@jbrowse/plugin-legacy-jbrowse 3.6.5 → 4.0.0

package/dist/JBrowse1Connection/jb1ToJb2.js

@@ -1,408 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.convertTrackConfig = convertTrackConfig;
-exports.createRefSeqsAdapter = createRefSeqsAdapter;
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
-    var _a, _b, _c, _d, _e;
-    const jb2TrackConfig = {
-        trackId: (0, util_1.objectHash)(jb1TrackConfig),
-        name: jb1TrackConfig.key || jb1TrackConfig.label,
-    };
-    const description = jb1TrackConfig.metadata &&
-        (jb1TrackConfig.metadata.description || jb1TrackConfig.metadata.Description);
-    if (description) {
-        jb2TrackConfig.description = description;
-    }
-    const category = jb1TrackConfig.category || ((_a = jb1TrackConfig.metadata) === null || _a === void 0 ? void 0 : _a.category);
-    jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
-    const { storeClass } = jb1TrackConfig;
-    if (!jb1TrackConfig.urlTemplate) {
-        if (!(storeClass === null || storeClass === void 0 ? void 0 : storeClass.endsWith('FromConfig'))) {
-            const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
-            console.warn(`Could not import JBrowse1 track "${trackIdentifier}" because it does not have a "urlTemplate" or is not a "FromConfig" track`);
-            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
-        }
-        return generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig);
-    }
-    const resolveUrlTemplate = (urlTemplate) => {
-        return new URL(urlTemplate, `${dataRoot}/`).href
-            .replaceAll(/%7B/gi, '{')
-            .replaceAll(/%7D/gi, '}');
-    };
-    const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate);
-    if (storeClass) {
-        if (storeClass === 'JBrowse/Store/SeqFeature/BAM') {
-            const adapter = {
-                type: 'BamAdapter',
-                bamLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-            };
-            if (jb1TrackConfig.baiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                };
-            }
-            else if (jb1TrackConfig.csiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                    indexType: 'CSI',
-                };
-            }
-            else {
-                adapter.index = {
-                    location: { uri: `${urlTemplate}.bai`, locationType: 'UriLocation' },
-                };
-            }
-            return {
-                ...jb2TrackConfig,
-                type: 'AlignmentsTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/CRAM') {
-            const adapter = {
-                type: 'CramAdapter',
-                cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                sequenceAdapter,
-            };
-            adapter.craiLocation = jb1TrackConfig.craiUrlTemplate
-                ? {
-                    uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
-                    locationType: 'UriLocation',
-                }
-                : {
-                    uri: `${urlTemplate}.crai`,
-                    locationType: 'UriLocation',
-                };
-            return {
-                ...jb2TrackConfig,
-                type: 'AlignmentsTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/NCList') {
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter: {
-                    type: 'NCListAdapter',
-                    rootUrlTemplate: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
-            storeClass === 'JBrowse/Store/BigWig') {
-            if ((_b = jb1TrackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('XYPlot')) {
-                jb2TrackConfig.defaultRendering = 'xyplot';
-            }
-            else if ((_c = jb1TrackConfig.type) === null || _c === void 0 ? void 0 : _c.endsWith('Density')) {
-                jb2TrackConfig.defaultRendering = 'density';
-            }
-            return {
-                ...jb2TrackConfig,
-                type: 'QuantitativeTrack',
-                adapter: {
-                    type: 'BigWigAdapter',
-                    bigWigLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/VCFTabix') {
-            const adapter = {
-                type: 'VcfTabixAdapter',
-                vcfGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-            };
-            if (jb1TrackConfig.tbiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                };
