@jbrowse/plugin-sequence 2.1.0 → 2.1.2

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js

@@ -1,34 +1,18 @@
 "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 __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 io_1 = require("@jbrowse/core/util/io");
-var configuration_1 = require("@jbrowse/core/configuration");
-var IndexedFastaAdapter_1 = __importDefault(require("../IndexedFastaAdapter/IndexedFastaAdapter"));
-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;
-        var fastaLocation = (0, configuration_1.readConfObject)(config, 'fastaLocation');
-        var faiLocation = (0, configuration_1.readConfObject)(config, 'faiLocation');
-        var gziLocation = (0, configuration_1.readConfObject)(config, 'gziLocation');
+const indexedfasta_1 = require("@gmod/indexedfasta");
+const io_1 = require("@jbrowse/core/util/io");
+const configuration_1 = require("@jbrowse/core/configuration");
+const IndexedFastaAdapter_1 = __importDefault(require("../IndexedFastaAdapter/IndexedFastaAdapter"));
+class default_1 extends IndexedFastaAdapter_1.default {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const fastaLocation = (0, configuration_1.readConfObject)(config, 'fastaLocation');
+        const faiLocation = (0, configuration_1.readConfObject)(config, 'faiLocation');
+        const gziLocation = (0, configuration_1.readConfObject)(config, 'gziLocation');
         if (!fastaLocation) {
             throw new Error('must provide fastaLocation');
         }
@@ -38,15 +22,13 @@ var default_1 = /** @class */ (function (_super) {
         if (!gziLocation) {
             throw new Error('must provide gziLocation');
         }
-        var fastaOpts = {
-            fasta: (0, io_1.openLocation)(fastaLocation, _this.pluginManager),
-            fai: (0, io_1.openLocation)(faiLocation, _this.pluginManager),
-            gzi: (0, io_1.openLocation)(gziLocation, _this.pluginManager),
+        const fastaOpts = {
+            fasta: (0, io_1.openLocation)(fastaLocation, this.pluginManager),
+            fai: (0, io_1.openLocation)(faiLocation, this.pluginManager),
+            gzi: (0, io_1.openLocation)(gziLocation, this.pluginManager),
         };
-        _this.fasta = new indexedfasta_1.BgzipIndexedFasta(fastaOpts);
-        return _this;
+        this.fasta = new indexedfasta_1.BgzipIndexedFasta(fastaOpts);
     }
-    return default_1;
-}(IndexedFastaAdapter_1.default));
+}
 exports.default = default_1;
 //# sourceMappingURL=BgzipFastaAdapter.js.map

package/dist/BgzipFastaAdapter/BgzipFastaAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BgzipFastaAdapter.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/BgzipFastaAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qDAAsD;AAEtD,8CAAoD;AACpD,+DAA4D;AAE5D,qGAAqE;AAIrE,eAAqB,SAAQ,6BAAY;IACvC,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,aAAa,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC7D,MAAM,WAAW,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,aAAa,CAAC,CAAA;QACzD,MAAM,WAAW,GAAG,IAAA,8BAAc,EAAC,MAAM,EAAE,aAAa,CAAC,CAAA;QACzD,IAAI,CAAC,aAAa,EAAE;YAClB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;SAC9C;QACD,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QACD,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QACD,MAAM,SAAS,GAAG;YAChB,KAAK,EAAE,IAAA,iBAAY,EAAC,aAA6B,EAAE,IAAI,CAAC,aAAa,CAAC;YACtE,GAAG,EAAE,IAAA,iBAAY,EAAC,WAA2B,EAAE,IAAI,CAAC,aAAa,CAAC;YAClE,GAAG,EAAE,IAAA,iBAAY,EAAC,WAA2B,EAAE,IAAI,CAAC,aAAa,CAAC;SACnE,CAAA;QAED,IAAI,CAAC,KAAK,GAAG,IAAI,gCAAiB,CAAC,SAAS,CAAC,CAAA;IAC/C,CAAC;CACF;AA3BD,4BA2BC"}

package/dist/BgzipFastaAdapter/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)('BgzipFastaAdapter', {
     fastaLocation: {
         type: 'fileLocation',

package/dist/BgzipFastaAdapter/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,mBAAmB,EACnB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,gBAAgB,EAAE;QAChB,WAAW,EAAE,wBAAwB;QACrC,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,2BAA2B;YAChC,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,mBAAmB,EACnB;IACE,aAAa,EAAE;QACb,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE;KACzE;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,gBAAgB,EAAE;QAChB,WAAW,EAAE,wBAAwB;QACrC,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,2BAA2B;YAChC,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,wBAAwB;YAC7B,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/BgzipFastaAdapter/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/BgzipFastaAdapter/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: 'BgzipFastaAdapter',
+        configSchema: configSchema_1.default,
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BgzipFastaAdapter'))).then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/BgzipFastaAdapter/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/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,mBAAmB;QACzB,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,qBAAqB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/ChromSizesAdapter/ChromSizesAdapter.js

