Examples with KAlignerParameters2 com.milaboratory.core.alignment.kaligner2.KAlignerParameters2 used on opensource projects

Example 1 with KAlignerParameters2

use of com.milaboratory.core.alignment.kaligner2.KAlignerParameters2 in project mixcr by milaboratory.

the class VDJCAlignerS method extractBatchParameters.

@Override
protected BatchAlignerWithBaseParameters extractBatchParameters(KGeneAlignmentParameters init) {
    final BatchAlignerWithBaseParameters p = init.getParameters().clone();
    if (p instanceof KAlignerParameters) {
        KAlignerParameters p1 = (KAlignerParameters) p;
        p1.setAbsoluteMinScore(init.getMinSumScore());
        p1.setRelativeMinScore(init.getRelativeMinScore());
    } else if (p instanceof KAlignerParameters2) {
        KAlignerParameters2 p2 = (KAlignerParameters2) p;
        p2.setAbsoluteMinScore(init.getMinSumScore());
        p2.setRelativeMinScore(init.getRelativeMinScore());
    } else
        throw new RuntimeException();
    return p;
}