Method run

src/openms_gui/source/VISUAL/TOPPASOutputFileListVertex.cpp:85–249

  }

  void TOPPASOutputFileListVertex::run()
  {
    __DEBUG_BEGIN_METHOD__

    // copy tmp files to output dir

    // get incoming edge and preceding vertex
    TOPPASEdge* e = *inEdgesBegin();
    RoundPackages pkg = e->getSourceVertex()->getOutputFiles();
    if (pkg.empty())
    {
      std::cerr << "A problem occurred while grabbing files from the parent tool. This is a bug, please report it!" << std::endl;
      __DEBUG_END_METHOD__
      return;
    }

    String full_dir = createOutputDir(); // create output dir

    round_total_ = (int) pkg.size(); // take number of rounds from previous tool(s) - should all be equal
    round_counter_ = 0; // once round_counter_ reaches round_total_, we are done

    // clear output file list
    output_files_.clear();
    output_files_.resize(pkg.size()); // #rounds

    files_total_ = 0;
    files_written_ = 0;

    const TOPPASScene* ts = qobject_cast<TOPPASScene*>(scene());
    bool dry_run = ts->isDryRun();

    int param_index_src = e->getSourceOutParam();
    int param_index_me = e->getTargetInParam();
    for (Size round = 0; round < pkg.size(); ++round)
    {
      foreach(const QString &f, pkg[round][param_index_src].filenames.get())
      {
        if (!dry_run && !File::exists(f))
        {
          OPENMS_LOG_ERROR << "The file '" << String(f) << "' does not exist!" << std::endl;
          throw Exception::FileNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, f.toStdString());
        }
        QString new_file = full_dir.toQString()
            + QDir::separator()
            + File::basename(f).toQString();

        // remove "_tmp<number>" if its a suffix
        QRegExp rx("_tmp\\d+$");
        int tmp_index = rx.indexIn(new_file);
        if (tmp_index != -1)
        {
          new_file = new_file.left(tmp_index);
        }

        // get file type and rename
        FileTypes::Type ft = FileTypes::UNKNOWN;
        if (!dry_run)
        {