@@ -1,138 +1,42 @@
 "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);
+Object.defineProperty(exports, "__esModule", { value: true });
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const io_1 = require("@jbrowse/core/util/io");
+class default_1 extends BaseAdapter_1.BaseAdapter {
+    async setupPre() {
+        const pm = this.pluginManager;
+        const file = (0, io_1.openLocation)(this.getConf('chromSizesLocation'), pm);
+        const data = await file.readFile('utf8');
+        return Object.fromEntries(data
+            .split('\n')
+            .map(f => f.trim())
+            .filter(f => !!f)
+            .map((line) => {
+            const [name, length] = line.split('\t');
+            return [name, +length];
+        }));
     }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
+    async setup() {
+        if (!this.setupP) {
+            this.setupP = this.setupPre().catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
         }
-        finally { if (e) throw e.error; }
+        return this.setupP;
     }
-    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 default_1 = /** @class */ (function (_super) {
-    __extends(default_1, _super);
-    function default_1() {
-        return _super !== null && _super.apply(this, arguments) || this;
+    async getRegions() {
+        const refSeqs = await this.setup();
+        return Object.keys(refSeqs).map(refName => ({
+            refName,
+            start: 0,
+            end: refSeqs[refName],
+        }));
     }
-    default_1.prototype.setupPre = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var pm, file, data;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        pm = this.pluginManager;
-                        file = (0, io_1.openLocation)(this.getConf('chromSizesLocation'), pm);
-                        return [4 /*yield*/, file.readFile('utf8')];
-                    case 1:
-                        data = _a.sent();
-                        return [2 /*return*/, Object.fromEntries(data
-                                .split('\n')
-                                .map(function (f) { return f.trim(); })
-                                .filter(function (f) { return !!f; })
-                                .map(function (line) {
-                                var _a = __read(line.split('\t'), 2), name = _a[0], length = _a[1];
-                                return [name, +length];
-                            }))];
-                }
-            });
-        });
-    };
-    default_1.prototype.setup = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var _this = this;
-            return __generator(this, function (_a) {
-                if (!this.setupP) {
-                    this.setupP = this.setupPre().catch(function (e) {
-                        _this.setupP = undefined;
-                        throw e;
-                    });
-                }
-                return [2 /*return*/, this.setupP];
-            });
-        });
-    };
-    default_1.prototype.getRegions = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var refSeqs;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.setup()];
-                    case 1:
-                        refSeqs = _a.sent();
-                        return [2 /*return*/, Object.keys(refSeqs).map(function (refName) { return ({
-                                refName: refName,
-                                start: 0,
-                                end: refSeqs[refName],
-                            }); })];
-                }
-            });
-        });
-    };
-    default_1.prototype.getHeader = function () {
+    getHeader() {
         return {};
-    };
-    default_1.prototype.freeResources = function ( /* { region } */) { };
-    return default_1;
-}(BaseAdapter_1.BaseAdapter));
+    }
+    freeResources( /* { region } */) { }
+}
 exports.default = default_1;
 //# sourceMappingURL=ChromSizesAdapter.js.map

package/dist/ChromSizesAdapter/ChromSizesAdapter.js.map

@@ -1 +1 @@
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package/dist/ChromSizesAdapter/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)('ChromSizesAdapter', {
     chromSizesLocation: {
         type: 'fileLocation',

