@jbrowse/plugin-config 2.0.0 → 2.1.2

package/dist/FromConfigAdapter/FromConfigSequenceAdapter.js

@@ -1,202 +1,71 @@
 "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 __values = (this && this.__values) || function(o) {
-    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
-    if (m) return m.call(o);
-    if (o && typeof o.length === "number") return {
-        next: function () {
-            if (o && i >= o.length) o = void 0;
-            return { value: o && o[i++], done: !o };
-        }
-    };
-    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
-};
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-var rxjs_1 = require("@jbrowse/core/util/rxjs");
-var operators_1 = require("rxjs/operators");
-var FromConfigAdapter_1 = __importDefault(require("./FromConfigAdapter"));
-var FromConfigSequenceAdapter = /** @class */ (function (_super) {
-    __extends(FromConfigSequenceAdapter, _super);
-    function FromConfigSequenceAdapter() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
+const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const operators_1 = require("rxjs/operators");
+const FromConfigAdapter_1 = __importDefault(require("./FromConfigAdapter"));
+class FromConfigSequenceAdapter extends FromConfigAdapter_1.default {
     /**
      * Fetch features for a certain region
      * @param region - Region
      * @returns Observable of Feature objects in the region
      */
-    FromConfigSequenceAdapter.prototype.getFeatures = function (region) {
-        var _this = this;
-        // TODO: restore commented version below once TSDX supports Rollup v2
-        // xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45
-        // return ObservableCreate<Feature>(async observer => {
-        //   const feats = await super.getFeatures(region).pipe(toArray()).toPromise()
-        var superGetFeatures = _super.prototype.getFeatures;
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var feats, feat;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, superGetFeatures
-                            .call(this, region)
-                            .pipe((0, operators_1.toArray)())
-                            .toPromise()];
-                    case 1:
-                        feats = _a.sent();
-                        feat = feats[0];
-                        observer.next(new simpleFeature_1.default(__assign(__assign({}, feat.toJSON()), { uniqueId: "".concat(feat.id(), ":").concat(region.start, "-").concat(region.end), end: region.end, start: region.start, seq: feat
-                                .get('seq')
-                                .slice(Math.max(region.start - feat.get('start'), 0), Math.max(region.end - feat.get('start'), 0)) })));
-                        observer.complete();
-                        return [2 /*return*/];
-                }
-            });
-        }); });
-    };
+    getFeatures(region) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const feats = await super.getFeatures(region).pipe((0, operators_1.toArray)()).toPromise();
+            const feat = feats[0];
+            observer.next(new simpleFeature_1.default({
+                ...feat.toJSON(),
+                uniqueId: `${feat.id()}:${region.start}-${region.end}`,
+                end: region.end,
+                start: region.start,
+                seq: feat
+                    .get('seq')
+                    .slice(Math.max(region.start - feat.get('start'), 0), Math.max(region.end - feat.get('start'), 0)),
+            }));
+            observer.complete();
+        });
+    }
     /**
      * Get refName, start, and end for all features after collapsing any overlaps
      */
-    FromConfigSequenceAdapter.prototype.getRegions = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var regions, _a, _b, _c, refName, features, currentRegion, features_1, features_1_1, feature;
-            var e_1, _d, e_2, _e;
-            return __generator(this, function (_f) {
-                regions = [];
-                try {
-                    // recall: features are stored in this object sorted by start coordinate
-                    for (_a = __values(this.features), _b = _a.next(); !_b.done; _b = _a.next()) {
-                        _c = __read(_b.value, 2), refName = _c[0], features = _c[1];
