| 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 |