@jbrowse/plugin-sequence 2.0.0 → 2.1.2

package/dist/GCContentAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/GCContentAdapter/configSchema.ts"],"names":[],"mappings":";;AACA,6DAAiE;AAEjE,mBAAe,UAAC,aAA4B;IAC1C,OAAO,IAAA,mCAAmB,EACxB,kBAAkB,EAClB;QACE,eAAe,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;KACpE,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACH,CAAC,EAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/GCContentAdapter/configSchema.ts"],"names":[],"mappings":";;AACA,+DAAiE;AAEjE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,OAAO,IAAA,mCAAmB,EACxB,kBAAkB,EAClB;QACE,eAAe,EAAE,aAAa,CAAC,yBAAyB,CAAC,SAAS,CAAC;KACpE,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACH,CAAC,CAAA"}

package/dist/GCContentAdapter/index.d.ts

@@ -1,6 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => {
-    configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    getAdapterClass: () => Promise<typeof import("./GCContentAdapter").default>;
-};
+declare const _default: (pluginManager: PluginManager) => void;
 export default _default;

package/dist/GCContentAdapter/index.js

@@ -26,11 +26,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (function (pluginManager) {
-    return {
-        configSchema: pluginManager.load(configSchema_1.default),
-        getAdapterClass: function () { return Promise.resolve().then(function () { return __importStar(require('./GCContentAdapter')); }).then(function (r) { return r.default; }); },
-    };
-});
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'GCContentAdapter',
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        configSchema: (0, configSchema_1.default)(pluginManager),
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./GCContentAdapter'))).then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/GCContentAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GCContentAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,gEAA0C;AAE1C,mBAAe,UAAC,aAA4B;IAC1C,OAAO;QACL,YAAY,EAAE,aAAa,CAAC,IAAI,CAAC,sBAAa,CAAC;QAC/C,eAAe,EAAE,cAAM,OAAA,iEAAO,oBAAoB,OAAE,IAAI,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,OAAO,EAAT,CAAS,CAAC,EAAjD,CAAiD;KACzE,CAAA;AACH,CAAC,EAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GCContentAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAA0C;AAE1C,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,kBAAkB;QACxB,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,YAAY,EAAE,IAAA,sBAAa,EAAC,aAAa,CAAC;QAC1C,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,oBAAoB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -1,190 +1,96 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            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;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var indexedfasta_1 = require("@gmod/indexedfasta");
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var io_1 = require("@jbrowse/core/util/io");
-var rxjs_1 = require("@jbrowse/core/util/rxjs");
-var util_1 = require("@jbrowse/core/util");
-var abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
-var QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
-var default_1 = /** @class */ (function (_super) {
-    __extends(default_1, _super);
-    function default_1(config, getSubAdapter, pluginManager) {
-        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
-        _this.seqCache = new abortable_promise_cache_1.default({
+const indexedfasta_1 = require("@gmod/indexedfasta");
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const io_1 = require("@jbrowse/core/util/io");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const util_1 = require("@jbrowse/core/util");
+const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
+const QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
+class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        this.seqCache = new abortable_promise_cache_1.default({
             cache: new QuickLRU_1.default({ maxSize: 200 }),
-            fill: function (args, signal) { return __awaiter(_this, void 0, void 0, function () {
-                var refName, start, end;
-                return __generator(this, function (_a) {
-                    refName = args.refName, start = args.start, end = args.end;
-                    return [2 /*return*/, this.fasta.getSequence(refName, start, end, __assign(__assign({}, args), { signal: signal }))];
-                });
-            }); },
+            fill: async (args, signal) => {
+                const { refName, start, end } = args;
+                return this.fasta.getSequence(refName, start, end, { ...args, signal });
+            },
         });
-        var fastaLocation = _this.getConf('fastaLocation');
-        var faiLocation = _this.getConf('faiLocation');
-        var fastaOpts = {
-            fasta: (0, io_1.openLocation)(fastaLocation, _this.pluginManager),
-            fai: (0, io_1.openLocation)(faiLocation, _this.pluginManager),
+        const fastaLocation = this.getConf('fastaLocation');
+        const faiLocation = this.getConf('faiLocation');
+        const fastaOpts = {
+            fasta: (0, io_1.openLocation)(fastaLocation, this.pluginManager),
+            fai: (0, io_1.openLocation)(faiLocation, this.pluginManager),
         };
-        _this.fasta = new indexedfasta_1.IndexedFasta(fastaOpts);
-        return _this;
+        this.fasta = new indexedfasta_1.IndexedFasta(fastaOpts);
     }
-    default_1.prototype.getRefNames = function (opts) {
+    getRefNames(opts) {
         return this.fasta.getSequenceNames(opts);
-    };
-    default_1.prototype.getRegions = function (opts) {
-        return __awaiter(this, void 0, void 0, function () {
-            var seqSizes;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.fasta.getSequenceSizes(opts)];
