@jbrowse/plugin-sequence 3.6.5 → 4.0.0

package/dist/createExtensionPoints.d.ts

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

package/dist/createExtensionPoints.js

@@ -1,86 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = ExtensionPointsF;
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function ExtensionPointsF(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const regexGuess = /\.2bit$/i;
-            const adapterName = 'TwoBitAdapter';
-            const fileName = (0, tracks_1.getFileName)(file);
-            const obj = {
-                type: adapterName,
-                twoBitLocation: file,
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
-            }
-            if (adapterHint === adapterName) {
-                return obj;
-            }
-            return adapterGuesser(file, index, adapterHint);
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-        return (adapterName) => {
-            if (adapterName === 'TwoBitAdapter') {
-                return 'ReferenceSequenceTrack';
-            }
-            return trackTypeGuesser(adapterName);
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const regexGuess = /\.(fa|fasta|fas|fna|mfa)$/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;
-            }
-            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;
-            }
-            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);
-        };
-    });
-}

package/dist/index.d.ts

@@ -1,6 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default class SequencePlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}

package/dist/index.js

@@ -1,35 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const BgzipFastaAdapter_1 = __importDefault(require("./BgzipFastaAdapter"));
-const ChromSizesAdapter_1 = __importDefault(require("./ChromSizesAdapter"));
-const DivSequenceRenderer_1 = __importDefault(require("./DivSequenceRenderer"));
-const IndexedFastaAdapter_1 = __importDefault(require("./IndexedFastaAdapter"));
-const LinearReferenceSequenceDisplay_1 = __importDefault(require("./LinearReferenceSequenceDisplay"));
-const ReferenceSequenceTrack_1 = __importDefault(require("./ReferenceSequenceTrack"));
-const SequenceSearchAdapter_1 = __importDefault(require("./SequenceSearchAdapter"));
-const TwoBitAdapter_1 = __importDefault(require("./TwoBitAdapter"));
-const UnindexedFastaAdapter_1 = __importDefault(require("./UnindexedFastaAdapter"));
-const createExtensionPoints_1 = __importDefault(require("./createExtensionPoints"));
-class SequencePlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'SequencePlugin';
-    }
-    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, UnindexedFastaAdapter_1.default)(pluginManager);
-        (0, SequenceSearchAdapter_1.default)(pluginManager);
-        (0, ReferenceSequenceTrack_1.default)(pluginManager);
-        (0, LinearReferenceSequenceDisplay_1.default)(pluginManager);
-        (0, createExtensionPoints_1.default)(pluginManager);
-    }
-}
-exports.default = SequencePlugin;