@jbrowse/core/esm/BaseFeatureWidget/SequenceFeatureDetails/useSequenceData.js

JBrowse 2 core libraries used by plugins

import { revcom } from "../../util/index.js";
import { calculateUTRs2, calculateUTRs, filterSuccessiveElementsWithSameStartAndEndCoord, revlist, } from "../util.js";
function prepareSubfeatures(feature) {
    const { start, subfeatures } = feature;
    return (subfeatures
        ?.sort((a, b) => a.start - b.start)
        .map(sub => ({
        ...sub,
        start: sub.start - start,
        end: sub.end - start,
    })) || []);
}
function processFeatureData(children, feature) {
    const featureType = feature.type?.toLowerCase();
    const isMatureProteinRegion = featureType === 'mature_protein_region_of_cds';
    const cds = isMatureProteinRegion
        ? [{ start: 0, end: feature.end - feature.start, type: 'CDS' }]
        : filterSuccessiveElementsWithSameStartAndEndCoord(children.filter(sub => {
            const type = sub.type?.toLowerCase();
            return type === 'cds' || type === 'mature_protein_region_of_cds';
        }));
    const exons = filterSuccessiveElementsWithSameStartAndEndCoord(children.filter(sub => sub.type === 'exon'));
    let utr = filterSuccessiveElementsWithSameStartAndEndCoord(children.filter(sub => sub.type?.match(/utr/i)));
    if (!utr.length && cds.length && exons.length) {
        utr = calculateUTRs(cds, exons);
    }
    else if (!utr.length && cds.length && !exons.length) {
        utr = calculateUTRs2(cds, {
            start: 0,
            end: feature.end - feature.start,
            type: 'gene',
        });
    }
    return {
        cds,
        exons,
        utr,
    };
}
function handleReverseStrand(sequence, cds, exons, utr) {
    const { seq, upstream = '', downstream = '' } = sequence;
    return {
        sequence: {
            seq: revcom(seq),
            upstream: downstream ? revcom(downstream) : '',
            downstream: upstream ? revcom(upstream) : '',
        },
        cds: revlist(cds, seq.length),
        exons: revlist(exons, seq.length),
        utr: revlist(utr, seq.length),
    };
}
export function useSequenceData({ feature, sequence, }) {
    const children = prepareSubfeatures(feature);
    const { cds, exons, utr } = processFeatureData(children, feature);
    if (!sequence || 'error' in sequence) {
        return undefined;
    }
    else {
        const { sequence: adjustedSequence, cds: adjustedCds, exons: adjustedExons, utr: adjustedUtr, } = feature.strand === -1
            ? handleReverseStrand(sequence, cds, exons, utr)
            : { sequence, cds, exons, utr };
        const { seq, upstream, downstream } = adjustedSequence;
        return {
            seq,
            upstream,
            downstream,
            cds: adjustedCds,
            exons: adjustedExons,
            utr: adjustedUtr,
        };
    }
}