@gmod/jbrowse/src/JBrowse/Store/SeqFeature/_SpanCache.js

JBrowse - client-side genome browser

class SpanFeature {
    constructor(feat) {
        this.start = Math.min(feat._get('start'), feat._get('next_pos'))
        this.end = Math.max(feat._get('end'), feat._get('next_pos'))
        this.feat = feat
    }
    id() {
        return this.feat.id()
    }
    get(field) {
        return this._get(field.toLowerCase())
    }
    _get(field) {
        if(field === 'start') {
            return this.start
        } else if(field === 'end') {
            return this.end
        }

        return this.feat.get(field)
    }
    pairedFeature() { return true }
    children() {}
}


function canBePaired(alignment) {
    return alignment._get('multi_segment_template') &&
        !alignment._get('multi_segment_next_segment_unmapped') &&
        (alignment._get('multi_segment_first') || alignment._get('multi_segment_last')) &&
        !(alignment._get('secondary_alignment') || alignment._get('supplementary_alignment'))
}

define([
    'dojo/_base/declare',
    'JBrowse/Util',
],
function(
    declare,
    Util
) {

return declare(null, {
    constructor(args) {
        this.featureCache = {}
    },

    pairFeatures(query, records, featCallback, errorCallback) {
        for(let i = 0; i < records.length; i++) {
            let feat
            if (canBePaired(records[i])) {
                let name = records[i]._get('name')
                if(!this.featureCache[name]) {
                    this.featureCache[name] = new SpanFeature(records[i])
                }
            }
            else if(Util.intersect(records[i]._get('start'), records[i]._get('end'), query.start, query.end)) {
                let feat = records[i]
                featCallback(feat)
            }
        }
        Object.entries(this.featureCache).forEach(([k, v]) => {
            if (Util.intersect(v._get('start'), v._get('end'), query.start, query.end)) {
                featCallback(v)
            }
        })
    },


    cleanFeatureCache(query) {
        Object.entries(this.featureCache).forEach(([k, v]) => {
            if (!Util.intersect(v._get('start'), v._get('end'), query.start, query.end)) {
                delete this.featureCache[k]
            }
        })
    }
});
});