-                        currentRegion = void 0;
-                        try {
-                            for (features_1 = (e_2 = void 0, __values(features)), features_1_1 = features_1.next(); !features_1_1.done; features_1_1 = features_1.next()) {
-                                feature = features_1_1.value;
-                                if (currentRegion &&
-                                    currentRegion.end >= feature.get('start') &&
-                                    currentRegion.start <= feature.get('end')) {
-                                    currentRegion.end = feature.get('end');
-                                }
-                                else {
-                                    if (currentRegion) {
-                                        regions.push(currentRegion);
-                                    }
-                                    currentRegion = {
-                                        refName: refName,
-                                        start: feature.get('start'),
-                                        end: feature.get('end'),
-                                    };
-                                }
-                            }
-                        }
-                        catch (e_2_1) { e_2 = { error: e_2_1 }; }
-                        finally {
-                            try {
-                                if (features_1_1 && !features_1_1.done && (_e = features_1.return)) _e.call(features_1);
-                            }
-                            finally { if (e_2) throw e_2.error; }
-                        }
-                        if (currentRegion) {
-                            regions.push(currentRegion);
-                        }
-                    }
+    async getRegions() {
+        const regions = [];
+        // recall: features are stored in this object sorted by start coordinate
+        for (const [refName, features] of this.features) {
+            let currentRegion;
+            for (const feature of features) {
+                if (currentRegion &&
+                    currentRegion.end >= feature.get('start') &&
+                    currentRegion.start <= feature.get('end')) {
+                    currentRegion.end = feature.get('end');
                 }
-                catch (e_1_1) { e_1 = { error: e_1_1 }; }
-                finally {
-                    try {
-                        if (_b && !_b.done && (_d = _a.return)) _d.call(_a);
+                else {
+                    if (currentRegion) {
+                        regions.push(currentRegion);
                     }
-                    finally { if (e_1) throw e_1.error; }
+                    currentRegion = {
+                        refName,
+                        start: feature.get('start'),
+                        end: feature.get('end'),
+                    };
                 }
-                return [2 /*return*/, regions];
-            });
-        });
-    };
+            }
+            if (currentRegion) {
+                regions.push(currentRegion);
+            }
+        }
+        return regions;
+    }
     /**
      * 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
      */
-    FromConfigSequenceAdapter.prototype.freeResources = function ( /* { region } */) { };
-    return FromConfigSequenceAdapter;
-}(FromConfigAdapter_1.default));
+    freeResources( /* { region } */) { }
+}
 exports.default = FromConfigSequenceAdapter;
 //# sourceMappingURL=FromConfigSequenceAdapter.js.map

package/dist/FromConfigAdapter/FromConfigSequenceAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"FromConfigSequenceAdapter.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/FromConfigSequenceAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,mFAAyE;AACzE,gDAA0D;AAE1D,4CAAwC;AACxC,0EAAmD;AAEnD;IAAuD,6CAAiB;IAAxE;;IA8EA,CAAC;IA7EC;;;;OAIG;IACH,+CAAW,GAAX,UAAY,MAAwB;QAApC,iBA6BC;QA5BC,qEAAqE;QACrE,+EAA+E;QAC/E,uDAAuD;QACvD,8EAA8E;QAC9E,IAAM,gBAAgB,GAAG,iBAAM,WAAW,CAAA;QAC1C,OAAO,IAAA,uBAAgB,EAAU,UAAM,QAAQ;;;;4BAC/B,qBAAM,gBAAgB;6BACjC,IAAI,CAAC,IAAI,EAAE,MAAM,CAAC;6BAClB,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC;6BACf,SAAS,EAAE,EAAA;;wBAHR,KAAK,GAAG,SAGA;wBACR,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;wBACrB,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