npm - jbrowse-plugin-mafviewer - Versions diffs - 1.0.3 → 1.0.4 - Mend

jbrowse-plugin-mafviewer 1.0.3 → 1.0.4

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.

Files changed (18) hide show

package/CHANGELOG.md +3 -0
package/README.md +183 -0
package/dist/jbrowse-plugin-mafviewer.umd.development.js +78 -78
package/dist/jbrowse-plugin-mafviewer.umd.development.js.map +1 -1
package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +1 -1
package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +1 -1
package/package.json +8 -10
package/src/BigMafAdapter/BigMafAdapter.ts +8 -18
package/src/LinearMafDisplay/components/ColorLegend.tsx +5 -3
package/src/LinearMafDisplay/components/ReactComponent.tsx +4 -1
package/src/LinearMafDisplay/components/SetRowHeight.tsx +2 -2
package/src/LinearMafDisplay/components/YScaleBars.tsx +6 -2
package/src/LinearMafDisplay/renderSvg.tsx +2 -2
package/src/LinearMafDisplay/stateModel.ts +35 -10
package/src/LinearMafRenderer/LinearMafRenderer.ts +33 -28
package/src/LinearMafRenderer/components/ReactComponent.tsx +4 -1
package/src/MafAddTrackWorkflow/AddTrackWorkflow.tsx +1 -0
package/src/MafTabixAdapter/MafTabixAdapter.ts +2 -13

package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"jbrowse-plugin-mafviewer.umd.production.min.js","sources":["../src/BigMafAdapter/configSchema.ts","../node_modules/tslib/tslib.es6.mjs","../node_modules/rxjs/dist/esm5/internal/util/isFunction.js","../node_modules/rxjs/dist/esm5/internal/util/createErrorClass.js","../node_modules/rxjs/dist/esm5/internal/util/UnsubscriptionError.js","../node_modules/rxjs/dist/esm5/internal/util/arrRemove.js","../node_modules/rxjs/dist/esm5/internal/Subscription.js","../node_modules/rxjs/dist/esm5/internal/config.js","../node_modules/rxjs/dist/esm5/internal/scheduler/timeoutProvider.js","../node_modules/rxjs/dist/esm5/internal/util/noop.js","../node_modules/rxjs/dist/esm5/internal/Subscriber.js","../node_modules/rxjs/dist/esm5/internal/util/reportUnhandledError.js","../node_modules/rxjs/dist/esm5/internal/util/lift.js","../node_modules/rxjs/dist/esm5/internal/operators/OperatorSubscriber.js","../node_modules/rxjs/dist/esm5/internal/util/EmptyError.js","../node_modules/rxjs/dist/esm5/internal/firstValueFrom.js","../node_modules/rxjs/dist/esm5/internal/operators/toArray.js","../node_modules/rxjs/dist/esm5/internal/operators/reduce.js","../node_modules/rxjs/dist/esm5/internal/operators/scanInternals.js","../src/BigMafAdapter/BigMafAdapter.ts","../src/LinearMafDisplay/components/SetRowHeight.tsx","../src/LinearMafDisplay/components/RectBg.tsx","../src/LinearMafDisplay/components/ColorLegend.tsx","../src/LinearMafDisplay/components/YScaleBars.tsx","../src/LinearMafDisplay/components/ReactComponent.tsx","../src/LinearMafRenderer/configSchema.ts","../src/LinearMafRenderer/LinearMafRenderer.ts","../src/LinearMafRenderer/components/ReactComponent.tsx","../src/MafTabixAdapter/configSchema.ts","../src/MafTabixAdapter/MafTabixAdapter.ts","../src/MafAddTrackWorkflow/AddTrackWorkflow.tsx","../src/LinearMafDisplay/renderSvg.tsx","../src/index.ts","../src/BigMafAdapter/index.ts","../src/MafTrack/index.ts","../src/MafTrack/configSchema.ts","../src/LinearMafDisplay/index.ts","../src/LinearMafDisplay/configSchema.ts","../src/LinearMafDisplay/stateModel.ts","../src/LinearMafRenderer/index.ts","../src/MafTabixAdapter/index.ts","../src/MafAddTrackWorkflow/index.ts"],"sourcesContent":[null,"/****************************************************************************\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 /\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 ? 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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 = {}, verb(\"next\"), verb(\"throw\"), verb(\"return\"), i[Symbol.asyncIterator] = function () { return this; }, i;\n function verb(n) { if (g[n]) i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 \|\| resume(n, v); }); }; }\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\nexport function __importStar(mod) {\n if (mod && mod.__esModule) return mod;\n var result = {};\n if (mod != null) for (var k in mod) if (k !== \"default\" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);\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;\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 }\n if (typeof dispose !== \"function\") throw new TypeError(\"Object not disposable.\");\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 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 ? 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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 /\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;\n return g = { next: verb(0), \"throw\": verb(1), \"return\": verb(2) }, typeof Symbol === \"function\" && (g[Symbol.iterator] = function() { return this; }), g;\n function verb(n) { return function (v) { return step([n, v]); }; }\n function step(op) {\n if (f) throw new TypeError(\"Generator is already executing.\");\n while (g && (g = 0, op[0] && (_ = 0)), _) try {\n if (f = 1, y && (t = op[0] & 2 ? y[\"return\"] : op[0] ? y[\"throw\"] \|\| ((t = y[\"return\"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;\n if (y = 0, t) op = [op[0] & 2, t.value];\n switch (op[0]) {\n case 0: case 1: t = op; break;\n case 4: _.label++; return { value: op[1], done: false };\n case 5: _.label++; y = op[1]; op = [0]; continue;\n case 7: op = _.ops.pop(); _.trys.pop(); continue;\n default:\n if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 \|\| op[0] === 2)) { _ = 0; continue; }\n if (op[0] === 3 && (!t \|\| (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }\n if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }\n if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }\n if (t[2]) _.ops.pop();\n _.trys.pop(); continue;\n }\n op = body.call(thisArg, _);\n } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }\n if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };\n }\n}\n\nexport var __createBinding = Object.create ? (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 = {}, verb(\"next\"), verb(\"throw\"), verb(\"return\"), i[Symbol.asyncIterator] = function () { return this; }, i;\n function verb(n) { if (g[n]) i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 \|\| resume(n, v); }); }; }\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\nexport function __importStar(mod) {\n if (mod && mod.__esModule) return mod;\n var result = {};\n if (mod != null) for (var k in mod) if (k !== \"default\" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);\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;\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 }\n if (typeof dispose !== \"function\") throw new TypeError(\"Object not disposable.\");\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 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 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package/package.json CHANGED Viewed

