| 23 | XQuestResultXMLFile::~XQuestResultXMLFile() = default; |
| 24 | |
| 25 | void XQuestResultXMLFile::load(const String & filename, |
| 26 | std::vector < PeptideIdentification > & pep_ids, |
| 27 | std::vector< ProteinIdentification > & prot_ids |
| 28 | ) |
| 29 | { |
| 30 | Internal::XQuestResultXMLHandler handler(filename, pep_ids, prot_ids); |
| 31 | this->parse_(filename, &handler); |
| 32 | |
| 33 | this->n_hits_ = handler.getNumberOfHits(); |
| 34 | this->min_score_ = handler.getMinScore(); |
| 35 | this->max_score_ = handler.getMaxScore(); |
| 36 | |
| 37 | // this helper function adds additional explicit "xl_target_decoy" meta values derived from parsed data |
| 38 | OPXLHelper::addXLTargetDecoyMV(pep_ids); |
| 39 | // this helper function adds beta peptide accessions |
| 40 | OPXLHelper::addBetaAccessions(pep_ids); |
| 41 | // this helper function bases the ranked lists of labeled XLMS searches on each light spectrum instead of pairs |
| 42 | // the second parameter here should be the maximal number of hits per spectrum, |
| 43 | // but using the total number of hits we will just keep everything contained in the file |
| 44 | // (just reassigned to single spectra and re-ranked by score) |
| 45 | pep_ids = OPXLHelper::combineTopRanksFromPairs(pep_ids, this->n_hits_); |
| 46 | OPXLHelper::removeBetaPeptideHits(pep_ids); |
| 47 | OPXLHelper::computeDeltaScores(pep_ids); |
| 48 | } |
| 49 | |
| 50 | int XQuestResultXMLFile::getNumberOfHits() const |
| 51 | { |
nothing calls this directly
no test coverage detected