package/dist/ChromSizesAdapter/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,mBAAmB,EACnB;IACE,kBAAkB,EAAE;QAClB,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,8BAA8B;YACnC,YAAY,EAAE,aAAa;SAC5B;KACF;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/ChromSizesAdapter/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/ChromSizesAdapter/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: 'ChromSizesAdapter',
+        configSchema: configSchema_1.default,
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./ChromSizesAdapter'))).then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/ChromSizesAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/ChromSizesAdapter/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,mBAAmB;QACzB,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,qBAAqB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -1,79 +1,43 @@
 "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);
-};
-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 });
 /* eslint-disable @typescript-eslint/no-explicit-any */
-var react_1 = __importDefault(require("react"));
-var color_1 = require("@jbrowse/core/util/color");
-var ui_1 = require("@jbrowse/core/ui");
-var mobx_react_1 = require("mobx-react");
-var util_1 = require("@jbrowse/core/util");
+const react_1 = __importDefault(require("react"));
+const color_1 = require("@jbrowse/core/util/color");
+const ui_1 = require("@jbrowse/core/ui");
+const mobx_react_1 = require("mobx-react");
+const util_1 = require("@jbrowse/core/util");
 function Translation(props) {
-    var codonTable = props.codonTable, seq = props.seq, frame = props.frame, bpPerPx = props.bpPerPx, region = props.region, height = props.height, y = props.y, _a = props.reverse, reverse = _a === void 0 ? false : _a, theme = props.theme;
-    var scale = bpPerPx;
+    const { codonTable, seq, frame, bpPerPx, region, height, y, reverse = false, theme, } = props;
+    const scale = bpPerPx;
     // the tilt variable normalizes the frame to where we are starting from,
     // which increases consistency across blocks
-    var tilt = 3 - (region.start % 3);
+    const tilt = 3 - (region.start % 3);
     // the effectiveFrame incorporates tilt and the frame to say what the
     // effective frame that is plotted. The +3 is for when frame is -2 and this
     // can otherwise result in effectiveFrame -1
-    var effectiveFrame = (frame + tilt + 3) % 3;
-    var seqSliced = seq.slice(effectiveFrame);
-    var translated = [];
-    for (var i = 0; i < seqSliced.length; i += 3) {
-        var codon = seqSliced.slice(i, i + 3);
-        var normalizedCodon = reverse ? (0, util_1.revcom)(codon) : codon;
-        var aminoAcid = codonTable[normalizedCodon] || '';
+    const effectiveFrame = (frame + tilt + 3) % 3;
+    const seqSliced = seq.slice(effectiveFrame);
+    const translated = [];
+    for (let i = 0; i < seqSliced.length; i += 3) {
+        const codon = seqSliced.slice(i, i + 3);
+        const normalizedCodon = reverse ? (0, util_1.revcom)(codon) : codon;
+        const aminoAcid = codonTable[normalizedCodon] || '';
         translated.push({ letter: aminoAcid, codon: normalizedCodon.toUpperCase() });
     }
-    var w = (1 / scale) * 3;
-    var drop = region.start === 0 ? 0 : w;
-    var render = 1 / bpPerPx >= 12;
-    var width = (region.end - region.start) / bpPerPx;
-    var map = ['#d8d8d8', '#adadad', '#8f8f8f'].reverse();
-    return (react_1.default.createElement(react_1.default.Fragment, null, translated.map(function (element, index) {
-        var x = region.reversed
+    const w = (1 / scale) * 3;
+    const drop = region.start === 0 ? 0 : w;
+    const render = 1 / bpPerPx >= 12;
+    const width = (region.end - region.start) / bpPerPx;
+    const map = ['#d8d8d8', '#adadad', '#8f8f8f'].reverse();
+    return (react_1.default.createElement(react_1.default.Fragment, null, translated.map((element, index) => {
+        const x = region.reversed
             ? width - (w * (index + 1) + effectiveFrame / scale - drop)
             : w * index + effectiveFrame / scale - drop;
-        var letter = element.letter, codon = element.codon;
-        return (react_1.default.createElement(react_1.default.Fragment, { key: "".concat(index, "-").concat(letter) },
+        const { letter, codon } = element;
+        return (react_1.default.createElement(react_1.default.Fragment, { key: `${index}-${letter}` },
             react_1.default.createElement("rect", { x: x, y: y, width: render ? w : w + 0.7 /* small fudge factor when zoomed out*/, height: height, stroke: render ? '#555' : 'none', fill: util_1.defaultStarts.includes(codon)
                     ? theme.palette.startCodon
                     : util_1.defaultStops.includes(codon)
@@ -83,58 +47,56 @@ function Translation(props) {
     })));
 }
 function DNA(props) {
-    var bpPerPx = props.bpPerPx, region = props.region, feature = props.feature, theme = props.theme, height = props.height, seq = props.seq, y = props.y;
-    var render = 1 / bpPerPx >= 12;
-    var _a = __read((0, util_1.bpSpanPx)(feature.get('start'), feature.get('end'), region, bpPerPx), 2), leftPx = _a[0], rightPx = _a[1];
-    var reverse = region.reversed;
-    var len = feature.get('end') - feature.get('start');
-    var w = Math.max((rightPx - leftPx) / len, 0.8);
-    return (react_1.default.createElement(react_1.default.Fragment, null, seq.split('').map(function (letter, index) {
