@jbrowse/plugin-sequence 3.6.5 → 4.0.0

package/dist/ChromSizesAdapter/ChromSizesAdapter.js

@@ -1,40 +0,0 @@
-"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");
-class ChromSizesAdapter extends BaseAdapter_1.BaseAdapter {
-    async setupPre() {
-        const pm = this.pluginManager;
-        const file = (0, io_1.openLocation)(this.getConf('chromSizesLocation'), pm);
-        const data = await file.readFile('utf8');
-        return Object.fromEntries(data
-            .split(/\n|\r\n|\r/)
-            .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;
-            });
-        }
-        return this.setupP;
-    }
-    async getRegions() {
-        const refSeqs = await this.setup();
-        return Object.keys(refSeqs).map(refName => ({
-            refName,
-            start: 0,
-            end: refSeqs[refName],
-        }));
-    }
-    getHeader() {
-        return {};
-    }
-}
-exports.default = ChromSizesAdapter;

package/dist/ChromSizesAdapter/configSchema.d.ts

@@ -1,10 +0,0 @@
-declare const ChromSizesAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    chromSizesLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default ChromSizesAdapter;

package/dist/ChromSizesAdapter/configSchema.js

@@ -1,27 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const ChromSizesAdapter = (0, configuration_1.ConfigurationSchema)('ChromSizesAdapter', {
-    chromSizesLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/species.chrom.sizes',
-            locationType: 'UriLocation',
-        },
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                chromSizesLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = ChromSizesAdapter;

package/dist/ChromSizesAdapter/index.d.ts

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

package/dist/ChromSizesAdapter/index.js

@@ -1,52 +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 = ChromSizesAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function ChromSizesAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'ChromSizesAdapter',
-        displayName: 'Chrom sizes adapter',
-        configSchema: configSchema_1.default,
-        adapterMetadata: {
-            hiddenFromGUI: true,
-        },
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./ChromSizesAdapter'))).then(r => r.default),
-    }));
-}

package/dist/DivSequenceRenderer/components/DivSequenceRendering.d.ts

@@ -1,18 +0,0 @@
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Feature, Region } from '@jbrowse/core/util';
-declare const DivSequenceRendering: ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, showForward, showReverse, showTranslation, }: {
-    exportSVG?: {
-        rasterizeLayers: boolean;
-    };
-    features: Map<string, Feature>;
-    regions: Region[];
-    colorByCDS: boolean;
-    bpPerPx: number;
-    rowHeight: number;
-    sequenceHeight: number;
-    config: AnyConfigurationModel;
-    showForward?: boolean;
-    showReverse?: boolean;
-    showTranslation?: boolean;
-}) => import("react/jsx-runtime").JSX.Element;
-export default DivSequenceRendering;

