@jbrowse/plugin-comparative-adapters 2.17.0 → 3.0.0

package/dist/DeltaAdapter/configSchema.d.ts

@@ -1,33 +1,19 @@
 declare const DeltaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     deltaLocation: {
         type: string;
         defaultValue: {

package/dist/DeltaAdapter/configSchema.js

@@ -1,41 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config DeltaAdapter
- * #category adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const DeltaAdapter = (0, configuration_1.ConfigurationSchema)('DeltaAdapter', {
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the target assembly name',
     },
-    /**
-     * #slot
-     * alternative to assembly names
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the query assembly name',
     },
-    /**
-     * #slot
-     */
     deltaLocation: {
         type: 'fileLocation',
         defaultValue: {

package/dist/DeltaAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function DeltaAdapterF(pluginManager: PluginManager): void;

package/dist/DeltaAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -35,7 +45,7 @@ function DeltaAdapterF(pluginManager) {
         displayName: 'MUMmer delta adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./DeltaAdapter'))).then(r => r.default),
     }));

package/dist/DeltaAdapter/util.d.ts

@@ -1,5 +1,4 @@
-import type { Buffer } from 'buffer';
-export declare function paf_delta2paf(buffer: Buffer): {
+export declare function paf_delta2paf(buffer: Uint8Array): {
     qname: string;
     qstart: number;
     qend: number;

package/dist/DeltaAdapter/util.js

@@ -1,33 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.paf_delta2paf = paf_delta2paf;
-/* paf2delta from paftools.js in the minimap2 repository, license reproduced below
- *
- * The MIT License
- *
- * Copyright (c) 2018-     Dana-Farber Cancer Institute
- *               2017-2018 Broad Institute, Inc.
- *
- * Permission is hereby granted, free of charge, to any person obtaining
- * a copy of this software and associated documentation files (the
- * "Software"), to deal in the Software without restriction, including
- * without limitation the rights to use, copy, modify, merge, publish,
- * distribute, sublicense, and/or sell copies of the Software, and to
- * permit persons to whom the Software is furnished to do so, subject to
- * the following conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- */
 function paf_delta2paf(buffer) {
     let rname = '';
     let qname = '';
@@ -47,7 +20,7 @@ function paf_delta2paf(buffer) {
     let i = 0;
     const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
-        const n = buffer.indexOf('\n', blockStart);
+        const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
             break;
         }
@@ -125,7 +98,7 @@ function paf_delta2paf(buffer) {
                     }
                     else {
                         cigar.push((1 << 4) | 2);
-                    } // deletion
+                    }
                 }
                 else {
                     const l = -d - 1;
@@ -139,7 +112,7 @@ function paf_delta2paf(buffer) {
                     }
                     else {
                         cigar.push((1 << 4) | 1);
-                    } // insertion
+                    }
                 }
             }
         }

package/dist/GuessAdapter/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function GuessAdapterF(pluginManager: PluginManager): void;

package/dist/GuessAdapter/index.js

@@ -0,0 +1,74 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = GuessAdapterF;
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const syntenyTypes_1 = require("../syntenyTypes");
+function GuessAdapterF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
+        return (file, index, adapterHint) => {
+            const fileName = (0, tracks_1.getFileName)(file);
+            const indexName = index && (0, tracks_1.getFileName)(index);
+            if ((0, util_1.testAdapter)(fileName, /\.paf(.gz)?/i, adapterHint, 'PAFAdapter')) {
+                return {
+                    type: 'PAFAdapter',
+                    pafLocation: file,
+                };
+            }
+            else if (adapterHint === 'BlastTabularAdapter') {
+                return {
+                    type: 'BlastTabularAdapter',
+                    blastTableLocation: file,
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.anchors.simple(.gz)?/i, adapterHint, 'MCScanSimpleAnchorsAdapter')) {
+                return {
+                    type: 'MCScanSimpleAnchorsAdapter',
+                    mcscanSimpleAnchorsLocation: file,
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.anchors(.gz)?/i, adapterHint, 'MCScanAnchorsAdapter')) {
+                return {
+                    type: 'MCScanAnchorsAdapter',
+                    mcscanAnchorsLocation: file,
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.delta(.gz)?/i, adapterHint, 'DeltaAdapter')) {
+                return {
+                    type: 'DeltaAdapter',
+                    deltaLocation: file,
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.chain(.gz)?/i, adapterHint, 'ChainAdapter')) {
+                return {
+                    type: 'ChainAdapter',
+                    chainLocation: file,
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.out(.gz)?/i, adapterHint, 'MashMapAdapter')) {
+                return {
+                    type: 'MashMapAdapter',
+                    outLocation: file,
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.pif\.gz/i, adapterHint, 'PairwiseIndexedPAFAdapter')) {
+                return {
+                    type: 'PairwiseIndexedPAFAdapter',
+                    pifGzLocation: file,
+                    index: {
+                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
+                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else {
+                return adapterGuesser(file, index, adapterHint);
+            }
+        };
+    });
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
+        return (adapterName) => syntenyTypes_1.syntenyTypes.includes(adapterName)
+            ? 'SyntenyTrack'
+            : trackTypeGuesser(adapterName);
+    });
+}

