_parentage_1);\n }\n finally { if (e_1) throw e_1.error; }\n }\n }\n else {\n _parentage.remove(this);\n }\n }\n var initialFinalizer = this.initialTeardown;\n if (isFunction(initialFinalizer)) {\n try {\n initialFinalizer();\n }\n catch (e) {\n errors = e instanceof UnsubscriptionError ? e.errors : [e];\n }\n }\n var _finalizers = this._finalizers;\n if (_finalizers) {\n this._finalizers = null;\n try {\n for (var _finalizers_1 = __values(_finalizers), _finalizers_1_1 = _finalizers_1.next(); !_finalizers_1_1.done; _finalizers_1_1 = _finalizers_1.next()) {\n var finalizer = _finalizers_1_1.value;\n try {\n execFinalizer(finalizer);\n }\n catch (err) {\n errors = errors !== null && errors !== void 0 ? errors : [];\n if (err instanceof UnsubscriptionError) {\n errors = __spreadArray(__spreadArray([], __read(errors)), __read(err.errors));\n }\n else {\n errors.push(err);\n }\n }\n }\n }\n catch (e_2_1) { e_2 = { error: e_2_1 }; }\n finally {\n try {\n if (_finalizers_1_1 && !_finalizers_1_1.done && (_b = _finalizers_1.return)) _b.call(_finalizers_1);\n }\n finally { if (e_2) throw e_2.error; }\n }\n }\n if (errors) {\n throw new UnsubscriptionError(errors);\n }\n }\n };\n Subscription.prototype.add = function (teardown) {\n var _a;\n if (teardown && teardown !== this) {\n if (this.closed) {\n execFinalizer(teardown);\n }\n else {\n if (teardown instanceof Subscription) {\n if (teardown.closed || teardown._hasParent(this)) {\n return;\n }\n teardown._addParent(this);\n }\n (this._finalizers = (_a = this._finalizers) !== null && _a !== void 0 ? _a : []).push(teardown);\n }\n }\n };\n Subscription.prototype._hasParent = function (parent) {\n var _parentage = this._parentage;\n return _parentage === parent || (Array.isArray(_parentage) && _parentage.includes(parent));\n };\n Subscription.prototype._addParent = function (parent) {\n var _parentage = this._parentage;\n this._parentage = Array.isArray(_parentage) ? (_parentage.push(parent), _parentage) : _parentage ? [_parentage, parent] : parent;\n };\n Subscription.prototype._removeParent = function (parent) {\n var _parentage = this._parentage;\n if (_parentage === parent) {\n this._parentage = null;\n }\n else if (Array.isArray(_parentage)) {\n arrRemove(_parentage, parent);\n }\n };\n Subscription.prototype.remove = function (teardown) {\n var _finalizers = this._finalizers;\n _finalizers && arrRemove(_finalizers, teardown);\n if (teardown instanceof Subscription) {\n teardown._removeParent(this);\n }\n };\n Subscription.EMPTY = (function () {\n var empty = new Subscription();\n empty.closed = true;\n return empty;\n })();\n return Subscription;\n}());\nexport { Subscription };\nexport var EMPTY_SUBSCRIPTION = Subscription.EMPTY;\nexport function isSubscription(value) {\n return (value instanceof Subscription ||\n (value && 'closed' in value && isFunction(value.remove) && isFunction(value.add) && isFunction(value.unsubscribe)));\n}\nfunction execFinalizer(finalizer) {\n if (isFunction(finalizer)) {\n finalizer();\n }\n else {\n finalizer.unsubscribe();\n }\n}\n//# sourceMappingURL=Subscription.js.map","export var config = {\n onUnhandledError: null,\n onStoppedNotification: null,\n Promise: undefined,\n useDeprecatedSynchronousErrorHandling: false,\n useDeprecatedNextContext: false,\n};\n//# sourceMappingURL=config.js.map","import { __read, __spreadArray } from \"tslib\";\nexport var timeoutProvider = {\n setTimeout: function (handler, timeout) {\n var args = [];\n for (var _i = 2; _i < arguments.length; _i++) {\n args[_i - 2] = arguments[_i];\n }\n var delegate = timeoutProvider.delegate;\n if (delegate === null || delegate === void 0 ? void 0 : delegate.setTimeout) {\n return delegate.setTimeout.apply(delegate, __spreadArray([handler, timeout], __read(args)));\n }\n return setTimeout.apply(void 0, __spreadArray([handler, timeout], __read(args)));\n },\n clearTimeout: function (handle) {\n var delegate = timeoutProvider.delegate;\n return ((delegate === null || delegate === void 0 ? void 0 : delegate.clearTimeout) || clearTimeout)(handle);\n },\n delegate: undefined,\n};\n//# sourceMappingURL=timeoutProvider.js.map","export function noop() { }\n//# sourceMappingURL=noop.js.map","import { __extends } from \"tslib\";\nimport { isFunction } from './util/isFunction';\nimport { isSubscription, Subscription } from './Subscription';\nimport { config } from './config';\nimport { reportUnhandledError } from './util/reportUnhandledError';\nimport { noop } from './util/noop';\nimport { nextNotification, errorNotification, COMPLETE_NOTIFICATION } from './NotificationFactories';\nimport { timeoutProvider } from './scheduler/timeoutProvider';\nimport { captureError } from './util/errorContext';\nvar Subscriber = (function (_super) {\n __extends(Subscriber, _super);\n function Subscriber(destination) {\n var _this = _super.call(this) || this;\n _this.isStopped = false;\n if (destination) {\n _this.destination = destination;\n if (isSubscription(destination)) {\n destination.add(_this);\n }\n }\n else {\n _this.destination = EMPTY_OBSERVER;\n }\n return _this;\n }\n Subscriber.create = function (next, error, complete) {\n return new SafeSubscriber(next, error, complete);\n };\n Subscriber.prototype.next = function (value) {\n if (this.isStopped) {\n handleStoppedNotification(nextNotification(value), this);\n }\n else {\n this._next(value);\n }\n };\n Subscriber.prototype.error = function (err) {\n if (this.isStopped) {\n handleStoppedNotification(errorNotification(err), this);\n }\n else {\n this.isStopped = true;\n this._error(err);\n }\n };\n Subscriber.prototype.complete = function () {\n if (this.isStopped) {\n handleStoppedNotification(COMPLETE_NOTIFICATION, this);\n }\n else {\n this.isStopped = true;\n this._complete();\n }\n };\n Subscriber.prototype.unsubscribe = function () {\n if (!this.closed) {\n this.isStopped = true;\n _super.prototype.unsubscribe.call(this);\n this.destination = null;\n }\n };\n Subscriber.prototype._next = function (value) {\n this.destination.next(value);\n };\n Subscriber.prototype._error = function (err) {\n try {\n this.destination.error(err);\n }\n finally {\n this.unsubscribe();\n }\n };\n Subscriber.prototype._complete = function () {\n try {\n this.destination.complete();\n }\n finally {\n this.unsubscribe();\n }\n };\n return Subscriber;\n}(Subscription));\nexport { Subscriber };\nvar _bind = Function.prototype.bind;\nfunction bind(fn, thisArg) {\n return _bind.call(fn, thisArg);\n}\nvar ConsumerObserver = (function () {\n function ConsumerObserver(partialObserver) {\n this.partialObserver = partialObserver;\n }\n ConsumerObserver.prototype.next = function (value) {\n var partialObserver = this.partialObserver;\n if (partialObserver.next) {\n try {\n partialObserver.next(value);\n }\n catch (error) {\n handleUnhandledError(error);\n }\n }\n };\n ConsumerObserver.prototype.error = function (err) {\n var partialObserver = this.partialObserver;\n if (partialObserver.error) {\n try {\n partialObserver.error(err);\n }\n catch (error) {\n handleUnhandledError(error);\n }\n }\n else {\n handleUnhandledError(err);\n }\n };\n ConsumerObserver.prototype.complete = function () {\n var partialObserver = this.partialObserver;\n if (partialObserver.complete) {\n try {\n partialObserver.complete();\n }\n catch (error) {\n handleUnhandledError(error);\n }\n }\n };\n return ConsumerObserver;\n}());\nvar SafeSubscriber = (function (_super) {\n __extends(SafeSubscriber, _super);\n function SafeSubscriber(observerOrNext, error, complete) {\n var _this = _super.call(this) || this;\n var partialObserver;\n if (isFunction(observerOrNext) || !observerOrNext) {\n partialObserver = {\n next: (observerOrNext !== null && observerOrNext !== void 0 ? observerOrNext : undefined),\n error: error !== null && error !== void 0 ? error : undefined,\n complete: complete !== null && complete !== void 0 ? complete : undefined,\n };\n }\n else {\n var context_1;\n if (_this && config.useDeprecatedNextContext) {\n context_1 = Object.create(observerOrNext);\n context_1.unsubscribe = function () { return _this.unsubscribe(); };\n partialObserver = {\n next: observerOrNext.next && bind(observerOrNext.next, context_1),\n error: observerOrNext.error && bind(observerOrNext.error, context_1),\n complete: observerOrNext.complete && bind(observerOrNext.complete, context_1),\n };\n }\n else {\n partialObserver = observerOrNext;\n }\n }\n _this.destination = new ConsumerObserver(partialObserver);\n return _this;\n }\n return SafeSubscriber;\n}(Subscriber));\nexport { SafeSubscriber };\nfunction handleUnhandledError(error) {\n if (config.useDeprecatedSynchronousErrorHandling) {\n captureError(error);\n }\n else {\n reportUnhandledError(error);\n }\n}\nfunction defaultErrorHandler(err) {\n throw err;\n}\nfunction handleStoppedNotification(notification, subscriber) {\n var onStoppedNotification = config.onStoppedNotification;\n onStoppedNotification && timeoutProvider.setTimeout(function () { return onStoppedNotification(notification, subscriber); });\n}\nexport var EMPTY_OBSERVER = {\n closed: true,\n next: noop,\n error: defaultErrorHandler,\n complete: noop,\n};\n//# sourceMappingURL=Subscriber.js.map","import { config } from '../config';\nimport { timeoutProvider } from '../scheduler/timeoutProvider';\nexport function reportUnhandledError(err) {\n timeoutProvider.setTimeout(function () {\n var onUnhandledError = config.onUnhandledError;\n if (onUnhandledError) {\n onUnhandledError(err);\n }\n else {\n throw err;\n }\n });\n}\n//# sourceMappingURL=reportUnhandledError.js.map","import { isFunction } from './isFunction';\nexport function hasLift(source) {\n return isFunction(source === null || source === void 0 ? void 0 : source.lift);\n}\nexport function operate(init) {\n return function (source) {\n if (hasLift(source)) {\n return source.lift(function (liftedSource) {\n try {\n return init(liftedSource, this);\n }\n catch (err) {\n this.error(err);\n }\n });\n }\n throw new TypeError('Unable to lift unknown Observable type');\n };\n}\n//# sourceMappingURL=lift.js.map","import { __extends } from \"tslib\";\nimport { Subscriber } from '../Subscriber';\nexport function createOperatorSubscriber(destination, onNext, onComplete, onError, onFinalize) {\n return new OperatorSubscriber(destination, onNext, onComplete, onError, onFinalize);\n}\nvar OperatorSubscriber = (function (_super) {\n __extends(OperatorSubscriber, _super);\n function OperatorSubscriber(destination, onNext, onComplete, onError, onFinalize, shouldUnsubscribe) {\n var _this = _super.call(this, destination) || this;\n _this.onFinalize = onFinalize;\n _this.shouldUnsubscribe = shouldUnsubscribe;\n _this._next = onNext\n ? function (value) {\n try {\n onNext(value);\n }\n catch (err) {\n destination.error(err);\n }\n }\n : _super.prototype._next;\n _this._error = onError\n ? function (err) {\n try {\n onError(err);\n }\n catch (err) {\n destination.error(err);\n }\n finally {\n this.unsubscribe();\n }\n }\n : _super.prototype._error;\n _this._complete = onComplete\n ? function () {\n try {\n onComplete();\n }\n catch (err) {\n destination.error(err);\n }\n finally {\n this.unsubscribe();\n }\n }\n : _super.prototype._complete;\n return _this;\n }\n OperatorSubscriber.prototype.unsubscribe = function () {\n var _a;\n if (!this.shouldUnsubscribe || this.shouldUnsubscribe()) {\n var closed_1 = this.closed;\n _super.prototype.unsubscribe.call(this);\n !closed_1 && ((_a = this.onFinalize) === null || _a === void 0 ? void 0 : _a.call(this));\n }\n };\n return OperatorSubscriber;\n}(Subscriber));\nexport { OperatorSubscriber };\n//# sourceMappingURL=OperatorSubscriber.js.map","import { createErrorClass } from './createErrorClass';\nexport var EmptyError = createErrorClass(function (_super) { return function EmptyErrorImpl() {\n _super(this);\n this.name = 'EmptyError';\n this.message = 'no elements in sequence';\n}; });\n//# sourceMappingURL=EmptyError.js.map","import { EmptyError } from './util/EmptyError';\nimport { SafeSubscriber } from './Subscriber';\nexport function firstValueFrom(source, config) {\n var hasConfig = typeof config === 'object';\n return new Promise(function (resolve, reject) {\n var subscriber = new SafeSubscriber({\n next: function (value) {\n resolve(value);\n subscriber.unsubscribe();\n },\n error: reject,\n complete: function () {\n if (hasConfig) {\n resolve(config.defaultValue);\n }\n else {\n reject(new EmptyError());\n }\n },\n });\n source.subscribe(subscriber);\n });\n}\n//# sourceMappingURL=firstValueFrom.js.map","import { reduce } from './reduce';\nimport { operate } from '../util/lift';\nvar arrReducer = function (arr, value) { return (arr.push(value), arr); };\nexport function toArray() {\n return operate(function (source, subscriber) {\n reduce(arrReducer, [])(source).subscribe(subscriber);\n });\n}\n//# sourceMappingURL=toArray.js.map","import { scanInternals } from './scanInternals';\nimport { operate } from '../util/lift';\nexport function reduce(accumulator, seed) {\n return operate(scanInternals(accumulator, seed, arguments.length >= 2, false, true));\n}\n//# sourceMappingURL=reduce.js.map","import { createOperatorSubscriber } from './OperatorSubscriber';\nexport function scanInternals(accumulator, seed, hasSeed, emitOnNext, emitBeforeComplete) {\n return function (source, subscriber) {\n var hasState = hasSeed;\n var state = seed;\n var index = 0;\n source.subscribe(createOperatorSubscriber(subscriber, function (value) {\n var i = index++;\n state = hasState\n ?\n accumulator(state, value, i)\n :\n ((hasState = true), value);\n emitOnNext && subscriber.next(state);\n }, emitBeforeComplete &&\n (function () {\n hasState && subscriber.next(state);\n subscriber.complete();\n })));\n };\n}\n//# 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1
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{
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2