@@ -1,5 +1,5 @@
 {
-  "version": "1.0.3",
+  "version": "1.0.4",
   "name": "jbrowse-plugin-mafviewer",
   "keywords": [
     "jbrowse",
@@ -25,16 +25,11 @@
   },
   "scripts": {
     "clean": "rimraf dist",
-    "start": "npm-run-all --sequential clean --parallel start:*",
-    "start:watch": "cross-env JB_NPM=false NODE_ENV=development rollup --config --watch --bundleConfigAsCjs",
-    "start:server": "serve --cors --listen $npm_package_config_port .",
-    "prebuild": "npm-run-all clean",
+    "start": "node esbuild.mjs",
+    "prebuild": "npm run clean",
     "build": "rollup --config --bundleConfigAsCjs",
-    "browse": "npm-run-all jbrowse:*",
-    "jbrowse:configure": "cp jbrowse_config.json .jbrowse/config.json",
-    "jbrowse:serve": "cross-var serve --listen $npm_package_config_browse_port .jbrowse",
     "lint": "eslint --ext .js,.ts,.jsx,.tsx src/",
-    "prepack": "npm-run-all build",
+    "prepack": "npm run build",
     "postversion": "git push --follow-tags"
   },
   "jbrowse-plugin": {
@@ -44,6 +39,7 @@
     "@babel/core": "^7.16.5",
     "@babel/preset-react": "^7.10.4",
     "@emotion/react": "^11.10.4",
+    "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
     "@jbrowse/cli": "^2.6.1",
     "@jbrowse/core": "^2.6.1",
     "@jbrowse/development-tools": "^2.1.1",
@@ -62,6 +58,7 @@
     "cross-env": "^7.0.3",
     "cross-var": "^1.1.0",
     "cypress": "^13.3.2",
+    "esbuild": "^0.19.5",
     "eslint": "^8.36.0",
     "eslint-config-prettier": "^9.0.0",
     "eslint-config-react-app": "^7.0.1",
@@ -71,10 +68,11 @@
     "eslint-plugin-prettier": "^5.0.1",
     "eslint-plugin-react": "^7.20.3",
     "eslint-plugin-react-hooks": "^4.0.8",
+    "eslint-plugin-react-refresh": "^0.4.3",
+    "eslint-plugin-unicorn": "^48.0.1",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.1",
     "mobx-state-tree": "5.2.0",
-    "npm-run-all": "^4.1.5",
     "prettier": "^3.0.0",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",