-            }
-            else if (jb1TrackConfig.csiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                    indexType: 'CSI',
-                };
-            }
-            else {
-                adapter.index = {
-                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
-                };
-            }
-            return {
-                ...jb2TrackConfig,
-                type: 'VariantTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/VCFTribble') {
-            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, `VCFTribble (${urlTemplate})`, jb2TrackConfig.category);
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter: {
-                    type: 'Gff3Adapter',
-                    gffLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/GFF3Tabix') {
-            const adapter = {
-                type: 'Gff3TabixAdapter',
-                gffGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-            };
-            if (jb1TrackConfig.tbiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                };
-            }
-            else if (jb1TrackConfig.csiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                    indexType: 'CSI',
-                };
-            }
-            else {
-                adapter.index = {
-                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
-                };
-            }
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/BED') {
-            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, `BED (${urlTemplate})`, jb2TrackConfig.category);
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/BEDTabix') {
-            const adapter = {
-                type: 'BedTabixAdapter',
-                bedGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-            };
-            if (jb1TrackConfig.tbiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                };
-            }
-            else if (jb1TrackConfig.csiUrlTemplate) {
-                adapter.index = {
-                    location: {
-                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-                        locationType: 'UriLocation',
-                    },
-                    indexType: 'CSI',
-                };
-            }
-            else {
-                adapter.index = {
-                    location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
-                };
-            }
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {
-            return {
-                ...jb2TrackConfig,
-                type: 'FeatureTrack',
-                adapter: {
-                    type: 'GtfAdapter',
-                    gtfLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' ||
-            storeClass === 'JBrowse/Store/Sequence/StaticChunked') {
-            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, `StaticChunked (${urlTemplate})`, jb2TrackConfig.category);
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/UnindexedFasta') {
-            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, `UnindexedFasta (${urlTemplate})`, jb2TrackConfig.category);
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta') {
-            const adapter = {
-                type: 'IndexedFastaAdapter',
-                fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-            };
-            adapter.faiLocation = jb1TrackConfig.faiUrlTemplate
-                ? {
-                    uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-                    locationType: 'UriLocation',
-                }
-                : {
-                    uri: `${urlTemplate}.fai`,
-                    locationType: 'UriLocation',
-                };
-            return {
-                ...jb2TrackConfig,
-                type: 'SequenceTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta') {
-            const adapter = {
-                type: 'BgzipFastaAdapter',
-                fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-            };
-            adapter.faiLocation = jb1TrackConfig.faiUrlTemplate
-                ? {
-                    uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-                    locationType: 'UriLocation',
-                }
-                : {
-                    uri: `${urlTemplate}.fai`,
