@jbrowse/plugin-sequence 2.0.0 → 2.1.2

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

package/dist/TwoBitAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/TwoBitAdapter/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,eAAe;QACrB,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,CAAC,kDAAO,iBAAiB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACtE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/dist/createExtensionPoints.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/createExtensionPoints.js

@@ -0,0 +1,86 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const tracks_1 = require("@jbrowse/core/util/tracks");
+exports.default = (pluginManager) => {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.2bit$/i;
+            const adapterName = 'TwoBitAdapter';
+            const fileName = (0, tracks_1.getFileName)(file);
+            const obj = {
+                type: adapterName,
+                twoBitLocation: file,
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => {
+            if (adapterName === 'TwoBitAdapter') {
+                return 'ReferenceSequenceTrack';
+            }
+            return trackTypeGuesser(adapterName);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i;
+            const adapterName = 'IndexedFastaAdapter';
+            const fileName = (0, tracks_1.getFileName)(file);
+            const obj = {
+                type: adapterName,
+                fastaLocation: file,
+                faiLocation: index || (0, tracks_1.makeIndex)(file, '.fai'),
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => {
+            if (adapterName === 'IndexedFastaAdapter') {
+                return 'ReferenceSequenceTrack';
+            }
+            return trackTypeGuesser(adapterName);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i;
+            const adapterName = 'BgzipFastaAdapter';
+            const fileName = (0, tracks_1.getFileName)(file);
+            const obj = {
+                type: adapterName,
+                faiLocation: (0, tracks_1.makeIndex)(file, '.fai'),
+                gziLocation: (0, tracks_1.makeIndex)(file, '.gzi'),
+            };
+            if (regexGuess.test(fileName) && !adapterHint) {
+                return obj;
+            }
+            else if (adapterHint === adapterName) {
+                return obj;
+            }
+            return adapterGuesser(file, index, adapterHint);
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => {
+            if (adapterName === 'BgzipFastaAdapter') {
+                return 'ReferenceSequenceTrack';
+            }
+            return trackTypeGuesser(adapterName);
+        };
+    });
+};
+//# sourceMappingURL=createExtensionPoints.js.map

package/dist/createExtensionPoints.js.map

@@ -0,0 +1 @@
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package/dist/index.js

