Examples with NucleotideSequence com.milaboratory.core.sequence.NucleotideSequence used on opensource projects

Example 81 with NucleotideSequence

use of com.milaboratory.core.sequence.NucleotideSequence in project mixcr by milaboratory.

the class TargetBuilder method generateSequence.

public static NucleotideSequence generateSequence(VDJCGenes genes, String model, RandomGenerator rg) {
    // Pre-processing
    model = preProcessModel(model);
    // Building sequence
    SequenceBuilder<NucleotideSequence> builder = NucleotideSequence.ALPHABET.createBuilder();
    // builder.ensureCapacity(model.length());
    Matcher matcher = modelParserPattern.matcher(model);
    ReferencePoint leftPoint = null;
    ReferencePoint rightPoint;
    int prevPosition = 0;
    while (matcher.find()) {
        if (matcher.start() != prevPosition)
            throw new IllegalArgumentException("Can't parse " + model.substring(prevPosition, matcher.start()));
        prevPosition = matcher.end();
        String rpGroup = matcher.group(refPointGroupId);
        String gf1Group = matcher.group(geneFeaturePoint1GroupId);
        String gf2Group = matcher.group(geneFeaturePoint2GroupId);
        String nGroup = matcher.group(nGroupId);
        String atgcGroup = matcher.group(atgcGroupId);
        if (rpGroup != null)
            leftPoint = ReferencePoint.parse(rpGroup);
        else if (gf1Group != null) {
            leftPoint = ReferencePoint.parse(gf1Group);
            rightPoint = ReferencePoint.parse(gf2Group);
            GeneFeature geneFeature = new GeneFeature(leftPoint, rightPoint);
            VDJCGene gene = genes.geneByGeneType(geneFeature.getGeneType());
            NucleotideSequence seqGF = gene.getFeature(geneFeature);
            if (seqGF == null)
                throw new RuntimeException("No sequence for feature " + geneFeature);
            builder.append(seqGF);
            leftPoint = rightPoint;
        } else if (nGroup != null)
            for (int j = 0; j < nGroup.length(); j++) builder.append((byte) rg.nextInt(4));
        else if (atgcGroup != null)
            builder.append(new NucleotideSequence(atgcGroup));
        else {
            for (int i = 0; i < 4; i++) {
                GeneType geneType = GeneType.VDJC_REFERENCE[i];
                String group = matcher.group(i + vGroupId);
                if (group != null) {
                    if (leftPoint == null || leftPoint.getGeneType() != geneType)
                        throw new IllegalArgumentException("No reference point for " + group);
                    rightPoint = leftPoint.move(group.length());
                    GeneFeature geneFeature = new GeneFeature(leftPoint, rightPoint);
                    VDJCGene gene = genes.geneByGeneType(geneType);
                    NucleotideSequence seqGF = gene.getFeature(geneFeature);
                    if (seqGF == null)
                        throw new RuntimeException("No sequence for feature " + geneFeature);
                    for (int j = 0; j < seqGF.size(); j++) {
                        char ch = group.charAt(j);
                        byte n = seqGF.codeAt(j);
                        if (Character.isLowerCase(ch))
                            builder.append((byte) ((n + 1 + rg.nextInt(3)) % 3));
                        else
                            builder.append(n);
                    }
                }
            }
        }
    }
    if (model.length() != prevPosition)
        throw new IllegalArgumentException("Can't parse " + model.substring(prevPosition, model.length()));
    return builder.createAndDestroy();
}