@jbrowse/plugin-sequence 2.1.0 → 2.1.3

package/dist/DivSequenceRenderer/components/DivSequenceRendering.js.map

@@ -1 +1 @@
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package/dist/DivSequenceRenderer/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)('DivSequenceRenderer', {
     height: {
         type: 'number',

package/dist/DivSequenceRenderer/configSchema.js.map

@@ -1 +1 @@
-{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/DivSequenceRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,qBAAqB,EACrB;IACE,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,2CAA2C;QACxD,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/DivSequenceRenderer/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,qBAAqB,EACrB;IACE,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,2CAA2C;QACxD,YAAY,EAAE,EAAE;KACjB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/DivSequenceRenderer/index.d.ts

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

package/dist/DivSequenceRenderer/index.js

@@ -3,9 +3,29 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = exports.ReactComponent = void 0;
-var DivSequenceRendering_1 = require("./components/DivSequenceRendering");
-Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(DivSequenceRendering_1).default; } });
-var configSchema_1 = require("./configSchema");
-Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+const FeatureRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType"));
+const DivSequenceRendering_1 = __importDefault(require("./components/DivSequenceRendering"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+/* adjust in both directions */
+class DivSequenceRenderer extends FeatureRendererType_1.default {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    getExpandedRegion(region) {
+        return {
+            ...region,
+            start: Math.max(region.start - 3, 0),
+            end: region.end + 3,
+        };
+    }
+}
+exports.default = (pluginManager) => {
+    pluginManager.addRendererType(() => new DivSequenceRenderer({
+        name: 'DivSequenceRenderer',
+        ReactComponent: DivSequenceRendering_1.default,
+        configSchema: configSchema_1.default,
+        pluginManager,
+    }));
+};
 //# sourceMappingURL=index.js.map

package/dist/DivSequenceRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/DivSequenceRenderer/index.ts"],"names":[],"mappings":";;;;;AAGA,4HAAmG;AACnG,6FAA8D;AAC9D,kEAAyC;AAEzC,+BAA+B;AAC/B,MAAM,mBAAoB,SAAQ,6BAAmB;IAArD;;QACE,gBAAW,GAAG,IAAI,CAAA;IASpB,CAAC;IAPC,iBAAiB,CAAC,MAAc;QAC9B,OAAO;YACL,GAAG,MAAM;YACT,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,GAAG,CAAC,EAAE,CAAC,CAAC;YACpC,GAAG,EAAE,MAAM,CAAC,GAAG,GAAG,CAAC;SACpB,CAAA;IACH,CAAC;CACF;AAED,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,mBAAmB,CAAC;QACtB,IAAI,EAAE,qBAAqB;QAC3B,cAAc,EAAd,8BAAc;QACd,YAAY,EAAZ,sBAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/GCContentAdapter/GCContentAdapter.d.ts

@@ -1,6 +1,5 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Feature, Region } from '@jbrowse/core/util';
 export default class extends BaseFeatureDataAdapter {
     private windowSize;
     private windowDelta;
@@ -8,11 +7,6 @@ export default class extends BaseFeatureDataAdapter {
     static capabilities: string[];
     configure(): Promise<BaseFeatureDataAdapter>;
     getRefNames(): Promise<string[]>;
-    /**
-     * Fetch features for a certain region
-     * @param param -
-     * @returns Observable of Feature objects in the region
-     */
     getFeatures(query: Region, opts: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region