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"version": 3,
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3
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+
"sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/Plugin\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes\"];", "module.exports = JBrowseExports[\"@jbrowse/core/configuration\"];", "module.exports = JBrowseExports[\"@jbrowse/core/data_adapters/BaseAdapter\"];", "module.exports = JBrowseExports[\"mobx-state-tree\"];", "module.exports = JBrowseExports[\"@jbrowse/core/util\"];", "module.exports = JBrowseExports[\"@jbrowse/core/util/rxjs\"];", "module.exports = JBrowseExports[\"react\"];", "module.exports = JBrowseExports[\"mobx-react\"];", "module.exports = JBrowseExports[\"@mui/material\"];", "module.exports = JBrowseExports[\"@jbrowse/core/ui\"];", "module.exports = JBrowseExports[\"tss-react/mui\"];", "import React from 'react'\n\nconst RectBg = (props: {\n x: number\n y: number\n width: number\n height: number\n color?: string\n}) => {\n const { color = 'rgb(255,255,255,0.8)' } = props\n return <rect {...props} fill={color} />\n}\n\nexport default RectBg\n", "import React from 'react'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { LinearMafDisplayModel } from '../stateModel'\nimport RectBg from './RectBg'\n\nconst ColorLegend = observer(function ({\n model,\n labelWidth,\n svgFontSize,\n}: {\n model: LinearMafDisplayModel\n svgFontSize: number\n labelWidth: number\n}) {\n const { samples, rowHeight } = model\n const canDisplayLabel = rowHeight >= 10\n const boxHeight = Math.min(20, rowHeight)\n\n return (\n <>\n {samples.map((sample, idx) => (\n <RectBg\n key={`${sample.id}-${idx}`}\n y={idx * rowHeight}\n x={0}\n width={labelWidth + 5}\n height={boxHeight}\n color={sample.color}\n />\n ))}\n {canDisplayLabel\n ? samples.map((sample, idx) => (\n <text\n key={`${sample.id}-${idx}`}\n y={idx * rowHeight + rowHeight / 2}\n dominantBaseline=\"middle\"\n x={2}\n fontSize={svgFontSize}\n >\n {sample.label}\n </text>\n ))\n : null}\n </>\n )\n})\n\nexport default ColorLegend\n", "import React from 'react'\nimport { measureText, getContainingView } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\n\n// locals\nimport { LinearMafDisplayModel } from '../stateModel'\nimport ColorLegend from './ColorLegend'\n\nconst Wrapper = observer(function ({\n children,\n model,\n exportSVG,\n}: {\n model: LinearMafDisplayModel\n children: React.ReactNode\n exportSVG?: boolean\n}) {\n if (exportSVG) {\n return <>{children}</>\n } else {\n const { rowHeight, samples } = model\n return (\n <svg\n style={{\n position: 'absolute',\n top: 0,\n left: 0,\n pointerEvents: 'none',\n height: samples.length * rowHeight,\n width: getContainingView(model).width,\n }}\n >\n {children}\n </svg>\n )\n }\n})\n\nexport function max(arr: number[], init = Number.NEGATIVE_INFINITY) {\n let max = init\n for (const entry of arr) {\n max = Math.max(entry, max)\n }\n return max\n}\n\nexport const YScaleBars = observer(function (props: {\n model: LinearMafDisplayModel\n orientation?: string\n exportSVG?: boolean\n}) {\n const { model } = props\n const { rowHeight, samples } = model\n const svgFontSize = Math.min(Math.max(rowHeight, 10), 14)\n const canDisplayLabel = rowHeight >= 10\n const minWidth = 20\n\n const labelWidth = max(\n samples\n .map(s => measureText(s.label, svgFontSize))\n .map(width => (canDisplayLabel ? width : minWidth)),\n )\n\n return (\n <Wrapper {...props}>\n <ColorLegend\n model={model}\n labelWidth={labelWidth}\n svgFontSize={svgFontSize}\n />\n </Wrapper>\n )\n})\n\nexport default YScaleBars\n", "import React from 'react'\nimport { getContainingView } from '@jbrowse/core/util'\nimport {\n ExportSvgDisplayOptions,\n LinearGenomeViewModel,\n} from '@jbrowse/plugin-linear-genome-view'\n\n// locals\nimport { LinearMafDisplayModel } from './stateModel'\nimport YScaleBars from './components/YScaleBars'\n\nexport async function renderSvg(\n self: LinearMafDisplayModel,\n opts: ExportSvgDisplayOptions,\n superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>,\n) {\n const { height, id } = self\n const { offsetPx, width } = getContainingView(self) as LinearGenomeViewModel\n const clipid = `mafclip-${id}`\n return (\n <>\n <defs>\n <clipPath id={clipid}>\n <rect x={0} y={0} width={width} height={height} />\n </clipPath>\n </defs>\n <g clipPath={`url(#${clipid})`}>\n <g id=\"snpcov\">{await superRenderSvg(opts)}</g>\n <g transform={`translate(${Math.max(-offsetPx, 0)})`}>\n <YScaleBars model={self} orientation=\"left\" exportSVG />\n </g>\n </g>\n </>\n )\n}\n", "module.exports = JBrowseExports[\"@jbrowse/core/util/io\"];", "import Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nimport { version } from '../package.json'\nimport BigMafAdapterF from './BigMafAdapter'\nimport MafTrackF from './MafTrack'\nimport LinearMafDisplayF from './LinearMafDisplay'\nimport LinearMafRendererF from './LinearMafRenderer'\nimport MafTabixAdapterF from './MafTabixAdapter'\nimport TaffyAdapterF from './TaffyAdapter'\nimport MafAddTrackWorkflowF from './MafAddTrackWorkflow'\n\nexport default class MafViewerPlugin extends Plugin {\n name = 'MafViewerPlugin'\n version = version\n\n install(pluginManager: PluginManager) {\n BigMafAdapterF(pluginManager)\n MafTrackF(pluginManager)\n LinearMafDisplayF(pluginManager)\n LinearMafRendererF(pluginManager)\n MafTabixAdapterF(pluginManager)\n TaffyAdapterF(pluginManager)\n MafAddTrackWorkflowF(pluginManager)\n }\n\n configure(_pluginManager: PluginManager) {}\n}\n", "{\n \"version\": \"1.0.8\",\n \"name\": \"jbrowse-plugin-mafviewer\",\n \"keywords\": [\n \"jbrowse\",\n \"jbrowse2\"\n ],\n \"main\": \"dist/index.js\",\n \"module\": \"dist/index.esm.js\",\n \"typings\": \"dist/index.d.ts\",\n \"files\": [\n \"dist\",\n \"src\"\n ],\n \"scripts\": {\n \"clean\": \"rimraf dist\",\n \"start\": \"node esbuild.mjs\",\n \"prebuild\": \"npm run clean\",\n \"build\": \"tsc && NODE_ENV=production node esbuild.mjs\",\n \"lint\": \"eslint --report-unused-disable-directives --max-warnings 0\",\n \"prepack\": \"npm run build\",\n \"postversion\": \"git push --follow-tags\"\n },\n \"devDependencies\": {\n \"@babel/core\": \"^7.16.5\",\n \"@babel/preset-react\": \"^7.10.4\",\n \"@emotion/react\": \"^11.10.4\",\n \"@fal-works/esbuild-plugin-global-externals\": \"^2.1.2\",\n \"@jbrowse/core\": \"^2.6.1\",\n \"@jbrowse/plugin-data-management\": \"^2.7.1\",\n \"@jbrowse/plugin-linear-genome-view\": \"^2.7.1\",\n \"@mui/material\": \"^6.2.0\",\n \"@mui/system\": \"^6.2.0\",\n \"@mui/x-data-grid\": \"^7.2.0\",\n \"@types/node\": \"^22.10.2\",\n \"@types/react\": \"^19.0.1\",\n \"@typescript-eslint/eslint-plugin\": \"^8.18.0\",\n \"@typescript-eslint/parser\": \"^8.18.0\",\n \"chalk\": \"^5.3.0\",\n \"esbuild\": \"^0.24.0\",\n \"eslint\": \"^9.17.0\",\n \"eslint-plugin-react\": \"^7.20.3\",\n \"eslint-plugin-react-hooks\": \"^5.1.0\",\n \"eslint-plugin-unicorn\": \"^56.0.1\",\n \"mobx\": \"^6.0.0\",\n \"mobx-react\": \"^9.0.1\",\n \"mobx-state-tree\": \"5.4.1\",\n \"prettier\": \"^3.4.2\",\n \"pretty-bytes\": \"^6.1.1\",\n \"react\": \"^19.0.0\",\n \"react-dom\": \"^19.0.0\",\n \"rimraf\": \"^6.0.1\",\n \"rxjs\": \"^7.8.1\",\n \"serve\": \"^14.2.0\",\n \"tss-react\": \"^4.8.6\",\n \"typescript\": \"^5.1.6\",\n \"typescript-eslint\": \"^8.18.0\"\n }\n}\n", "import PluginManager from '@jbrowse/core/PluginManager'\nimport { AdapterType } from '@jbrowse/core/pluggableElementTypes'\nimport configSchema from './configSchema'\nimport BigMafAdapter from './BigMafAdapter'\n\nexport default function BigMafAdapterF(pluginManager: PluginManager) {\n return pluginManager.addAdapterType(\n () =>\n new AdapterType({\n name: 'BigMafAdapter',\n AdapterClass: BigMafAdapter,\n configSchema,\n }),\n )\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\n/**\n * #config BigMafAdapter\n * used to configure BigMaf adapter\n */\nfunction x() {} // eslint-disable-line @typescript-eslint/no-unused-vars\n\nconst configSchema = ConfigurationSchema(\n 'BigMafAdapter',\n {\n /**\n * #slot\n */\n samples: {\n type: 'frozen',\n description: 'string[] or {id:string,label:string,color?:string}[]',\n defaultValue: [],\n },\n /**\n * #slot\n */\n bigBedLocation: {\n type: 'fileLocation',\n defaultValue: {\n uri: '/path/to/my.bb',\n locationType: 'UriLocation',\n },\n },\n },\n { explicitlyTyped: true },\n)\n\nexport default configSchema\n", "import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getSnapshot } from 'mobx-state-tree'\nimport { Feature, Region, SimpleFeature } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { firstValueFrom, toArray } from 'rxjs'\n\ninterface OrganismRecord {\n chr: string\n start: number\n srcSize: number\n strand: number\n unknown: number\n data: string\n}\nexport default class BigMafAdapter extends BaseFeatureDataAdapter {\n public setupP?: Promise<{ adapter: BaseFeatureDataAdapter }>\n\n async setup() {\n if (!this.getSubAdapter) {\n throw new Error('no getSubAdapter available')\n }\n const adapter = await this.getSubAdapter({\n ...getSnapshot(this.config),\n type: 'BigBedAdapter',\n })\n return {\n adapter: adapter.dataAdapter as BaseFeatureDataAdapter,\n }\n }\n async setupPre() {\n if (!this.setupP) {\n this.setupP = this.setup().catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n\n async getRefNames() {\n const { adapter } = await this.setup()\n return adapter.getRefNames()\n }\n\n async getHeader() {\n const { adapter } = await this.setup()\n return adapter.getHeader()\n }\n\n getFeatures(query: Region) {\n return ObservableCreate<Feature>(async observer => {\n const { adapter } = await this.setup()\n const features = await firstValueFrom(\n adapter.getFeatures(query).pipe(toArray()),\n )\n for (const feature of features) {\n const maf = feature.get('mafBlock') as string\n const blocks = maf.split(';')\n let aln: string | undefined\n const alns = [] as string[]\n const alignments = {} as Record<string, OrganismRecord>\n const blocks2 = [] as string[]\n for (const block of blocks) {\n if (block.startsWith('s')) {\n if (aln) {\n alns.push(block.split(/ +/)[6])\n blocks2.push(block)\n } else {\n aln = block.split(/ +/)[6]\n alns.push(aln)\n blocks2.push(block)\n }\n }\n }\n\n for (let i = 0; i < blocks2.length; i++) {\n const elt = blocks2[i]\n const ad = elt.split(/ +/)\n const y = ad[1].split('.')\n const org = y[0]\n const chr = y[1]\n\n alignments[org] = {\n chr: chr,\n start: +ad[1],\n srcSize: +ad[2],\n strand: ad[3] === '+' ? 1 : -1,\n unknown: +ad[4],\n data: alns[i],\n }\n }\n observer.next(\n new SimpleFeature({\n id: feature.id(),\n data: {\n start: feature.get('start'),\n end: feature.get('end'),\n refName: feature.get('refName'),\n seq: alns[0],\n alignments: alignments,\n },\n }),\n )\n }\n observer.complete()\n })\n }\n freeResources(): void {}\n}\n", "/******************************************************************************\nCopyright (c) Microsoft Corporation.\n\nPermission to use, copy, modify, and/or distribute this software for any\npurpose with or without fee is hereby granted.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH\nREGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY\nAND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,\nINDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM\nLOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR\nOTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR\nPERFORMANCE OF THIS SOFTWARE.\n***************************************************************************** */\n/* global Reflect, Promise, SuppressedError, Symbol, Iterator */\n\nvar extendStatics = function(d, b) {\n extendStatics = Object.setPrototypeOf ||\n ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||\n function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };\n return extendStatics(d, b);\n};\n\nexport function __extends(d, b) {\n if (typeof b !== \"function\" && b !== null)\n throw new TypeError(\"Class extends value \" + String(b) + \" is not a constructor or null\");\n extendStatics(d, b);\n function __() { this.constructor = d; }\n d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());\n}\n\nexport var __assign = function() {\n __assign = Object.assign || function __assign(t) {\n for (var s, i = 1, n = arguments.length; i < n; i++) {\n s = arguments[i];\n for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p)) t[p] = s[p];\n }\n return t;\n }\n return __assign.apply(this, arguments);\n}\n\nexport function __rest(s, e) {\n var t = {};\n for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)\n t[p] = s[p];\n if (s != null && typeof Object.getOwnPropertySymbols === \"function\")\n for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {\n if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))\n t[p[i]] = s[p[i]];\n }\n return t;\n}\n\nexport function __decorate(decorators, target, key, desc) {\n var c = arguments.length, r = c < 3 ? target : desc === null ? desc = Object.getOwnPropertyDescriptor(target, key) : desc, d;\n if (typeof Reflect === \"object\" && typeof Reflect.decorate === \"function\") r = Reflect.decorate(decorators, target, key, desc);\n else for (var i = decorators.length - 1; i >= 0; i--) if (d = decorators[i]) r = (c < 3 ? d(r) : c > 3 ? d(target, key, r) : d(target, key)) || r;\n return c > 3 && r && Object.defineProperty(target, key, r), r;\n}\n\nexport function __param(paramIndex, decorator) {\n return function (target, key) { decorator(target, key, paramIndex); }\n}\n\nexport function __esDecorate(ctor, descriptorIn, decorators, contextIn, initializers, extraInitializers) {\n function accept(f) { if (f !== void 0 && typeof f !