package/dist/DivSequenceRenderer/components/DivSequenceRendering.js

@@ -1,103 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-function Translation({ codonTable, seq, frame, width, bpPerPx, colorByCDS, region, seqStart, height, y, reverse = false, }) {
-    var _a, _b;
-    const normalizedFrame = Math.abs(frame) - 1;
-    const seqFrame = seqStart % 3;
-    const frameShift = (normalizedFrame - seqFrame + 3) % 3;
-    const theme = (0, material_1.useTheme)();
-    const frameShiftAdjustedSeqLength = seq.length - frameShift;
-    const multipleOfThreeLength = frameShiftAdjustedSeqLength - (frameShiftAdjustedSeqLength % 3);
-    const seqSliced = seq.slice(frameShift, frameShift + multipleOfThreeLength);
-    const translated = [];
-    for (let i = 0; i < seqSliced.length; i += 3) {
-        const codon = seqSliced.slice(i, i + 3);
-        const normalizedCodon = reverse ? (0, util_1.revcom)(codon) : codon;
-        const aminoAcid = codonTable[normalizedCodon] || '';
-        translated.push({
-            letter: aminoAcid,
-            codon: normalizedCodon.toUpperCase(),
-        });
-    }
-    const codonWidth = (1 / bpPerPx) * 3;
-    const renderLetter = 1 / bpPerPx >= 12;
-    const frameOffset = frameShift / bpPerPx;
-    const startOffset = (region.start - seqStart) / bpPerPx;
-    const offset = frameOffset - startOffset;
-    const dark = theme.palette.mode === 'dark' ? 'dark' : 'main';
-    const defaultFill = colorByCDS
-        ? (_a = theme.palette.framesCDS.at(frame)) === null || _a === void 0 ? void 0 : _a[dark]
-        : (_b = theme.palette.frames.at(frame)) === null || _b === void 0 ? void 0 : _b[dark];
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("rect", { x: 0, y: y, width: width, height: height, fill: defaultFill }), translated.map((element, index) => {
-                const x = region.reversed
-                    ? width - (index + 1) * codonWidth - offset
-                    : codonWidth * index + offset;
-                const { letter, codon } = element;
-                const codonFill = util_1.defaultStarts.includes(codon)
-                    ? theme.palette.startCodon
-                    : util_1.defaultStops.includes(codon)
-                        ? theme.palette.stopCodon
-                        : undefined;
-                return !(renderLetter || codonFill) ? null : ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("rect", { x: x, y: y, width: renderLetter
-                                ? codonWidth
-                                : codonWidth + 0.7, height: height, stroke: renderLetter ? '#555' : 'none', fill: codonFill || 'none' }), renderLetter ? ((0, jsx_runtime_1.jsx)("text", { x: x + codonWidth / 2, fontSize: height - 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", children: letter })) : null] }, `${index}-${letter}`));
-            })] }));
-}
-function Sequence({ bpPerPx, region, feature, sequenceType, height, seq, y, }) {
-    const render = 1 / bpPerPx >= 12;
-    const s = feature.get('start');
-    const e = feature.get('end');
-    const [leftPx, rightPx] = (0, util_1.bpSpanPx)(s, e, region, bpPerPx);
-    const reverse = region.reversed;
-    const len = e - s;
-    const w = Math.max((rightPx - leftPx) / len, 0.8);
-    const theme = (0, material_1.useTheme)();
-    return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: seq.split('').map((letter, index) => {
-            const color = sequenceType === 'dna'
-                ?
-                    theme.palette.bases[letter.toUpperCase()]
-                : undefined;
-            const dark = theme.palette.mode === 'dark';
-            const x = reverse ? rightPx - (index + 1) * w : leftPx + index * w;
-            return ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("rect", { x: x, y: y, width: w, height: height, fill: color ? (dark ? color.dark : color.main) : '#aaa', stroke: render ? '#555' : 'none' }), render ? ((0, jsx_runtime_1.jsx)("text", { x: x + w / 2, y: y + height / 2, dominantBaseline: "middle", textAnchor: "middle", fontSize: height - 2, fill: color ? theme.palette.getContrastText(color.main) : 'black', children: letter })) : null] }, `${letter}-${index}`));
-        }) }));
-}
-function SequenceSVG({ regions, width, colorByCDS, features = new Map(), showReverse = true, showForward = true, showTranslation = true, sequenceType = 'dna', bpPerPx, rowHeight, }) {
-    const region = regions[0];
-    const codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
-    const [feature] = [...features.values()];
-    if (!feature) {
-        return null;
-    }
-    const seq = feature.get('seq');
-    if (!seq) {
-        return null;
-    }
-    let currY = -rowHeight;
-    const showSequence = bpPerPx <= 1;
-    const forwardFrames = showTranslation && showForward ? [3, 2, 1] : [];
-    const reverseFrames = showTranslation && showReverse ? [-1, -2, -3] : [];
-    const [topFrames, bottomFrames] = region.reversed
-        ? [reverseFrames.toReversed(), forwardFrames.toReversed()]
-        : [forwardFrames, reverseFrames];
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [topFrames.map(index => ((0, jsx_runtime_1.jsx)(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), height: rowHeight, reverse: region.reversed }, `translation-${index}`))), showForward && showSequence ? ((0, jsx_runtime_1.jsx)(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? (0, util_1.complement)(seq) : seq, bpPerPx: bpPerPx })) : null, showReverse && showSequence ? ((0, jsx_runtime_1.jsx)(Sequence, { height: rowHeight, sequenceType: sequenceType, y: (currY += rowHeight), feature: feature, region: region, seq: region.reversed ? seq : (0, util_1.complement)(seq), bpPerPx: bpPerPx })) : null, bottomFrames.map(index => ((0, jsx_runtime_1.jsx)(Translation, { width: width, colorByCDS: colorByCDS, seq: seq, y: (currY += rowHeight), codonTable: codonTable, frame: index, bpPerPx: bpPerPx, region: region, seqStart: feature.get('start'), height: rowHeight, reverse: !region.reversed }, `rev-translation-${index}`)))] }));
-}
-function Wrapper({ exportSVG, width, totalHeight, children, }) {
-    return exportSVG ? (children) : ((0, jsx_runtime_1.jsx)("svg", { "data-testid": "sequence_track", width: width, height: totalHeight, style: {
-            display: 'block',
-            width,
-            height: totalHeight,
-            userSelect: 'none',
-        }, children: children }));
-}
-const DivSequenceRendering = (0, mobx_react_1.observer)(function ({ exportSVG, features, regions, colorByCDS, bpPerPx, rowHeight, sequenceHeight, showForward, showReverse, showTranslation, }) {
-    const region = regions[0];
-    const width = Math.ceil((region.end - region.start) / bpPerPx);
-    return ((0, jsx_runtime_1.jsx)(Wrapper, { exportSVG: exportSVG, totalHeight: sequenceHeight, width: width, children: (0, jsx_runtime_1.jsx)(SequenceSVG, { width: width, showReverse: showReverse, showForward: showForward, showTranslation: showTranslation, colorByCDS: colorByCDS, bpPerPx: bpPerPx, rowHeight: rowHeight, features: features, regions: regions }) }));
-});
-exports.default = DivSequenceRendering;