package/dist/MCScanAddTrackComponent/MCScanAddTrackComponent.d.ts

@@ -0,0 +1,2 @@
+declare const MCScanAddTrackComponent: ({ model }: any) => import("react/jsx-runtime").JSX.Element;
+export default MCScanAddTrackComponent;

package/dist/MCScanAddTrackComponent/MCScanAddTrackComponent.js

@@ -0,0 +1,39 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const MCScanAddTrackComponent = (0, mobx_react_1.observer)(function ({ model }) {
+    var _a, _b;
+    const session = (0, util_1.getSession)(model);
+    const [r0, setR0] = (0, react_1.useState)((_a = session.assemblies[0]) === null || _a === void 0 ? void 0 : _a.name);
+    const [r1, setR1] = (0, react_1.useState)((_b = session.assemblies[0]) === null || _b === void 0 ? void 0 : _b.name);
+    const [bed1Location, setBed1Location] = (0, react_1.useState)();
+    const [bed2Location, setBed2Location] = (0, react_1.useState)();
+    (0, react_1.useEffect)(() => {
+        model.setMixinData({
+            adapter: {
+                assemblyNamees: [r0, r1],
+                bed1Location,
+                bed2Location,
+            },
+        });
+    }, [model, bed1Location, bed2Location, r0, r1]);
+    return ((0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 20 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "JBrowse requires the two BED files that specify the genomic locations of the genes in the .anchors files" }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { session: session, label: "BED1 assembly", helperText: "", selected: r0, onChange: asm => {
+                    setR0(asm);
+                }, TextFieldProps: {
+                    fullWidth: true,
+                } }), (0, jsx_runtime_1.jsx)(ui_1.AssemblySelector, { session: session, label: "BED2 assembly", helperText: "", selected: r1, onChange: asm => {
+                    setR1(asm);
+                }, TextFieldProps: {
+                    fullWidth: true,
+                } }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: "BED1", inline: true, description: "", location: bed1Location, setLocation: loc => {
+                    setBed1Location(loc);
+                } }), (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { name: "BED2", inline: true, description: "", location: bed2Location, setLocation: loc => {
+                    setBed2Location(loc);
+                } })] }));
+});
+exports.default = MCScanAddTrackComponent;

package/dist/MCScanAddTrackComponent/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function MCScanAddTrackComponentF(pluginManager: PluginManager): void;

package/dist/MCScanAddTrackComponent/index.js

@@ -0,0 +1,46 @@
+"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 () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = MCScanAddTrackComponentF;
+const react_1 = require("react");
+const syntenyTypes_1 = require("../syntenyTypes");
+const MCScanAddTrackComponent = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./MCScanAddTrackComponent'))));
+function MCScanAddTrackComponentF(pluginManager) {
+    pluginManager.addToExtensionPoint('Core-addTrackComponent', (comp, { model }) => {
+        return syntenyTypes_1.mcscanTypes.includes(model.trackAdapterType)
+            ? MCScanAddTrackComponent
+            : comp;
+    });
+}

package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts

@@ -1,5 +1,6 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 interface BareFeature {
     strand: number;
     refName: string;
@@ -24,11 +25,6 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources(): void;
 }
 export {};

