Method storeISO

src/openms/source/FORMAT/MSstatsFile.cpp:449–676

}

void MSstatsFile::storeISO(const String& filename,
                                   const ConsensusMap& consensus_map,
                                   const ExperimentalDesign& design,
                                   const StringList& reannotate_filenames,
                                   const String& bioreplicate,
                                   const String& condition,
                                   const String& mixture,
                                   const String& retention_time_summarization_method)
{
  // Experimental Design file
  const ExperimentalDesign::SampleSection& sampleSection = design.getSampleSection();

  checkConditionISO_(sampleSection, bioreplicate, condition, mixture);

  if (consensus_map.getProteinIdentifications().empty())
  {
    throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
                                     "No protein information found in the ConsensusXML.");
  }

  // warn if we have more than one protein ID run
  //TODO actually allow having more than one inference run e.g. for different conditions
  if (consensus_map.getProteinIdentifications().size() > 1)
  {
    OPENMS_LOG_WARN << "Found " +
                       String(consensus_map.getProteinIdentifications().size()) +
                       " protein runs in consensusXML. Using first one only to parse inference data for now." << std::endl;
  }

  if (!consensus_map.getProteinIdentifications()[0].hasInferenceData())
  {
    OPENMS_LOG_WARN << "No inference was performed on the first run, defaulting to one-peptide-rule." << std::endl;
  }

  // Maps run in MSstats input to run for OpenMS
  map< unsigned, unsigned > msstats_run_to_openms_fractiongroup;

  // Mapping of filepath and label to sample and fraction
  map< pair< String, unsigned >, unsigned> path_label_to_sample = design.getPathLabelToSampleMapping(true);
  map< pair< String, unsigned >, unsigned> path_label_to_fraction = design.getPathLabelToFractionMapping(true);
  map< pair< String, unsigned >, unsigned> path_label_to_fractiongroup = design.getPathLabelToFractionGroupMapping(true);

  // The Retention Time is additionally written to the output as soon as the user wants to resolve multiple peptides manually
  bool rt_summarization_manual(retention_time_summarization_method == "manual");

  if (!rt_summarization_manual)
  {
    OPENMS_LOG_WARN << "WARNING: rt_summarization set to something else than 'manual' but MSstatsTMT does aggregation of"
            " intensities of peptide-chargestate combinations in the same file itself."
            " Reverting to 'manual'" << endl;
    rt_summarization_manual = true;
  }

  ExperimentalDesign::MSFileSection msfile_section = design.getMSFileSection();

  // Extract the Spectra Filepath column from the design
  std::vector<String> design_filenames;
  for (ExperimentalDesign::MSFileSectionEntry const& f : msfile_section)