@@ -1,270 +1,36 @@
 "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 __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 });
-var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-var models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-var FeatureRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType"));
-var TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-var tracks_1 = require("@jbrowse/core/util/tracks");
-var BgzipFastaAdapter_1 = require("./BgzipFastaAdapter");
-var ChromSizesAdapter_1 = require("./ChromSizesAdapter");
-var DivSequenceRenderer_1 = require("./DivSequenceRenderer");
-var IndexedFastaAdapter_1 = require("./IndexedFastaAdapter");
-var LinearReferenceSequenceDisplay_1 = require("./LinearReferenceSequenceDisplay");
-var TwoBitAdapter_1 = require("./TwoBitAdapter");
-var GCContentAdapter_1 = __importDefault(require("./GCContentAdapter"));
-var referenceSeqTrackConfig_1 = require("./referenceSeqTrackConfig");
-/* adjust in both directions */
-var DivSequenceRenderer = /** @class */ (function (_super) {
-    __extends(DivSequenceRenderer, _super);
-    function DivSequenceRenderer() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.supportsSVG = true;
-        return _this;
+const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+const TwoBitAdapter_1 = __importDefault(require("./TwoBitAdapter"));
+const DivSequenceRenderer_1 = __importDefault(require("./DivSequenceRenderer"));
+const BgzipFastaAdapter_1 = __importDefault(require("./BgzipFastaAdapter"));
+const ChromSizesAdapter_1 = __importDefault(require("./ChromSizesAdapter"));
+const IndexedFastaAdapter_1 = __importDefault(require("./IndexedFastaAdapter"));
+const GCContentAdapter_1 = __importDefault(require("./GCContentAdapter"));
+const SequenceSearchAdapter_1 = __importDefault(require("./SequenceSearchAdapter"));
+const ReferenceSequenceTrack_1 = __importDefault(require("./ReferenceSequenceTrack"));
+const LinearReferenceSequenceDisplay_1 = __importDefault(require("./LinearReferenceSequenceDisplay"));
+const createExtensionPoints_1 = __importDefault(require("./createExtensionPoints"));
+class SequencePlugin extends Plugin_1.default {
+    constructor() {
+        super(...arguments);
+        this.name = 'SequencePlugin';
     }
-    DivSequenceRenderer.prototype.getExpandedRegion = function (region) {
-        return __assign(__assign({}, region), { start: Math.max(region.start - 3, 0), end: region.end + 3 });
-    };
-    return DivSequenceRenderer;
-}(FeatureRendererType_1.default));
-var SequencePlugin = /** @class */ (function (_super) {
-    __extends(SequencePlugin, _super);
-    function SequencePlugin() {
-        var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this.name = 'SequencePlugin';
-        return _this;
+    install(pluginManager) {
+        (0, DivSequenceRenderer_1.default)(pluginManager);
+        (0, TwoBitAdapter_1.default)(pluginManager);
+        (0, BgzipFastaAdapter_1.default)(pluginManager);
+        (0, ChromSizesAdapter_1.default)(pluginManager);
+        (0, IndexedFastaAdapter_1.default)(pluginManager);
+        (0, GCContentAdapter_1.default)(pluginManager);
+        (0, SequenceSearchAdapter_1.default)(pluginManager);
+        (0, ReferenceSequenceTrack_1.default)(pluginManager);
+        (0, LinearReferenceSequenceDisplay_1.default)(pluginManager);
+        (0, createExtensionPoints_1.default)(pluginManager);
     }
-    SequencePlugin.prototype.install = function (pluginManager) {
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'TwoBitAdapter',
-                configSchema: TwoBitAdapter_1.configSchema,
-                adapterMetadata: {
-                    category: null,
-                    hiddenFromGUI: true,
-                    displayName: null,
-                    description: null,
-                },
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./TwoBitAdapter/TwoBitAdapter')); }).then(function (r) { return r.default; });
-                },
-            });
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-            return function (file, index, adapterHint) {
-                var regexGuess = /\.2bit$/i;
-                var adapterName = 'TwoBitAdapter';
-                var fileName = (0, tracks_1.getFileName)(file);
-                var obj = {
-                    type: adapterName,
-                    twoBitLocation: file,
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
-            return function (adapterName) {
-                if (adapterName === 'TwoBitAdapter') {
-                    return 'ReferenceSequenceTrack';
-                }
-                return trackTypeGuesser(adapterName);
-            };
-        });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'ChromSizesAdapter',
-                configSchema: ChromSizesAdapter_1.configSchema,
-                adapterMetadata: {
-                    category: null,
-                    hiddenFromGUI: true,
-                    displayName: null,
-                    description: null,
-                },
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./ChromSizesAdapter/ChromSizesAdapter')); }).then(function (r) { return r.default; });
-                },
-            });
-        });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'IndexedFastaAdapter',
-                configSchema: IndexedFastaAdapter_1.configSchema,
-                adapterMetadata: {
-                    category: null,