-                    case 1:
-                        seqSizes = _a.sent();
-                        return [2 /*return*/, Object.keys(seqSizes).map(function (refName) { return ({
-                                refName: refName,
-                                start: 0,
-                                end: seqSizes[refName],
-                            }); })];
-                }
-            });
+    }
+    async getRegions(opts) {
+        const seqSizes = await this.fasta.getSequenceSizes(opts);
+        return Object.keys(seqSizes).map(refName => ({
+            refName,
+            start: 0,
+            end: seqSizes[refName],
+        }));
+    }
+    async getHeader() {
+        if (this.header) {
+            return this.header;
+        }
+        const loc = this.getConf('metadataLocation');
+        if (loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml') {
+            return null;
+        }
+        this.header = (0, io_1.openLocation)(loc)
+            .readFile('utf8')
+            .catch(e => {
+            this.header = undefined;
+            throw e;
         });
-    };
-    default_1.prototype.getHeader = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var loc;
-            var _this = this;
-            return __generator(this, function (_a) {
-                if (this.header) {
-                    return [2 /*return*/, this.header];
-                }
-                loc = this.getConf('metadataLocation');
-                if (loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml') {
-                    return [2 /*return*/, null];
-                }
-                this.header = (0, io_1.openLocation)(loc)
-                    .readFile('utf8')
-                    .catch(function (e) {
-                    _this.header = undefined;
-                    throw e;
-                });
-                return [2 /*return*/, this.header];
-            });
+        return this.header;
+    }
+    getFeatures(region, opts) {
+        const { refName, start, end } = region;
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const size = await this.fasta.getSequenceSize(refName, opts);
+            const regionEnd = size !== undefined ? Math.min(size, end) : end;
+            const chunks = [];
+            const chunkSize = 128000;
+            const s = start - (start % chunkSize);
+            const e = end + (chunkSize - (end % chunkSize));
+            for (let chunkStart = s; chunkStart < e; chunkStart += chunkSize) {
+                const r = {
+                    refName,
+                    start: chunkStart,
+                    end: chunkStart + chunkSize,
+                };
+                chunks.push(this.seqCache.get(JSON.stringify(r), r, opts === null || opts === void 0 ? void 0 : opts.signal));
+            }
+            const seq = (await Promise.all(chunks))
+                .join('')
+                .slice(start - s)
+                .slice(0, end - start);
+            if (seq) {
+                observer.next(new util_1.SimpleFeature({
+                    id: `${refName} ${start}-${regionEnd}`,
+                    data: { refName, start, end: regionEnd, seq },
+                }));
+            }
+            observer.complete();
         });
-    };
-    default_1.prototype.getFeatures = function (region, opts) {
-        var _this = this;
-        var refName = region.refName, start = region.start, end = region.end;
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var size, regionEnd, chunks, chunkSize, s, e, chunkStart, r, seq;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.fasta.getSequenceSize(refName, opts)];
-                    case 1:
-                        size = _a.sent();
-                        regionEnd = size !== undefined ? Math.min(size, end) : end;
-                        chunks = [];
-                        chunkSize = 128000;
-                        s = start - (start % chunkSize);
-                        e = end + (chunkSize - (end % chunkSize));
-                        for (chunkStart = s; chunkStart < e; chunkStart += chunkSize) {
-                            r = {
-                                refName: refName,
-                                start: chunkStart,
-                                end: chunkStart + chunkSize,
-                            };
-                            chunks.push(this.seqCache.get(JSON.stringify(r), r, opts === null || opts === void 0 ? void 0 : opts.signal));
-                        }
-                        return [4 /*yield*/, Promise.all(chunks)];
-                    case 2:
-                        seq = (_a.sent())
-                            .join('')
-                            .slice(start - s)
-                            .slice(0, end - start);
-                        if (seq) {
-                            observer.next(new util_1.SimpleFeature({
-                                id: "".concat(refName, " ").concat(start, "-").concat(regionEnd),
-                                data: { refName: refName, start: start, end: regionEnd, seq: seq },
-                            }));
-                        }
-                        observer.complete();
-                        return [2 /*return*/];
-                }
-            });
-        }); });
-    };
+    }
     /**
      * called to provide a hint that data tied to a certain region
      * will not be needed for the forseeable future and can be purged
      * from caches, etc
      */
-    default_1.prototype.freeResources = function ( /* { region } */) { };
-    return default_1;
-}(BaseAdapter_1.BaseSequenceAdapter));
+    freeResources( /* { region } */) { }
+}
 exports.default = default_1;
 //# sourceMappingURL=IndexedFastaAdapter.js.map