package/dist/DivSequenceRenderer/configSchema.d.ts

@@ -1,8 +0,0 @@
-declare const DivSequenceRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    height: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default DivSequenceRenderer;

package/dist/DivSequenceRenderer/configSchema.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const DivSequenceRenderer = (0, configuration_1.ConfigurationSchema)('DivSequenceRenderer', {
-    height: {
-        type: 'number',
-        description: 'height in pixels of each line of sequence',
-        defaultValue: 16,
-    },
-}, { explicitlyTyped: true });
-exports.default = DivSequenceRenderer;

package/dist/DivSequenceRenderer/index.d.ts

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

package/dist/DivSequenceRenderer/index.js

@@ -1,30 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = DivSequenceRendererF;
-const FeatureRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType"));
-const DivSequenceRendering_1 = __importDefault(require("./components/DivSequenceRendering"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-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,
-        };
-    }
-}
-function DivSequenceRendererF(pluginManager) {
-    pluginManager.addRendererType(() => new DivSequenceRenderer({
-        name: 'DivSequenceRenderer',
-        ReactComponent: DivSequenceRendering_1.default,
-        configSchema: configSchema_1.default,
-        pluginManager,
-    }));
-}

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -1,25 +0,0 @@
-import { IndexedFasta } from '@gmod/indexedfasta';
-import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import type { Feature } from '@jbrowse/core/util';
-import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
-export default class IndexedFastaAdapter extends BaseSequenceAdapter {
-    protected setupP?: Promise<{
-        fasta: IndexedFasta;
-    }>;
-    private seqCache;
-    getRefNames(_opts?: BaseOptions): Promise<string[]>;
-    getRegions(_opts?: BaseOptions): Promise<{
-        refName: string;
-        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>;
-}

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js

@@ -1,112 +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 abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
-const indexedfasta_1 = require("@gmod/indexedfasta");
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const util_1 = require("@jbrowse/core/util");
-const QuickLRU_1 = __importDefault(require("@jbrowse/core/util/QuickLRU"));
-const io_1 = require("@jbrowse/core/util/io");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const stopToken_1 = require("@jbrowse/core/util/stopToken");
-class IndexedFastaAdapter extends BaseAdapter_1.BaseSequenceAdapter {
-    constructor() {
-        super(...arguments);
-        this.seqCache = new abortable_promise_cache_1.default({
-            cache: new QuickLRU_1.default({ maxSize: 200 }),
-            fill: async (args) => {
-                const { refName, start, end, fasta } = args;
-                return fasta.getSequence(refName, start, end);
-            },
-        });
-    }
-    async getRefNames(_opts) {
-        const { fasta } = await this.setup();
-        return fasta.getSequenceNames();
-    }
-    async getRegions(_opts) {
-        const { fasta } = await this.setup();
-        const seqSizes = await fasta.getSequenceSizes();
-        return Object.keys(seqSizes).map(refName => ({
-            refName,
-            start: 0,
-            end: seqSizes[refName],
-        }));
-    }
-    async setupPre() {
-        const fastaLocation = this.getConf('fastaLocation');
-        const faiLocation = this.getConf('faiLocation');
-        return {
-            fasta: new indexedfasta_1.IndexedFasta({
-                fasta: (0, io_1.openLocation)(fastaLocation, this.pluginManager),
-                fai: (0, io_1.openLocation)(faiLocation, this.pluginManager),
-            }),
-        };
-    }
-    async getHeader() {
-        const loc = this.getConf('metadataLocation');
-        return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'
-            ? null
-            : (0, io_1.openLocation)(loc, this.pluginManager).readFile('utf8');
-    }
-    async setup() {
-        if (!this.setupP) {
-            this.setupP = this.setupPre().catch((e) => {
-                this.setupP = undefined;
-                throw e;
-            });
-        }
-        return this.setupP;
-    }
-    getFeatures(region, opts) {
-        const { statusCallback = () => { }, stopToken } = opts || {};
-        const { refName, start, end } = region;
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            await (0, util_1.updateStatus2)('Downloading sequence', statusCallback, stopToken, async () => {
-                const { fasta } = await this.setup();
-                const size = await fasta.getSequenceSize(refName);
-                const regionEnd = Math.min(size || 0, end);
-                const chunks = [];
-                const chunkSize = 128000;
-                const s = start - (start % chunkSize);
-                const e = end + (chunkSize - (end % chunkSize));
-                for (let chunkStart = s; chunkStart < e; chunkStart += chunkSize) {
-                    const r = {
-                        refName,
-                        start: chunkStart,
-                        end: chunkStart + chunkSize,
-                    };
-                    (0, stopToken_1.checkStopToken)(stopToken);
-                    const res = await this.seqCache.get(JSON.stringify(r), {
-                        ...r,
-                        fasta,
-                    });
-                    if (!res) {
-                        break;
-                    }
-                    chunks.push(res);
-                }
-                const seq = chunks
-                    .filter(f => !!f)
-                    .join('')
-                    .slice(start - s)
-                    .slice(0, end - start);
-                if (seq) {
-                    observer.next(new util_1.SimpleFeature({
-                        id: `${refName}-${start}-${regionEnd}`,
-                        data: {
-                            refName,
-                            start,
-                            end: regionEnd,
-                            seq,
-                        },
-                    }));
-                }
-            });
-            observer.complete();
-        });
-    }
-}
-exports.default = IndexedFastaAdapter;

