@gmod/nclist/dist/nclist.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 quick_lru_1 = __importDefault(require("quick-lru"));
const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
const util_ts_1 = require("./util.js");
class NCList {
    constructor({ readFile, cacheSize = 100 }) {
        this.topList = [];
        this.chunkCache = new abortable_promise_cache_1.default({
            cache: new quick_lru_1.default({ maxSize: cacheSize }),
            fill: this.readChunkItems.bind(this),
        });
        this.readFile = readFile;
        if (!this.readFile) {
            throw new Error(`must provide a "readFile" function`);
        }
    }
    importExisting(nclist, attrs, baseURL, lazyUrlTemplate, lazyClass) {
        this.topList = nclist;
        this.attrs = attrs;
        this.start = attrs.makeFastGetter('Start');
        this.end = attrs.makeFastGetter('End');
        this.lazyClass = lazyClass;
        this.baseURL = baseURL;
        this.lazyUrlTemplate = lazyUrlTemplate;
    }
    binarySearch(arr, item, getter) {
        let low = -1;
        let high = arr.length;
        let mid;
        while (high - low > 1) {
            mid = (low + high) >>> 1;
            if (getter(arr[mid]) >= item) {
                high = mid;
            }
            else {
                low = mid;
            }
        }
        // if we're iterating rightward, return the high index;
        // if leftward, the low index
        if (getter === this.end) {
            return high;
        }
        return low;
    }
    readChunkItems(chunkNum) {
        const url = (0, util_ts_1.newURL)(this.lazyUrlTemplate.replaceAll(/\{Chunk\}/gi, chunkNum), this.baseURL);
        return (0, util_ts_1.readJSON)(url, this.readFile, { defaultContent: [] });
    }
    async *iterateSublist(arr, from, to, inc, searchGet, testGet, path) {
        const getChunk = this.attrs.makeGetter('Chunk');
        const getSublist = this.attrs.makeGetter('Sublist');
        const pendingPromises = [];
        for (let i = this.binarySearch(arr, from, searchGet); i < arr.length && i >= 0 && inc * testGet(arr[i]) < inc * to; i += inc) {
            if (arr[i][0] === this.lazyClass) {
                // this is a lazily-loaded chunk of the nclist
                const chunkNum = getChunk(arr[i]);
                const chunkItemsP = this.chunkCache
                    .get(chunkNum, chunkNum)
                    .then(item => [item, chunkNum]);
                pendingPromises.push(chunkItemsP);
            }
            else {
                // this is just a regular feature
                yield [arr[i], path.concat(i)];
            }
            // if this node has a contained sublist, process that too
            const sublist = getSublist(arr[i]);
            if (sublist) {
                yield* this.iterateSublist(sublist, from, to, inc, searchGet, testGet, path.concat(i));
            }
        }
        for (const p of pendingPromises) {
            const [item, chunkNum] = await p;
            if (item) {
                yield* this.iterateSublist(item, from, to, inc, searchGet, testGet, [
                    ...path,
                    chunkNum,
                ]);
            }
        }
    }
    async *iterate(from, to) {
        // calls the given function once for each of the
        // intervals that overlap the given interval
        // if from <= to, iterates left-to-right, otherwise iterates right-to-left
        // inc: iterate leftward or rightward
        const inc = from > to ? -1 : 1;
        // searchGet: search on start or end
        const searchGet = from > to ? this.start : this.end;
        // testGet: test on start or end
        const testGet = from > to ? this.end : this.start;
        if (this.topList.length > 0) {
            yield* this.iterateSublist(this.topList, from, to, inc, searchGet, testGet, [0]);
        }
    }
    async histogram(from, to, numBins) {
        // calls callback with a histogram of the feature density
        // in the given interval
        const result = new Array(numBins);
        result.fill(0);
        const binWidth = (to - from) / numBins;
        for await (const feat of this.iterate(from, to)) {
            const firstBin = Math.max(0, ((this.start(feat) - from) / binWidth) | 0);
            const lastBin = Math.min(numBins, ((this.end(feat) - from) / binWidth) | 0);
            for (let bin = firstBin; bin <= lastBin; bin += 1) {
                result[bin] += 1;
            }
        }
        return result;
    }
}
exports.default = NCList;
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