== \"function\") throw new TypeError(\"Function expected\"); return f; }\n var kind = contextIn.kind, key = kind === \"getter\" ? \"get\" : kind === \"setter\" ? \"set\" : \"value\";\n var target = !descriptorIn && ctor ? contextIn[\"static\"] ? ctor : ctor.prototype : null;\n var descriptor = descriptorIn || (target ? Object.getOwnPropertyDescriptor(target, contextIn.name) : {});\n var _, done = false;\n for (var i = decorators.length - 1; i >= 0; i--) {\n var context = {};\n for (var p in contextIn) context[p] = p === \"access\" ? {} : contextIn[p];\n for (var p in contextIn.access) context.access[p] = contextIn.access[p];\n context.addInitializer = function (f) { if (done) throw new TypeError(\"Cannot add initializers after decoration has completed\"); extraInitializers.push(accept(f || null)); };\n var result = (0, decorators[i])(kind === \"accessor\" ? { get: descriptor.get, set: descriptor.set } : descriptor[key], context);\n if (kind === \"accessor\") {\n if (result === void 0) continue;\n if (result === null || typeof result !== \"object\") throw new TypeError(\"Object expected\");\n if (_ = accept(result.get)) descriptor.get = _;\n if (_ = accept(result.set)) descriptor.set = _;\n if (_ = accept(result.init)) initializers.unshift(_);\n }\n else if (_ = accept(result)) {\n if (kind === \"field\") initializers.unshift(_);\n else descriptor[key] = _;\n }\n }\n if (target) Object.defineProperty(target, contextIn.name, descriptor);\n done = true;\n};\n\nexport function __runInitializers(thisArg, initializers, value) {\n var useValue = arguments.length > 2;\n for (var i = 0; i < initializers.length; i++) {\n value = useValue ? initializers[i].call(thisArg, value) : initializers[i].call(thisArg);\n }\n return useValue ? value : void 0;\n};\n\nexport function __propKey(x) {\n return typeof x === \"symbol\" ? x : \"\".concat(x);\n};\n\nexport function __setFunctionName(f, name, prefix) {\n if (typeof name === \"symbol\") name = name.description ? \"[\".concat(name.description, \"]\") : \"\";\n return Object.defineProperty(f, \"name\", { configurable: true, value: prefix ? \"\".concat(prefix, \" \", name) : name });\n};\n\nexport function __metadata(metadataKey, metadataValue) {\n if (typeof Reflect === \"object\" && typeof Reflect.metadata === \"function\") return Reflect.metadata(metadataKey, metadataValue);\n}\n\nexport function __awaiter(thisArg, _arguments, P, generator) {\n function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }\n return new (P || (P = Promise))(function (resolve, reject) {\n function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }\n function rejected(value) { try { step(generator[\"throw\"](value)); } catch (e) { reject(e); } }\n function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }\n step((generator = generator.apply(thisArg, _arguments || [])).next());\n });\n}\n\nexport function __generator(thisArg, body) {\n var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g = Object.create((typeof Iterator === \"function\" ? 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(function(o, m, k, k2) {\n if (k2 === undefined) k2 = k;\n var desc = Object.getOwnPropertyDescriptor(m, k);\n if (!desc || (\"get\" in desc ? !m.__esModule : desc.writable || desc.configurable)) {\n desc = { enumerable: true, get: function() { return m[k]; } };\n }\n Object.defineProperty(o, k2, desc);\n}) : (function(o, m, k, k2) {\n if (k2 === undefined) k2 = k;\n o[k2] = m[k];\n});\n\nexport function __exportStar(m, o) {\n for (var p in m) if (p !== \"default\" && !Object.prototype.hasOwnProperty.call(o, p)) __createBinding(o, m, p);\n}\n\nexport function __values(o) {\n var s = typeof Symbol === \"function\" && Symbol.iterator, m = s && o[s], i = 0;\n if (m) return m.call(o);\n if (o && typeof o.length === \"number\") return {\n next: function () {\n if (o && i >= o.length) o = void 0;\n return { value: o && o[i++], done: !o };\n }\n };\n throw new TypeError(s ? \"Object is not iterable.\" : \"Symbol.iterator is not defined.\");\n}\n\nexport function __read(o, n) {\n var m = typeof Symbol === \"function\" && o[Symbol.iterator];\n if (!m) return o;\n var i = m.call(o), r, ar = [], e;\n try {\n while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);\n }\n catch (error) { e = { error: error }; }\n finally {\n try {\n if (r && !r.done && (m = i[\"return\"])) m.call(i);\n }\n finally { if (e) throw e.error; }\n }\n return ar;\n}\n\n/** @deprecated */\nexport function __spread() {\n for (var ar = [], i = 0; i < arguments.length; i++)\n ar = ar.concat(__read(arguments[i]));\n return ar;\n}\n\n/** @deprecated */\nexport function __spreadArrays() {\n for (var s = 0, i = 0, il = arguments.length; i < il; i++) s += arguments[i].length;\n for (var r = Array(s), k = 0, i = 0; i < il; i++)\n for (var a = arguments[i], j = 0, jl = a.length; j < jl; j++, k++)\n r[k] = a[j];\n return r;\n}\n\nexport function __spreadArray(to, from, pack) {\n if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {\n if (ar || !(i in from)) {\n if (!ar) ar = Array.prototype.slice.call(from, 0, i);\n ar[i] = from[i];\n }\n }\n return to.concat(ar || Array.prototype.slice.call(from));\n}\n\nexport function __await(v) {\n return this instanceof __await ? (this.v = v, this) : new __await(v);\n}\n\nexport function __asyncGenerator(thisArg, _arguments, generator) {\n if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\n var g = generator.apply(thisArg, _arguments || []), i, q = [];\n return i = Object.create((typeof AsyncIterator === \"function\" ? AsyncIterator : Object).prototype), verb(\"next\"), verb(\"throw\"), verb(\"return\", awaitReturn), i[Symbol.asyncIterator] = function () { return this; }, i;\n function awaitReturn(f) { return function (v) { return Promise.resolve(v).then(f, reject); }; }\n function verb(n, f) { if (g[n]) { i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; if (f) i[n] = f(i[n]); } }\n function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }\n function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }\n function fulfill(value) { resume(\"next\", value); }\n function reject(value) { resume(\"throw\", value); }\n function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }\n}\n\nexport function __asyncDelegator(o) {\n var i, p;\n return i = {}, verb(\"next\"), verb(\"throw\", function (e) { throw e; }), verb(\"return\"), i[Symbol.iterator] = function () { return this; }, i;\n function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: false } : f ? f(v) : v; } : f; }\n}\n\nexport function __asyncValues(o) {\n if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\n var m = o[Symbol.asyncIterator], i;\n return m ? m.call(o) : (o = typeof __values === \"function\" ? __values(o) : o[Symbol.iterator](), i = {}, verb(\"next\"), verb(\"throw\"), verb(\"return\"), i[Symbol.asyncIterator] = function () { return this; }, i);\n function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }\n function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }\n}\n\nexport function __makeTemplateObject(cooked, raw) {\n if (Object.defineProperty) { Object.defineProperty(cooked, \"raw\", { value: raw }); } else { cooked.raw = raw; }\n return cooked;\n};\n\nvar __setModuleDefault = Object.create ? (function(o, v) {\n Object.defineProperty(o, \"default\", { enumerable: true, value: v });\n}) : function(o, v) {\n o[\"default\"] = v;\n};\n\nvar ownKeys = function(o) {\n ownKeys = Object.getOwnPropertyNames || function (o) {\n var ar = [];\n for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;\n return ar;\n };\n return ownKeys(o);\n};\n\nexport function __importStar(mod) {\n if (mod && mod.__esModule) return mod;\n var result = {};\n if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== \"default\") __createBinding(result, mod, k[i]);\n __setModuleDefault(result, mod);\n return result;\n}\n\nexport function __importDefault(mod) {\n return (mod && mod.__esModule) ? mod : { default: mod };\n}\n\nexport function __classPrivateFieldGet(receiver, state, kind, f) {\n if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a getter\");\n if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot read private member from an object whose class did not declare it\");\n return kind === \"m\" ? f : kind === \"a\" ? f.call(receiver) : f ? f.value : state.get(receiver);\n}\n\nexport function __classPrivateFieldSet(receiver, state, value, kind, f) {\n if (kind === \"m\") throw new TypeError(\"Private method is not writable\");\n if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a setter\");\n if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot write private member to an object whose class did not declare it\");\n return (kind === \"a\" ? f.call(receiver, value) : f ? f.value = value : state.set(receiver, value)), value;\n}\n\nexport function __classPrivateFieldIn(state, receiver) {\n if (receiver === null || (typeof receiver !== \"object\" && typeof receiver !== \"function\")) throw new TypeError(\"Cannot use 'in' operator on non-object\");\n return typeof state === \"function\" ? receiver === state : state.has(receiver);\n}\n\nexport function __addDisposableResource(env, value, async) {\n if (value !== null && value !== void 0) {\n if (typeof value !== \"object\" && typeof value !== \"function\") throw new TypeError(\"Object expected.\");\n var dispose, inner;\n if (async) {\n if (!Symbol.asyncDispose) throw new TypeError(\"Symbol.asyncDispose is not defined.\");\n dispose = value[Symbol.asyncDispose];\n }\n if (dispose === void 0) {\n if (!Symbol.dispose) throw new TypeError(\"Symbol.dispose is not defined.\");\n dispose = value[Symbol.dispose];\n if (async) inner = dispose;\n }\n if (typeof dispose !== \"function\") throw new TypeError(\"Object not disposable.\");\n if (inner) dispose = function() { try { inner.call(this); } catch (e) { return Promise.reject(e); } };\n env.stack.push({ value: value, dispose: dispose, async: async });\n }\n else if (async) {\n env.stack.push({ async: true });\n }\n return value;\n}\n\nvar _SuppressedError = typeof SuppressedError === \"function\" ? SuppressedError : function (error, suppressed, message) {\n var e = new Error(message);\n return e.name = \"SuppressedError\", e.error = error, e.suppressed = suppressed, e;\n};\n\nexport function __disposeResources(env) {\n function fail(e) {\n env.error = env.hasError ? new _SuppressedError(e, env.error, \"An error was suppressed during disposal.\") : e;\n env.hasError = true;\n }\n var r, s = 0;\n function next() {\n while (r = env.stack.pop()) {\n try {\n if (!r.async && s === 1) return s = 0, env.stack.push(r), Promise.resolve().then(next);\n if (r.dispose) {\n var result = r.dispose.call(r.value);\n if (r.async) return s |= 2, Promise.resolve(result).then(next, function(e) { fail(e); return next(); });\n }\n else s |= 1;\n }\n catch (e) {\n fail(e);\n }\n }\n if (s === 1) return env.hasError ? Promise.reject(env.error) : Promise.resolve();\n if (env.hasError) throw env.error;\n }\n return next();\n}\n\nexport function __rewriteRelativeImportExtension(path, preserveJsx) {\n if (typeof path === \"string\" && /^\\.\\.?\\//.test(path)) {\n return path.replace(/\\.(tsx)$|((?:\\.d)?)((?:\\.[^./]+?)?)\\.([cm]?)ts$/i, function (m, tsx, d, ext, cm) {\n return tsx ? preserveJsx ? \".jsx\" : \".js\" : d && (!ext || !cm) ? m : (d + ext + \".\" + cm.toLowerCase() + \"js\");\n });\n }\n return path;\n}\n\nexport default {\n __extends,\n __assign,\n __rest,\n __decorate,\n __param,\n __esDecorate,\n __runInitializers,\n __propKey,\n __setFunctionName,\n __metadata,\n __awaiter,\n __generator,\n __createBinding,\n __exportStar,\n __values,\n __read,\n __spread,\n __spreadArrays,\n __spreadArray,\n __await,\n __asyncGenerator,\n __asyncDelegator,\n __asyncValues,\n __makeTemplateObject,\n __importStar,\n __importDefault,\n __classPrivateFieldGet,\n __classPrivateFieldSet,\n __classPrivateFieldIn,\n __addDisposableResource,\n __disposeResources,\n __rewriteRelativeImportExtension,\n};\n", "/**\n * Returns true if the object is a function.\n * @param value The value to check\n */\nexport function isFunction(value: any): value is (...args: any[]) => any {\n return typeof value === 'function';\n}\n", "/**\n * Used to create Error subclasses until the community moves away from ES5.\n *\n * This is because compiling from TypeScript down to ES5 has issues with subclassing Errors\n * as well as other built-in types: https://github.com/Microsoft/TypeScript/issues/12123\n *\n * @param createImpl A factory function to create the actual constructor implementation. The returned\n * function should be a named function that calls `_super` internally.\n */\nexport function createErrorClass<T>(createImpl: (_super: any) => any): T {\n const _super = (instance: any) => {\n Error.call(instance);\n instance.stack = new Error().stack;\n };\n\n const ctorFunc = createImpl(_super);\n ctorFunc.prototype = Object.create(Error.prototype);\n ctorFunc.prototype.constructor = ctorFunc;\n return ctorFunc;\n}\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface UnsubscriptionError extends Error {\n readonly errors: any[];\n}\n\nexport interface UnsubscriptionErrorCtor {\n /**\n * @deprecated Internal implementation detail. Do not construct error instances.\n * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n */\n new (errors: any[]): UnsubscriptionError;\n}\n\n/**\n * An error thrown when one or more errors have occurred during the\n * `unsubscribe` of a {@link Subscription}.\n */\nexport const UnsubscriptionError: UnsubscriptionErrorCtor = createErrorClass(\n (_super) =>\n function UnsubscriptionErrorImpl(this: any, errors: (Error | string)[]) {\n _super(this);\n this.message = errors\n ? `${errors.length} errors occurred during unsubscription:\n${errors.map((err, i) => `${i + 1}) ${err.toString()}`).join('\\n ')}`\n : '';\n this.name = 'UnsubscriptionError';\n this.errors = errors;\n }\n);\n", "/**\n * Removes an item from an array, mutating it.