package/dist/GCContentAdapter/GCContentAdapter.js

@@ -1,194 +1,89 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
-var __assign = (this && this.__assign) || function () {
-    __assign = Object.assign || function(t) {
-        for (var s, i = 1, n = arguments.length; i < n; i++) {
-            s = arguments[i];
-            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
-                t[p] = s[p];
-        }
-        return t;
-    };
-    return __assign.apply(this, arguments);
-};
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var rxjs_1 = require("@jbrowse/core/util/rxjs");
-var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
-var configuration_1 = require("@jbrowse/core/configuration");
-var operators_1 = require("rxjs/operators");
-var default_1 = /** @class */ (function (_super) {
-    __extends(default_1, _super);
-    function default_1() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.windowSize = 1000;
-        _this.windowDelta = 1000;
-        _this.gcMode = 'content';
-        return _this;
-    }
-    default_1.prototype.configure = function () {
-        var _a;
-        return __awaiter(this, void 0, void 0, function () {
-            var sequenceAdapter, dataAdapter;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        sequenceAdapter = (0, configuration_1.readConfObject)(this.config, 'sequenceAdapter');
-                        return [4 /*yield*/, ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, sequenceAdapter))];
-                    case 1:
-                        dataAdapter = _b.sent();
-                        if (!dataAdapter) {
-                            throw new Error('Error getting subadapter');
-                        }
-                        return [2 /*return*/, dataAdapter.dataAdapter];
-                }
-            });
-        });
-    };
-    default_1.prototype.getRefNames = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var sequenceAdapter;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        sequenceAdapter = _a.sent();
-                        return [2 /*return*/, sequenceAdapter.getRefNames()];
-                }
-            });
-        });
-    };
-    /**
-     * Fetch features for a certain region
-     * @param param -
-     * @returns Observable of Feature objects in the region
-     */
-    default_1.prototype.getFeatures = function (query, opts) {
-        var _this = this;
+const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+const rxjs_1 = require("@jbrowse/core/util/rxjs");
+const util_1 = require("@jbrowse/core/util");
+const operators_1 = require("rxjs/operators");
+class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
         this.windowSize = 1000;
         this.windowDelta = 1000;
         this.gcMode = 'content';
-        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
-            var sequenceAdapter, hw, f, queryStart, queryEnd, ret, feats, residues, i, r, nc, ng, len, j, pos, score;
+    }
+    async configure() {
+        var _a;
+        const adapter = await ((_a = this.getSubAdapter) === null || _a === void 0 ? void 0 : _a.call(this, this.getConf('sequenceAdapter')));
+        if (!adapter) {
+            throw new Error('Error getting subadapter');
+        }
+        return adapter.dataAdapter;
+    }
+    async getRefNames() {
+        const adapter = await this.configure();
+        return adapter.getRefNames();
+    }
+    getFeatures(query, opts) {
+        return (0, rxjs_1.ObservableCreate)(async (observer) => {
             var _a;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0: return [4 /*yield*/, this.configure()];
-                    case 1:
-                        sequenceAdapter = _b.sent();
-                        hw = this.windowSize === 1 ? 1 : this.windowSize / 2 // Half the window size
-                        ;
-                        f = this.windowSize === 1;
-                        queryStart = query.start, queryEnd = query.end;
-                        queryStart = Math.max(0, queryStart - hw);
-                        queryEnd += hw;
-                        if (queryEnd < 0 || queryStart > queryEnd) {
-                            observer.complete();
-                            return [2 /*return*/];
-                        }
-                        ret = sequenceAdapter.getFeatures(__assign(__assign({}, query), { start: queryStart, end: queryEnd }));
-                        return [4 /*yield*/, ret.pipe((0, operators_1.toArray)()).toPromise()];
-                    case 2:
-                        feats = _b.sent();
-                        residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
-                        for (i = hw; i < residues.length - hw; i += this.windowDelta) {
-                            r = f ? residues[i] : residues.slice(i - hw, i + hw);
-                            nc = 0;
-                            ng = 0;
-                            len = 0;
-                            for (j = 0; j < r.length; j++) {
-                                if (r[j] === 'c' || r[j] === 'C') {
-                                    nc++;
-                                }
-                                else if (r[j] === 'g' || r[j] === 'G') {
-                                    ng++;
-                                }
-                                if (r[j] !== 'N') {
-                                    len++;
-                                }
-                            }
-                            pos = queryStart;
-                            score = void 0;
-                            if (this.gcMode === 'content') {
-                                score = (ng + nc) / (len || 1);
-                            }
-                            else if (this.gcMode === 'skew') {
-                                score = (ng - nc) / (ng + nc || 1);
-                            }
-                            observer.next(new simpleFeature_1.default({
-                                uniqueId: "".concat(this.id, "_").concat(pos + i),
-                                start: pos + i,
-                                end: pos + i + this.windowDelta,
-                                score: score,
-                            }));
-                        }
-                        observer.complete();
-                        return [2 /*return*/];
+            const sequenceAdapter = await this.configure();
+            const hw = this.windowSize === 1 ? 1 : this.windowSize / 2; // Half the window size
+            const f = this.windowSize === 1;
+            let { start: queryStart, end: queryEnd } = query;
+            queryStart = Math.max(0, queryStart - hw);
+            queryEnd += hw;
+            if (queryEnd < 0 || queryStart > queryEnd) {
+                observer.complete();
+                return;
+            }
+            const ret = sequenceAdapter.getFeatures({
+                ...query,
+                start: queryStart,
+                end: queryEnd,
+            }, opts);
+            const feats = await ret.pipe((0, operators_1.toArray)()).toPromise();
+            const residues = ((_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq')) || '';
+            for (let i = hw; i < residues.length - hw; i += this.windowDelta) {
+                const r = f ? residues[i] : residues.slice(i - hw, i + hw);
+                let nc = 0;
+                let ng = 0;
+                let len = 0;
+                for (let j = 0; j < r.length; j++) {
+                    if (r[j] === 'c' || r[j] === 'C') {
+                        nc++;
+                    }
+                    else if (r[j] === 'g' || r[j] === 'G') {
+                        ng++;
+                    }
+                    if (r[j] !== 'N') {
+                        len++;
+                    }
                 }
-            });
-        }); });
-    };
+                const pos = queryStart;
+                let score;
+                if (this.gcMode === 'content') {
+                    score = (ng + nc) / (len || 1);
+                }
+                else if (this.gcMode === 'skew') {
+                    score = (ng - nc) / (ng + nc || 1);
+                }
+                observer.next(new util_1.SimpleFeature({
+                    uniqueId: `${this.id}_${pos + i}`,
+                    start: pos + i,
+                    end: pos + i + this.windowDelta,
+                    score,
+                }));
+            }
+            observer.complete();
+        });
+    }
     /**
      * called to provide a hint that data tied to a certain region
      * will not be needed for the forseeable future and can be purged
      * from caches, etc
      */
-    default_1.prototype.freeResources = function ( /* { region } */) { };
-    default_1.capabilities = ['hasLocalStats'];
-    return default_1;
-}(BaseAdapter_1.BaseFeatureDataAdapter));
+    freeResources( /* { region } */) { }
+}
 exports.default = default_1;
+default_1.capabilities = ['hasLocalStats'];
 //# sourceMappingURL=GCContentAdapter.js.map