-                    locationType: 'UriLocation',
-                };
-            adapter.gziLocation = jb1TrackConfig.gziUrlTemplate
-                ? {
-                    uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
-                    locationType: 'UriLocation',
-                }
-                : {
-                    uri: `${urlTemplate}.gzi`,
-                    locationType: 'UriLocation',
-                };
-            return {
-                ...jb2TrackConfig,
-                type: 'ReferenceSequenceTrack',
-                adapter,
-            };
-        }
-        if (storeClass === 'JBrowse/Store/SeqFeature/TwoBit') {
-            return {
-                ...jb2TrackConfig,
-                type: 'ReferenceSequenceTrack',
-                adapter: {
-                    type: 'TwoBitAdapter',
-                    twoBitLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-                },
-            };
-        }
-    }
-    jb2TrackConfig.adapter = (0, tracks_1.guessAdapter)({ uri: urlTemplate, locationType: 'UriLocation' }, undefined, urlTemplate);
-    if (jb2TrackConfig.adapter.type === tracks_1.UNSUPPORTED) {
-        return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
-    }
-    if (jb2TrackConfig.adapter.type === tracks_1.UNKNOWN) {
-        return (0, tracks_1.generateUnknownTrackConf)(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
-    }
-    jb2TrackConfig.type = (0, tracks_1.guessTrackType)(jb2TrackConfig.adapter.type);
-    if (jb2TrackConfig.type === 'QuantitativeTrack') {
-        if ((_d = jb1TrackConfig.type) === null || _d === void 0 ? void 0 : _d.endsWith('XYPlot')) {
-            jb2TrackConfig.defaultRendering = 'xyplot';
-        }
-        else if ((_e = jb1TrackConfig.type) === null || _e === void 0 ? void 0 : _e.endsWith('Density')) {
-            jb2TrackConfig.defaultRendering = 'density';
-        }
-    }
-    return jb2TrackConfig;
-}
-function generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig) {
-    const jb1Features = jb1TrackConfig.features || [];
-    const jb2Features = jb1Features.map((feature) => {
-        const jb2Feature = JSON.parse(JSON.stringify(feature));
-        jb2Feature.refName = feature.seq_id;
-        jb2Feature.uniqueId = `${feature.seq_id}:${feature.start}-${feature.end}:${feature.name || ''}`;
-        return jb2Feature;
-    });
-    jb2TrackConfig.adapter = {
-        type: 'FromConfigAdapter',
-        features: jb2Features,
-    };
-    jb2TrackConfig.type = 'FeatureTrack';
-    return jb2TrackConfig;
-}
-async function createRefSeqsAdapter(refSeqs) {
-    if (typeof refSeqs === 'string') {
-        refSeqs = {
-            url: refSeqs,
-        };
-    }
-    if (refSeqs.url) {
-        if (/.fai$/.exec(refSeqs.url)) {
-            return {
-                type: 'IndexedFastaAdapter',
-                fastaLocation: {
-                    uri: refSeqs.url.slice(0, -4),
-                    locationType: 'UriLocation',
-                },
-                faiLocation: {
-                    uri: refSeqs.url,
-                    locationType: 'UriLocation',
-                },
-            };
-        }
-        if (/.2bit$/.exec(refSeqs.url)) {
-            return {
-                type: 'TwoBitAdapter',
-                twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },
-            };
-        }
-        if (/.fa$/.exec(refSeqs.url)) {
-            throw new Error('Unindexed FASTA adapter not available');
-        }
-        if (/.sizes/.exec(refSeqs.url)) {
-            throw new Error('chromosome SIZES adapter not available');
-        }
-        const refSeqsJson = await (0, io_1.openLocation)({
-            uri: refSeqs.url,
-            locationType: 'UriLocation',
-        }).readFile('utf8');
-        const refSeqsData = JSON.parse(refSeqsJson);
-        return refSeqAdapterFromConfig(refSeqsData);
-    }
-    if ('data' in refSeqs) {
-        return refSeqAdapterFromConfig(refSeqs.data || []);
-    }
-    throw new Error(`Could not determine adapter for JBrowse1 refSeqs: ${refSeqs.url || JSON.stringify(refSeqs)}`);
-}
-function refSeqAdapterFromConfig(refSeqsData) {
-    const features = refSeqsData.map((refSeq) => ({
-        refName: refSeq.name,
-        uniqueId: refSeq.name,
-        start: refSeq.start,
-        end: refSeq.end,
-    }));
-    return {
-        type: 'FromConfigAdapter',
-        features,
-    };
-}