package/dist/IndexedFastaAdapter/configSchema.d.ts

@@ -1,25 +0,0 @@
-declare const IndexedFastaAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    fastaLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    faiLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    metadataLocation: {
-        description: string;
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default IndexedFastaAdapter;

package/dist/IndexedFastaAdapter/configSchema.js

@@ -1,40 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const IndexedFastaAdapter = (0, configuration_1.ConfigurationSchema)('IndexedFastaAdapter', {
-    fastaLocation: {
-        type: 'fileLocation',
-        defaultValue: { uri: '/path/to/seq.fa', locationType: 'UriLocation' },
-    },
-    faiLocation: {
-        type: 'fileLocation',
-        defaultValue: { uri: '/path/to/seq.fa.fai', locationType: 'UriLocation' },
-    },
-    metadataLocation: {
-        description: 'Optional metadata file',
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/fa.metadata.yaml',
-            locationType: 'UriLocation',
-        },
-    },
-}, {
-    explicitlyTyped: true,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                fastaLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                faiLocation: {
-                    uri: `${snap.uri}.fai`,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = IndexedFastaAdapter;

package/dist/IndexedFastaAdapter/index.d.ts

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

package/dist/IndexedFastaAdapter/index.js

@@ -1,54 +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 = IndexedFastaAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function IndexedFastaAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => {
-        return new AdapterType_1.default({
-            name: 'IndexedFastaAdapter',
-            displayName: 'Indexed FASTA adapter',
-            configSchema: configSchema_1.default,
-            adapterMetadata: {
-                hiddenFromGUI: true,
-            },
-            getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./IndexedFastaAdapter'))).then(r => r.default),
-        });
-    });
-}

package/dist/LinearReferenceSequenceDisplay/configSchema.d.ts

@@ -1,9 +0,0 @@
-export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    renderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        height: {
-            type: string;
-            description: string;
-            defaultValue: number;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;

package/dist/LinearReferenceSequenceDisplay/configSchema.js

@@ -1,12 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = void 0;
-const configuration_1 = require("@jbrowse/core/configuration");
-const configSchema_1 = __importDefault(require("../DivSequenceRenderer/configSchema"));
-function x() { }
-exports.configSchema = (0, configuration_1.ConfigurationSchema)('LinearReferenceSequenceDisplay', {
-    renderer: configSchema_1.default,
-}, { explicitIdentifier: 'displayId', explicitlyTyped: true });

package/dist/LinearReferenceSequenceDisplay/index.d.ts

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

package/dist/LinearReferenceSequenceDisplay/index.js

@@ -1,21 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LinearReferenceSequenceDisplayF;
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const configSchema_1 = require("./configSchema");
-const model_1 = require("./model");
-function LinearReferenceSequenceDisplayF(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const stateModel = (0, model_1.modelFactory)(configSchema_1.configSchema);
-        return new pluggableElementTypes_1.DisplayType({
-            name: 'LinearReferenceSequenceDisplay',
-            configSchema: configSchema_1.configSchema,
-            stateModel,
-            displayName: 'Reference sequence display',
-            trackType: 'ReferenceSequenceTrack',
-            viewType: 'LinearGenomeView',
-            ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
-        });
-    });
-}