Examples with HiCHitCollection uk.ac.babraham.SeqMonk.DataTypes.Sequence.HiCHitCollection used on opensource projects

Example 21 with HiCHitCollection

use of uk.ac.babraham.SeqMonk.DataTypes.Sequence.HiCHitCollection in project SeqMonk by s-andrews.

the class HeatmapMatrix method getTotalCounts.

private void getTotalCounts(int[] cisCounts, int[] transCounts) {
    for (int p = 0; p < probes.length; p++) {
        if (p % 100 == 0) {
            Enumeration<ProgressListener> en = listeners.elements();
            while (en.hasMoreElements()) {
                en.nextElement().progressUpdated("Getting probe total counts", p, probes.length);
            }
            if (cancel) {
                return;
            }
        }
        HiCHitCollection hits = dataSet.getHiCReadsForProbe(probes[p].probe);
        String[] names = hits.getChromosomeNamesWithHits();
        for (int c = 0; c < names.length; c++) {
            if (names[c].equals(probes[p].probe.chromosome().name())) {
                cisCounts[p] = hits.getSourcePositionsForChromosome(names[c]).length;
            } else {
                transCounts[p] += hits.getSourcePositionsForChromosome(names[c]).length;
            }
        }
    }
}