package/dist/JBrowse1Connection/model.d.ts

@@ -1,75 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    name: import("mobx-state-tree").ISimpleType<string>;
-    tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            type: string;
-            defaultValue: string;
-            description: string;
-        };
-        assemblyNames: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
-} & {
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        dataDirLocation: {
-            type: string;
-            defaultValue: {
-                uri: string;
-                locationType: string;
-            };
-            description: string;
-        };
-        assemblyNames: {
-            description: string;
-            type: string;
-            defaultValue: never[];
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            type: string;
-            defaultValue: string;
-            description: string;
-        };
-        assemblyNames: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
-    type: import("mobx-state-tree").ISimpleType<"JBrowse1Connection">;
-}, {
-    connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
-} & {
-    afterAttach(): void;
-    addTrackConf(trackConf: Record<string, unknown> | ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
-    addTrackConfs(trackConfs: (Record<string, unknown> | ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
-    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
-    clear(): void;
-} & {
-    connect(): Promise<void>;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/JBrowse1Connection/model.js

@@ -1,82 +0,0 @@
-"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;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = stateModelFactory;
-const configuration_1 = require("@jbrowse/core/configuration");
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-const util_1 = require("@jbrowse/core/util");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const configSchema_1 = __importDefault(require("./configSchema"));
-function stateModelFactory(pluginManager) {
-    return mobx_state_tree_1.types
-        .compose('JBrowse1Connection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types.model({
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
-        type: mobx_state_tree_1.types.literal('JBrowse1Connection'),
-    }))
-        .actions(self => ({
-        async connect() {
-            var _a, _b;
-            const session = (0, util_1.getSession)(self);
-            try {
-                const dataDirLocation = (0, configuration_1.getConf)(self, 'dataDirLocation');
-                const { fetchJb1 } = await Promise.resolve().then(() => __importStar(require('./jb1ConfigLoad')));
-                const { convertTrackConfig } = await Promise.resolve().then(() => __importStar(require('./jb1ToJb2')));
-                const config = await fetchJb1(dataDirLocation);
-                const assemblyName = (0, configuration_1.getConf)(self, 'assemblyNames')[0];
-                if (!assemblyName) {
-                    throw new Error('assembly name required for JBrowse 1 connection');
-                }
-                const conf = session.assemblies.find(a => (0, configuration_1.readConfObject)(a, 'name') === assemblyName);
-                if (!conf) {
-                    throw new Error(`Assembly "${assemblyName}" not found`);
-                }
-                const sequenceAdapter = (0, configuration_1.readConfObject)(conf, ['sequence', 'adapter']);
-                const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => ({
-                    ...convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter),
-                    assemblyNames: [assemblyName],
-                }));
-                self.setTrackConfs(jb2Tracks);
-            }
-            catch (error) {
-                console.error(error);
-                session.notifyError(`There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`, error);
-                (_b = session.breakConnection) === null || _b === void 0 ? void 0 : _b.call(session, self.configuration);
-            }
-        },
-    }));
-}

package/dist/JBrowse1Connection/types.d.ts

@@ -1,91 +0,0 @@
-export interface ProtoTrack {
-    backendVersion?: number;
-    baseUrl?: string;
-    category?: string;
-    config?: Track;
-    dataRoot?: string;
-    features?: Feature[];
-    histograms?: Track;
-    index?: number;
-    key?: string;
-    label?: string;
-    metadata?: Metadata;
-    store?: Store | string;
-    storeClass?: string;
-    type?: string;
-    urlTemplate?: string;
-    baiUrlTemplate?: string;
-    craiUrlTemplate?: string;
-    tbiUrlTemplate?: string;
-    csiUrlTemplate?: string;
-    faiUrlTemplate?: string;
-    gziUrlTemplate?: string;
-    useAsRefSeqStore?: boolean;
-}
-export interface Track extends ProtoTrack {
-    label: string;
-}
-export interface Metadata {
-    category?: string;
-    description?: string;
-    Description?: string;
-}
-export interface Feature {
-    seq_id: string;
-    start: number;
-    end: number;
-    name?: string;
-}
-export interface Source {
-    url: string;
-    name?: string;
-    type?: string;
-}
-export interface TrackMetadata {
-    sources?: string | Source | (string | Source)[] | Record<string, Source>;
-}
-export interface Store extends ProtoTrack {
-    name?: string;
-}
-export interface Names {
-    baseUrl?: string;
-}
-export interface RefSeq {
-    name: string;
-    length: number;
-    end: number;
-    start: number;
-}
-export interface RefSeqs {
-    url?: string;
-    data?: RefSeq[];
-}
-export interface Include {
-    url: string;
-    cacheBuster?: boolean;
-    format?: string;
-    version?: number;
-}
-export interface Config {
-    baseUrl?: string;
-    cacheBuster?: boolean;
-    dataRoot?: string;
-    include?: string[];
-    names?: Record<string, string>;
-    nameUrl?: string;
-    refSeqs?: string | RefSeqs;
-    sourceUrl?: string;
-    stores?: Record<string, Store>;
-    trackMetadata?: TrackMetadata;
-    tracks?: Track | Track[] | Record<string, Track | ProtoTrack>;
-}
-export interface UriLocation {
-    uri: string;
-    baseUri?: string;
-    locationType: 'UriLocation';
-}
-export interface LocalPathLocation {
-    localPath: string;
-    locationType: 'LocalPathLocation';
-}
-export type JBLocation = UriLocation | LocalPathLocation;

package/dist/JBrowse1Connection/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/JBrowse1Connection/util.d.ts

@@ -1,8 +0,0 @@
-import type { Source, Track } from './types';
-export declare function isTrack(arg: any): arg is Track;
-export declare function isSource(arg: any): arg is Source;
-type Obj = Record<string, any>;
-export declare function deepUpdate(a: Obj, b: Obj): Obj;
-export declare function fillTemplate(template: string, fillWith: Obj): string;
-export declare function structuredClone(src: any): any;
-export {};