,uBACZ,IAAI,CAAC,MAAM,EAAE,KAChB,QAAQ,EAAE,UAAG,IAAI,CAAC,EAAE,EAAE,cAAI,MAAM,CAAC,KAAK,cAAI,MAAM,CAAC,GAAG,CAAE,EACtD,GAAG,EAAE,MAAM,CAAC,GAAG,EACf,KAAK,EAAE,MAAM,CAAC,KAAK,EACnB,GAAG,EAAE,IAAI;iCACN,GAAG,CAAC,KAAK,CAAC;iCACV,KAAK,CACJ,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,EAC7C,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAC5C,IACH,CACH,CAAA;wBAED,QAAQ,CAAC,QAAQ,EAAE,CAAA;;;;aACpB,CAAC,CAAA;IACJ,CAAC;IAED;;OAEG;IACG,8CAAU,GAAhB;;;;;gBACQ,OAAO,GAAG,EAAE,CAAA;;oBAElB,wEAAwE;oBACxE,KAAkC,KAAA,SAAA,IAAI,CAAC,QAAQ,CAAA,4CAAE;wBAAtC,KAAA,mBAAmB,EAAlB,OAAO,QAAA,EAAE,QAAQ,QAAA;wBACvB,aAAa,SAAA,CAAA;;4BACjB,KAAsB,4BAAA,SAAA,QAAQ,CAAA,CAAA,0FAAE;gCAArB,OAAO;gCAChB,IACE,aAAa;oCACb,aAAa,CAAC,GAAG,IAAI,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;oCACzC,aAAa,CAAC,KAAK,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EACzC;oCACA,aAAa,CAAC,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;iCACvC;qCAAM;oCACL,IAAI,aAAa,EAAE;wCACjB,OAAO,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;qCAC5B;oCACD,aAAa,GAAG;wCACd,OAAO,SAAA;wCACP,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;wCAC3B,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC;qCACxB,CAAA;iCACF;6BACF;;;;;;;;;wBACD,IAAI,aAAa,EAAE;4BACjB,OAAO,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;yBAC5B;qBACF;;;;;;;;;gBAED,sBAAO,OAAO,EAAA;;;KACf;IAED;;;;OAIG;IACH,iDAAa,GAAb,WAAc,gBAAgB,IAAS,CAAC;IAC1C,gCAAC;AAAD,CAAC,AA9ED,CAAuD,2BAAiB,GA8EvE"}
+{"version":3,"file":"FromConfigSequenceAdapter.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/FromConfigSequenceAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qFAAyE;AACzE,kDAA0D;AAE1D,8CAAwC;AACxC,4EAAmD;AAGnD,MAAqB,yBACnB,SAAQ,2BAAiB;IAGzB;;;;OAIG;IACH,WAAW,CAAC,MAAwB;QAClC,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,IAAA,mBAAO,GAAE,CAAC,CAAC,SAAS,EAAE,CAAA;YACzE,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACrB,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;gBAChB,GAAG,IAAI,CAAC,MAAM,EAAE;gBAChB,QAAQ,EAAE,GAAG,IAAI,CAAC,EAAE,EAAE,IAAI,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,GAAG,EAAE;gBACtD,GAAG,EAAE,MAAM,CAAC,GAAG;gBACf,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,GAAG,EAAE,IAAI;qBACN,GAAG,CAAC,KAAK,CAAC;qBACV,KAAK,CACJ,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,EAC7C,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAC5C;aACJ,CAAC,CACH,CAAA;YAED,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,UAAU;QACd,MAAM,OAAO,GAAG,EAAE,CAAA;QAElB,wEAAwE;QACxE,KAAK,MAAM,CAAC,OAAO,EAAE,QAAQ,CAAC,IAAI,IAAI,CAAC,QAAQ,EAAE;YAC/C,IAAI,aAAa,CAAA;YACjB,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE;gBAC9B,IACE,aAAa;oBACb,aAAa,CAAC,GAAG,IAAI,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;oBACzC,aAAa,CAAC,KAAK,IAAI,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EACzC;oBACA,aAAa,CAAC,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;iBACvC;qBAAM;oBACL,IAAI,aAAa,EAAE;wBACjB,OAAO,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;qBAC5B;oBACD,aAAa,GAAG;wBACd,OAAO;wBACP,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC;wBAC3B,GAAG,EAAE,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC;qBACxB,CAAA;iBACF;aACF;YACD,IAAI,aAAa,EAAE;gBACjB,OAAO,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;aAC5B;SACF;QAED,OAAO,OAAO,CAAA;IAChB,CAAC;IAED;;;;OAIG;IACH,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAzED,4CAyEC"}

package/dist/FromConfigAdapter/configSchema.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.sequenceConfigSchema = exports.regionsConfigSchema = exports.configSchema = void 0;
-var configuration_1 = require("@jbrowse/core/configuration");
+const configuration_1 = require("@jbrowse/core/configuration");
 exports.configSchema = (0, configuration_1.ConfigurationSchema)('FromConfigAdapter', {
     features: {
         type: 'frozen',

