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

Example 1 with RangeTranslationParameters

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

the class VDJCAlignmentsFormatter method drawAASequence.

public static void drawAASequence(MultiAlignmentHelper helper, SequencePartitioning partitioning, NucleotideSequence target) {
    List<RangeTranslationParameters> trParams = partitioning.getTranslationParameters(target.size());
    char[] line = new char[helper.size()];
    Arrays.fill(line, ' ');
    for (RangeTranslationParameters trParam : trParams) {
        NucleotideSequence mainSequence = target.getRange(trParam.range);
        NucleotideSequence leftover = trParam.codonLeftoverRange == null ? null : target.getRange(trParam.codonLeftoverRange);
        NucleotideSequence bigSeq = leftover == null ? mainSequence : trParam.leftIncompleteCodonRange() != null ? leftover.concatenate(mainSequence) : mainSequence.concatenate(leftover);
        AminoAcidSequence aa = AminoAcidSequence.translate(bigSeq, trParam.translationParameters);
        int aaPosition = 0;
        int ntPosition = trParam.range.getFrom() + AminoAcidSequence.convertAAPositionToNt(aaPosition, mainSequence.size(), trParam.translationParameters);
        if (aa.codeAt(aaPosition) == AminoAcidAlphabet.INCOMPLETE_CODON) {
            line[helper.subjectToAlignmentPosition(ntPosition)] = // '_'
            AminoAcidSequence.ALPHABET.codeToSymbol(aa.codeAt(aaPosition));
            ++aaPosition;
        }
        while (aaPosition < aa.size() && aa.codeAt(aaPosition) != AminoAcidAlphabet.INCOMPLETE_CODON) {
            ntPosition = trParam.range.getFrom() + AminoAcidSequence.convertAAPositionToNt(aaPosition, mainSequence.size(), trParam.translationParameters);
            line[helper.subjectToAlignmentPosition(ntPosition + 1)] = AminoAcidSequence.ALPHABET.codeToSymbol(aa.codeAt(aaPosition));
            ++aaPosition;
        }
        if (aaPosition < aa.size() && aa.codeAt(aaPosition) == AminoAcidAlphabet.INCOMPLETE_CODON) {
            ntPosition = trParam.range.getFrom() + AminoAcidSequence.convertAAPositionToNt(aaPosition, mainSequence.size(), trParam.translationParameters);
            line[helper.subjectToAlignmentPosition(ntPosition)] = AminoAcidSequence.ALPHABET.codeToSymbol(aa.codeAt(aaPosition));
        }
    }
    helper.addAnnotationString("", new String(line));
}