@gmod/nclist/dist/lazy_array.js

Read features from JBrowse 1 format nested containment list JSON

"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
//@ts-nocheck
const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
const util_ts_1 = require("./util.js");
/**
 * For a JSON array that gets too large to load in one go, this class
 * helps break it up into chunks and provides an
 * async API for using the information in the array.
 */
class LazyArray {
    constructor({ urlTemplate, chunkSize, length, cacheSize = 100, readFile }, baseUrl) {
        this.urlTemplate = urlTemplate;
        this.chunkSize = chunkSize;
        this.length = length;
        this.baseUrl = baseUrl === undefined ? '' : baseUrl;
        this.readFile = readFile;
        if (!readFile) {
            throw new Error('must provide readFile callback');
        }
        this.chunkCache = new abortable_promise_cache_1.default({
            cache: new quick_lru_1.default({ maxSize: cacheSize }),
            fill: this.getChunk.bind(this),
        });
    }
    /**
     * call the callback on one element of the array
     * @param i index
     * @param callback callback, gets called with (i, value, param)
     * @param param (optional) callback will get this as its last parameter
     */
    index(i, callback, param) {
        this.range(i, i, callback, undefined, param);
    }
    /**
     * async generator for the elements in the range [start,end]
     *
     * @param start index of first element to call the callback on
     * @param end index of last element to call the callback on
     */
    async *range(start, end) {
        start = Math.max(0, start);
        end = Math.min(end, this.length - 1);
        const firstChunk = Math.floor(start / this.chunkSize);
        const lastChunk = Math.floor(end / this.chunkSize);
        const chunkreadFiles = [];
        for (let chunk = firstChunk; chunk <= lastChunk; chunk += 1) {
            chunkreadFiles.push(this.chunkCache.get(chunk, chunk));
        }
        for (const elt of chunkreadFiles) {
            const [chunkNumber, chunkData] = await elt;
            yield* this.filterChunkData(start, end, chunkNumber, chunkData);
        }
    }
    async getChunk(chunkNumber) {
        let url = this.urlTemplate.replaceAll(/\{Chunk\}/gi, chunkNumber);
        if (this.baseUrl) {
            url = (0, util_ts_1.newURL)(url, this.baseUrl);
        }
        const data = await (0, util_ts_1.readJSON)(url, this.readFile);
        return [chunkNumber, data];
    }
    *filterChunkData(queryStart, queryEnd, chunkNumber, chunkData) {
        // index (in the overall lazy array) of the first position in this chunk
        const firstIndex = chunkNumber * this.chunkSize;
        const chunkStart = Math.max(0, queryStart - firstIndex);
        const chunkEnd = Math.min(queryEnd - firstIndex, this.chunkSize - 1);
        for (let i = chunkStart; i <= chunkEnd; i += 1) {
            yield [i + firstIndex, chunkData[i]];
        }
    }
}
exports.default = LazyArray;
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