package/dist/FromConfigAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/configSchema.ts"],"names":[],"mappings":";;;AAAA,6DAAiE;AAEpD,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAC7C,mBAAmB,EACnB;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAEY,QAAA,mBAAmB,GAAG,IAAA,mCAAmB,EACpD,0BAA0B,EAC1B;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAEY,QAAA,oBAAoB,GAAG,IAAA,mCAAmB,EACrD,2BAA2B,EAC3B;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/FromConfigAdapter/configSchema.ts"],"names":[],"mappings":";;;AAAA,+DAAiE;AAEpD,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAC7C,mBAAmB,EACnB;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAEY,QAAA,mBAAmB,GAAG,IAAA,mCAAmB,EACpD,0BAA0B,EAC1B;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA;AAEY,QAAA,oBAAoB,GAAG,IAAA,mCAAmB,EACrD,2BAA2B,EAC3B;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,EAAE;KACjB;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,eAAe;KAC9B;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,WAAW,EAAE,CAC3D,CAAA"}

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -1,113 +1,27 @@
 "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 __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 __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var io_1 = require("@jbrowse/core/util/io");
-var configuration_1 = require("@jbrowse/core/configuration");
-var RefNameAliasAdapter = /** @class */ (function (_super) {
-    __extends(RefNameAliasAdapter, _super);
-    function RefNameAliasAdapter() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    RefNameAliasAdapter.prototype.getRefNameAliases = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var loc, results, refColumn;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        loc = (0, configuration_1.readConfObject)(this.config, 'location');
-                        if (loc.uri === '' || loc.uri === '/path/to/my/aliases.txt') {
-                            return [2 /*return*/, []];
-                        }
-                        return [4 /*yield*/, (0, io_1.openLocation)(loc).readFile('utf8')];
-                    case 1:
-                        results = _a.sent();
-                        refColumn = (0, configuration_1.readConfObject)(this.config, 'refNameColumn');
-                        return [2 /*return*/, results
-                                .trim()
-                                .split('\n')
-                                .filter(function (f) { return !!f && !f.startsWith('#'); })
-                                .map(function (row) {
-                                var aliases = row.split('\t');
-                                var _a = __read(aliases.splice(refColumn, 1), 1), refName = _a[0];
-                                return { refName: refName, aliases: aliases.filter(function (f) { return !!f.trim(); }) };
-                            })];
-                }
-            });
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const io_1 = require("@jbrowse/core/util/io");
+const configuration_1 = require("@jbrowse/core/configuration");
+class RefNameAliasAdapter extends BaseAdapter_1.BaseAdapter {
+    async getRefNameAliases() {
+        const loc = (0, configuration_1.readConfObject)(this.config, 'location');
+        if (loc.uri === '' || loc.uri === '/path/to/my/aliases.txt') {
+            return [];
+        }
+        const results = await (0, io_1.openLocation)(loc).readFile('utf8');
+        const refColumn = (0, configuration_1.readConfObject)(this.config, 'refNameColumn');
+        return results
+            .trim()
+            .split('\n')
+            .filter(f => !!f && !f.startsWith('#'))
+            .map(row => {
+            const aliases = row.split('\t');
+            const [refName] = aliases.splice(refColumn, 1);
+            return { refName, aliases: aliases.filter(f => !!f.trim()) };
         });
-    };
-    RefNameAliasAdapter.prototype.freeResources = function () {
-        return __awaiter(this, void 0, void 0, function () { return __generator(this, function (_a) {
-            return [2 /*return*/];
-        }); });
-    };
-    return RefNameAliasAdapter;
-}(BaseAdapter_1.BaseAdapter));
+    }
+    async freeResources() { }
+}
 exports.default = RefNameAliasAdapter;
 //# sourceMappingURL=RefNameAliasAdapter.js.map

