Function START_SECTION

src/tests/class_tests/openms/source/MzIdentMLFile_test.cpp:43–105

  delete ptr;
}
END_SECTION

START_SECTION(void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids) )
{
  std::vector<ProteinIdentification> protein_ids;
  std::vector<PeptideIdentification> peptide_ids;
  std::vector<String> fm{"Carbamidomethyl (C)", "Xlink:DTSSP[88] (Protein N-term)"};
  MzIdentMLFile().load(OPENMS_GET_TEST_DATA_PATH("MzIdentMLFile_msgf_mini.mzid"), protein_ids, peptide_ids);

  TEST_EQUAL(protein_ids.size(),2)
  TEST_EQUAL(protein_ids[0].getHits().size(),2)
  TEST_EQUAL(protein_ids[1].getHits().size(),1)
  TEST_EQUAL(peptide_ids.size(),5)
  TEST_EQUAL(peptide_ids[0].getHits().size(),1)
  TEST_EQUAL(peptide_ids[1].getHits().size(),1)
  TEST_EQUAL(peptide_ids[2].getHits().size(),1)
  TEST_EQUAL(peptide_ids[3].getHits().size(),1)
  TEST_EQUAL(peptide_ids[4].getHits().size(),1)

  /////////////// protein id 1 //////////////////
  TEST_EQUAL(protein_ids[0].getSearchEngine(),"MS-GF+")
  TEST_EQUAL(protein_ids[0].getSearchEngineVersion(),"Beta (v9979)")
  TEST_NOT_EQUAL(protein_ids[0].getDateTime().getDate(),"0000-00-00")
  TEST_NOT_EQUAL(protein_ids[0].getDateTime().getTime(),"00:00:00")
  TEST_EQUAL(protein_ids[0].getSearchParameters().db,"database.fasta")
  TEST_EQUAL(protein_ids[0].getSearchParameters().missed_cleavages, 1000)
  ABORT_IF(protein_ids[0].getSearchParameters().fixed_modifications.size() != fm.size())
  for (size_t i = 0; i < fm.size(); ++i)
  {
    TEST_EQUAL(protein_ids[0].getSearchParameters().fixed_modifications[i], fm[i]);
  }
  TEST_REAL_SIMILAR(protein_ids[0].getSearchParameters().fragment_mass_tolerance,0)
  TEST_REAL_SIMILAR(protein_ids[0].getSearchParameters().precursor_mass_tolerance,20)

  //ProteinGroups not nupported yet, also no ProteinDetection, too few input here
  //  TEST_EQUAL(protein_ids[0].getProteinGroups().size(), 0);
  //  TEST_EQUAL(protein_ids[0].getIndistinguishableProteins().size(), 0);

  //protein hit 1
  TEST_EQUAL(protein_ids[0].getHits()[0].getAccession(),"sp|P0A9K9|SLYD_ECOLI")
  TEST_EQUAL(protein_ids[0].getHits()[0].getSequence(),"")
  //protein hit 2
  TEST_EQUAL(protein_ids[0].getHits()[1].getAccession(),"sp|P0A786|PYRB_ECOLI")
  TEST_EQUAL(protein_ids[0].getHits()[1].getSequence(),"")

  //peptide id s
  TEST_EQUAL(peptide_ids[0].getScoreType(),"MS-GF:RawScore")
  TEST_REAL_SIMILAR(peptide_ids[0].getHits()[0].getScore(),195)
  TEST_EQUAL(peptide_ids[0].getHits()[0].getSequence().toString(),"LATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQETQGR")
  TEST_EQUAL(peptide_ids[0].getSpectrumReference(),"controllerType=0 controllerNumber=1 scan=32805")
  TEST_EQUAL(peptide_ids[1].getScoreType(),"MS-GF:RawScore")
  TEST_REAL_SIMILAR(peptide_ids[1].getHits()[0].getScore(),182)
  TEST_EQUAL(peptide_ids[1].getHits()[0].getSequence().toString(),"FLAETDQGPVPVEITAVEDDHVVVDGNHMLAGQNLK")
  TEST_EQUAL(peptide_ids[1].getSpectrumReference(),"controllerType=0 controllerNumber=1 scan=26090")
  TEST_EQUAL(peptide_ids[2].getScoreType(),"MS-GF:RawScore")
  TEST_REAL_SIMILAR(peptide_ids[2].getHits()[0].getScore(),191)
  TEST_EQUAL(peptide_ids[2].getHits()[0].getSequence().toString(),"FLAETDQGPVPVEITAVEDDHVVVDGNHMLAGQNLK")
  TEST_EQUAL(peptide_ids[2].getSpectrumReference(),"controllerType=0 controllerNumber=1 scan=26157")