mascotdatparser.cpp

pappso::pappso_double
MascotDatParser::getEvalueExperimental(
  pappso::pappso_double ion_score,
  SummaryLine &summary_line,
  pappso::pappso_double confidence_interval) const
{
  // Evalue experimental  Homology threshold (QPlughole value from .dat file).
  pappso::pappso_double eval =
    (ion_score - summary_line.plug_hole) / (pappso::pappso_double)10;
  eval = confidence_interval / pow((pappso::pappso_double)10, eval);
}

void
MascotDatParser::setVariableModifications(PeptideXtpSp &peptide_sp,
                                          QString variable_modifications_string)
{
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
           << variable_modifications_string;
  //
  for(unsigned int i = 0; i < variable_modifications_string.size(); i++)
    {
      qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
               << variable_modifications_string.mid(i, 1).toUInt() << " "
               << variable_modifications_string;
      if(variable_modifications_string.mid(i, 1).toUInt() > 0)
        {
          MascotModification mascot_modification = _delta_modification_list
            [variable_modifications_string.mid(i, 1).toUInt() - 1];
          try
            {
              if(i > 0)
                {
                  peptide_sp.get()->addAaModification(
                    mascot_modification.modification, i - 1);
                }
              else
                {
                  peptide_sp.get()->addAaModification(
                    mascot_modification.modification, i);
                }
            }
          catch(pappso::PappsoException &error)
            {
              throw pappso::PappsoException(
                QObject::tr("ERROR adding modification %1 to peptide %2 at "
                            "position %3 :\n %4")
                  .arg(mascot_modification.modification->getAccession())
                  .arg(peptide_sp.get()->toAbsoluteString())
                  .arg(i)
                  .arg(error.qwhat()));
            }
        }
    }
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}