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"RefNameAliasAdapter.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/RefNameAliasAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uEAGgD;AAChD,4CAAoD;AACpD,6DAA4D;AAE5D;IACU,uCAAW;IADrB;;IAuBA,CAAC;IAnBO,+CAAiB,GAAvB;;;;;;wBACQ,GAAG,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,CAAA;wBACnD,IAAI,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,GAAG,CAAC,GAAG,KAAK,yBAAyB,EAAE;4BAC3D,sBAAO,EAAE,EAAA;yBACV;wBACe,qBAAM,IAAA,iBAAY,EAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAA;;wBAAlD,OAAO,GAAG,SAAwC;wBAClD,SAAS,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;wBAC9D,sBAAO,OAAO;iCACX,IAAI,EAAE;iCACN,KAAK,CAAC,IAAI,CAAC;iCACX,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAzB,CAAyB,CAAC;iCACtC,GAAG,CAAC,UAAA,GAAG;gCACN,IAAM,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gCACzB,IAAA,KAAA,OAAY,OAAO,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,IAAA,EAAvC,OAAO,QAAgC,CAAA;gCAC9C,OAAO,EAAE,OAAO,SAAA,EAAE,OAAO,EAAE,OAAO,CAAC,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,EAAV,CAAU,CAAC,EAAE,CAAA;4BAC9D,CAAC,CAAC,EAAA;;;;KACL;IAEK,2CAAa,GAAnB;;;;KAAwB;IAC1B,0BAAC;AAAD,CAAC,AAvBD,CACU,yBAAW,GAsBpB"}
+{"version":3,"file":"RefNameAliasAdapter.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/RefNameAliasAdapter.ts"],"names":[],"mappings":";;AAAA,yEAGgD;AAChD,8CAAoD;AACpD,+DAA4D;AAE5D,MAAqB,mBACnB,SAAQ,yBAAW;IAGnB,KAAK,CAAC,iBAAiB;QACrB,MAAM,GAAG,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,CAAA;QACnD,IAAI,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,GAAG,CAAC,GAAG,KAAK,yBAAyB,EAAE;YAC3D,OAAO,EAAE,CAAA;SACV;QACD,MAAM,OAAO,GAAG,MAAM,IAAA,iBAAY,EAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QACxD,MAAM,SAAS,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC9D,OAAO,OAAO;aACX,IAAI,EAAE;aACN,KAAK,CAAC,IAAI,CAAC;aACX,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;aACtC,GAAG,CAAC,GAAG,CAAC,EAAE;YACT,MAAM,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC/B,MAAM,CAAC,OAAO,CAAC,GAAG,OAAO,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YAC9C,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,CAAA;QAC9D,CAAC,CAAC,CAAA;IACN,CAAC;IAED,KAAK,CAAC,aAAa,KAAI,CAAC;CACzB;AAvBD,sCAuBC"}

package/dist/RefNameAliasAdapter/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)('RefNameAliasAdapter', {
     location: {
         type: 'fileLocation',

package/dist/RefNameAliasAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,qBAAqB,EACrB;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,qBAAqB,EACrB;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/index.js

@@ -1,19 +1,4 @@
 "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 __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -42,84 +27,66 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ConfigurationEditor = exports.JsonEditor = void 0;
-var react_1 = require("react");
-var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-var WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
-var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-var ConfigurationEditorWidget_1 = require("./ConfigurationEditorWidget");
-var FromConfigAdapter_1 = require("./FromConfigAdapter");
-var RefNameAliasAdapter_1 = require("./RefNameAliasAdapter");
-var LazyConfigurationEditorComponent = (0, react_1.lazy)(function () { return Promise.resolve().then(function () { return __importStar(require('./ConfigurationEditorWidget/components/ConfigurationEditor')); }); });
+const react_1 = require("react");
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
+const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const ConfigurationEditorWidget_1 = require("./ConfigurationEditorWidget");
+const FromConfigAdapter_1 = require("./FromConfigAdapter");
+const RefNameAliasAdapter_1 = require("./RefNameAliasAdapter");
+const LazyConfigurationEditorComponent = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./ConfigurationEditorWidget/components/ConfigurationEditor'))));
 exports.ConfigurationEditor = LazyConfigurationEditorComponent;
-var default_1 = /** @class */ (function (_super) {
-    __extends(default_1, _super);
-    function default_1() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.name = 'ConfigurationPlugin';
-        return _this;
+class default_1 extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'ConfigurationPlugin';
     }
-    default_1.prototype.install = function (pluginManager) {
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'FromConfigAdapter',
-                configSchema: FromConfigAdapter_1.configSchema,
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./FromConfigAdapter/FromConfigAdapter')); }).then(function (r) { return r.default; });
-                },
