| enforced_encoding_ | XMLFile | protected |
| enforceEncoding_(const String &encoding) | XMLFile | protected |
| getMaxScore() const | XQuestResultXMLFile | |
| getMinScore() const | XQuestResultXMLFile | |
| getNumberOfHits() const | XQuestResultXMLFile | |
| getVersion() const | XMLFile | |
| getxQuestBase64EncodedSpectrum_(const PeakSpectrum &spec, String header) | XQuestResultXMLFile | privatestatic |
| isValid(const String &filename, std::ostream &os) | XMLFile | |
| load(const String &filename, std::vector< std::vector< PeptideIdentification > > &csms, std::vector< ProteinIdentification > &prot_ids, Size min_n_hits_per_spectrum=0, bool load_to_peptideHit=false) | XQuestResultXMLFile | |
| max_score_ | XQuestResultXMLFile | private |
| min_score_ | XQuestResultXMLFile | private |
| n_hits_ | XQuestResultXMLFile | private |
| parse_(const String &filename, XMLHandler *handler) | XMLFile | protected |
| save_(const String &filename, XMLHandler *handler) const | XMLFile | protected |
| schema_location_ | XMLFile | protected |
| schema_version_ | XMLFile | protected |
| wrap_(const String &input, Size width, String &output) | XQuestResultXMLFile | privatestatic |
| writeXQuestXML(String out_file, String base_name, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra, String precursor_mass_tolerance_unit, String fragment_mass_tolerance_unit, double precursor_mass_tolerance, double fragment_mass_tolerance, double fragment_mass_tolerance_xlinks, String cross_link_name, double cross_link_mass_light, DoubleList cross_link_mass_mono_link, String in_fasta, String in_decoy_fasta, StringList cross_link_residue1, StringList cross_link_residue2, double cross_link_mass_iso_shift, String enzyme_name, Size missed_cleavages) | XQuestResultXMLFile | static |
| writeXQuestXMLSpec(String out_file, String base_name, const OPXLDataStructs::PreprocessedPairSpectra &preprocessed_pair_spectra, const std::vector< std::pair< Size, Size > > &spectrum_pairs, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra) | XQuestResultXMLFile | static |
| writeXQuestXMLSpec(String out_file, String base_name, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra) | XQuestResultXMLFile | static |
| XMLFile() | XMLFile | |
| XMLFile(const String &schema_location, const String &version) | XMLFile | |
| XQuestResultXMLFile() | XQuestResultXMLFile | |
| ~XMLFile() | XMLFile | virtual |
| ~XQuestResultXMLFile() | XQuestResultXMLFile | |