package/src/BigMafAdapter/BigMafAdapter.ts CHANGED Viewed

@@ -61,29 +61,19 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
         const alignments = {} as Record<string, OrganismRecord>
         const blocks2 = [] as string[]
         for (const block of blocks) {
-          if (block[0] === 's') {
-            if (!aln) {
-              aln = block.split(/ +/)[6]
-              alns.push(aln)
+          if (block.startsWith('s')) {
+            if (aln) {
+              alns.push(block.split(/ +/)[6])
               blocks2.push(block)
             } else {
-              alns.push(block.split(/ +/)[6])
+              aln = block.split(/ +/)[6]
+              alns.push(aln)
               blocks2.push(block)
             }
           }
         }
-        const alns2 = alns.map(() => '')
-        if (aln) {
-          for (let i = 0; i < aln?.length; i++) {
-            if (aln[i] !== '-') {
-              for (let j = 0; j < alns.length; j++) {
-                alns2[j] += alns[j][i]
-              }
-            }
-          }
-        }
+        // eslint-disable-next-line unicorn/no-for-loop
         for (let i = 0; i < blocks2.length; i++) {
           const elt = blocks2[i]
           const ad = elt.split(/ +/)
@@ -97,7 +87,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
             srcSize: +ad[2],
             strand: ad[3] === '+' ? 1 : -1,
             unknown: +ad[4],
-            data: alns2[i],
+            data: alns[i],
           }
         }
         observer.next(
@@ -107,7 +97,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
               start: feature.get('start'),
               end: feature.get('end'),
               refName: feature.get('refName'),
-              seq: alns2[0],
+              seq: alns[0],
               alignments: alignments,
             },
           }),

package/src/LinearMafDisplay/components/ColorLegend.tsx CHANGED Viewed

@@ -8,12 +8,13 @@ import RectBg from './RectBg'
 const ColorLegend = observer(function ({
   model,
   labelWidth,
+  svgFontSize,
 }: {
   model: LinearMafDisplayModel
+  svgFontSize: number
   labelWidth: number
 }) {
   const { samples, rowHeight } = model
-  const svgFontSize = Math.min(rowHeight, 10)
   const canDisplayLabel = rowHeight >= 10
   const boxHeight = Math.min(20, rowHeight)
@@ -22,7 +23,7 @@ const ColorLegend = observer(function ({
       {samples.map((sample, idx) => (
         <RectBg
           key={`${sample.id}-${idx}`}
-          y={idx * rowHeight + 1}
+          y={idx * rowHeight}
           x={0}
           width={labelWidth + 5}
           height={boxHeight}
@@ -33,7 +34,8 @@ const ColorLegend = observer(function ({
         ? samples.map((sample, idx) => (
             <text
               key={`${sample.id}-${idx}`}
-              y={idx * rowHeight + 14}
+              y={idx * rowHeight + rowHeight / 2}
+              dominantBaseline="middle"
               x={2}
               fontSize={svgFontSize}
             >

package/src/LinearMafDisplay/components/ReactComponent.tsx CHANGED Viewed

@@ -2,8 +2,11 @@ import React from 'react'
 import { getEnv } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 import YScaleBars from './YScaleBars'
+import { LinearMafDisplayModel } from '../stateModel'
-const LinearMafDisplay = observer(function (props: any) {
+const LinearMafDisplay = observer(function (props: {
+  model: LinearMafDisplayModel
+}) {
   const { model } = props
   const { pluginManager } = getEnv(model)

package/src/LinearMafDisplay/components/SetRowHeight.tsx CHANGED Viewed

@@ -20,8 +20,8 @@ const SetRowHeightDialog = observer(function (props: {
   model: {
     rowHeight?: number
     rowProportion?: number
-    setRowHeight: Function
-    setRowProportion: Function
+    setRowHeight: (arg: number) => void
+    setRowProportion: (arg: number) => void
   }
   handleClose: () => void
 }) {

package/src/LinearMafDisplay/components/YScaleBars.tsx CHANGED Viewed

@@ -43,7 +43,7 @@ export const YScaleBars = observer(function (props: {
 }) {
   const { model } = props
   const { rowHeight, samples } = model
-  const svgFontSize = Math.min(rowHeight, 12)
+  const svgFontSize = Math.min(Math.max(rowHeight, 10), 14)
   const canDisplayLabel = rowHeight >= 10
   const minWidth = 20
@@ -55,7 +55,11 @@ export const YScaleBars = observer(function (props: {
   return (
     <Wrapper {...props}>
-      <ColorLegend model={model} labelWidth={labelWidth} />
+      <ColorLegend
+        model={model}
+        labelWidth={labelWidth}
+        svgFontSize={svgFontSize}
+      />
     </Wrapper>
   )
 })

package/src/LinearMafDisplay/renderSvg.tsx CHANGED Viewed

@@ -14,9 +14,9 @@ export async function renderSvg(
   opts: ExportSvgDisplayOptions,
   superRenderSvg: (opts: ExportSvgDisplayOptions) => Promise<React.ReactNode>,
 ) {
-  const { height } = self
+  const { height, id } = self
   const { offsetPx, width } = getContainingView(self) as LinearGenomeViewModel
-  const clipid = `mafclip-${self.id}`
+  const clipid = `mafclip-${id}`
   return (
     <>
       <defs>