Method parseTwoTableFile_

src/openms/source/FORMAT/ExperimentalDesignFile.cpp:303–440

    }

    ExperimentalDesign ExperimentalDesignFile::parseTwoTableFile_(const TextFile& text_file, const String& tsv_file, bool require_spectra_file)
    {
      ExperimentalDesign::MSFileSection msfile_section;
      bool has_sample(false);
      bool has_label(false);

      // Attributes of the sample section
      std::vector< std::vector < String > > sample_content_;
      std::map< String, Size > sample_sample_to_rowindex_;
      std::map< String, Size > sample_columnname_to_columnindex_;

      // Maps the column header string to the column index for
      // the file section
      std::map <String, Size> fs_column_header_to_index;

      unsigned line_number(0);

      enum ParseState { RUN_HEADER, RUN_CONTENT, SAMPLE_HEADER, SAMPLE_CONTENT };

      ParseState state(RUN_HEADER);
      Size n_col = 0;

      for (String s : text_file)
      {
        // skip empty lines (except in state RUN_CONTENT, where the sample table is read)
        const String line(s.trim());
	      // also skip comment lines
        if (line.hasPrefix("#") || (line.empty() && state != RUN_CONTENT))
        {
          continue;
        }

        // Now split the line into individual cells
        StringList cells;
        line.split("\t", cells);

        // Trim whitespace from all cells (so , foo , and  ,foo, is the same)
        std::transform(cells.begin(), cells.end(), cells.begin(),
                       [](String cell) -> String { return cell.trim(); });

        if (state == RUN_HEADER)
        {
          state = RUN_CONTENT;
          parseHeader_(
            cells,
            tsv_file,
            fs_column_header_to_index,
            {"Fraction_Group", "Fraction", "Spectra_Filepath"},
            {"Label", "Sample"}, false
          );
          has_label = fs_column_header_to_index.find("Label") != fs_column_header_to_index.end();
          has_sample = fs_column_header_to_index.find("Sample") != fs_column_header_to_index.end();
          
          n_col = fs_column_header_to_index.size();
        }
        // End of file section lines, empty line separates file and sample section
        else if (state == RUN_CONTENT && line.empty())
        {