Method getScanIdentifier

src/openms/source/FORMAT/PercolatorInfile.cpp:37–57

uses spectrum_reference, if empty uses spectrum_id, if also empty fall back to using index

  // uses spectrum_reference, if empty uses spectrum_id, if also empty fall back to using index
  String PercolatorInfile::getScanIdentifier(const PeptideIdentification& pid, size_t index)
  {
    // MSGF+ uses this field, is empty if not specified
    String scan_identifier = pid.getSpectrumReference();

    if (scan_identifier.empty())
    {
      // XTandem uses this (integer) field
      // these ids are 1-based in contrast to the index which is 0-based. This might be problematic to use for merging
      if (pid.metaValueExists("spectrum_id") && !pid.getMetaValue("spectrum_id").toString().empty())
      {
        scan_identifier = "scan=" + pid.getMetaValue("spectrum_id").toString();
      }
      else
      {
        scan_identifier = "index=" + String(index); // fall back
        OPENMS_LOG_WARN << "no known spectrum identifiers, using index [1,n] - use at own risk." << endl;
      }
    }
    return scan_identifier.removeWhitespaces();
  }

  vector<PeptideIdentification> PercolatorInfile::load(
    const String& pin_file,