Examples with ClonalSequence com.milaboratory.mixcr.basictypes.ClonalSequence used on opensource projects

Example 1 with ClonalSequence

use of com.milaboratory.mixcr.basictypes.ClonalSequence in project mixcr by milaboratory.

the class CloneAccumulator method rebuildClonalSequence.

public void rebuildClonalSequence() {
    SequenceQuality newQuality = aggregator.getQuality();
    final NSequenceWithQuality[] updated = new NSequenceWithQuality[sequence.size()];
    int pointer = 0;
    for (int i = 0; i < updated.length; i++) {
        final NucleotideSequence s = this.sequence.get(i).getSequence();
        updated[i] = new NSequenceWithQuality(s, newQuality.getRange(pointer, pointer + s.size()));
        pointer += s.size();
    }
    sequence = new ClonalSequence(updated);
    return;
}