Examples with NSequenceWithQualityPrintHelper com.milaboratory.util.NSequenceWithQualityPrintHelper used on opensource projects

Example 1 with NSequenceWithQualityPrintHelper

use of com.milaboratory.util.NSequenceWithQualityPrintHelper in project mixcr by milaboratory.

the class ActionExportAlignmentsPretty method outputVerbose.

public void outputVerbose(PrintStream output, final VDJCAlignments alignments) {
    output.println(">>> Read ids: " + Arrays.toString(alignments.getReadIds()).replace("[", "").replace("]", ""));
    output.println();
    output.println(">>> Target sequences (input sequences):");
    output.println();
    for (int i = 0; i < alignments.numberOfTargets(); i++) {
        output.println("Sequence" + i + ":");
        final VDJCPartitionedSequence partitionedTarget = alignments.getPartitionedTarget(i);
        printGeneFeatures(new Filter<GeneFeature>() {

            @Override
            public boolean accept(GeneFeature object) {
                return partitionedTarget.getPartitioning().isAvailable(object);
            }
        }, output, "Contains features: ");
        output.println();
        output.print(new NSequenceWithQualityPrintHelper(alignments.getTarget(i), LINE_OFFSET, LINE_LENGTH));
    }
    if (alignments.numberOfTargets() > 1) {
        // Printing a set of available gene features for a full read
        output.println(">>> Gene features that can be extracted from this paired-read: ");
        printGeneFeatures(new Filter<GeneFeature>() {

            @Override
            public boolean accept(GeneFeature object) {
                return alignments.getFeature(object) != null;
            }
        }, output, "");
    }
    output.println();
    for (GeneType geneType : GeneType.values()) {
        output.println(">>> Alignments with " + geneType.getLetter() + " gene:");
        output.println();
        boolean exists = false;
        VDJCHit[] hits = alignments.getHits(geneType);
        if (hits.length > 0) {
            hits = actionParameters.isOnlyTop() ? new VDJCHit[] { hits[0] } : hits;
            for (VDJCHit hit : hits) {
                exists = true;
                output.println(hit.getGene().getName() + " (total score = " + hit.getScore() + ")");
                for (int i = 0; i < alignments.numberOfTargets(); i++) {
                    Alignment<NucleotideSequence> alignment = hit.getAlignment(i);
                    if (alignment == null)
                        continue;
                    output.println("Alignment of Sequence" + i + " (score = " + (alignment == null ? "NaN" : alignment.getScore()) + "):");
                    if (alignment != null) {
                        for (AlignmentHelper subHelper : alignment.getAlignmentHelper().split(LINE_LENGTH, LINE_OFFSET)) {
                            output.println(subHelper.toStringWithSeq2Quality(alignments.getTarget(i).getQuality()));
                            output.println();
                        }
                        if (actionParameters.printGeneSequence()) {
                            output.println("Gene sequence:");
                            output.println(alignment.getSequence1());
                            output.println();
                        }
                    }
                }
            }
        }
        if (!exists) {
            output.println("No hits.");
            output.println();
        }
    }
    char[] ll = new char[94];
    Arrays.fill(ll, '=');
    output.println(ll);
    output.println();
}