\n * @param arr The array to remove the item from\n * @param item The item to remove\n */\nexport function arrRemove<T>(arr: T[] | undefined | null, item: T) {\n if (arr) {\n const index = arr.indexOf(item);\n 0 <= index && arr.splice(index, 1);\n }\n}\n", "import { isFunction } from './util/isFunction';\nimport { UnsubscriptionError } from './util/UnsubscriptionError';\nimport { SubscriptionLike, TeardownLogic, Unsubscribable } from './types';\nimport { arrRemove } from './util/arrRemove';\n\n/**\n * Represents a disposable resource, such as the execution of an Observable. A\n * Subscription has one important method, `unsubscribe`, that takes no argument\n * and just disposes the resource held by the subscription.\n *\n * Additionally, subscriptions may be grouped together through the `add()`\n * method, which will attach a child Subscription to the current Subscription.\n * When a Subscription is unsubscribed, all its children (and its grandchildren)\n * will be unsubscribed as well.\n *\n * @class Subscription\n */\nexport class Subscription implements SubscriptionLike {\n /** @nocollapse */\n public static EMPTY = (() => {\n const empty = new Subscription();\n empty.closed = true;\n return empty;\n })();\n\n /**\n * A flag to indicate whether this Subscription has already been unsubscribed.\n */\n public closed = false;\n\n private _parentage: Subscription[] | Subscription | null = null;\n\n /**\n * The list of registered finalizers to execute upon unsubscription. Adding and removing from this\n * list occurs in the {@link #add} and {@link #remove} methods.\n */\n private _finalizers: Exclude<TeardownLogic, void>[] | null = null;\n\n /**\n * @param initialTeardown A function executed first as part of the finalization\n * process that is kicked off when {@link #unsubscribe} is called.\n */\n constructor(private initialTeardown?: () => void) {}\n\n /**\n * Disposes the resources held by the subscription. May, for instance, cancel\n * an ongoing Observable execution or cancel any other type of work that\n * started when the Subscription was created.\n * @return {void}\n */\n unsubscribe(): void {\n let errors: any[] | undefined;\n\n if (!this.closed) {\n this.closed = true;\n\n // Remove this from it's parents.\n const { _parentage } = this;\n if (_parentage) {\n this._parentage = null;\n if (Array.isArray(_parentage)) {\n for (const parent of _parentage) {\n parent.remove(this);\n }\n } else {\n _parentage.remove(this);\n }\n }\n\n const { initialTeardown: initialFinalizer } = this;\n if (isFunction(initialFinalizer)) {\n try {\n initialFinalizer();\n } catch (e) {\n errors = e instanceof UnsubscriptionError ? e.errors : [e];\n }\n }\n\n const { _finalizers } = this;\n if (_finalizers) {\n this._finalizers = null;\n for (const finalizer of _finalizers) {\n try {\n execFinalizer(finalizer);\n } catch (err) {\n errors = errors ?? [];\n if (err instanceof UnsubscriptionError) {\n errors = [...errors, ...err.errors];\n } else {\n errors.push(err);\n }\n }\n }\n }\n\n if (errors) {\n throw new UnsubscriptionError(errors);\n }\n }\n }\n\n /**\n * Adds a finalizer to this subscription, so that finalization will be unsubscribed/called\n * when this subscription is unsubscribed. If this subscription is already {@link #closed},\n * because it has already been unsubscribed, then whatever finalizer is passed to it\n * will automatically be executed (unless the finalizer itself is also a closed subscription).\n *\n * Closed Subscriptions cannot be added as finalizers to any subscription. Adding a closed\n * subscription to a any subscription will result in no operation. (A noop).\n *\n * Adding a subscription to itself, or adding `null` or `undefined` will not perform any\n * operation at all. (A noop).\n *\n * `Subscription` instances that are added to this instance will automatically remove themselves\n * if they are unsubscribed. Functions and {@link Unsubscribable} objects that you wish to remove\n * will need to be removed manually with {@link #remove}\n *\n * @param teardown The finalization logic to add to this subscription.\n */\n add(teardown: TeardownLogic): void {\n // Only add the finalizer if it's not undefined\n // and don't add a subscription to itself.\n if (teardown && teardown !== this) {\n if (this.closed) {\n // If this subscription is already closed,\n // execute whatever finalizer is handed to it automatically.\n execFinalizer(teardown);\n } else {\n if (teardown instanceof Subscription) {\n // We don't add closed subscriptions, and we don't add the same subscription\n // twice. Subscription unsubscribe is idempotent.\n if (teardown.closed || teardown._hasParent(this)) {\n return;\n }\n teardown._addParent(this);\n }\n (this._finalizers = this._finalizers ?? []).push(teardown);\n }\n }\n }\n\n /**\n * Checks to see if a this subscription already has a particular parent.\n * This will signal that this subscription has already been added to the parent in question.\n * @param parent the parent to check for\n */\n private _hasParent(parent: Subscription) {\n const { _parentage } = this;\n return _parentage === parent || (Array.isArray(_parentage) && _parentage.includes(parent));\n }\n\n /**\n * Adds a parent to this subscription so it can be removed from the parent if it\n * unsubscribes on it's own.\n *\n * NOTE: THIS ASSUMES THAT {@link _hasParent} HAS ALREADY BEEN CHECKED.\n * @param parent The parent subscription to add\n */\n private _addParent(parent: Subscription) {\n const { _parentage } = this;\n this._parentage = Array.isArray(_parentage) ? (_parentage.push(parent), _parentage) : _parentage ? [_parentage, parent] : parent;\n }\n\n /**\n * Called on a child when it is removed via {@link #remove}.\n * @param parent The parent to remove\n */\n private _removeParent(parent: Subscription) {\n const { _parentage } = this;\n if (_parentage === parent) {\n this._parentage = null;\n } else if (Array.isArray(_parentage)) {\n arrRemove(_parentage, parent);\n }\n }\n\n /**\n * Removes a finalizer from this subscription that was previously added with the {@link #add} method.\n *\n * Note that `Subscription` instances, when unsubscribed, will automatically remove themselves\n * from every other `Subscription` they have been added to. This means that using the `remove` method\n * is not a common thing and should be used thoughtfully.\n *\n * If you add the same finalizer instance of a function or an unsubscribable object to a `Subscription` instance\n * more than once, you will need to call `remove` the same number of times to remove all instances.\n *\n * All finalizer instances are removed to free up memory upon unsubscription.\n *\n * @param teardown The finalizer to remove from this subscription\n */\n remove(teardown: Exclude<TeardownLogic, void>): void {\n const { _finalizers } = this;\n _finalizers && arrRemove(_finalizers, teardown);\n\n if (teardown instanceof Subscription) {\n teardown._removeParent(this);\n }\n }\n}\n\nexport const EMPTY_SUBSCRIPTION = Subscription.EMPTY;\n\nexport function isSubscription(value: any): value is Subscription {\n return (\n value instanceof Subscription ||\n (value && 'closed' in value && isFunction(value.remove) && isFunction(value.add) && isFunction(value.unsubscribe))\n );\n}\n\nfunction execFinalizer(finalizer: Unsubscribable | (() => void)) {\n if (isFunction(finalizer)) {\n finalizer();\n } else {\n finalizer.unsubscribe();\n }\n}\n", "import { Subscriber } from './Subscriber';\nimport { ObservableNotification } from './types';\n\n/**\n * The {@link GlobalConfig} object for RxJS. It is used to configure things\n * like how to react on unhandled errors.\n */\nexport const config: GlobalConfig = {\n onUnhandledError: null,\n onStoppedNotification: null,\n Promise: undefined,\n useDeprecatedSynchronousErrorHandling: false,\n useDeprecatedNextContext: false,\n};\n\n/**\n * The global configuration object for RxJS, used to configure things\n * like how to react on unhandled errors. Accessible via {@link config}\n * object.\n */\nexport interface GlobalConfig {\n /**\n * A registration point for unhandled errors from RxJS. These are errors that\n * cannot were not handled by consuming code in the usual subscription path. For\n * example, if you have this configured, and you subscribe to an observable without\n * providing an error handler, errors from that subscription will end up here. This\n * will _always_ be called asynchronously on another job in the runtime. This is because\n * we do not want errors thrown in this user-configured handler to interfere with the\n * behavior of the library.\n */\n onUnhandledError: ((err: any) => void) | null;\n\n /**\n * A registration point for notifications that cannot be sent to subscribers because they\n * have completed, errored or have been explicitly unsubscribed. By default, next, complete\n * and error notifications sent to stopped subscribers are noops. However, sometimes callers\n * might want a different behavior. For example, with sources that attempt to report errors\n * to stopped subscribers, a caller can configure RxJS to throw an unhandled error instead.\n * This will _always_ be called asynchronously on another job in the runtime. This is because\n * we do not want errors thrown in this user-configured handler to interfere with the\n * behavior of the library.\n */\n onStoppedNotification: ((notification: ObservableNotification<any>, subscriber: Subscriber<any>) => void) | null;\n\n /**\n * The promise constructor used by default for {@link Observable#toPromise toPromise} and {@link Observable#forEach forEach}\n * methods.\n *\n * @deprecated As of version 8, RxJS will no longer support this sort of injection of a\n * Promise constructor. If you need a Promise implementation other than native promises,\n * please polyfill/patch Promise as you see appropriate. Will be removed in v8.\n */\n Promise?: PromiseConstructorLike;\n\n /**\n * If true, turns on synchronous error rethrowing, which is a deprecated behavior\n * in v6 and higher. This behavior enables bad patterns like wrapping a subscribe\n * call in a try/catch block. It also enables producer interference, a nasty bug\n * where a multicast can be broken for all observers by a downstream consumer with\n * an unhandled error. DO NOT USE THIS FLAG UNLESS IT'S NEEDED TO BUY TIME\n * FOR MIGRATION REASONS.\n *\n * @deprecated As of version 8, RxJS will no longer support synchronous throwing\n * of unhandled errors. All errors will be thrown on a separate call stack to prevent bad\n * behaviors described above. Will be removed in v8.\n */\n useDeprecatedSynchronousErrorHandling: boolean;\n\n /**\n * If true, enables an as-of-yet undocumented feature from v5: The ability to access\n * `unsubscribe()` via `this` context in `next` functions created in observers passed\n * to `subscribe`.\n *\n * This is being removed because the performance was severely problematic, and it could also cause\n * issues when types other than POJOs are passed to subscribe as subscribers, as they will likely have\n * their `this` context overwritten.\n *\n * @deprecated As of version 8, RxJS will no longer support altering the\n * context of next functions provided as part of an observer to Subscribe. Instead,\n * you will have access to a subscription or a signal or token that will allow you to do things like\n * unsubscribe and test closed status. Will be removed in v8.\n */\n useDeprecatedNextContext: boolean;\n}\n", "import type { TimerHandle } from './timerHandle';\ntype SetTimeoutFunction = (handler: () => void, timeout?: number, ...args: any[]) => TimerHandle;\ntype ClearTimeoutFunction = (handle: TimerHandle) => void;\n\ninterface TimeoutProvider {\n setTimeout: SetTimeoutFunction;\n clearTimeout: ClearTimeoutFunction;\n delegate:\n | {\n setTimeout: SetTimeoutFunction;\n clearTimeout: ClearTimeoutFunction;\n }\n | undefined;\n}\n\nexport const timeoutProvider: TimeoutProvider = {\n // When accessing the delegate, use the variable rather than `this` so that\n // the functions can be called without being bound to the provider.\n setTimeout(handler: () => void, timeout?: number, ...args) {\n const { delegate } = timeoutProvider;\n if (delegate?.setTimeout) {\n return delegate.setTimeout(handler, timeout, ...args);\n }\n return setTimeout(handler, timeout, ...args);\n },\n clearTimeout(handle) {\n const { delegate } = timeoutProvider;\n return (delegate?.clearTimeout || clearTimeout)(handle as any);\n },\n delegate: undefined,\n};\n", "import { config } from '../config';\nimport { timeoutProvider } from '../scheduler/timeoutProvider';\n\n/**\n * Handles an error on another job either with the user-configured {@link onUnhandledError},\n * or by throwing it on that new job so it can be picked up by `window.onerror`, `process.on('error')`, etc.\n *\n * This should be called whenever there is an error that is out-of-band with the subscription\n * or when an error hits a terminal boundary of the subscription and no error handler was provided.\n *\n * @param err the error to report\n */\nexport function reportUnhandledError(err: any) {\n timeoutProvider.setTimeout(() => {\n const { onUnhandledError } = config;\n if (onUnhandledError) {\n // Execute the user-configured error handler.\n onUnhandledError(err);\n } else {\n // Throw so it is picked up by the runtime's uncaught error mechanism.\n throw err;\n }\n });\n}\n", "/* tslint:disable:no-empty */\nexport function noop() { }\n", "import { CompleteNotification, NextNotification, ErrorNotification } from './types';\n\n/**\n * A completion object optimized for memory use and created to be the\n * same \"shape\" as other notifications in v8.\n * @internal\n */\nexport const COMPLETE_NOTIFICATION = (() => createNotification('C', undefined, undefined) as CompleteNotification)();\n\n/**\n * Internal use only. Creates an optimized error notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function errorNotification(error: any): ErrorNotification {\n return createNotification('E', undefined, error) as any;\n}\n\n/**\n * Internal use only. Creates an optimized next notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function nextNotification<T>(value: T) {\n return createNotification('N', value, undefined) as NextNotification<T>;\n}\n\n/**\n * Ensures that all notifications created internally have the same \"shape\" in v8.