package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const util_2 = require("../util");
 class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -42,9 +42,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         };
     }
     async hasDataForRefName() {
-        // determining this properly is basically a call to getFeatures so is not
-        // really that important, and has to be true or else getFeatures is never
-        // called (BaseFeatureDataAdapter filters it out)
         return true;
     }
     getAssemblyNames() {
@@ -53,7 +50,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getRefNames(opts = {}) {
         var _a;
-        // @ts-expect-error
         const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
         const { feats } = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
@@ -70,8 +66,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { assemblyNames, feats } = await this.setup(opts);
-            // The index of the assembly name in the region list corresponds to
-            // the adapter in the subadapters list
             const index = assemblyNames.indexOf(region.assemblyName);
             if (index !== -1) {
                 const flip = index === 0;
@@ -84,8 +78,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                             ...f1,
                             uniqueId: `${index}-${rowNum}`,
                             syntenyId: rowNum,
-                            // note: strand would be -1 if the two features are on opposite
-                            // strands, indicating inverted alignment
                             strand: f1.strand * f2.strand,
                             assemblyName: assemblyNames[+!flip],
                             score,
@@ -100,12 +92,7 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = MCScanAnchorsAdapter;

package/dist/MCScanAnchorsAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     mcscanAnchorsLocation: {
         type: string;
         defaultValue: {
@@ -9,9 +6,6 @@ declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configur
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     bed1Location: {
         type: string;
         defaultValue: {
@@ -19,9 +13,6 @@ declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configur
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     bed2Location: {
         type: string;
         defaultValue: {
@@ -29,9 +20,6 @@ declare const MCScanAnchorsAdapter: import("@jbrowse/core/configuration/configur
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];

package/dist/MCScanAnchorsAdapter/configSchema.js

@@ -1,14 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config MCScanAnchorsAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const MCScanAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanAnchorsAdapter', {
-    /**
-     * #slot
-     */
     mcscanAnchorsLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -16,9 +10,6 @@ const MCScanAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanAnc
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed1Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -26,9 +17,6 @@ const MCScanAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanAnc
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     bed2Location: {
         type: 'fileLocation',
         defaultValue: {
@@ -36,9 +24,6 @@ const MCScanAnchorsAdapter = (0, configuration_1.ConfigurationSchema)('MCScanAnc
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],

package/dist/MCScanAnchorsAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function MCScanAnchorsAdapterF(pluginManager: PluginManager): void;

package/dist/MCScanAnchorsAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -35,7 +45,7 @@ function MCScanAnchorsAdapterF(pluginManager) {
         displayName: 'MCScan anchors adapter',
         configSchema: configSchema_1.default,
         adapterMetadata: {
-            hiddenFromGUI: true,
+            category: 'Synteny adapters',
         },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./MCScanAnchorsAdapter'))).then(r => r.default),
     }));

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts

@@ -1,6 +1,7 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util/simpleFeature';
+import type { Region } from '@jbrowse/core/util/types';
 interface BareFeature {
     refName: string;
     start: number;
@@ -32,11 +33,6 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
     getAssemblyNames(): string[];
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
     freeResources(): void;
 }
 export {};

package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const io_1 = require("@jbrowse/core/util/io");
 const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const util_2 = require("../util");
@@ -56,9 +56,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         };
     }
     async hasDataForRefName() {
-        // determining this properly is basically a call to getFeatures
-        // so is not really that important, and has to be true or else
-        // getFeatures is never called (BaseFeatureDataAdapter filters it out)
         return true;
     }
     getAssemblyNames() {
@@ -67,7 +64,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async getRefNames(opts = {}) {
         var _a;
-        // @ts-expect-error
         const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
         const { feats } = await this.setup(opts);
         const idx = this.getAssemblyNames().indexOf(r1);
@@ -91,8 +87,6 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { assemblyNames, feats } = await this.setup(opts);
-            // The index of the assembly name in the region list corresponds to
-            // the adapter in the subadapters list
             const index = assemblyNames.indexOf(region.assemblyName);
             if (index !== -1) {
                 const flip = index === 0;
@@ -132,12 +126,7 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    /**
-     * called to provide a hint that data tied to a certain region
-     * will not be needed for the foreseeable future and can be purged
-     * from caches, etc
-     */
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 MCScanAnchorsAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = MCScanAnchorsAdapter;