| accession_to_id_ | FeatureXMLFile | protected | 
  | 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 | 
  | begin_ | ProgressLogger | mutableprotected | 
  | characters(const XMLCh *const chars, const XMLSize_t length) | FeatureXMLFile | protectedvirtual | 
  | CMD enum value | ProgressLogger |  | 
  | current_chull_ | FeatureXMLFile | protected | 
  | current_feature_ | FeatureXMLFile | protected | 
  | cv_terms_ | XMLHandler | protected | 
  | cvStringToEnum_(const Size section, const String &term, const char *message, const SignedSize result_on_error=0) | XMLHandler | inlineprotected | 
  | dim_ | FeatureXMLFile | protected | 
  | disable_parsing_ | FeatureXMLFile | protected | 
  | dlg_ | ProgressLogger | mutableprotected | 
  | end_ | ProgressLogger | mutableprotected | 
  | endElement(const XMLCh *const , const XMLCh *const , const XMLCh *const qname) | FeatureXMLFile | protectedvirtual | 
  | endProgress() const | ProgressLogger |  | 
  | enforced_encoding_ | XMLFile | protected | 
  | enforceEncoding_(const String &encoding) | XMLFile | protected | 
  | 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 | 
  | expected_size_ | FeatureXMLFile | protected | 
  | fatalError(const xercesc::SAXParseException &exception) | XMLHandler | protected | 
  | fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | XMLHandler | protected | 
  | FeatureXMLFile() | FeatureXMLFile |  | 
  | file_ | XMLHandler | protected | 
  | getLogType() const | ProgressLogger |  | 
  | getOptions() | FeatureXMLFile |  | 
  | getOptions() const | FeatureXMLFile |  | 
  | getVersion() const | XMLFile |  | 
  | GUI enum value | ProgressLogger |  | 
  | hull_position_ | FeatureXMLFile | protected | 
  | id_identifier_ | FeatureXMLFile | protected | 
  | identifier_id_ | FeatureXMLFile | protected | 
  | in_description_ | FeatureXMLFile | protected | 
  | isValid(const String &filename, std::ostream &os=std::cerr) | XMLFile |  | 
  | last_invoke_ | ProgressLogger | mutableprotected | 
  | last_meta_ | FeatureXMLFile | protected | 
  | LOAD enum value | XMLHandler | protected | 
  | load(const String &filename, FeatureMap<> &feature_map) | FeatureXMLFile |  | 
  | loadSize(const String &filename) | FeatureXMLFile |  | 
  | LogType enum name | ProgressLogger |  | 
  | map_ | FeatureXMLFile | protected | 
  | model_desc_ | FeatureXMLFile | protected | 
  | NONE enum value | ProgressLogger |  | 
  | 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 | 
  | options_ | FeatureXMLFile | protected | 
  | param_ | FeatureXMLFile | protected | 
  | parse_(const String &filename, XMLHandler *handler) | XMLFile | protected | 
  | pep_hit_ | FeatureXMLFile | protected | 
  | pep_id_ | FeatureXMLFile | protected | 
  | ProgressLogger() | ProgressLogger |  | 
  | prot_hit_ | FeatureXMLFile | protected | 
  | prot_id_ | FeatureXMLFile | protected | 
  | proteinid_to_accession_ | FeatureXMLFile | protected | 
  | recursion_depth_ | ProgressLogger | protectedstatic | 
  | reset() | XMLHandler | protected | 
  | resetMembers_() | FeatureXMLFile | protected | 
  | save_(const String &filename, XMLHandler *handler) const | XMLFile | protected | 
  | schema_location_ | XMLFile | protected | 
  | schema_version_ | XMLFile | protected | 
  | search_param_ | FeatureXMLFile | protected | 
  | setLogType(LogType type) const | ProgressLogger |  | 
  | setOptions(const FeatureFileOptions &) | FeatureXMLFile |  | 
  | setProgress(SignedSize value) const | ProgressLogger |  | 
  | size_only_ | FeatureXMLFile | protected | 
  | sm_ | XMLHandler | protected | 
  | startElement(const XMLCh *const , const XMLCh *const , const XMLCh *const qname, const xercesc::Attributes &attributes) | FeatureXMLFile | protectedvirtual | 
  | startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger |  | 
  | stop_watch_ | ProgressLogger | mutableprotected | 
  | STORE enum value | XMLHandler | protected | 
  | store(const String &filename, const FeatureMap<> &feature_map) | FeatureXMLFile |  | 
  | subordinate_feature_level_ | FeatureXMLFile | protected | 
  | type_ | ProgressLogger | mutableprotected | 
  | updateCurrentFeature_(bool create) | FeatureXMLFile | protected | 
  | value_ | ProgressLogger | mutableprotected | 
  | 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 | 
  | writeFeature_(const String &filename, std::ostream &os, const Feature &feat, const String &identifier_prefix, UInt64 identifier, UInt indentation_level) | FeatureXMLFile | protected | 
  | writePeptideIdentification_(const String &filename, std::ostream &os, const PeptideIdentification &id, const String &tag_name, UInt indentation_level) | FeatureXMLFile | protected | 
  | writeTo(std::ostream &) | XMLHandler | inlineprotectedvirtual | 
  | writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const | XMLHandler | protected | 
  | XMLFile() | XMLFile |  | 
  | XMLFile(const String &schema_location, const String &version) | XMLFile |  | 
  | XMLHandler(const String &filename, const String &version) | XMLHandler | protected | 
  | ~FeatureXMLFile() | FeatureXMLFile |  | 
  | ~ProgressLogger() | ProgressLogger |  | 
  | ~XMLFile() | XMLFile | virtual | 
  | ~XMLHandler() | XMLHandler | protectedvirtual |