\n *\n * TODO: This is only exported to support a crazy legacy test in `groupBy`.\n * @internal\n */\nexport function createNotification(kind: 'N' | 'E' | 'C', value: any, error: any) {\n return {\n kind,\n value,\n error,\n };\n}\n", "import { config } from '../config';\n\nlet context: { errorThrown: boolean; error: any } | null = null;\n\n/**\n * Handles dealing with errors for super-gross mode. Creates a context, in which\n * any synchronously thrown errors will be passed to {@link captureError}. Which\n * will record the error such that it will be rethrown after the call back is complete.\n * TODO: Remove in v8\n * @param cb An immediately executed function.\n */\nexport function errorContext(cb: () => void) {\n if (config.useDeprecatedSynchronousErrorHandling) {\n const isRoot = !context;\n if (isRoot) {\n context = { errorThrown: false, error: null };\n }\n cb();\n if (isRoot) {\n const { errorThrown, error } = context!;\n context = null;\n if (errorThrown) {\n throw error;\n }\n }\n } else {\n // This is the general non-deprecated path for everyone that\n // isn't crazy enough to use super-gross mode (useDeprecatedSynchronousErrorHandling)\n cb();\n }\n}\n\n/**\n * Captures errors only in super-gross mode.\n * @param err the error to capture\n */\nexport function captureError(err: any) {\n if (config.useDeprecatedSynchronousErrorHandling && context) {\n context.errorThrown = true;\n context.error = err;\n }\n}\n", "import { isFunction } from './util/isFunction';\nimport { Observer, ObservableNotification } from './types';\nimport { isSubscription, Subscription } from './Subscription';\nimport { config } from './config';\nimport { reportUnhandledError } from './util/reportUnhandledError';\nimport { noop } from './util/noop';\nimport { nextNotification, errorNotification, COMPLETE_NOTIFICATION } from './NotificationFactories';\nimport { timeoutProvider } from './scheduler/timeoutProvider';\nimport { captureError } from './util/errorContext';\n\n/**\n * Implements the {@link Observer} interface and extends the\n * {@link Subscription} class. While the {@link Observer} is the public API for\n * consuming the values of an {@link Observable}, all Observers get converted to\n * a Subscriber, in order to provide Subscription-like capabilities such as\n * `unsubscribe`. Subscriber is a common type in RxJS, and crucial for\n * implementing operators, but it is rarely used as a public API.\n *\n * @class Subscriber<T>\n */\nexport class Subscriber<T> extends Subscription implements Observer<T> {\n /**\n * A static factory for a Subscriber, given a (potentially partial) definition\n * of an Observer.\n * @param next The `next` callback of an Observer.\n * @param error The `error` callback of an\n * Observer.\n * @param complete The `complete` callback of an\n * Observer.\n * @return A Subscriber wrapping the (partially defined)\n * Observer represented by the given arguments.\n * @nocollapse\n * @deprecated Do not use. Will be removed in v8. There is no replacement for this\n * method, and there is no reason to be creating instances of `Subscriber` directly.\n * If you have a specific use case, please file an issue.\n */\n static create<T>(next?: (x?: T) => void, error?: (e?: any) => void, complete?: () => void): Subscriber<T> {\n return new SafeSubscriber(next, error, complete);\n }\n\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n protected isStopped: boolean = false;\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n protected destination: Subscriber<any> | Observer<any>; // this `any` is the escape hatch to erase extra type param (e.g. R)\n\n /**\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n * There is no reason to directly create an instance of Subscriber. This type is exported for typings reasons.\n */\n constructor(destination?: Subscriber<any> | Observer<any>) {\n super();\n if (destination) {\n this.destination = destination;\n // Automatically chain subscriptions together here.\n // if destination is a Subscription, then it is a Subscriber.\n if (isSubscription(destination)) {\n destination.add(this);\n }\n } else {\n this.destination = EMPTY_OBSERVER;\n }\n }\n\n /**\n * The {@link Observer} callback to receive notifications of type `next` from\n * the Observable, with a value. The Observable may call this method 0 or more\n * times.\n * @param {T} [value] The `next` value.\n * @return {void}\n */\n next(value?: T): void {\n if (this.isStopped) {\n handleStoppedNotification(nextNotification(value), this);\n } else {\n this._next(value!);\n }\n }\n\n /**\n * The {@link Observer} callback to receive notifications of type `error` from\n * the Observable, with an attached `Error`. Notifies the Observer that\n * the Observable has experienced an error condition.\n * @param {any} [err] The `error` exception.\n * @return {void}\n */\n error(err?: any): void {\n if (this.isStopped) {\n handleStoppedNotification(errorNotification(err), this);\n } else {\n this.isStopped = true;\n this._error(err);\n }\n }\n\n /**\n * The {@link Observer} callback to receive a valueless notification of type\n * `complete` from the Observable. Notifies the Observer that the Observable\n * has finished sending push-based notifications.\n * @return {void}\n */\n complete(): void {\n if (this.isStopped) {\n handleStoppedNotification(COMPLETE_NOTIFICATION, this);\n } else {\n this.isStopped = true;\n this._complete();\n }\n }\n\n unsubscribe(): void {\n if (!this.closed) {\n this.isStopped = true;\n super.unsubscribe();\n this.destination = null!;\n }\n }\n\n protected _next(value: T): void {\n this.destination.next(value);\n }\n\n protected _error(err: any): void {\n try {\n this.destination.error(err);\n } finally {\n this.unsubscribe();\n }\n }\n\n protected _complete(): void {\n try {\n this.destination.complete();\n } finally {\n this.unsubscribe();\n }\n }\n}\n\n/**\n * This bind is captured here because we want to be able to have\n * compatibility with monoid libraries that tend to use a method named\n * `bind`. In particular, a library called Monio requires this.\n */\nconst _bind = Function.prototype.bind;\n\nfunction bind<Fn extends (...args: any[]) => any>(fn: Fn, thisArg: any): Fn {\n return _bind.call(fn, thisArg);\n}\n\n/**\n * Internal optimization only, DO NOT EXPOSE.\n * @internal\n */\nclass ConsumerObserver<T> implements Observer<T> {\n constructor(private partialObserver: Partial<Observer<T>>) {}\n\n next(value: T): void {\n const { partialObserver } = this;\n if (partialObserver.next) {\n try {\n partialObserver.next(value);\n } catch (error) {\n handleUnhandledError(error);\n }\n }\n }\n\n error(err: any): void {\n const { partialObserver } = this;\n if (partialObserver.error) {\n try {\n partialObserver.error(err);\n } catch (error) {\n handleUnhandledError(error);\n }\n } else {\n handleUnhandledError(err);\n }\n }\n\n complete(): void {\n const { partialObserver } = this;\n if (partialObserver.complete) {\n try {\n partialObserver.complete();\n } catch (error) {\n handleUnhandledError(error);\n }\n }\n }\n}\n\nexport class SafeSubscriber<T> extends Subscriber<T> {\n constructor(\n observerOrNext?: Partial<Observer<T>> | ((value: T) => void) | null,\n error?: ((e?: any) => void) | null,\n complete?: (() => void) | null\n ) {\n super();\n\n let partialObserver: Partial<Observer<T>>;\n if (isFunction(observerOrNext) || !observerOrNext) {\n // The first argument is a function, not an observer. The next\n // two arguments *could* be observers, or they could be empty.\n partialObserver = {\n next: (observerOrNext ?? undefined) as (((value: T) => void) | undefined),\n error: error ?? undefined,\n complete: complete ?? undefined,\n };\n } else {\n // The first argument is a partial observer.\n let context: any;\n if (this && config.useDeprecatedNextContext) {\n // This is a deprecated path that made `this.unsubscribe()` available in\n // next handler functions passed to subscribe. This only exists behind a flag\n // now, as it is *very* slow.\n context = Object.create(observerOrNext);\n context.unsubscribe = () => this.unsubscribe();\n partialObserver = {\n next: observerOrNext.next && bind(observerOrNext.next, context),\n error: observerOrNext.error && bind(observerOrNext.error, context),\n complete: observerOrNext.complete && bind(observerOrNext.complete, context),\n };\n } else {\n // The \"normal\" path. Just use the partial observer directly.\n partialObserver = observerOrNext;\n }\n }\n\n // Wrap the partial observer to ensure it's a full observer, and\n // make sure proper error handling is accounted for.\n this.destination = new ConsumerObserver(partialObserver);\n }\n}\n\nfunction handleUnhandledError(error: any) {\n if (config.useDeprecatedSynchronousErrorHandling) {\n captureError(error);\n } else {\n // Ideal path, we report this as an unhandled error,\n // which is thrown on a new call stack.\n reportUnhandledError(error);\n }\n}\n\n/**\n * An error handler used when no error handler was supplied\n * to the SafeSubscriber -- meaning no error handler was supplied\n * do the `subscribe` call on our observable.\n * @param err The error to handle\n */\nfunction defaultErrorHandler(err: any) {\n throw err;\n}\n\n/**\n * A handler for notifications that cannot be sent to a stopped subscriber.\n * @param notification The notification being sent\n * @param subscriber The stopped subscriber\n */\nfunction handleStoppedNotification(notification: ObservableNotification<any>, subscriber: Subscriber<any>) {\n const { onStoppedNotification } = config;\n onStoppedNotification && timeoutProvider.setTimeout(() => onStoppedNotification(notification, subscriber));\n}\n\n/**\n * The observer used as a stub for subscriptions where the user did not\n * pass any arguments to `subscribe`. Comes with the default error handling\n * behavior.\n */\nexport const EMPTY_OBSERVER: Readonly<Observer<any>> & { closed: true } = {\n closed: true,\n next: noop,\n error: defaultErrorHandler,\n complete: noop,\n};\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { OperatorFunction } from '../types';\nimport { isFunction } from './isFunction';\n\n/**\n * Used to determine if an object is an Observable with a lift function.\n */\nexport function hasLift(source: any): source is { lift: InstanceType<typeof Observable>['lift'] } {\n return isFunction(source?.lift);\n}\n\n/**\n * Creates an `OperatorFunction`. Used to define operators throughout the library in a concise way.\n * @param init The logic to connect the liftedSource to the subscriber at the moment of subscription.\n */\nexport function operate<T, R>(\n init: (liftedSource: Observable<T>, subscriber: Subscriber<R>) => (() => void) | void\n): OperatorFunction<T, R> {\n return (source: Observable<T>) => {\n if (hasLift(source)) {\n return source.lift(function (this: Subscriber<R>, liftedSource: Observable<T>) {\n try {\n return init(liftedSource, this);\n } catch (err) {\n this.error(err);\n }\n });\n }\n throw new TypeError('Unable to lift unknown Observable type');\n };\n}\n", "import { Subscriber } from '../Subscriber';\n\n/**\n * Creates an instance of an `OperatorSubscriber`.\n * @param destination The downstream subscriber.\n * @param onNext Handles next values, only called if this subscriber is not stopped or closed. Any\n * error that occurs in this function is caught and sent to the `error` method of this subscriber.\n * @param onError Handles errors from the subscription, any errors that occur in this handler are caught\n * and send to the `destination` error handler.\n * @param onComplete Handles completion notification from the subscription. Any errors that occur in\n * this handler are sent to the `destination` error handler.\n * @param onFinalize Additional teardown logic here. This will only be called on teardown if the\n * subscriber itself is not already closed. This is called after all other teardown logic is executed.\n */\nexport function createOperatorSubscriber<T>(\n destination: Subscriber<any>,\n onNext?: (value: T) => void,\n onComplete?: () => void,\n onError?: (err: any) => void,\n onFinalize?: () => void\n): Subscriber<T> {\n return new OperatorSubscriber(destination, onNext, onComplete, onError, onFinalize);\n}\n\n/**\n * A generic helper for allowing operators to be created with a Subscriber and\n * use closures to capture necessary state from the operator function itself.\n */\nexport class OperatorSubscriber<T> extends Subscriber<T> {\n /**\n * Creates an instance of an `OperatorSubscriber`.\n * @param destination The downstream subscriber.\n * @param onNext Handles next values, only called if this subscriber is not stopped or closed. Any\n * error that occurs in this function is caught and sent to the `error` method of this subscriber.\n * @param onError Handles errors from the subscription, any errors that occur in this handler are caught\n * and send to the `destination` error handler.\n * @param onComplete Handles completion notification from the subscription. Any errors that occur in\n * this handler are sent to the `destination` error handler.\n * @param onFinalize Additional finalization logic here. This will only be called on finalization if the\n * subscriber itself is not already closed. This is called after all other finalization logic is executed.\n * @param shouldUnsubscribe An optional check to see if an unsubscribe call should truly unsubscribe.\n * NOTE: This currently **ONLY** exists to support the strange behavior of {@link groupBy}, where unsubscription\n * to the resulting observable does not actually disconnect from the source if there are active subscriptions\n * to any grouped observable. (DO NOT EXPOSE OR USE EXTERNALLY!!!)