Examples with Joining io.repseq.core.GeneType.Joining used on opensource projects

Example 1 with Joining

use of io.repseq.core.GeneType.Joining in project mixcr by milaboratory.

the class FullSeqAssembler method buildClone.

/* ================================= Re-align and build final clone ====================================== */
private Clone buildClone(double count, BranchSequences targets) {
    Alignment<NucleotideSequence>[] vTopHitAlignments = new Alignment[targets.ranges.length], jTopHitAlignments = new Alignment[targets.ranges.length];
    VDJCHit hit = clone.getBestHit(Variable);
    if (hit == null)
        throw new UnsupportedOperationException("No V hit.");
    NucleotideSequence vTopReferenceSequence = hit.getGene().getFeature(hit.getAlignedFeature());
    hit = clone.getBestHit(Joining);
    if (hit == null)
        throw new UnsupportedOperationException("No J hit.");
    NucleotideSequence jTopReferenceSequence = hit.getGene().getFeature(hit.getAlignedFeature());
    // Excessive optimization
    CachedIntArray cachedIntArray = new CachedIntArray();
    int assemblingFeatureLength = targets.assemblingFeatureLength;
    for (int i = 0; i < targets.ranges.length; i++) {
        Range range = targets.ranges[i];
        NucleotideSequence sequence = targets.sequences[i].getSequence();
        // Asserts
        if (range.getFrom() < N_LEFT_DUMMIES + lengthV && range.getTo() >= N_LEFT_DUMMIES + lengthV && i != targets.assemblingFeatureTargetId)
            throw new RuntimeException();
        if (range.getTo() >= rightAssemblingFeatureBound && range.getFrom() < rightAssemblingFeatureBound && i != targets.assemblingFeatureTargetId)
            throw new RuntimeException();
        if (range.getTo() < N_LEFT_DUMMIES + lengthV) {
            boolean floatingLeftBound = !parameters.alignedRegionsOnly && i == 0 && alignerParameters.getVAlignerParameters().getParameters().isFloatingLeftBound();
            // Can be reduced to a single statement
            if (range.getFrom() < N_LEFT_DUMMIES)
                // This target contain extra non-V nucleotides on the left
                vTopHitAlignments[i] = alignLinearSeq1FromRight(((LinearGapAlignmentScoring<NucleotideSequence>) alignerParameters.getVAlignerParameters().getScoring()), vTopReferenceSequence, sequence.getSequence(), 0, range.getTo() - N_LEFT_DUMMIES, 0, sequence.size(), !floatingLeftBound, cachedIntArray);
            else if (floatingLeftBound)
                vTopHitAlignments[i] = alignLinearSeq1FromRight(((LinearGapAlignmentScoring<NucleotideSequence>) alignerParameters.getVAlignerParameters().getScoring()), vTopReferenceSequence, sequence.getSequence(), range.getFrom() - N_LEFT_DUMMIES, range.length(), 0, sequence.size(), false, cachedIntArray);
            else
                vTopHitAlignments[i] = Aligner.alignGlobal(alignerParameters.getVAlignerParameters().getScoring(), vTopReferenceSequence, sequence, range.getFrom() - N_LEFT_DUMMIES, range.length(), 0, sequence.size());
        } else if (i == targets.assemblingFeatureTargetId) {
            /*
                 *  V gene
                 */
            boolean vFloatingLeftBound = !parameters.alignedRegionsOnly && i == 0 && alignerParameters.getVAlignerParameters().getParameters().isFloatingLeftBound();
            // Can be reduced to a single statement
            if (range.getFrom() < N_LEFT_DUMMIES)
                // This target contain extra non-V nucleotides on the left
                vTopHitAlignments[i] = alignLinearSeq1FromRight(((LinearGapAlignmentScoring<NucleotideSequence>) alignerParameters.getVAlignerParameters().getScoring()), vTopReferenceSequence, sequence.getSequence(), 0, lengthV, 0, targets.assemblingFeatureOffset, !vFloatingLeftBound, cachedIntArray);
            else if (vFloatingLeftBound)
                vTopHitAlignments[i] = alignLinearSeq1FromRight(((LinearGapAlignmentScoring<NucleotideSequence>) alignerParameters.getVAlignerParameters().getScoring()), vTopReferenceSequence, sequence.getSequence(), range.getFrom() - N_LEFT_DUMMIES, lengthV - (range.getFrom() - N_LEFT_DUMMIES), 0, targets.assemblingFeatureOffset, false, cachedIntArray);
            else
                vTopHitAlignments[i] = Aligner.alignGlobal(alignerParameters.getVAlignerParameters().getScoring(), vTopReferenceSequence, sequence, range.getFrom() - N_LEFT_DUMMIES, lengthV - (range.getFrom() - N_LEFT_DUMMIES), 0, targets.assemblingFeatureOffset);