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js.map

@@ -1 +1 @@
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package/dist/IndexedFastaAdapter/configSchema.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
+const configuration_1 = require("@jbrowse/core/configuration");
 exports.default = (0, configuration_1.ConfigurationSchema)('IndexedFastaAdapter', {
     fastaLocation: {
         type: 'fileLocation',

package/dist/IndexedFastaAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,qBAAqB,EACrB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,iBAAiB,EAAE,YAAY,EAAE,aAAa,EAAE;KACtE;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,qBAAqB,EAAE,YAAY,EAAE,aAAa,EAAE;KAC1E;IACD,gBAAgB,EAAE;QAChB,WAAW,EAAE,wBAAwB;QACrC,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,2BAA2B;YAChC,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/IndexedFastaAdapter/index.d.ts

@@ -1 +1,3 @@
-export { default as configSchema } from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/IndexedFastaAdapter/index.js

@@ -1,9 +1,44 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = void 0;
-var configSchema_1 = require("./configSchema");
-Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+exports.default = (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'IndexedFastaAdapter',
+        configSchema: configSchema_1.default,
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./IndexedFastaAdapter'))).then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/IndexedFastaAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,kGAAyE;AAEzE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,qBAAW,CAAC;QACd,IAAI,EAAE,qBAAqB;QAC3B,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE;YACf,QAAQ,EAAE,IAAI;YACd,aAAa,EAAE,IAAI;YACnB,WAAW,EAAE,IAAI;YACjB,WAAW,EAAE,IAAI;SAClB;QACD,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,uBAAuB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACvD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/LinearReferenceSequenceDisplay/configSchema.js

@@ -1,7 +1,10 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.configSchema = void 0;
-var configuration_1 = require("@jbrowse/core/configuration");
-var DivSequenceRenderer_1 = require("../DivSequenceRenderer");
-exports.configSchema = (0, configuration_1.ConfigurationSchema)('LinearReferenceSequenceDisplay', { renderer: DivSequenceRenderer_1.configSchema }, { explicitIdentifier: 'displayId', explicitlyTyped: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const configSchema_1 = __importDefault(require("../DivSequenceRenderer/configSchema"));
+exports.configSchema = (0, configuration_1.ConfigurationSchema)('LinearReferenceSequenceDisplay', { renderer: configSchema_1.default }, { explicitIdentifier: 'displayId', explicitlyTyped: true });
 //# sourceMappingURL=configSchema.js.map

package/dist/LinearReferenceSequenceDisplay/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/configSchema.ts"],"names":[],"mappings":";;;AAAA,6DAAiE;AACjE,8DAAwF;AAE3E,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAC7C,gCAAgC,EAChC,EAAE,QAAQ,EAAE,kCAA+B,EAAE,EAC7C,EAAE,kBAAkB,EAAE,WAAW,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/configSchema.ts"],"names":[],"mappings":";;;;;;AAAA,+DAAiE;AACjE,uFAAgG;AAEnF,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAC7C,gCAAgC,EAChC,EAAE,QAAQ,EAAE,sBAA+B,EAAE,EAC7C,EAAE,kBAAkB,EAAE,WAAW,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA"}

package/dist/LinearReferenceSequenceDisplay/index.d.ts

@@ -1,2 +1,3 @@
-export { configSchema } from './configSchema';
-export { modelFactory } from './model';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/LinearReferenceSequenceDisplay/index.js

