@jbrowse/plugin-config 2.0.0 → 2.1.2

package/dist/ConfigurationEditorWidget/model.js

@@ -1,20 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var mobx_state_tree_1 = require("mobx-state-tree");
-var mst_1 = require("@jbrowse/core/util/types/mst");
-exports.default = (function (pluginManager) {
-    return mobx_state_tree_1.types
-        .model('ConfigurationEditorWidget', {
-        id: mst_1.ElementId,
-        type: mobx_state_tree_1.types.literal('ConfigurationEditorWidget'),
-        // If you add different types of targets, don't forget to account for that
-        // in the key of ./components/ConfigurationEditor.js
-        target: mobx_state_tree_1.types.safeReference(pluginManager.pluggableConfigSchemaType('track')),
-    })
-        .actions(function (self) { return ({
-        setTarget: function (newTarget) {
-            self.target = newTarget;
-        },
-    }); });
-});
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mst_1 = require("@jbrowse/core/util/types/mst");
+exports.default = (pluginManager) => mobx_state_tree_1.types
+    .model('ConfigurationEditorWidget', {
+    id: mst_1.ElementId,
+    type: mobx_state_tree_1.types.literal('ConfigurationEditorWidget'),
+    // If you add different types of targets, don't forget to account for that
+    // in the key of ./components/ConfigurationEditor.js
+    target: mobx_state_tree_1.types.safeReference(pluginManager.pluggableConfigSchemaType('track')),
+})
+    .actions(self => ({
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    setTarget(newTarget) {
+        self.target = newTarget;
+    },
+}));
 //# sourceMappingURL=model.js.map

package/dist/ConfigurationEditorWidget/model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/ConfigurationEditorWidget/model.ts"],"names":[],"mappings":";;AAAA,qDAAuC;AACvC,sDAAwD;AAGxD,kBAAe,CAAC,aAA4B,EAAE,EAAE,CAC9C,uBAAK;KACF,KAAK,CAAC,2BAA2B,EAAE;IAClC,EAAE,EAAE,eAAS;IACb,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,2BAA2B,CAAC;IAChD,0EAA0E;IAC1E,oDAAoD;IACpD,MAAM,EAAE,uBAAK,CAAC,aAAa,CACzB,aAAa,CAAC,yBAAyB,CAAC,OAAO,CAAC,CACjD;CACF,CAAC;KACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAChB,8DAA8D;IAC9D,SAAS,CAAC,SAAc;QACtB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;IACzB,CAAC;CACF,CAAC,CAAC,CAAA"}

package/dist/FromConfigAdapter/FromConfigAdapter.js

@@ -1,120 +1,30 @@
 "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 __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 __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
-    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
-        if (ar || !(i in from)) {
-            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
-            ar[i] = from[i];
-        }
-    }
-    return to.concat(ar || Array.prototype.slice.call(from));
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-var rxjs_1 = require("@jbrowse/core/util/rxjs");
-var configuration_1 = require("@jbrowse/core/configuration");
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const configuration_1 = require("@jbrowse/core/configuration");
 /**
  * Adapter that just returns the features defined in its `features` configuration
  * key, like:
  *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
  */
-var FromConfigAdapter = /** @class */ (function (_super) {
-    __extends(FromConfigAdapter, _super);
-    function FromConfigAdapter(conf, getSubAdapter, pluginManager) {
-        var _this = _super.call(this, conf, getSubAdapter, pluginManager) || this;
-        var feats = (0, configuration_1.readConfObject)(conf, 'features');
-        _this.features = FromConfigAdapter.makeFeatures(feats || []);
-        return _this;
+class FromConfigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
+    constructor(conf, getSubAdapter, pluginManager) {
+        super(conf, getSubAdapter, pluginManager);
+        const feats = (0, configuration_1.readConfObject)(conf, 'features');
+        this.features = FromConfigAdapter.makeFeatures(feats || []);
     }
-    FromConfigAdapter.makeFeatures = function (fdata) {
-        var e_1, _a;
-        var features = new Map();
-        for (var i = 0; i < fdata.length; i += 1) {
+    static makeFeatures(fdata) {
+        const features = new Map();
+        for (let i = 0; i < fdata.length; i += 1) {
             if (fdata[i]) {
-                var f = this.makeFeature(fdata[i]);
-                var refName = f.get('refName');
-                var bucket = features.get(refName);
+                const f = this.makeFeature(fdata[i]);
+                const refName = f.get('refName');
+                let bucket = features.get(refName);
                 if (!bucket) {
                     bucket = [];
                     features.set(refName, bucket);
@@ -122,62 +32,38 @@ var FromConfigAdapter = /** @class */ (function (_super) {
                 bucket.push(f);
             }
         }
-        try {
-            // sort the features on each reference sequence by start coordinate
-            for (var _b = __values(features.values()), _c = _b.next(); !_c.done; _c = _b.next()) {
-                var refFeatures = _c.value;
-                refFeatures.sort(function (a, b) { return a.get('start') - b.get('start'); });
-            }
-        }
-        catch (e_1_1) { e_1 = { error: e_1_1 }; }
-        finally {
-            try {
-                if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
-            }
-            finally { if (e_1) throw e_1.error; }
+        // sort the features on each reference sequence by start coordinate
+        for (const refFeatures of features.values()) {
+            refFeatures.sort((a, b) => a.get('start') - b.get('start'));
         }
         return features;
-    };
-    FromConfigAdapter.makeFeature = function (data) {
+    }
+    static makeFeature(data) {
         return new simpleFeature_1.default(data);
-    };
-    FromConfigAdapter.prototype.getRefNames = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            return __generator(this, function (_a) {
-                return [2 /*return*/, __spreadArray([], __read(this.features.keys()), false)];
-            });
-        });
-    };
-    FromConfigAdapter.prototype.getRefNameAliases = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            return __generator(this, function (_a) {
-                return [2 /*return*/, Array.from(this.features.values()).map(function (featureArray) { return ({
-                        refName: featureArray[0].get('refName'),
-                        aliases: featureArray[0].get('aliases'),
-                    }); })];
-            });
-        });
-    };
-    FromConfigAdapter.prototype.getFeatures = function (region) {
-        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 features, i, f;
-            return __generator(this, function (_a) {
-                features = this.features.get(refName) || [];
-                for (i = 0; i < features.length; i++) {
-                    f = features[i];
-                    if (f.get('end') > start && f.get('start') < end) {
-                        observer.next(f);
-                    }
+    }
+    async getRefNames() {
+        return [...this.features.keys()];
+    }
+    async getRefNameAliases() {
+        return Array.from(this.features.values()).map(featureArray => ({
+            refName: featureArray[0].get('refName'),
+            aliases: featureArray[0].get('aliases'),
+        }));
+    }
+    getFeatures(region) {
+        const { refName, start, end } = region;
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
+            const features = this.features.get(refName) || [];
+            for (let i = 0; i < features.length; i++) {
+                const f = features[i];
+                if (f.get('end') > start && f.get('start') < end) {
+                    observer.next(f);
                 }
-                observer.complete();
-                return [2 /*return*/];
-            });
-        }); });
-    };
-    FromConfigAdapter.prototype.freeResources = function ( /* { region } */) { };
-    return FromConfigAdapter;
-}(BaseAdapter_1.BaseFeatureDataAdapter));
+            }
+            observer.complete();
+        });
+    }
+    freeResources( /* { region } */) { }
+}
 exports.default = FromConfigAdapter;
 //# sourceMappingURL=FromConfigAdapter.js.map

