| ActionMode enum name | XMLHandler | protected |
| analysis_summary_ | PepXMLFile | private |
| asBool_(const String &in) | XMLHandler | inlineprotected |
| asDateTime_(String date_string) | XMLHandler | inlineprotected |
| asDouble_(const String &in) | XMLHandler | inlineprotected |
| asFloat_(const String &in) | XMLHandler | inlineprotected |
| asInt_(const String &in) | XMLHandler | inlineprotected |
| asInt_(const XMLCh *in) | XMLHandler | inlineprotected |
| asUInt_(const String &in) | XMLHandler | inlineprotected |
| attributeAsDouble_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsDouble_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| attributeAsDoubleList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsDoubleList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| attributeAsInt_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsInt_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| attributeAsIntList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsIntList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| attributeAsString_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsString_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| attributeAsStringList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| attributeAsStringList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| characters(const XMLCh *const chars, const XMLSize_t length) | XMLHandler | protectedvirtual |
| charge_ | PepXMLFile | private |
| checked_base_name_ | PepXMLFile | private |
| current_analysis_result_ | PepXMLFile | private |
| current_base_name_ | PepXMLFile | private |
| current_modifications_ | PepXMLFile | private |
| current_peptide_ | PepXMLFile | private |
| current_proteins_ | PepXMLFile | private |
| current_sequence_ | PepXMLFile | private |
| cv_terms_ | XMLHandler | protected |
| cvStringToEnum_(const Size section, const String &term, const char *message, const SignedSize result_on_error=0) | XMLHandler | inlineprotected |
| date_ | PepXMLFile | private |
| endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) | PepXMLFile | protectedvirtual |
| enforced_encoding_ | XMLFile | protected |
| enforceEncoding_(const String &encoding) | XMLFile | protected |
| enzyme_ | PepXMLFile | private |
| equal_(const XMLCh *a, const XMLCh *b) const | XMLHandler | inlineprotected |
| error(const xercesc::SAXParseException &exception) | XMLHandler | protected |
| error(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | XMLHandler | protected |
| error_message_ | XMLHandler | mutableprotected |
| errorString() | XMLHandler | protected |
| exp_name_ | PepXMLFile | private |
| experiment_label_ | PepXMLFile | private |
| fatalError(const xercesc::SAXParseException &exception) | XMLHandler | protected |
| fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | XMLHandler | protected |
| file_ | XMLHandler | protected |
| fixed_modifications_ | PepXMLFile | private |
| getVersion() const | XMLFile | |
| hydrogen_ | PepXMLFile | private |
| hydrogen_mass_ | PepXMLFile | private |
| isValid(const String &filename, std::ostream &os) | XMLFile | |
| keep_native_name_ | PepXMLFile | private |
| keepNativeSpectrumName(bool keep) | PepXMLFile | inline |
| load(const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name, const SpectrumMetaDataLookup &lookup) | PepXMLFile | |
| load(const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name="") | PepXMLFile | |
| LOAD enum value | XMLHandler | protected |
| lookup_ | PepXMLFile | private |
| makeScanMap_() | PepXMLFile | private |
| matchModification_(const double mass, const String &origin, String &modification_description) | PepXMLFile | private |
| mod_tol_ | PepXMLFile | privatestatic |
| mz_ | PepXMLFile | private |
| native_spectrum_name_ | PepXMLFile | private |
| open_tags_ | XMLHandler | protected |
| optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected |
| optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inlineprotected |
| params_ | PepXMLFile | private |
| parse_(const String &filename, XMLHandler *handler) | XMLFile | protected |
| peptide_hit_ | PepXMLFile | private |
| peptides_ | PepXMLFile | private |
| PepXMLFile() | PepXMLFile | |
| prot_id_ | PepXMLFile | private |
| proteins_ | PepXMLFile | private |
| readRTMZCharge_(const xercesc::Attributes &attributes) | PepXMLFile | private |
| reset() | XMLHandler | protected |
| rt_ | PepXMLFile | private |
| save_(const String &filename, XMLHandler *handler) const | XMLFile | protected |
| scan_map_ | PepXMLFile | private |
| schema_location_ | XMLFile | protected |
| schema_version_ | XMLFile | protected |
| search_engine_ | PepXMLFile | private |
| search_id_ | PepXMLFile | private |
| search_score_summary_ | PepXMLFile | private |
| search_summary_ | PepXMLFile | private |
| seen_experiment_ | PepXMLFile | private |
| sm_ | XMLHandler | protected |
| startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) | PepXMLFile | protectedvirtual |
| status_ | PepXMLFile | private |
| 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=false) | PepXMLFile | |
| STORE enum value | XMLHandler | protected |
| swath_assay_ | PepXMLFile | private |
| use_precursor_data_ | PepXMLFile | private |
| variable_modifications_ | PepXMLFile | private |
| version_ | XMLHandler | protected |
| warning(const xercesc::SAXParseException &exception) | XMLHandler | protected |
| warning(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | XMLHandler | protected |
| writeTo(std::ostream &) | XMLHandler | protectedvirtual |
| writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const | XMLHandler | protected |
| writeXMLEscape(const String &to_escape) | XMLHandler | inlineprotectedstatic |
| wrong_experiment_ | PepXMLFile | private |
| XMLFile() | XMLFile | |
| XMLFile(const String &schema_location, const String &version) | XMLFile | |
| XMLHandler(const String &filename, const String &version) | XMLHandler | protected |
| xtandem_artificial_mod_tol_ | PepXMLFile | privatestatic |
| ~PepXMLFile() | PepXMLFile | virtual |
| ~XMLFile() | XMLFile | virtual |
| ~XMLHandler() | XMLHandler | protectedvirtual |