| ActionMode enum name | XMLHandler | protected | 
  | 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_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) | 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_ | 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=std::cerr) | XMLFile |  | 
  | load(const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name, const MSExperiment<> &experiment, bool use_precursor_data=false) | PepXMLFile |  | 
  | load(const String &filename, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides, const String &experiment_name="") | PepXMLFile |  | 
  | LOAD enum value | XMLHandler | protected | 
  | makeScanMap_() | PepXMLFile | private | 
  | matchModification_(const DoubleReal mass, const String &origin, String &modification_description) | PepXMLFile | private | 
  | mz_ | PepXMLFile | private | 
  | mz_tol_ | PepXMLFile | private | 
  | open_tags_ | XMLHandler | protected | 
  | optionalAttributeAsDouble_(DoubleReal &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inlineprotected | 
  | optionalAttributeAsDouble_(DoubleReal &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 | 
  | rt_tol_ | 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 | 
  | seen_experiment_ | PepXMLFile | private | 
  | sm_ | XMLHandler | protected | 
  | startElement(const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes) | PepXMLFile | protectedvirtual | 
  | store(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids) | PepXMLFile |  | 
  | STORE enum value | XMLHandler | protected | 
  | 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 | inlineprotectedvirtual | 
  | writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const | XMLHandler | protected | 
  | wrong_experiment_ | PepXMLFile | private | 
  | XMLFile() | XMLFile |  | 
  | XMLFile(const String &schema_location, const String &version) | XMLFile |  | 
  | XMLHandler(const String &filename, const String &version) | XMLHandler | protected | 
  | ~PepXMLFile() | PepXMLFile | virtual | 
  | ~XMLFile() | XMLFile | virtual | 
  | ~XMLHandler() | XMLHandler | protectedvirtual |