@@ -1,8 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.modelFactory = exports.configSchema = void 0;
-var configSchema_1 = require("./configSchema");
-Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return configSchema_1.configSchema; } });
-var model_1 = require("./model");
-Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return model_1.modelFactory; } });
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const configSchema_1 = require("./configSchema");
+const model_1 = require("./model");
+exports.default = (pluginManager) => {
+    pluginManager.addDisplayType(() => {
+        const stateModel = (0, model_1.modelFactory)(configSchema_1.configSchema);
+        return {
+            name: 'LinearReferenceSequenceDisplay',
+            configSchema: configSchema_1.configSchema,
+            stateModel,
+            trackType: 'ReferenceSequenceTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
+        };
+    });
+};
 //# sourceMappingURL=index.js.map

package/dist/LinearReferenceSequenceDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/index.ts"],"names":[],"mappings":";;;AAAA,+CAA6C;AAApC,4GAAA,YAAY,OAAA;AACrB,iCAAsC;AAA7B,qGAAA,YAAY,OAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/index.ts"],"names":[],"mappings":";;AACA,kFAA+E;AAE/E,iDAA6C;AAC7C,mCAAsC;AAEtC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,UAAU,GAAG,IAAA,oBAAY,EAAC,2BAAY,CAAC,CAAA;QAC7C,OAAO;YACL,IAAI,EAAE,gCAAgC;YACtC,YAAY,EAAZ,2BAAY;YACZ,UAAU;YACV,SAAS,EAAE,wBAAwB;YACnC,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,sDAA0B;SAC3C,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}

package/dist/LinearReferenceSequenceDisplay/model.d.ts

@@ -182,7 +182,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
     }): Promise<JSX.Element>;
 } & {

package/dist/LinearReferenceSequenceDisplay/model.js

@@ -1,21 +1,10 @@
 "use strict";
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.modelFactory = void 0;
-var mobx_state_tree_1 = require("mobx-state-tree");
-var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-var configuration_1 = require("@jbrowse/core/configuration");
-var util_1 = require("@jbrowse/core/util");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
 function modelFactory(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearReferenceSequenceDisplay', plugin_linear_genome_view_1.BaseLinearDisplay, mobx_state_tree_1.types.model({
@@ -26,15 +15,22 @@ function modelFactory(configSchema) {
         showTranslation: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, true),
         height: 180,
     }))
-        .views(function (self) {
-        var superRenderProps = self.renderProps;
+        .views(self => {
+        const { renderProps: superRenderProps } = self;
         return {
-            renderProps: function () {
-                var showForward = self.showForward, showReverse = self.showReverse, showTranslation = self.showTranslation;
-                return __assign(__assign({}, superRenderProps()), { rpcDriverName: self.rpcDriverName, config: self.configuration.renderer, showForward: showForward, showReverse: showReverse, showTranslation: showTranslation });
+            renderProps() {
+                const { showForward, showReverse, showTranslation } = self;
+                return {
+                    ...superRenderProps(),
+                    rpcDriverName: self.rpcDriverName,
+                    config: self.configuration.renderer,
+                    showForward,
+                    showReverse,
+                    showTranslation,
+                };
             },
-            regionCannotBeRendered: function ( /* region */) {
-                var view = (0, util_1.getContainingView)(self);
+            regionCannotBeRendered( /* region */) {
+                const view = (0, util_1.getContainingView)(self);
                 if (view && view.bpPerPx >= 1) {
                     return 'Zoom in to see sequence';
                 }
@@ -45,25 +41,25 @@ function modelFactory(configSchema) {
             },
         };
     })
-        .actions(function (self) { return ({
-        toggleShowForward: function () {
+        .actions(self => ({
+        toggleShowForward() {
             self.showForward = !self.showForward;
         },
-        toggleShowReverse: function () {
+        toggleShowReverse() {
             self.showReverse = !self.showReverse;
         },
-        toggleShowTranslation: function () {
+        toggleShowTranslation() {
             self.showTranslation = !self.showTranslation;
         },
-    }); })
-        .views(function (self) { return ({
-        trackMenuItems: function () {
+    }))
+        .views(self => ({
+        trackMenuItems() {
             return [
                 {
                     label: 'Show forward',
                     type: 'checkbox',
                     checked: self.showForward,
-                    onClick: function () {
+                    onClick: () => {
                         self.toggleShowForward();
                     },
                 },
@@ -71,7 +67,7 @@ function modelFactory(configSchema) {
                     label: 'Show reverse',
                     type: 'checkbox',
                     checked: self.showReverse,
-                    onClick: function () {
+                    onClick: () => {
                         self.toggleShowReverse();
                     },
                 },
@@ -79,13 +75,13 @@ function modelFactory(configSchema) {
                     label: 'Show translation',
                     type: 'checkbox',
                     checked: self.showTranslation,
-                    onClick: function () {
+                    onClick: () => {
                         self.toggleShowTranslation();
                     },
                 },
             ];
         },
-    }); });
+    }));
 }
 exports.modelFactory = modelFactory;
 //# sourceMappingURL=model.js.map

package/dist/LinearReferenceSequenceDisplay/model.js.map

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