-                    hiddenFromGUI: true,
-                    displayName: null,
-                    description: null,
-                },
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./IndexedFastaAdapter/IndexedFastaAdapter')); }).then(function (r) { return r.default; });
-                },
-            });
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-            return function (file, index, adapterHint) {
-                var regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i;
-                var adapterName = 'IndexedFastaAdapter';
-                var fileName = (0, tracks_1.getFileName)(file);
-                var obj = {
-                    type: adapterName,
-                    fastaLocation: file,
-                    faiLocation: index || (0, tracks_1.makeIndex)(file, '.fai'),
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
-            return function (adapterName) {
-                if (adapterName === 'IndexedFastaAdapter') {
-                    return 'ReferenceSequenceTrack';
-                }
-                return trackTypeGuesser(adapterName);
-            };
-        });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default({
-                name: 'BgzipFastaAdapter',
-                configSchema: BgzipFastaAdapter_1.configSchema,
-                adapterMetadata: {
-                    category: null,
-                    hiddenFromGUI: true,
-                    displayName: null,
-                    description: null,
-                },
-                getAdapterClass: function () {
-                    return Promise.resolve().then(function () { return __importStar(require('./BgzipFastaAdapter/BgzipFastaAdapter')); }).then(function (r) { return r.default; });
-                },
-            });
-        });
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-            return function (file, index, adapterHint) {
-                var regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i;
-                var adapterName = 'BgzipFastaAdapter';
-                var fileName = (0, tracks_1.getFileName)(file);
-                var obj = {
-                    type: adapterName,
-                    faiLocation: (0, tracks_1.makeIndex)(file, '.fai'),
-                    gziLocation: (0, tracks_1.makeIndex)(file, '.gzi'),
-                };
-                if (regexGuess.test(fileName) && !adapterHint) {
-                    return obj;
-                }
-                else if (adapterHint === adapterName) {
-                    return obj;
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
-            return function (adapterName) {
-                if (adapterName === 'BgzipFastaAdapter') {
-                    return 'ReferenceSequenceTrack';
-                }
-                return trackTypeGuesser(adapterName);
-            };
-        });
-        pluginManager.addAdapterType(function () {
-            return new AdapterType_1.default(__assign({ name: 'GCContentAdapter', adapterMetadata: {
-                    category: null,
-                    hiddenFromGUI: true,
-                    displayName: null,
-                    description: null,
-                } }, pluginManager.load(GCContentAdapter_1.default)));
-        });
-        pluginManager.addTrackType(function () {
-            var configSchema = (0, referenceSeqTrackConfig_1.createReferenceSeqTrackConfig)(pluginManager);
-            return new TrackType_1.default({
-                name: 'ReferenceSequenceTrack',
-                configSchema: configSchema,
-                stateModel: (0, models_1.createBaseTrackModel)(pluginManager, 'ReferenceSequenceTrack', configSchema),
-            });
-        });
-        pluginManager.addDisplayType(function () {
-            var stateModel = (0, LinearReferenceSequenceDisplay_1.modelFactory)(LinearReferenceSequenceDisplay_1.configSchema);
-            return {
-                name: 'LinearReferenceSequenceDisplay',
-                configSchema: LinearReferenceSequenceDisplay_1.configSchema,
-                stateModel: stateModel,
-                trackType: 'ReferenceSequenceTrack',
-                viewType: 'LinearGenomeView',
-                ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
-            };
-        });
-        pluginManager.addRendererType(function () {
-            return new DivSequenceRenderer({
-                name: 'DivSequenceRenderer',
-                ReactComponent: DivSequenceRenderer_1.ReactComponent,
-                configSchema: DivSequenceRenderer_1.configSchema,
-                pluginManager: pluginManager,
-            });
-        });
-    };
-    return SequencePlugin;
-}(Plugin_1.default));
+}
 exports.default = SequencePlugin;
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;AAAA,kEAAyC;AAGzC,oEAA4C;AAC5C,gFAAwD;AACxD,4EAAoD;AACpD,4EAAoD;AACpD,gFAAwD;AACxD,0EAAkD;AAClD,oFAA4D;AAC5D,sFAA8D;AAC9D,sGAA8E;AAC9E,oFAA2D;AAE3D,MAAqB,cAAe,SAAQ,gBAAM;IAAlD;;QACE,SAAI,GAAG,gBAAgB,CAAA;IAczB,CAAC;IAZC,OAAO,CAAC,aAA4B;QAClC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,uBAAc,EAAC,aAAa,CAAC,CAAA;QAC7B,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,2BAAkB,EAAC,aAAa,CAAC,CAAA;QACjC,IAAA,6BAAoB,EAAC,aAAa,CAAC,CAAA;QACnC,IAAA,0BAAiB,EAAC,aAAa,CAAC,CAAA;QAChC,IAAA,+BAAsB,EAAC,aAAa,CAAC,CAAA;QACrC,IAAA,gCAAuB,EAAC,aAAa,CAAC,CAAA;QACtC,IAAA,wCAA+B,EAAC,aAAa,CAAC,CAAA;QAC9C,IAAA,+BAAqB,EAAC,aAAa,CAAC,CAAA;IACtC,CAAC;CACF;AAfD,iCAeC"}

