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

JBrowse - client-side genome browser

/**
 * Mixin that adds getRegionFeatureDensities method to a store
 */

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

return declare( null, {

    getRegionFeatureDensities(query, successCallback, errorCallback) {
        let numBins
        let basesPerBin

        this.scoreMax = this.scoreMax || 0;

        if (query.numBins) {
            numBins = query.numBins;
            basesPerBin = (query.end - query.start)/numBins
        } else if (query.basesPerBin) {
            basesPerBin = query.basesPerBin || query.ref.basesPerBin
            numBins = Math.ceil((query.end-query.start)/basesPerBin)
        } else {
            throw new Error('numBins or basesPerBin arg required for getRegionFeatureDensities')
        }

        const statEntry = (function (basesPerBin, stats) {
            for (var i = 0; i < stats.length; i++) {
                if (stats[i].basesPerBin >= basesPerBin) {
                    return stats[i]
                }
            }
            return undefined
        })(basesPerBin, [])

        const stats = {}
        stats.basesPerBin = basesPerBin

        stats.max = 0
        const firstServerBin = Math.floor( query.start / basesPerBin)
        const histogram = []
        const binRatio = 1 / basesPerBin

        let binStart
        let binEnd

        for (var bin = 0 ; bin < numBins ; bin++) {
            histogram[bin] = 0
        }
        this._getFeatures(query,
            feature => {
                let binValue = Math.round( (feature.get('start') - query.start )* binRatio)
                let binValueEnd = Math.round( (feature.get('end')- query.start )* binRatio)
                for(let bin = binValue; bin <= binValueEnd; bin++) {
                    if(bin >= 0 && bin < numBins) {
                        histogram[bin] = (histogram[bin] || 0) + 1
                        if (histogram[bin] > stats.max) {
                            stats.max = histogram[bin]
                            if(stats.max > this.scoreMax) {
                                this.scoreMax = stats.max
                            }
                        }
                    }
                }
            },
            () => {
                stats.max = this.scoreMax
                successCallback({ bins: histogram, stats: stats})
            },
            errorCallback
        );

    }

});
});