Ejemplo n.º 1
0
      bool
      isFileSimilar(const std::string& filename_1,
                    const std::string& filename_2)
      {
        fuzzy_message.clear();
        FuzzyStringComparator fsc;
        fsc.setAcceptableAbsolute(absdiff_max_allowed);
        fsc.setAcceptableRelative(ratio_max_allowed);
        fsc.setVerboseLevel(2);
        fsc.setWhitelist(whitelist);
        std::ostringstream os;
        fsc.setLogDestination(os);
        fsc.use_prefix_ = true;

        bool result = fsc.compareFiles(filename_1, filename_2);

        fuzzy_message = os.str();
        absdiff = fsc.absdiff_max_;
        ratio = fsc.ratio_max_;
        line_num_1_max = fsc.line_num_1_max_;
        line_num_2_max = fsc.line_num_2_max_;

        return result;
      }
    Param p = test_ffm.getParameters();
    p.setValue("mz_scoring_13C", "true");
    test_ffm.setParameters(p);
    test_ffm.run(splitted_mt, test_fm, chromatograms);
    TEST_EQUAL(test_fm.size(), 93);

    // run with default settings (from paper using charge+isotope# dependent distances)
    p.setValue("report_convex_hulls", "true");
    p.setValue("mz_scoring_13C", "false");
    test_ffm.setParameters(p);
    test_ffm.run(splitted_mt, test_fm, chromatograms);
    TEST_EQUAL(test_fm.size(), 91);
    // --> this gives less features, i.e. more isotope clusters (but the input data is simulated and highly weird -- should be replaced at some point)

    // test annotation of input
    String tmp_file;
    NEW_TMP_FILE(tmp_file);
    FeatureXMLFile().store(tmp_file, test_fm);
    TEST_EQUAL(fsc.compareFiles(tmp_file, OPENMS_GET_TEST_DATA_PATH("FeatureFindingMetabo_output1.featureXML")), true);

}
END_SECTION


/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST



START_SECTION(void store(String filename, const std::vector<ProteinIdentification>& protein_ids, const std::vector<PeptideIdentification>& peptide_ids, const String& document_id="") )

  //store and load data
  std::vector<ProteinIdentification> protein_ids, protein_ids2;
  std::vector<PeptideIdentification> peptide_ids, peptide_ids2;
  String document_id, document_id2;
  String input_path = OPENMS_GET_TEST_DATA_PATH("IdXMLFile_whole.idXML");
  IdXMLFile().load(input_path, protein_ids2, peptide_ids2, document_id2);
  String filename;
  NEW_TMP_FILE(filename)
  IdXMLFile().store(filename, protein_ids2, peptide_ids2, document_id2);

  FuzzyStringComparator fuzzy;
  fuzzy.setWhitelist(ListUtils::create<String>("<?xml-stylesheet"));
  fuzzy.setAcceptableAbsolute(0.0001);
  bool result = fuzzy.compareFiles(input_path, filename);
  TEST_EQUAL(result, true);
END_SECTION


START_SECTION([EXTRA] static bool isValid(const String& filename))
  std::vector<ProteinIdentification> protein_ids, protein_ids2;
  std::vector<PeptideIdentification> peptide_ids, peptide_ids2;
  String filename;
  IdXMLFile f;

  //test if empty file is valid
  NEW_TMP_FILE(filename)
  f.store(filename, protein_ids2, peptide_ids2);
  TEST_EQUAL(f.isValid(filename, std::cerr),true);
Ejemplo n.º 4
0
  // load, store, and reload data
  std::vector<ProteinIdentification> protein_ids, protein_ids2;
  std::vector<PeptideIdentification> peptide_ids, peptide_ids2;
  String document_id, document_id2;
  String target_file = OPENMS_GET_TEST_DATA_PATH("IdXMLFile_whole.idXML");
  IdXMLFile().load(target_file, protein_ids2, peptide_ids2, document_id2);

  String actual_file;
  NEW_TMP_FILE(actual_file)
  IdXMLFile().store(actual_file, protein_ids2, peptide_ids2, document_id2);

  FuzzyStringComparator fuzzy;
  fuzzy.setWhitelist(ListUtils::create<String>("<?xml-stylesheet"));
  fuzzy.setAcceptableAbsolute(0.0001);
  bool result = fuzzy.compareFiles(actual_file, target_file);
  TEST_EQUAL(result, true);
END_SECTION


START_SECTION([EXTRA] static bool isValid(const String& filename))
  std::vector<ProteinIdentification> protein_ids, protein_ids2;
  std::vector<PeptideIdentification> peptide_ids, peptide_ids2;
  String filename;
  IdXMLFile f;

  //test if empty file is valid
  NEW_TMP_FILE(filename)
  f.store(filename, protein_ids2, peptide_ids2);
  TEST_EQUAL(f.isValid(filename, std::cerr),true);