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);
// 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);