Ejemplos de CRef::GetLineNumber en C++ (Cpp)

Ejemplo n.º 1

Archivo: blast_fasta_input.cpp Proyecto: svn2github/ncbi_tk

CRef<CSeq_entry>
CShortReadFastaInputSource::x_ReadFastqOneSeq(CRef<ILineReader> line_reader)
{
    CTempString line;
    CTempString id;
    CRef<CSeq_entry> retval;

    // first read defline
    ++(*line_reader);
    line = **line_reader;

    // skip empty lines
    while (!line_reader->AtEOF() && line.empty()) {
        ++(*line_reader);
        line = **line_reader;
    }

    if (line[0] != '@') {
        NCBI_THROW(CInputException, eInvalidInput, (string)"FASTQ parse error:"
                   " defline expected at line: " +
                   NStr::IntToString(line_reader->GetLineNumber()));
    }

    id = x_ParseDefline(line);
    CRef<CSeq_id> seqid(new CSeq_id);
    seqid->Set(CSeq_id::e_Local, id);

    // read sequence
    ++(*line_reader);
    line = **line_reader;
    // skip empty lines
    while (!line_reader->AtEOF() && line.empty()) {
        ++(*line_reader);
        line = **line_reader;
    }

    // set up sequence
    if (line.length() > 0) {
        CRef<CSeq_entry> seq_entry(new CSeq_entry);
        CBioseq& bioseq = seq_entry->SetSeq();
        bioseq.SetInst().SetMol(CSeq_inst::eMol_na);
        bioseq.SetInst().SetRepr(CSeq_inst::eRepr_raw);
        bioseq.SetId().clear();
        bioseq.SetId().push_back(seqid);
        bioseq.SetInst().SetLength(line.length());
        bioseq.SetInst().SetSeq_data().SetIupacna(CIUPACna(line.data()));
        bioseq.SetDescr();

        m_BasesAdded += line.length();
        retval = seq_entry;
    }
    
    // read and skip second defline
    ++(*line_reader);
    line = **line_reader;
    // skip empty lines
    while (!line_reader->AtEOF() && line.empty()) {
        ++(*line_reader);
        line = **line_reader;
    }

    if (line[0] != '+') {
        NCBI_THROW(CInputException, eInvalidInput, (string)"FASTQ parse error:"
                   " defline expected at line: " +
                   NStr::IntToString(line_reader->GetLineNumber()));
    }

    // read and skip quality scores
    ++(*line_reader);
    line = **line_reader;
    // skip empty lines
    while (!line_reader->AtEOF() && line.empty()) {
        ++(*line_reader);
        line = **line_reader;
    }

    return retval;
}