package/esm/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/esm/BgzipFastaAdapter/index.js

@@ -1,2 +1,16 @@
-export { default as configSchema } from './configSchema';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'BgzipFastaAdapter',
+        configSchema,
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        getAdapterClass: () => import('./BgzipFastaAdapter').then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/BgzipFastaAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BgzipFastaAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AAEzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,mBAAmB;QACzB,YAAY;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,MAAM,CAAC,qBAAqB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACrD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}

package/esm/ChromSizesAdapter/ChromSizesAdapter.d.ts

@@ -1,19 +1,19 @@
 import { RegionsAdapter, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Instance } from 'mobx-state-tree';
-import MyConfigSchema from './configSchema';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class extends BaseAdapter implements RegionsAdapter {
-    protected refSeqs: Promise<Record<string, number>>;
-    protected source: string;
-    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    private init;
+    protected setupP?: Promise<{
+        [key: string]: number;
+    }>;
+    setupPre(): Promise<{
+        [k: string]: number;
+    }>;
+    setup(): Promise<{
+        [key: string]: number;
+    }>;
     getRegions(): Promise<{
         refName: string;
         start: number;
         end: number;
     }[]>;
-    getFeatures(): void;
     getHeader(): {};
     freeResources(): void;
 }

package/esm/ChromSizesAdapter/ChromSizesAdapter.js

@@ -1,42 +1,36 @@
 import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { openLocation } from '@jbrowse/core/util/io';
-import { readConfObject } from '@jbrowse/core/configuration';
 export default class extends BaseAdapter {
-    constructor(config, getSubAdapter, pluginManager) {
-        super(config, getSubAdapter, pluginManager);
-        const chromSizesLocation = readConfObject(config, 'chromSizesLocation');
-        if (!chromSizesLocation) {
-            throw new Error('must provide chromSizesLocation');
-        }
-        const file = openLocation(chromSizesLocation, this.pluginManager);
-        this.source = file.toString();
-        this.refSeqs = this.init(file);
-    }
-    async init(file) {
+    async setupPre() {
+        const pm = this.pluginManager;
+        const file = openLocation(this.getConf('chromSizesLocation'), pm);
         const data = await file.readFile('utf8');
-        const refSeqs = {};
-        if (!data.length) {
-            throw new Error(`Could not read file ${file.toString()}`);
+        return Object.fromEntries(data
+            .split('\n')
+            .map(f => f.trim())
+            .filter(f => !!f)
+            .map((line) => {
+            const [name, length] = line.split('\t');
+            return [name, +length];
+        }));
+    }
+    async setup() {
+        if (!this.setupP) {
+            this.setupP = this.setupPre().catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
         }
-        data.split('\n').forEach((line) => {
-            if (line.length) {
-                const [name, length] = line.split('\t');
-                refSeqs[name] = +length;
-            }
-        });
-        return refSeqs;
+        return this.setupP;
     }
     async getRegions() {
-        const refSeqs = await this.refSeqs;
+        const refSeqs = await this.setup();
         return Object.keys(refSeqs).map(refName => ({
             refName,
             start: 0,
             end: refSeqs[refName],
         }));
     }
-    getFeatures() {
-        throw new Error('sequence not available');
-    }
     getHeader() {
         return {};
     }

package/esm/ChromSizesAdapter/ChromSizesAdapter.js.map

@@ -1 +1 @@
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package/esm/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/esm/ChromSizesAdapter/index.js

@@ -1,2 +1,16 @@
-export { default as configSchema } from './configSchema';
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default (pluginManager) => {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'ChromSizesAdapter',
+        configSchema,
+        adapterMetadata: {
+            category: null,
+            hiddenFromGUI: true,
+            displayName: null,
+            description: null,
+        },
+        getAdapterClass: () => import('./ChromSizesAdapter').then(r => r.default),
+    }));
+};
 //# sourceMappingURL=index.js.map

package/esm/ChromSizesAdapter/index.js.map

@@ -1 +1 @@
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