\n */\n constructor(\n destination: Subscriber<any>,\n onNext?: (value: T) => void,\n onComplete?: () => void,\n onError?: (err: any) => void,\n private onFinalize?: () => void,\n private shouldUnsubscribe?: () => boolean\n ) {\n // It's important - for performance reasons - that all of this class's\n // members are initialized and that they are always initialized in the same\n // order. This will ensure that all OperatorSubscriber instances have the\n // same hidden class in V8. This, in turn, will help keep the number of\n // hidden classes involved in property accesses within the base class as\n // low as possible. If the number of hidden classes involved exceeds four,\n // the property accesses will become megamorphic and performance penalties\n // will be incurred - i.e. inline caches won't be used.\n //\n // The reasons for ensuring all instances have the same hidden class are\n // further discussed in this blog post from Benedikt Meurer:\n // https://benediktmeurer.de/2018/03/23/impact-of-polymorphism-on-component-based-frameworks-like-react/\n super(destination);\n this._next = onNext\n ? function (this: OperatorSubscriber<T>, value: T) {\n try {\n onNext(value);\n } catch (err) {\n destination.error(err);\n }\n }\n : super._next;\n this._error = onError\n ? function (this: OperatorSubscriber<T>, err: any) {\n try {\n onError(err);\n } catch (err) {\n // Send any errors that occur down stream.\n destination.error(err);\n } finally {\n // Ensure finalization.\n this.unsubscribe();\n }\n }\n : super._error;\n this._complete = onComplete\n ? function (this: OperatorSubscriber<T>) {\n try {\n onComplete();\n } catch (err) {\n // Send any errors that occur down stream.\n destination.error(err);\n } finally {\n // Ensure finalization.\n this.unsubscribe();\n }\n }\n : super._complete;\n }\n\n unsubscribe() {\n if (!this.shouldUnsubscribe || this.shouldUnsubscribe()) {\n const { closed } = this;\n super.unsubscribe();\n // Execute additional teardown if we have any and we didn't already do so.\n !closed && this.onFinalize?.();\n }\n }\n}\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface EmptyError extends Error {}\n\nexport interface EmptyErrorCtor {\n /**\n * @deprecated Internal implementation detail. Do not construct error instances.\n * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n */\n new (): EmptyError;\n}\n\n/**\n * An error thrown when an Observable or a sequence was queried but has no\n * elements.\n *\n * @see {@link first}\n * @see {@link last}\n * @see {@link single}\n * @see {@link firstValueFrom}\n * @see {@link lastValueFrom}\n *\n * @class EmptyError\n */\nexport const EmptyError: EmptyErrorCtor = createErrorClass((_super) => function EmptyErrorImpl(this: any) {\n _super(this);\n this.name = 'EmptyError';\n this.message = 'no elements in sequence';\n});\n", "import { Observable } from './Observable';\nimport { EmptyError } from './util/EmptyError';\nimport { SafeSubscriber } from './Subscriber';\n\nexport interface FirstValueFromConfig<T> {\n defaultValue: T;\n}\n\nexport function firstValueFrom<T, D>(source: Observable<T>, config: FirstValueFromConfig<D>): Promise<T | D>;\nexport function firstValueFrom<T>(source: Observable<T>): Promise<T>;\n\n/**\n * Converts an observable to a promise by subscribing to the observable,\n * and returning a promise that will resolve as soon as the first value\n * arrives from the observable. The subscription will then be closed.\n *\n * If the observable stream completes before any values were emitted, the\n * returned promise will reject with {@link EmptyError} or will resolve\n * with the default value if a default was specified.\n *\n * If the observable stream emits an error, the returned promise will reject\n * with that error.\n *\n * **WARNING**: Only use this with observables you *know* will emit at least one value,\n * *OR* complete. If the source observable does not emit one value or complete, you will\n * end up with a promise that is hung up, and potentially all of the state of an\n * async function hanging out in memory. To avoid this situation, look into adding\n * something like {@link timeout}, {@link take}, {@link takeWhile}, or {@link takeUntil}\n * amongst others.\n *\n * ## Example\n *\n * Wait for the first value from a stream and emit it from a promise in\n * an async function\n *\n * ```ts\n * import { interval, firstValueFrom } from 'rxjs';\n *\n * async function execute() {\n * const source$ = interval(2000);\n * const firstNumber = await firstValueFrom(source$);\n * console.log(`The first number is ${ firstNumber }`);\n * }\n *\n * execute();\n *\n * // Expected output:\n * // 'The first number is 0'\n * ```\n *\n * @see {@link lastValueFrom}\n *\n * @param source the observable to convert to a promise\n * @param config a configuration object to define the `defaultValue` to use if the source completes without emitting a value\n */\nexport function firstValueFrom<T, D>(source: Observable<T>, config?: FirstValueFromConfig<D>): Promise<T | D> {\n const hasConfig = typeof config === 'object';\n return new Promise<T | D>((resolve, reject) => {\n const subscriber = new SafeSubscriber<T>({\n next: (value) => {\n resolve(value);\n subscriber.unsubscribe();\n },\n error: reject,\n complete: () => {\n if (hasConfig) {\n resolve(config!.defaultValue);\n } else {\n reject(new EmptyError());\n }\n },\n });\n source.subscribe(subscriber);\n });\n}\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { createOperatorSubscriber } from './OperatorSubscriber';\n\n/**\n * A basic scan operation. This is used for `scan` and `reduce`.\n * @param accumulator The accumulator to use\n * @param seed The seed value for the state to accumulate\n * @param hasSeed Whether or not a seed was provided\n * @param emitOnNext Whether or not to emit the state on next\n * @param emitBeforeComplete Whether or not to emit the before completion\n */\n\nexport function scanInternals<V, A, S>(\n accumulator: (acc: V | A | S, value: V, index: number) => A,\n seed: S,\n hasSeed: boolean,\n emitOnNext: boolean,\n emitBeforeComplete?: undefined | true\n) {\n return (source: Observable<V>, subscriber: Subscriber<any>) => {\n // Whether or not we have state yet. This will only be\n // false before the first value arrives if we didn't get\n // a seed value.\n let hasState = hasSeed;\n // The state that we're tracking, starting with the seed,\n // if there is one, and then updated by the return value\n // from the accumulator on each emission.\n let state: any = seed;\n // An index to pass to the accumulator function.\n let index = 0;\n\n // Subscribe to our source. All errors and completions are passed through.\n source.subscribe(\n createOperatorSubscriber(\n subscriber,\n (value) => {\n // Always increment the index.\n const i = index++;\n // Set the state\n state = hasState\n ? // We already have state, so we can get the new state from the accumulator\n accumulator(state, value, i)\n : // We didn't have state yet, a seed value was not provided, so\n\n // we set the state to the first value, and mark that we have state now\n ((hasState = true), value);\n\n // Maybe send it to the consumer.\n emitOnNext && subscriber.next(state);\n },\n // If an onComplete was given, call it, otherwise\n // just pass through the complete notification to the consumer.\n emitBeforeComplete &&\n (() => {\n hasState && subscriber.next(state);\n subscriber.complete();\n })\n )\n );\n };\n}\n", "import { scanInternals } from './scanInternals';\nimport { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\n\nexport function reduce<V, A = V>(accumulator: (acc: A | V, value: V, index: number) => A): OperatorFunction<V, V | A>;\nexport function reduce<V, A>(accumulator: (acc: A, value: V, index: number) => A, seed: A): OperatorFunction<V, A>;\nexport function reduce<V, A, S = A>(accumulator: (acc: A | S, value: V, index: number) => A, seed: S): OperatorFunction<V, A>;\n\n/**\n * Applies an accumulator function over the source Observable, and returns the\n * accumulated result when the source completes, given an optional seed value.\n *\n * <span class=\"informal\">Combines together all values emitted on the source,\n * using an accumulator function that knows how to join a new source value into\n * the accumulation from the past.</span>\n *\n * \n *\n * Like\n * [Array.prototype.reduce()](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Array/reduce),\n * `reduce` applies an `accumulator` function against an accumulation and each\n * value of the source Observable (from the past) to reduce it to a single\n * value, emitted on the output Observable. Note that `reduce` will only emit\n * one value, only when the source Observable completes. It is equivalent to\n * applying operator {@link scan} followed by operator {@link last}.\n *\n * Returns an Observable that applies a specified `accumulator` function to each\n * item emitted by the source Observable. If a `seed` value is specified, then\n * that value will be used as the initial value for the accumulator. If no seed\n * value is specified, the first item of the source is used as the seed.\n *\n * ## Example\n *\n * Count the number of click events that happened in 5 seconds\n *\n * ```ts\n * import { fromEvent, takeUntil, interval, map, reduce } from 'rxjs';\n *\n * const clicksInFiveSeconds = fromEvent(document, 'click')\n * .pipe(takeUntil(interval(5000)));\n *\n * const ones = clicksInFiveSeconds.pipe(map(() => 1));\n * const seed = 0;\n * const count = ones.pipe(reduce((acc, one) => acc + one, seed));\n *\n * count.subscribe(x => console.log(x));\n * ```\n *\n * @see {@link count}\n * @see {@link expand}\n * @see {@link mergeScan}\n * @see {@link scan}\n *\n * @param {function(acc: A, value: V, index: number): A} accumulator The accumulator function\n * called on each source value.\n * @param {A} [seed] The initial accumulation value.\n * @return A function that returns an Observable that emits a single value that\n * is the result of accumulating the values emitted by the source Observable.\n */\nexport function reduce<V, A>(accumulator: (acc: V | A, value: V, index: number) => A, seed?: any): OperatorFunction<V, V | A> {\n return operate(scanInternals(accumulator, seed, arguments.length >= 2, false, true));\n}\n", "import { reduce } from './reduce';\nimport { OperatorFunction } from '../types';\nimport { operate } from '../util/lift';\n\nconst arrReducer = (arr: any[], value: any) => (arr.push(value), arr);\n\n/**\n * Collects all source emissions and emits them as an array when the source completes.\n *\n * <span class=\"informal\">Get all values inside an array when the source completes</span>\n *\n * \n *\n * `toArray` will wait until the source Observable completes before emitting\n * the array containing all emissions. When the source Observable errors no\n * array will be emitted.\n *\n * ## Example\n *\n * ```ts\n * import { interval, take, toArray } from 'rxjs';\n *\n * const source = interval(1000);\n * const example = source.pipe(\n * take(10),\n * toArray()\n * );\n *\n * example.subscribe(value => console.log(value));\n *\n * // output: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]\n * ```\n *\n * @return A function that returns an Observable that emits an array of items\n * emitted by the source Observable when source completes.\n */\nexport function toArray<T>(): OperatorFunction<T, T[]> {\n // Because arrays are mutable, and we're mutating the array in this\n // reducer process, we have to encapsulate the creation of the initial\n // array within this `operate` function.\n return operate((source, subscriber) => {\n reduce(arrReducer, [] as T[])(source).subscribe(subscriber);\n });\n}\n", "import PluginManager from '@jbrowse/core/PluginManager'\nimport {\n TrackType,\n createBaseTrackModel,\n} from '@jbrowse/core/pluggableElementTypes'\nimport configSchemaF from './configSchema'\n\nexport default function MafTrackF(pluginManager: PluginManager) {\n return pluginManager.addTrackType(() => {\n const configSchema = configSchemaF(pluginManager)\n return new TrackType({\n name: 'MafTrack',\n configSchema,\n displayName: 'MAF track',\n stateModel: createBaseTrackModel(pluginManager, 'MafTrack', configSchema),\n })\n })\n}\n", "import PluginManager from '@jbrowse/core/PluginManager'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'\n\nexport default function configSchemaF(pluginManager: PluginManager) {\n return ConfigurationSchema(\n 'MafTrack',\n {},\n {\n /**\n * #baseConfiguration\n */\n baseConfiguration: createBaseTrackConfig(pluginManager),\n /**\n * #identifier\n */\n explicitIdentifier: 'trackId',\n },\n )\n}\n", "import PluginManager from '@jbrowse/core/PluginManager'\nimport { DisplayType } from '@jbrowse/core/pluggableElementTypes'\nimport configSchemaF from './configSchema'\nimport stateModelFactory from './stateModel'\nimport ReactComponent from './components/ReactComponent'\n\nexport default function LinearMafDisplayF(pluginManager: PluginManager) {\n pluginManager.addDisplayType(() => {\n const configSchema = configSchemaF(pluginManager)\n const stateModel = stateModelFactory(configSchema, pluginManager)\n return new DisplayType({\n name: 'LinearMafDisplay',\n configSchema,\n stateModel,\n ReactComponent,\n viewType: 'LinearGenomeView',\n trackType: 'MafTrack',\n displayName: 'MAF display',\n })\n })\n}\n", "import PluginManager from '@jbrowse/core/PluginManager'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default function configSchemaF(pluginManager: PluginManager) {\n const LinearGenomePlugin = pluginManager.getPlugin(\n 'LinearGenomeViewPlugin',\n ) as import('@jbrowse/plugin-linear-genome-view').default\n const { baseLinearDisplayConfigSchema } = LinearGenomePlugin.exports\n return ConfigurationSchema(\n 'LinearMafDisplay',\n {\n /**\n * #slot\n */\n renderer: pluginManager.pluggableConfigSchemaType('renderer'),\n },\n {\n baseConfiguration: baseLinearDisplayConfigSchema,\n explicitlyTyped: true,\n },\n )\n}\n", "import { Instance, types } from 'mobx-state-tree'\nimport {\n AnyConfigurationModel,\n AnyConfigurationSchemaType,\n ConfigurationReference,\n getConf,\n} from '@jbrowse/core/configuration'\nimport { getEnv, getSession } from '@jbrowse/core/util'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { ExportSvgDisplayOptions } from '@jbrowse/plugin-linear-genome-view'\nimport SetRowHeightDialog from './components/SetRowHeight'\n\nfunction isStrs(array: unknown[]): array is string[] {\n return typeof array[0] === 'string'\n}\n\n/**\n * #stateModel LinearMafDisplay\n * extends LinearBasicDisplay\n */\nexport default function stateModelFactory(\n configSchema: AnyConfigurationSchemaType,\n pluginManager: PluginManager,\n) {\n const LinearGenomePlugin = pluginManager.getPlugin(\n 'LinearGenomeViewPlugin',\n ) as import('@jbrowse/plugin-linear-genome-view').default\n const { BaseLinearDisplay } = LinearGenomePlugin.exports\n\n return types\n .compose(\n 'LinearMafDisplay',\n BaseLinearDisplay,\n types.model({\n /**\n * #property\n */\n type: types.literal('LinearMafDisplay'),\n /**\n * #property\n */\n configuration: ConfigurationReference(configSchema),\n /**\n * #property\n */\n rowHeight: 15,\n /**\n * #property\n */\n rowProportion: 0.8,\n /**\n * #property\n */\n showAllLetters: false,\n /**\n * #property\n */\n mismatchRendering: true,\n }),\n )\n .volatile(() => ({\n /**\n * #volatile\n */\n prefersOffset: true,\n }))\n .actions(self => ({\n /**\n * #action\n */\n setRowHeight(n: number) {\n self.rowHeight = n\n },\n /**\n * #action\n */\n setRowProportion(n: number) {\n self.rowProportion = n\n },\n /**\n * #action\n */\n setShowAllLetters(f: boolean) {\n self.showAllLetters = f\n },\n /**\n * #action\n */\n setMismatchRendering(f: boolean) {\n self.mismatchRendering = f\n },\n }))\n .views(self => ({\n /**\n * #getter\n */\n get samples() {\n const r = self.adapterConfig.samples as\n | string[]\n | { id: string; label: string; color?: string }[]\n return isStrs(r)\n ? r.map(elt => ({ id: elt, label: elt, color: undefined }))\n : r\n },\n\n /**\n * #getter\n */\n get rendererTypeName() {\n return 'LinearMafRenderer'\n },\n /**\n * #getter\n */\n get rendererConfig(): AnyConfigurationModel {\n const configBlob = getConf(self, ['renderer']) || {}\n const config = configBlob as Omit<typeof configBlob, symbol>\n\n return self.rendererType.configSchema.create(\n {\n ...config,\n type: 'LinearMafRenderer',\n },\n getEnv(self),\n )\n },\n }))\n .views(self => {\n const {\n // eslint-disable-next-line @typescript-eslint/unbound-method\n trackMenuItems: superTrackMenuItems,\n // eslint-disable-next-line @typescript-eslint/unbound-method\n renderProps: superRenderProps,\n } = self\n return {\n /**\n * #method\n */\n renderProps() {\n const {\n showAllLetters,\n rendererConfig,\n samples,\n rowHeight,\n rowProportion,\n mismatchRendering,\n } = self\n return {\n ...superRenderProps(),\n config: rendererConfig,\n samples,\n rowHeight,\n rowProportion,\n showAllLetters,\n mismatchRendering,\n }\n },\n /**\n * #method\n */\n trackMenuItems() {\n return [\n ...superTrackMenuItems(),\n {\n label: 'Set row height',\n onClick: () => {\n getSession(self).queueDialog(handleClose => [\n SetRowHeightDialog,\n {\n model: self,\n handleClose,\n },\n ])\n },\n },\n {\n label: 'Show all letters',\n type: 'checkbox',\n checked: self.showAllLetters,\n onClick: () => {\n self.setShowAllLetters(!self.showAllLetters)\n },\n },\n {\n label: 'Draw mismatches as single color',\n type: 'checkbox',\n checked: !self.mismatchRendering,\n onClick: () => {\n self.setMismatchRendering(!self.mismatchRendering)\n },\n },\n ]\n },\n }\n })\n .actions(self => {\n // eslint-disable-next-line @typescript-eslint/unbound-method\n const { renderSvg: superRenderSvg } = self\n return {\n /**\n * #action\n */\n async renderSvg(opts: ExportSvgDisplayOptions) {\n const { renderSvg } = await import('./renderSvg')\n return renderSvg(self, opts, superRenderSvg)\n },\n }\n })\n}\n\nexport type LinearMafDisplayStateModel = ReturnType<typeof stateModelFactory>\nexport type LinearMafDisplayModel = Instance<LinearMafDisplayStateModel>\n", "import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n Button,\n DialogActions,\n DialogContent,\n TextField,\n Typography,\n} from '@mui/material'\nimport { Dialog } from '@jbrowse/core/ui'\nimport { makeStyles } from 'tss-react/mui'\n\nconst useStyles = makeStyles()({\n root: {\n width: 500,\n },\n})\n\nconst SetRowHeightDialog = observer(function (props: {\n model: {\n rowHeight?: number\n rowProportion?: number\n setRowHeight: (arg: number) => void\n setRowProportion: (arg: number) => void\n }\n handleClose: () => void\n}) {\n const { model, handleClose } = props\n const { classes } = useStyles()\n const [rowHeight, setRowHeight] = useState(`${model.rowHeight}`)\n const [rowProportion, setRowProportion] = useState(`${model.rowProportion}`)\n\n return (\n <Dialog open onClose={handleClose} title=\"Filter options\">\n <DialogContent className={classes.root}>\n <Typography>\n Set row height and the proportion of the row height to use for drawing\n each row\n </Typography>\n <TextField\n value={rowHeight}\n onChange={event => {\n setRowHeight(event.target.value)\n }}\n placeholder=\"Enter row height\"\n />\n <TextField\n value={rowProportion}\n onChange={event => {\n setRowProportion(event.target.value)\n }}\n placeholder=\"Enter row proportion\"\n />\n <DialogActions>\n <Button\n variant=\"contained\"\n color=\"primary\"\n type=\"submit\"\n autoFocus\n onClick={() => {\n model.setRowProportion(+rowProportion)\n model.setRowHeight(+rowHeight)\n handleClose()\n }}\n >\n Submit\n </Button>\n <Button\n variant=\"contained\"\n color=\"secondary\"\n onClick={() => {\n handleClose()\n }}\n >\n Cancel\n </Button>\n </DialogActions>\n </DialogContent>\n </Dialog>\n )\n})\nexport default SetRowHeightDialog\n", "import React from 'react'\nimport { getEnv } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\nimport YScaleBars from './YScaleBars'\nimport { LinearMafDisplayModel } from '../stateModel'\n\nconst LinearMafDisplay = observer(function (props: {\n model: LinearMafDisplayModel\n}) {\n const { model } = props\n const { pluginManager } = getEnv(model)\n\n const LinearGenomePlugin = pluginManager.getPlugin(\n 'LinearGenomeViewPlugin',\n ) as import('@jbrowse/plugin-linear-genome-view').default\n const { BaseLinearDisplayComponent } = LinearGenomePlugin.exports\n\n return (\n <div>\n <BaseLinearDisplayComponent {...props} />\n <YScaleBars model={model} />\n </div>\n )\n})\n\nexport default LinearMafDisplay\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\n/**\n * #config LinearMafRenderer\n */\nfunction x() {} // eslint-disable-line @typescript-eslint/no-unused-vars\n\nconst configSchema = ConfigurationSchema(\n 'LinearMafRenderer',\n {},\n {\n /**\n * #baseConfiguration\n */\n explicitlyTyped: true,\n },\n)\n\nexport default configSchema\n", "import { FeatureRendererType } from '@jbrowse/core/pluggableElementTypes'\nimport { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'\nimport { createJBrowseTheme } from '@jbrowse/core/ui'\nimport {\n Feature,\n Region,\n featureSpanPx,\n renderToAbstractCanvas,\n} from '@jbrowse/core/util'\nimport { getColorBaseMap, getContrastBaseMap } from './util'\n\ninterface Sample {\n id: string\n color?: string\n}\ninterface RenderArgs extends RenderArgsDeserialized {\n samples: Sample[]\n rowHeight: number\n rowProportion: number\n showAllLetters: boolean\n mismatchRendering: boolean\n}\n\nfunction makeImageData({\n ctx,\n renderArgs,\n}: {\n ctx: CanvasRenderingContext2D\n renderArgs: RenderArgs & { features: Map<string, Feature> }\n}) {\n const {\n regions,\n bpPerPx,\n rowHeight,\n showAllLetters,\n theme: configTheme,\n mismatchRendering,\n samples,\n rowProportion,\n features,\n } = renderArgs\n const [region] = regions\n const h = rowHeight * rowProportion\n const theme = createJBrowseTheme(configTheme)\n const colorForBase = getColorBaseMap(theme)\n const contrastForBase = getContrastBaseMap(theme)\n const sampleToRowMap = new Map(samples.map((s, i) => [s.id, i]))\n const scale = 1 / bpPerPx\n const f = 0.4\n const h2 = rowHeight / 2\n const hp2 = h / 2\n const offset = (rowHeight - h) / 2\n\n // sample as alignments\n ctx.font = 'bold 10px Courier New,monospace'\n\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx)\n const vals = feature.get('alignments') as Record<string, { data: string }>\n const seq = feature.get('seq').toLowerCase()\n for (const [sample, val] of Object.entries(vals)) {\n const origAlignment = val.data\n const alignment = origAlignment.toLowerCase()\n\n const row = sampleToRowMap.get(sample)\n if (row === undefined) {\n throw new Error(`unknown sample encountered: ${sample}`)\n }\n\n const t = rowHeight * row\n\n // gaps\n ctx.beginPath()\n ctx.fillStyle = 'black'\n for (let i = 0, o = 0; i < alignment.length; i++) {\n if (seq[i] !== '-') {\n if (alignment[i] === '-') {\n const l = leftPx + scale * o\n ctx.moveTo(l, t + h2)\n ctx.lineTo(l + scale + f, t + h2)\n }\n o++\n }\n }\n ctx.stroke()\n\n if (!showAllLetters) {\n // matches\n ctx.beginPath()\n ctx.fillStyle = 'lightgrey'\n for (let i = 0, o = 0; i < alignment.length; i++) {\n if (seq[i] !== '-') {\n const c = alignment[i]\n const l = leftPx + scale * o\n if (seq[i] === c && c !== '-') {\n ctx.rect(l, offset + t, scale + f, h)\n }\n o++\n }\n }\n ctx.fill()\n }\n\n // mismatches\n for (let i = 0, o = 0; i < alignment.length; i++) {\n const c = alignment[i]\n if (seq[i] !== '-') {\n if (c !== '-') {\n const l = leftPx + scale * o\n if (seq[i] !== c) {\n ctx.fillStyle = mismatchRendering\n ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n (colorForBase[c as keyof typeof colorForBase] ?? 'black')\n : 'orange'\n ctx.fillRect(l, offset + t, scale + f, h)\n } else if (showAllLetters) {\n ctx.fillStyle = mismatchRendering\n ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n (colorForBase[c as keyof typeof colorForBase] ?? 'black')\n : 'lightblue'\n ctx.fillRect(l, offset + t, scale + f, h)\n }\n }\n o++\n }\n }\n\n // font\n const charSizeW = 10\n if (scale >= charSizeW) {\n for (let i = 0, o = 0; i < alignment.length; i++) {\n if (seq[i] !== '-') {\n const l = leftPx + scale * o\n const offset = (scale - charSizeW) / 2 + 1\n const c = alignment[i]\n if ((showAllLetters || seq[i] !== c) && c !== '-') {\n ctx.fillStyle = contrastForBase[c] ?? 'white'\n ctx.fillText(origAlignment[i], l + offset, hp2 + t + 3)\n }\n o++\n }\n }\n }\n }\n }\n\n // second pass for insertions, has slightly improved look since the\n // insertions are always 'on top' of the other features\n for (const feature of features.values()) {\n const [leftPx] = featureSpanPx(feature, region, bpPerPx)\n const vals = feature.get('alignments') as Record<string, { data: string }>\n const seq = feature.get('seq').toLowerCase()\n\n for (const [sample, val] of Object.entries(vals)) {\n const origAlignment = val.data\n const alignment = origAlignment.toLowerCase()\n const row = sampleToRowMap.get(sample)\n if (row === undefined) {\n throw new Error(`unknown sample encountered: ${sample}`)\n }\n\n const t = rowHeight * row\n\n ctx.beginPath()\n ctx.fillStyle = 'purple'\n for (let i = 0, o = 0; i < alignment.length; i++) {\n let ins = ''\n while (seq[i] === '-') {\n if (alignment[i] !== '-') {\n ins += alignment[i]\n }\n i++\n }\n if (ins.length > 0) {\n const l = leftPx + scale * o - 1\n ctx.rect(l, offset + t + 1, 1, h - 1)\n ctx.rect(l - 2, offset + t, 5, 1)\n ctx.rect(l - 2, offset + t + h - 1, 5, 1)\n }\n o++\n }\n ctx.fill()\n }\n }\n}\nexport default class LinearMafRenderer extends FeatureRendererType {\n getExpandedRegion(region: Region) {\n const { start, end } = region\n const bpExpansion = 1\n\n return {\n // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit\n ...