            /*
                 *  J gene
                 */
            boolean jFloatingRightBound = !parameters.alignedRegionsOnly && i == targets.ranges.length - 1 && alignerParameters.getJAlignerParameters().getParameters().isFloatingRightBound();
            if (range.getTo() >= rightAssemblingFeatureBound + jLength)
                // This target contain extra non-J nucleotides on the right
                jTopHitAlignments[i] = alignLinearSeq1FromLeft(((LinearGapAlignmentScoring<NucleotideSequence>) alignerParameters.getJAlignerParameters().getScoring()), jTopReferenceSequence, sequence.getSequence(), jOffset, jLength, targets.assemblingFeatureOffset + assemblingFeatureLength, sequence.size() - (targets.assemblingFeatureOffset + assemblingFeatureLength), !jFloatingRightBound, cachedIntArray);
            else if (jFloatingRightBound)
                jTopHitAlignments[i] = alignLinearSeq1FromLeft(((LinearGapAlignmentScoring<NucleotideSequence>) alignerParameters.getJAlignerParameters().getScoring()), jTopReferenceSequence, sequence.getSequence(), jOffset, range.getTo() - rightAssemblingFeatureBound, targets.assemblingFeatureOffset + assemblingFeatureLength, sequence.size() - (targets.assemblingFeatureOffset + assemblingFeatureLength), false, cachedIntArray);
            else
                jTopHitAlignments[i] = Aligner.alignGlobal(alignerParameters.getJAlignerParameters().getScoring(), jTopReferenceSequence, sequence, jOffset, range.getTo() - rightAssemblingFeatureBound, targets.assemblingFeatureOffset + assemblingFeatureLength, sequence.size() - (targets.assemblingFeatureOffset + assemblingFeatureLength));
        } else if (range.getFrom() > rightAssemblingFeatureBound) {
            boolean floatingRightBound = !parameters.alignedRegionsOnly && i == targets.ranges.length - 1 && alignerParameters.getJAlignerParameters().getParameters().isFloatingRightBound();
            if (range.getTo() >= rightAssemblingFeatureBound + jLength)
                // This target contain extra non-J nucleotides on the right
                jTopHitAlignments[i] = alignLinearSeq1FromLeft(((LinearGapAlignmentScoring<NucleotideSequence>) alignerParameters.getJAlignerParameters().getScoring()), jTopReferenceSequence, sequence.getSequence(), jOffset + (range.getFrom() - rightAssemblingFeatureBound), jLength - (range.getFrom() - rightAssemblingFeatureBound), 0, sequence.size(), !floatingRightBound, cachedIntArray);
            else if (floatingRightBound)
                jTopHitAlignments[i] = alignLinearSeq1FromLeft(((LinearGapAlignmentScoring<NucleotideSequence>) alignerParameters.getJAlignerParameters().getScoring()), jTopReferenceSequence, sequence.getSequence(), jOffset + (range.getFrom() - rightAssemblingFeatureBound), range.length(), 0, sequence.size(), false, cachedIntArray);
            else
                jTopHitAlignments[i] = Aligner.alignGlobal(alignerParameters.getJAlignerParameters().getScoring(), jTopReferenceSequence, sequence, jOffset + (range.getFrom() - rightAssemblingFeatureBound), range.length(), 0, sequence.size());
        } else
            throw new RuntimeException();
    }
    NSequenceWithQuality assemblingFeatureSeq = targets.sequences[targets.assemblingFeatureTargetId].getRange(targets.assemblingFeatureOffset, targets.assemblingFeatureOffset + targets.assemblingFeatureLength);
    Clone clone = cloneFactory.create(0, count, geneScores, new NSequenceWithQuality[] { assemblingFeatureSeq });
    vTopHitAlignments[targets.assemblingFeatureTargetId] = mergeTwoAlignments(vTopHitAlignments[targets.assemblingFeatureTargetId], clone.getBestHit(Variable).getAlignment(0).move(targets.assemblingFeatureOffset));
    jTopHitAlignments[targets.assemblingFeatureTargetId] = mergeTwoAlignments(clone.getBestHit(Joining).getAlignment(0).move(targets.assemblingFeatureOffset), jTopHitAlignments[targets.assemblingFeatureTargetId]);
    EnumMap<GeneType, VDJCHit[]> hits = new EnumMap<>(GeneType.class);
    for (GeneType gt : GeneType.VDJC_REFERENCE) hits.put(gt, Arrays.stream(clone.getHits(gt)).map(h -> moveHitTarget(h, targets.assemblingFeatureTargetId, targets.assemblingFeatureOffset, targets.ranges.length)).toArray(VDJCHit[]::new));
    VDJCHit[] tmp = hits.get(Variable);
    tmp[0] = substituteAlignments(tmp[0], vTopHitAlignments);
    tmp = hits.get(Joining);
    tmp[0] = substituteAlignments(tmp[0], jTopHitAlignments);
    return new Clone(targets.sequences, hits, count, 0);
}