Method load

src/openms/source/FORMAT/MzTabFile.cpp:84–1540

  }

  void MzTabFile::load(const String& filename, MzTab& mz_tab)
  {
  TextFile tf(filename, true);

  MzTabMetaData mz_tab_metadata;
  MzTabProteinSectionRows mz_tab_protein_section_data;
  MzTabPeptideSectionRows mz_tab_peptide_section_data;
  MzTabPSMSectionRows mz_tab_psm_section_data;
  MzTabSmallMoleculeSectionRows mz_tab_small_molecule_section_data;
  map<Size, String> comment_rows;
  vector<Size> empty_rows;

  map<String, Size> protein_custom_opt_columns;  // map column name to original column index
  map<String, Size> peptide_custom_opt_columns;
  map<String, Size> psm_custom_opt_columns;
  map<String, Size> smallmolecule_custom_opt_columns;

  Size count_study_variable_description = 0;
  Size count_ms_run_location = 0;

  //  protein section column information
  Size protein_accession_index = 0;
  Size protein_description_index = 0;
  Size protein_taxid_index = 0;
  Size protein_species_index = 0;
  Size protein_database_index = 0;
  Size protein_database_version_index = 0;
  Size protein_search_engine_index = 0;
  map<Size, Size> protein_best_search_engine_score_to_column_index;  // score number to column index
  map<Size, std::pair<Size, Size> > protein_column_index_to_score_runs_pair;   // map column of the protein section to a search_engine_score[index1]_ms_run[index] index pair
  Size protein_reliability_index = 0;
  map<Size, Size> protein_num_psms_ms_run_indices;
  map<Size, Size> protein_num_peptides_distinct_ms_run_indices;
  map<Size, Size> protein_num_peptides_unique_ms_run_indices;
  Size protein_ambiguity_members_index = 0;
  Size protein_modifications_index = 0;
  Size protein_uri_index = 0;
  Size protein_go_terms_index = 0;
  Size protein_coverage_index = 0;
  map<Size, Size> protein_abundance_assay_indices;
  map<Size, Size> protein_abundance_study_variable_to_column_indices;
  map<Size, Size> protein_abundance_stdev_study_variable_to_column_indices;
  map<Size, Size> protein_abundance_std_error_study_variable_to_column_indices;

  //  peptide section column information
  Size peptide_sequence_index = 0;
  Size peptide_accession_index = 0;
  Size peptide_unique_index = 0;
  Size peptide_database_index = 0;
  Size peptide_database_version_index = 0;
  Size peptide_search_engine_index = 0;
  map<Size, Size> peptide_best_search_engine_score_to_column_index;
  map<Size, std::pair<Size, Size> > peptide_column_index_to_score_runs_pair; // map column of the peptide section to a search_engine_score[index1]_ms_run[index] index pair
  Size peptide_reliability_index = 0;
  Size peptide_modifications_index = 0;
  Size peptide_retention_time_index = 0;
  Size peptide_retention_time_window_index = 0;
  Size peptide_charge_index = 0;