void testStringSimilar(const char* /*file*/, int line,
const std::string& string_1,
const char* string_1_stringified,
const std::string& string_2,
const char* string_2_stringified
)
{
++TEST::test_count;
TEST::test_line = line;
TEST::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;
TEST::this_test = fsc.compareStrings(string_1, string_2);
TEST::fuzzy_message = os.str();
TEST::absdiff = fsc.absdiff_max_;
TEST::ratio = fsc.ratio_max_;
TEST::line_num_1_max = fsc.line_num_1_max_;
TEST::line_num_2_max = fsc.line_num_2_max_;
TEST::test = TEST::test && TEST::this_test;
TEST::initialNewline();
if (TEST::this_test)
{
std__cout << " + line " << line << ": TEST_STRING_SIMILAR("
<< string_1_stringified << ',' << string_2_stringified << "): "
"absolute: " << TEST::absdiff << " (" << TEST::absdiff_max_allowed
<< "), relative: " << TEST::ratio << " ("
<< TEST::ratio_max_allowed << ") +\n";
std__cout << "got:\n";
TEST::printWithPrefix(string_1, TEST::line_num_1_max);
std__cout << "expected:\n";
TEST::printWithPrefix(string_2, TEST::line_num_2_max);
}
else
{
std__cout << " - line " << TEST::test_line
<< ": TEST_STRING_SIMILAR(" << string_1_stringified << ','
<< string_2_stringified << ") ... -\n"
"got:\n";
TEST::printWithPrefix(string_1, TEST::line_num_1_max);
std__cout << "expected:\n";
TEST::printWithPrefix(string_2, TEST::line_num_2_max);
std__cout << "message: \n";
std__cout << TEST::fuzzy_message;
failed_lines_list.push_back(line);
}
}
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;
}
PeakMap input;
MzMLFile().load(OPENMS_GET_TEST_DATA_PATH("FeatureFindingMetabo_input1.mzML"), input);
FeatureMap test_fm;
std::vector<MassTrace> output_mt, splitted_mt, filtered_mt;
std::vector<std::vector< OpenMS::MSChromatogram > > chromatograms;
MassTraceDetection test_mtd;
test_mtd.run(input, output_mt);
ElutionPeakDetection test_epd;
test_epd.detectPeaks(output_mt, splitted_mt);
FuzzyStringComparator fsc;
fsc.setAcceptableRelative(1.001);
fsc.setAcceptableAbsolute(1);
StringList sl;
sl.push_back("xml-stylesheet");
sl.push_back("<featureMap");
sl.push_back("<feature id");
fsc.setWhitelist(sl);
//std::cout << "\n\n" << fsc.compareStrings("529090", "529091") << "\n\n\n";
START_SECTION((void run(std::vector< MassTrace > &, FeatureMap &, chromatograms &)))
{
FeatureFindingMetabo test_ffm;
// run with non-default setting (C13 isotope distance)
Param p = test_ffm.getParameters();
TEST_EQUAL(pes4[0].getAAAfter(), PeptideEvidence::UNKNOWN_AA)
END_SECTION
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)
END_SECTION
START_SECTION(void store(String filename, const std::vector<ProteinIdentification>& protein_ids, const std::vector<PeptideIdentification>& peptide_ids, const String& document_id="") )
// 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)