Examples with GeneFeature io.repseq.core.GeneFeature used on opensource projects

Example 41 with GeneFeature

use of io.repseq.core.GeneFeature in project mixcr by milaboratory.

the class IOUtil method registerGeneReferences.

public static void registerGeneReferences(PrimitivO output, List<VDJCGene> genes, HasFeatureToAlign featuresToAlign) {
    // Putting genes references and feature sequences to be serialized/deserialized as references
    for (VDJCGene gene : genes) {
        output.putKnownReference(gene);
        // Also put sequences of certain gene features of genes as known references if required
        if (featuresToAlign != null) {
            GeneFeature featureToAlign = featuresToAlign.getFeatureToAlign(gene.getGeneType());
            if (featureToAlign == null)
                continue;
            NucleotideSequence featureSequence = gene.getFeature(featureToAlign);
            if (featureSequence == null)
                continue;
            output.putKnownReference(gene.getFeature(featuresToAlign.getFeatureToAlign(gene.getGeneType())));
        }
    }
}