C++ (Cpp) Seq::FromString Examples

Example #1

File: MuscleUtils.cpp Project: ggrekhov/ugene

void convertMAlignment2SecVect(SeqVect& sv, const MultipleSequenceAlignment& ma, bool fixAlpha) {
    sv.Clear();

    MuscleContext *ctx = getMuscleContext();
    ctx->fillUidsVectors(ma->getNumRows());

    unsigned i=0;
    unsigned seq_count = 0;
    foreach(const MultipleSequenceAlignmentRow& row, ma->getMsaRows()) {
        Seq *ptrSeq = new Seq();
        QByteArray name =  row->getName().toLocal8Bit();
        ptrSeq->FromString(row->getCore().constData(), name.constData());
        //stripping gaps, original Seq::StripGaps fails on MSVC9
        Seq::iterator newEnd = std::remove(ptrSeq->begin(), ptrSeq->end(), U2Msa::GAP_CHAR);
        ptrSeq->erase(newEnd, ptrSeq->end());
        if (ptrSeq->Length()!=0) {
            ctx->tmp_uIds[seq_count] = ctx->input_uIds[i];
            sv.push_back(ptrSeq);
            seq_count++; 
        }
        i++;
    }
    if (fixAlpha) {
        sv.FixAlpha();
    }
}