| 348 | PepXMLFile::~PepXMLFile() = default; |
| 349 | |
| 350 | void PepXMLFile::store(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, const String& mz_file, const String& mz_name, bool peptideprophet_analyzed, double rt_tolerance) |
| 351 | { |
| 352 | ofstream f(filename.c_str()); |
| 353 | if (!f) |
| 354 | { |
| 355 | throw Exception::UnableToCreateFile(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename); |
| 356 | } |
| 357 | |
| 358 | String search_engine_name; |
| 359 | ProteinIdentification::SearchParameters search_params; |
| 360 | if (!protein_ids.empty()) |
| 361 | { |
| 362 | if (protein_ids.size() > 1) |
| 363 | { |
| 364 | warning(STORE, "More than one protein identification defined; only first search parameters are written into pepXML; search engine must be the same."); |
| 365 | } |
| 366 | search_params = protein_ids.begin()->getSearchParameters(); |
| 367 | if (protein_ids.begin()->getSearchEngine() == "XTandem") |
| 368 | { |
| 369 | search_engine_name = "X! Tandem"; |
| 370 | } |
| 371 | else if (protein_ids.begin()->getSearchEngine() == "Mascot") |
| 372 | { |
| 373 | search_engine_name = "MASCOT"; |
| 374 | } |
| 375 | else |
| 376 | { |
| 377 | search_engine_name = protein_ids.begin()->getSearchEngine(); |
| 378 | //Comet writes "Comet" in pep.xml, so this is ok |
| 379 | } |
| 380 | } |
| 381 | |
| 382 | f.precision(writtenDigits<double>(0.0)); |
| 383 | String raw_data; |
| 384 | String base_name; |
| 385 | SpectrumMetaDataLookup lookup; |
| 386 | lookup.rt_tolerance = rt_tolerance; |
| 387 | |
| 388 | // The mz-File (if given) |
| 389 | if (!mz_file.empty()) |
| 390 | { |
| 391 | base_name = FileHandler::stripExtension(File::basename(mz_file)); |
| 392 | raw_data = FileTypes::typeToName(FileHandler::getTypeByFileName(mz_file)); |
| 393 | |
| 394 | PeakMap experiment; |
| 395 | FileHandler fh; |
| 396 | fh.loadExperiment(mz_file, experiment, FileTypes::UNKNOWN, ProgressLogger::NONE, false, false); |
| 397 | lookup.readSpectra(experiment.getSpectra()); |
| 398 | } |
| 399 | else |
| 400 | { |
| 401 | base_name = FileHandler::stripExtension(File::basename(filename)); |
| 402 | raw_data = "mzML"; |
| 403 | } |
| 404 | // mz_name is input from IDFileConverter for 'base_name' attribute, only necessary if different from 'mz_file'. |
| 405 | if (!mz_name.empty()) |
| 406 | { |
| 407 | base_name = mz_name; |
nothing calls this directly
no test coverage detected