-        var color = theme.palette.bases[letter.toUpperCase()];
-        var x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
+    const { bpPerPx, region, feature, theme, height, seq, y } = props;
+    const render = 1 / bpPerPx >= 12;
+    const [leftPx, rightPx] = (0, util_1.bpSpanPx)(feature.get('start'), feature.get('end'), region, bpPerPx);
+    const reverse = region.reversed;
+    const len = feature.get('end') - feature.get('start');
+    const w = Math.max((rightPx - leftPx) / len, 0.8);
+    return (react_1.default.createElement(react_1.default.Fragment, null, seq.split('').map((letter, index) => {
+        const color = theme.palette.bases[letter.toUpperCase()];
+        const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
         return (react_1.default.createElement(react_1.default.Fragment, { key: index },
             react_1.default.createElement("rect", { x: x, y: y, width: w, height: height, fill: color ? color.main : '#aaa', stroke: render ? '#555' : 'none' }),
             render ? (react_1.default.createElement("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fill: color ? (0, color_1.contrastingTextColor)(color.main) : 'black' }, letter)) : null));
     })));
 }
-var SequenceSVG = function (_a) {
-    var regions = _a.regions, configTheme = _a.theme, _b = _a.features, features = _b === void 0 ? new Map() : _b, showReverse = _a.showReverse, showForward = _a.showForward, showTranslation = _a.showTranslation, bpPerPx = _a.bpPerPx;
-    var _c = __read(regions, 1), region = _c[0];
-    var theme = (0, ui_1.createJBrowseTheme)(configTheme);
-    var codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
-    var height = 20;
-    var _d = __read(__spreadArray([], __read(features.values()), false), 1), feature = _d[0];
+const SequenceSVG = ({ regions, theme: configTheme, features = new Map(), showReverse, showForward, showTranslation, bpPerPx, }) => {
+    const [region] = regions;
+    const theme = (0, ui_1.createJBrowseTheme)(configTheme);
+    const codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
+    const height = 20;
+    const [feature] = [...features.values()];
     if (!feature) {
         return null;
     }
-    var seq = feature.get('seq');
+    const seq = feature.get('seq');
     if (!seq) {
         return null;
     }
     // incrementer for the y-position of the current sequence being rendered
     // (applies to both translation rows and dna rows)
-    var currY = -20;
+    let currY = -20;
     return (react_1.default.createElement(react_1.default.Fragment, null,
         showTranslation && (region.reversed ? showReverse : showForward)
-            ? [2, 1, 0].map(function (index) { return (react_1.default.createElement(Translation, { key: "translation-".concat(index), seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: region.reversed })); })
+            ? [2, 1, 0].map(index => (react_1.default.createElement(Translation, { key: `translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: region.reversed })))
             : null,
         showForward ? (react_1.default.createElement(DNA, { height: height, y: (currY += 20), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx, theme: theme })) : null,
         showReverse ? (react_1.default.createElement(DNA, { height: height, y: (currY += 20), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx, theme: theme })) : null,
         showTranslation && (region.reversed ? showForward : showReverse)
-            ? [0, -1, -2].map(function (index) { return (react_1.default.createElement(Translation, { key: "rev-translation-".concat(index), seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: !region.reversed })); })
+            ? [0, -1, -2].map(index => (react_1.default.createElement(Translation, { key: `rev-translation-${index}`, seq: seq, y: (currY += 20), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, theme: theme, height: height, reverse: !region.reversed })))
             : null));
 };
-var Wrapper = function (_a) {
-    var exportSVG = _a.exportSVG, width = _a.width, totalHeight = _a.totalHeight, children = _a.children;
-    return exportSVG ? (react_1.default.createElement(react_1.default.Fragment, null, children)) : (react_1.default.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: { width: width, height: totalHeight } }, children));
+const Wrapper = ({ exportSVG, width, totalHeight, children }) => {
+    return exportSVG ? (react_1.default.createElement(react_1.default.Fragment, null, children)) : (react_1.default.createElement("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: { width, height: totalHeight } }, children));
 };
 function Sequence(props) {
-    var regions = props.regions, bpPerPx = props.bpPerPx;
-    var _a = __read(regions, 1), region = _a[0];
-    var width = (region.end - region.start) / bpPerPx;
-    var totalHeight = 200;
-    return (react_1.default.createElement(Wrapper, __assign({}, props, { totalHeight: totalHeight, width: width }),
-        react_1.default.createElement(SequenceSVG, __assign({}, props))));
+    const { regions, bpPerPx } = props;
+    const [region] = regions;
+    const width = (region.end - region.start) / bpPerPx;
+    const totalHeight = 200;
+    return (react_1.default.createElement(Wrapper, { ...props, totalHeight: totalHeight, width: width },
+        react_1.default.createElement(SequenceSVG, { ...props })));
 }
 exports.default = (0, mobx_react_1.observer)(Sequence);
 //# sourceMappingURL=DivSequenceRendering.js.map