-                adapterMetadata: {
-                    category: null,
-                    hiddenFromGUI: true,
-                    displayName: null,
-                    description: null,
-                },
-            });
-        });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'FromConfigRegionsAdapter',
-                configSchema: FromConfigAdapter_1.regionsConfigSchema,
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./FromConfigAdapter/FromConfigRegionsAdapter')); }).then(function (r) { return r.default; });
-                },
-                adapterMetadata: {
-                    category: null,
-                    hiddenFromGUI: true,
-                    displayName: null,
-                    description: null,
-                },
-            });
-        });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'FromConfigSequenceAdapter',
-                configSchema: FromConfigAdapter_1.sequenceConfigSchema,
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./FromConfigAdapter/FromConfigSequenceAdapter')); }).then(function (r) { return r.default; });
-                },
-                adapterMetadata: {
-                    category: null,
-                    hiddenFromGUI: true,
-                    displayName: null,
-                    description: null,
-                },
-            });
-        });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'RefNameAliasAdapter',
-                configSchema: RefNameAliasAdapter_1.configSchema,
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./RefNameAliasAdapter/RefNameAliasAdapter')); }).then(function (r) { return r.default; });
-                },
-                adapterMetadata: {
-                    category: null,
-                    hiddenFromGUI: true,
-                    displayName: null,
-                    description: null,
-                },
-            });
-        });
-        pluginManager.addWidgetType(function () {
+    install(pluginManager) {
+        pluginManager.addAdapterType(() => new AdapterType_1.default({
+            name: 'FromConfigAdapter',
+            configSchema: FromConfigAdapter_1.configSchema,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./FromConfigAdapter/FromConfigAdapter'))).then(r => r.default),
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+        }));
+        pluginManager.addAdapterType(() => new AdapterType_1.default({
+            name: 'FromConfigRegionsAdapter',
+            configSchema: FromConfigAdapter_1.regionsConfigSchema,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./FromConfigAdapter/FromConfigRegionsAdapter'))).then(r => r.default),
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+        }));
+        pluginManager.addAdapterType(() => new AdapterType_1.default({
+            name: 'FromConfigSequenceAdapter',
+            configSchema: FromConfigAdapter_1.sequenceConfigSchema,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./FromConfigAdapter/FromConfigSequenceAdapter'))).then(r => r.default),
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+        }));
+        pluginManager.addAdapterType(() => new AdapterType_1.default({
+            name: 'RefNameAliasAdapter',
+            configSchema: RefNameAliasAdapter_1.configSchema,
+            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./RefNameAliasAdapter/RefNameAliasAdapter'))).then(r => r.default),
+            adapterMetadata: {
+                category: null,
+                hiddenFromGUI: true,
+                displayName: null,
+                description: null,
+            },
+        }));
+        pluginManager.addWidgetType(() => {
             return new WidgetType_1.default({
                 name: 'ConfigurationEditorWidget',
                 HeadingComponent: ConfigurationEditorWidget_1.HeadingComponent,
@@ -128,9 +95,8 @@ var default_1 = /** @class */ (function (_super) {
                 ReactComponent: LazyConfigurationEditorComponent,
             });
         });
-    };
-    return default_1;
-}(Plugin_1.default));
+    }
+}
 exports.default = default_1;
 var JsonEditor_1 = require("./ConfigurationEditorWidget/components/JsonEditor");
 Object.defineProperty(exports, "JsonEditor", { enumerable: true, get: function () { return __importDefault(JsonEditor_1).default; } });