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package/dist/GCContentAdapter/configSchema.js

@@ -1,9 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var configuration_1 = require("@jbrowse/core/configuration");
-exports.default = (function (pluginManager) {
+const configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (pluginManager) => {
     return (0, configuration_1.ConfigurationSchema)('GCContentAdapter', {
         sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
     }, { explicitlyTyped: true });
-});
+};
 //# sourceMappingURL=configSchema.js.map

package/dist/GCContentAdapter/configSchema.js.map

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

package/dist/GCContentAdapter/index.d.ts

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

package/dist/GCContentAdapter/index.js

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

package/dist/GCContentAdapter/index.js.map

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

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -6,8 +6,9 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends BaseSequenceAdapter {
-    protected fasta: IndexedFasta;
-    protected header?: Promise<string>;
+    protected setupP?: Promise<{
+        fasta: IndexedFasta;
+    }>;
     private seqCache;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): Promise<string[]>;
@@ -16,7 +17,13 @@ export default class extends BaseSequenceAdapter {
         start: number;
         end: number;
     }[]>;
+    setupPre(): Promise<{
+        fasta: IndexedFasta;
+    }>;
     getHeader(): Promise<string | null>;
+    setup(): Promise<{
+        fasta: IndexedFasta;
+    }>;
     getFeatures(region: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     /**
      * called to provide a hint that data tied to a certain region