(region as Omit<typeof region, symbol>),\n start: Math.floor(Math.max(start - bpExpansion, 0)),\n end: Math.ceil(end + bpExpansion),\n }\n }\n async render(renderProps: RenderArgs) {\n const { regions, bpPerPx, samples, rowHeight } = renderProps\n const [region] = regions\n const height = samples.length * rowHeight + 100\n const width = (region.end - region.start) / bpPerPx\n const features = await this.getFeatures(renderProps)\n const res = await renderToAbstractCanvas(\n width,\n height,\n renderProps,\n ctx => {\n makeImageData({\n ctx,\n renderArgs: {\n ...renderProps,\n features,\n },\n })\n return undefined\n },\n )\n const results = await super.render({\n ...renderProps,\n ...res,\n width,\n height,\n })\n return {\n ...results,\n ...res,\n width,\n height,\n }\n }\n}\n", "import { Theme } from '@mui/material'\n\nexport function getContrastBaseMap(theme: Theme) {\n return Object.fromEntries(\n Object.entries(getColorBaseMap(theme)).map(([key, value]) => [\n key,\n theme.palette.getContrastText(value),\n ]),\n )\n}\n\nexport function getColorBaseMap(theme: Theme) {\n const { bases } = theme.palette\n return {\n a: bases.A.main,\n c: bases.C.main,\n g: bases.G.main,\n t: bases.T.main,\n }\n}\n", "import { PrerenderedCanvas } from '@jbrowse/core/ui'\nimport { observer } from 'mobx-react'\nimport React from 'react'\n\nconst LinearMafRendering = observer(function (props: {\n width: number\n height: number\n}) {\n return <PrerenderedCanvas {...props} />\n})\n\nexport default LinearMafRendering\n", "import PluginManager from '@jbrowse/core/PluginManager'\nimport configSchema from './configSchema'\nimport LinearMafRenderer from './LinearMafRenderer'\nimport ReactComponent from './components/ReactComponent'\n\nexport default function LinearMafRendererF(pluginManager: PluginManager) {\n pluginManager.addRendererType(\n () =>\n new LinearMafRenderer({\n name: 'LinearMafRenderer',\n ReactComponent,\n configSchema,\n pluginManager,\n }),\n )\n}\n", "import PluginManager from '@jbrowse/core/PluginManager'\nimport { AdapterType } from '@jbrowse/core/pluggableElementTypes'\nimport configSchema from './configSchema'\nimport MafTabixAdapter from './MafTabixAdapter'\n\nexport default function MafTabixAdapterF(pluginManager: PluginManager) {\n return pluginManager.addAdapterType(\n () =>\n new AdapterType({\n name: 'MafTabixAdapter',\n AdapterClass: MafTabixAdapter,\n configSchema,\n }),\n )\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\n/**\n * #config MafTabixAdapter\n * used to configure MafTabix adapter\n */\nfunction x() {} // eslint-disable-line @typescript-eslint/no-unused-vars\n\nconst configSchema = ConfigurationSchema(\n 'MafTabixAdapter',\n {\n /**\n * #slot\n */\n samples: {\n type: 'frozen',\n description: 'string[] or {id:string,label:string,color?:string}[]',\n defaultValue: [],\n },\n /**\n * #slot\n */\n bedGzLocation: {\n type: 'fileLocation',\n defaultValue: {\n uri: '/path/to/my.bed.gz.tbi',\n locationType: 'UriLocation',\n },\n },\n index: ConfigurationSchema('Index', {\n location: {\n type: 'fileLocation',\n defaultValue: {\n uri: '/path/to/my.bed.gz.tbi',\n },\n },\n indexType: {\n type: 'string',\n defaultValue: 'TBI',\n },\n }),\n },\n { explicitlyTyped: true },\n)\n\nexport default configSchema\n", "import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getSnapshot } from 'mobx-state-tree'\nimport { Feature, Region, SimpleFeature } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { firstValueFrom, toArray } from 'rxjs'\n\ninterface OrganismRecord {\n chr: string\n start: number\n srcSize: number\n strand: number\n unknown: number\n data: string\n}\n\nexport default class MafTabixAdapter extends BaseFeatureDataAdapter {\n public setupP?: Promise<{ adapter: BaseFeatureDataAdapter }>\n\n async setup() {\n const config = this.config\n if (!this.getSubAdapter) {\n throw new Error('no getSubAdapter available')\n }\n const adapter = await this.getSubAdapter({\n ...getSnapshot(config),\n type: 'BedTabixAdapter',\n })\n return {\n adapter: adapter.dataAdapter as BaseFeatureDataAdapter,\n }\n }\n async setupPre() {\n if (!this.setupP) {\n this.setupP = this.setup().catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n\n async getRefNames() {\n const { adapter } = await this.setup()\n return adapter.getRefNames()\n }\n\n async getHeader() {\n const { adapter } = await this.setup()\n return adapter.getHeader()\n }\n\n getFeatures(query: Region) {\n return ObservableCreate<Feature>(async observer => {\n const { adapter } = await this.setup()\n const features = await firstValueFrom(\n adapter.getFeatures(query).pipe(toArray()),\n )\n const samples = this.getConf('samples') as string[] | { id: string }[]\n const sampleStrings =\n typeof samples[0] === 'string'\n ? (samples as string[])\n : (samples as { id: string }[]).map(s => s.id)\n const sampleSet = new Set(sampleStrings)\n let i = 0\n for (const feature of features) {\n const data = (feature.get('field5') as string).split(',')\n const alignments = {} as Record<string, OrganismRecord>\n const alns = data.map(elt => elt.split(':')[5])\n\n for (const [j, elt] of data.entries()) {\n const ad = elt.split(':')\n const idx = ad[0].lastIndexOf('.')\n const org = ad[0].slice(0, idx)\n const last = ad[0].slice(idx + 1)\n const s = sampleSet.has(org)\n ? org\n : sampleStrings.find(f => ad[0].startsWith(f))\n if (s) {\n alignments[s] = {\n chr: last,\n start: +ad[1],\n srcSize: +ad[2],\n strand: ad[3] === '-' ? -1 : 1,\n unknown: +ad[4],\n data: alns[j],\n }\n } else if (i < 100) {\n console.error(`line not processed ${ad[0]}`)\n i++\n } else if (i > 100) {\n console.error('too many errors, not printing any more')\n }\n }\n\n observer.next(\n new SimpleFeature({\n id: feature.id(),\n data: {\n start: feature.get('start'),\n end: feature.get('end'),\n refName: feature.get('refName'),\n name: feature.get('name'),\n score: feature.get('score'),\n alignments,\n seq: alns[0],\n },\n }),\n )\n }\n observer.complete()\n })\n }\n freeResources(): void {}\n}\n", "import PluginManager from '@jbrowse/core/PluginManager'\nimport { AdapterType } from '@jbrowse/core/pluggableElementTypes'\nimport configSchema from './configSchema'\nimport TaffyAdapter from './TaffyAdapter'\n\nexport default function TaffyAdapterF(pluginManager: PluginManager) {\n return pluginManager.addAdapterType(\n () =>\n new AdapterType({\n name: 'TaffyAdapter',\n AdapterClass: TaffyAdapter,\n configSchema,\n }),\n )\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\n/**\n * #config TaffyAdapter\n * used to configure Taffy adapter\n */\nfunction x() {} // eslint-disable-line @typescript-eslint/no-unused-vars\n\nconst configSchema = ConfigurationSchema(\n 'TaffyAdapter',\n {\n /**\n * #slot\n */\n samples: {\n type: 'frozen',\n description: 'string[] or {id:string,label:string,color?:string}[]',\n defaultValue: [],\n },\n /**\n * #slot\n */\n tafLocation: {\n type: 'fileLocation',\n defaultValue: {\n uri: '/path/to/my.taf',\n locationType: 'UriLocation',\n },\n },\n /**\n * #slot\n */\n taiLocation: {\n type: 'fileLocation',\n defaultValue: {\n uri: '/path/to/my.taf.tai',\n locationType: 'UriLocation',\n },\n },\n },\n { explicitlyTyped: true },\n)\n\nexport default configSchema\n", "import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getSnapshot } from 'mobx-state-tree'\nimport { Feature, Region, SimpleFeature } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { openLocation } from '@jbrowse/core/util/io'\n\ninterface OrganismRecord {\n chr: string\n start: number\n srcSize: number\n strand: number\n unknown: number\n data: string\n}\n\ninterface ByteRange {\n chrStart: number\n fileOffst: number\n}\ntype IndexData = Record<string, ByteRange[]>\n\nexport default class TaffyAdapter extends BaseFeatureDataAdapter {\n public setupP?: Promise<IndexData>\n\n async getRefNames() {\n const data = await this.setup()\n return Object.keys(data)\n }\n\n setup() {\n if (!this.setupP) {\n this.setupP = this.readTaiFile().catch((e: unknown) => {\n this.setupP = undefined\n throw e\n })\n }\n return this.setupP\n }\n\n async readTaiFile() {\n const text = await openLocation(this.getConf('taiLocation')).readFile(\n 'utf8',\n )\n const entries = {} as IndexData\n let lastChr = ''\n for (const line of text.split('\\n').filter(line => line.trim())) {\n const [chr, chrStart, fileOffset] = line.split('\\t')\n const ref = chr === '*' ? lastChr : chr\n const r2 = ref.split('.').at(-1)!\n\n if (!entries[r2]) {\n entries[r2] = []\n }\n entries[r2].push({\n chrStart: +chrStart,\n fileOffst: +fileOffset,\n })\n lastChr = ref\n }\n return entries\n }\n\n getFeatures(query: Region) {\n return ObservableCreate<Feature>(async observer => {\n try {\n // const { tafLocation } = getSnapshot(this.config)\n // const byteRanges = await this.setup()\n //\n // for (const range of byteRanges[query.refName] || []) {\n // const response = await fetch(tafLocation, {\n // headers: {\n // Range: `bytes=${range.start}-${range.start + range.length - 1}`,\n // },\n // })\n //\n // const text = await response.text()\n // const lines = text.split('\\n').filter(line => line.trim())\n //\n // for (const line of lines) {\n // const [chr, start, srcSize, strand, unknown, data] =\n // line.split('\\t')\n //\n // // Only emit features that overlap with query region\n // const featureStart = parseInt(start, 10)\n // const featureEnd = featureStart + parseInt(srcSize, 10)\n //\n // if (\n // chr === query.refName &&\n // featureEnd >= query.start &&\n // featureStart <= query.end\n // ) {\n // observer.next(\n // new SimpleFeature({\n // uniqueId: `${chr}-${start}-${data}`,\n // refName: chr,\n // start: featureStart,\n // end: featureEnd,\n // strand: parseInt(strand, 10),\n // data: data,\n // }),\n // )\n // }\n // }\n // }\n observer.complete()\n } catch (e) {\n observer.error(e)\n }\n })\n }\n freeResources(): void {}\n}\n", "import PluginManager from '@jbrowse/core/PluginManager'\nimport { AddTrackWorkflowType } from '@jbrowse/core/pluggableElementTypes'\nimport { types } from 'mobx-state-tree'\n\n// locals\nimport MultiMAFWidget from './AddTrackWorkflow'\n\nexport default function MafAddTrackWorkflowF(pluginManager: PluginManager) {\n pluginManager.addAddTrackWorkflowType(\n () =>\n new AddTrackWorkflowType({\n name: 'MAF track',\n ReactComponent: MultiMAFWidget,\n stateModel: types.model({}),\n }),\n )\n}\n", "import React, { useState } from 'react'\nimport {\n Button,\n FormControl,\n FormControlLabel,\n FormLabel,\n Paper,\n Radio,\n RadioGroup,\n TextField,\n} from '@mui/material'\nimport { makeStyles } from 'tss-react/mui'\nimport {\n FileLocation,\n getSession,\n isSessionModelWithWidgets,\n isSessionWithAddTracks,\n} from '@jbrowse/core/util'\nimport { AddTrackModel } from '@jbrowse/plugin-data-management'\nimport { ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport { getRoot } from 'mobx-state-tree'\n\nconst useStyles = makeStyles()(theme => ({\n textbox: {\n width: '100%',\n },\n paper: {\n margin: theme.spacing(),\n padding: theme.spacing(),\n },\n submit: {\n marginTop: 25,\n marginBottom: 100,\n display: 'block',\n },\n}))\n\nexport default function MultiMAFWidget({ model }: { model: AddTrackModel }) {\n const { classes } = useStyles()\n const [samples, setSamples] = useState('')\n const [loc, setLoc] = useState<FileLocation>()\n const [indexLoc, setIndexLoc] = useState<FileLocation>()\n const [error, setError] = useState<unknown>()\n const [trackName, setTrackName] = useState('MAF track')\n const [fileTypeChoice, setFileTypeChoice] = useState('BigMafAdapter')\n const [indexTypeChoice, setIndexTypeChoice] = useState('TBI')\n\n const rootModel = getRoot<any>(model)\n return (\n <Paper className={classes.paper}>\n <Paper>\n {error ? <ErrorMessage error={error} /> : null}\n <FormControl>\n <FormLabel>File type</FormLabel>\n <RadioGroup\n value={fileTypeChoice}\n onChange={event => {\n setFileTypeChoice(event.target.value)\n }}\n >\n <FormControlLabel\n value=\"BigMafAdapter\"\n control={<Radio />}\n checked={fileTypeChoice === 'BigMafAdapter'}\n label=\"bigMaf\"\n />\n <FormControlLabel\n value=\"MafTabixAdapter\"\n control={<Radio />}\n checked={fileTypeChoice === 'MafTabixAdapter'}\n label=\"mafTabix\"\n />\n </RadioGroup>\n </FormControl>\n {fileTypeChoice === 'BigMafAdapter' ? (\n <FileSelector\n location={loc}\n name=\"Path to bigMaf\"\n rootModel={rootModel}\n setLocation={arg => {\n setLoc(arg)\n }}\n />\n ) : (\n <>\n <FormControl>\n <FormLabel>Index type</FormLabel>\n <RadioGroup\n value={fileTypeChoice}\n onChange={event => {\n setIndexTypeChoice(event.target.value)\n }}\n >\n <FormControlLabel\n value=\"TBI\"\n control={<Radio />}\n checked={indexTypeChoice === 'TBI'}\n label=\"TBI\"\n />\n <FormControlLabel\n value=\"CSI\"\n control={<Radio />}\n checked={indexTypeChoice === 'CSI'}\n label=\"CSI\"\n />\n </RadioGroup>\n </FormControl>\n <FileSelector\n location={loc}\n name=\"Path to MAF tabix\"\n setLocation={arg => {\n setLoc(arg)\n }}\n rootModel={rootModel}\n />\n <FileSelector\n location={indexLoc}\n name=\"Path to MAF tabix index\"\n setLocation={arg => {\n setIndexLoc(arg)\n }}\n rootModel={rootModel}\n />\n </>\n )}\n </Paper>\n <TextField\n multiline\n rows={10}\n value={samples}\n onChange={event => {\n setSamples(event.target.value)\n }}\n placeholder={\n 'Enter sample names from the MAF file, one per line, or JSON formatted array of samples'\n }\n variant=\"outlined\"\n fullWidth\n />\n\n <TextField\n value={trackName}\n helperText=\"Track name\"\n onChange={event => {\n setTrackName(event.target.value)\n }}\n />\n <Button\n variant=\"contained\"\n className={classes.submit}\n onClick={() => {\n try {\n const session = getSession(model)\n let sampleNames = [] as string[]\n try {\n sampleNames = JSON.parse(samples)\n } catch (e) {\n sampleNames = samples.split(/\\n|\\r\\n|\\r/)\n }\n\n const trackId = [\n `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,\n session.adminMode ? '' : '-sessionTrack',\n ].join('')\n\n if (isSessionWithAddTracks(session)) {\n session.addTrackConf({\n trackId,\n type: 'MafTrack',\n name: trackName,\n assemblyNames: [model.assembly],\n adapter:\n fileTypeChoice === 'BigMafAdapter'\n ? {\n type: fileTypeChoice,\n bigBedLocation: loc,\n samples: sampleNames,\n }\n : {\n type: fileTypeChoice,\n bedGzLocation: loc,\n index: {\n indexType: indexTypeChoice,\n location: indexLoc,\n },\n samples: sampleNames,\n },\n })\n\n model.view?.showTrack(trackId)\n }\n model.clearData()\n if (isSessionModelWithWidgets(session)) {\n session.hideWidget(model)\n }\n } catch (e) {\n setError(e)\n }\n }}\n >\n Submit\n </Button>\n </Paper>\n )\n}\n"],
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6
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+
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"configSchema_default", "import_BaseAdapter", "import_rxjs", "import_io", "TaffyAdapter", "data", "e", "text", "entries", "lastChr", "line", "chr", "chrStart", "fileOffset", "ref", "r2", "query", "observer", "TaffyAdapterF", "pluginManager", "TaffyAdapter", "configSchema_default", "import_pluggableElementTypes", "import_mobx_state_tree", "import_react", "import_material", "import_mui", "import_util", "import_ui", "import_mobx_state_tree", "useStyles", "theme", "MultiMAFWidget", "model", "classes", "samples", "setSamples", "loc", "setLoc", "indexLoc", "setIndexLoc", "error", "setError", "trackName", "setTrackName", "fileTypeChoice", "setFileTypeChoice", "indexTypeChoice", "setIndexTypeChoice", "rootModel", "React", "event", "arg", "session", "sampleNames", "trackId", "e", "MafAddTrackWorkflowF", "pluginManager", "MultiMAFWidget", "MafViewerPlugin", "Plugin", "version", "pluginManager", "BigMafAdapterF", "MafTrackF", "LinearMafDisplayF", "LinearMafRendererF", "MafTabixAdapterF", "TaffyAdapterF", "MafAddTrackWorkflowF", "_pluginManager"]
|
|
7
|
+
}
|