@jbrowse/core/esm/BaseFeatureWidget/util.js

JBrowse 2 core libraries used by plugins

export function stitch(subfeats, sequence) {
    return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
}
function getItemId(feat) {
    return `${feat.start}-${feat.end}`;
}
export function filterSuccessiveElementsWithSameStartAndEndCoord(list) {
    return list.filter((item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]));
}
export function revlist(list, seqlen) {
    return list
        .map(sub => ({
        ...sub,
        start: seqlen - sub.end,
        end: seqlen - sub.start,
    }))
        .sort((a, b) => a.start - b.start);
}
export function calculateUTRs(cds, exons) {
    if (!cds.length) {
        return [];
    }
    if (exons.length < cds.length) {
        console.warn('exons.length less than cds.length, cant calculate UTR properly', { exons, cds });
        return [];
    }
    const firstCds = cds.at(0);
    const lastCds = cds.at(-1);
    const firstCdsIdx = exons.findIndex(exon => exon.end >= firstCds.start && exon.start <= firstCds.start);
    const lastCdsIdx = exons.findIndex(exon => exon.end >= lastCds.end && exon.start <= lastCds.end);
    const lastCdsExon = exons[lastCdsIdx];
    const firstCdsExon = exons[firstCdsIdx];
    const fivePrimeUTRs = [
        ...exons.slice(0, firstCdsIdx),
        {
            start: firstCdsExon.start,
            end: firstCds.start,
        },
    ].map(elt => ({
        ...elt,
        type: 'five_prime_UTR',
    }));
    const threePrimeUTRs = [
        {
            start: lastCds.end,
            end: lastCdsExon.end,
        },
        ...exons.slice(lastCdsIdx + 1),
    ].map(elt => ({
        ...elt,
        type: 'three_prime_UTR',
    }));
    return [...fivePrimeUTRs, ...threePrimeUTRs];
}
export function calculateUTRs2(cds, parentFeat) {
    if (!cds.length) {
        return [];
    }
    const firstCds = cds.at(0);
    const lastCds = cds.at(-1);
    const fivePrimeUTRs = [
        {
            start: parentFeat.start,
            end: firstCds.start,
        },
    ].map(elt => ({
        ...elt,
        type: 'five_prime_UTR',
    }));
    const threePrimeUTRs = [
        {
            start: lastCds.end,
            end: parentFeat.end,
        },
    ].map(elt => ({
        ...elt,
        type: 'three_prime_UTR',
    }));
    return [...fivePrimeUTRs, ...threePrimeUTRs];
}
export function ellipses(slug) {
    return slug.length > 20 ? `${slug.slice(0, 20)}...` : slug;
}
export function replaceUndefinedWithNull(obj) {
    return JSON.parse(JSON.stringify(obj, (_, v) => (v === undefined ? null : v)));
}
export function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
    if (depth <= currentDepth) {
        return;
    }
    obj.subfeatures?.map(sub => {
        formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
        parse(sub);
    });
}