package/dist/FromConfigAdapter/FromConfigAdapter.js.map

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package/dist/FromConfigAdapter/FromConfigRegionsAdapter.js

@@ -1,163 +1,56 @@
 "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 __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 BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var configuration_1 = require("@jbrowse/core/configuration");
-var FromConfigAdapter_1 = __importDefault(require("./FromConfigAdapter"));
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const configuration_1 = require("@jbrowse/core/configuration");
+const FromConfigAdapter_1 = __importDefault(require("./FromConfigAdapter"));
 /**
  * Adapter that just returns the features defined in its `features` configuration
  * key, like:
  *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
  */
-var FromConfigRegionsAdapter = /** @class */ (function (_super) {
-    __extends(FromConfigRegionsAdapter, _super);
-    function FromConfigRegionsAdapter(config, getSubAdapter, pluginManager) {
-        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
-        var features = (0, configuration_1.readConfObject)(config, 'features');
-        _this.features = FromConfigAdapter_1.default.makeFeatures(features || []);
-        return _this;
+class FromConfigRegionsAdapter extends BaseAdapter_1.BaseAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const features = (0, configuration_1.readConfObject)(config, 'features');
+        this.features = FromConfigAdapter_1.default.makeFeatures(features || []);
     }
     /**
      * Get refName, start, and end for all features after collapsing any overlaps
      */
-    FromConfigRegionsAdapter.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'),
+                    };
                 }
-                // sort the regions by refName
-                regions.sort(function (a, b) { return a.refName.localeCompare(b.refName); });
-                return [2 /*return*/, regions];
-            });
-        });
-    };
-    FromConfigRegionsAdapter.prototype.freeResources = function ( /* { region } */) { };
-    return FromConfigRegionsAdapter;
-}(BaseAdapter_1.BaseAdapter));
+            }
+            if (currentRegion) {
+                regions.push(currentRegion);
+            }
+        }
+        // sort the regions by refName
+        regions.sort((a, b) => a.refName.localeCompare(b.refName));
+        return regions;
+    }
+    freeResources( /* { region } */) { }
+}
 exports.default = FromConfigRegionsAdapter;
 //# sourceMappingURL=FromConfigRegionsAdapter.js.map

package/dist/FromConfigAdapter/FromConfigRegionsAdapter.js.map

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package/dist/FromConfigAdapter/FromConfigSequenceAdapter.d.ts

@@ -1,7 +1,8 @@
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import FromConfigAdapter from './FromConfigAdapter';
-export default class FromConfigSequenceAdapter extends FromConfigAdapter {
+import { RegionsAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+export default class FromConfigSequenceAdapter extends FromConfigAdapter implements RegionsAdapter {
     /**
      * Fetch features for a certain region
      * @param region - Region