| ActionMode enum name | XMLHandler | protected |
| addProteinGroups_(MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::map< String, UInt > &accession_to_id) | IdXMLFile | 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 |
| CMD enum value | ProgressLogger | |
| ConsensusXMLFile class | IdXMLFile | friend |
| createFlankingAAXMLString_(const std::vector< PeptideEvidence > &pes) | IdXMLFile | protectedstatic |
| createPositionXMLString_(const std::vector< PeptideEvidence > &pes) | IdXMLFile | protectedstatic |
| current_logger_ | ProgressLogger | mutableprotected |
| cv_terms_ | XMLHandler | protected |
| cvStringToEnum_(const Size section, const String &term, const char *message, const SignedSize result_on_error=0) | XMLHandler | inlineprotected |
| document_id_ | IdXMLFile | protected |
| endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) | IdXMLFile | protectedvirtual |
| endProgress() const | ProgressLogger | |
| enforced_encoding_ | XMLFile | protected |
| enforceEncoding_(const String &encoding) | XMLFile | protected |
| 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 |
| fatalError(const xercesc::SAXParseException &exception) | XMLHandler | protected |
| fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | XMLHandler | protected |
| FeatureXMLFile class | IdXMLFile | friend |
| file_ | XMLHandler | protected |
| getLogType() const | ProgressLogger | |
| getProteinGroups_(std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name) | IdXMLFile | protected |
| getVersion() const | XMLFile | |
| GUI enum value | ProgressLogger | |
| id_ | IdXMLFile | protected |
| IdXMLFile() | IdXMLFile | |
| isValid(const String &filename, std::ostream &os) | XMLFile | |
| last_invoke_ | ProgressLogger | mutableprotected |
| last_meta_ | IdXMLFile | protected |
| LOAD enum value | XMLHandler | protected |
| load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids) | IdXMLFile | |
| load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, String &document_id) | IdXMLFile | |
| LogType enum name | ProgressLogger | |
| logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
| NONE enum value | ProgressLogger | |
| open_tags_ | XMLHandler | protected |
| operator=(const ProgressLogger &other) | ProgressLogger | |
| 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 |
| param_ | IdXMLFile | protected |
| parameters_ | IdXMLFile | protected |
| parse_(const String &filename, XMLHandler *handler) | XMLFile | protected |
| parseFragmentAnnotation_(const String &s, std::vector< PeptideHit::PeakAnnotation > &annotations) | IdXMLFile | protectedstatic |
| pep_hit_ | IdXMLFile | protected |
| pep_id_ | IdXMLFile | protected |
| pep_ids_ | IdXMLFile | protected |
| peptide_evidences_ | IdXMLFile | protected |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| prot_hit_ | IdXMLFile | protected |
| prot_id_ | IdXMLFile | protected |
| prot_id_in_run_ | IdXMLFile | protected |
| prot_ids_ | IdXMLFile | protected |
| proteinid_to_accession_ | IdXMLFile | protected |
| recursion_depth_ | ProgressLogger | protectedstatic |
| reset() | XMLHandler | protected |
| save_(const String &filename, XMLHandler *handler) const | XMLFile | protected |
| schema_location_ | XMLFile | protected |
| schema_version_ | XMLFile | protected |
| setLogType(LogType type) const | ProgressLogger | |
| setProgress(SignedSize value) const | ProgressLogger | |
| sm_ | XMLHandler | protected |
| startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) | IdXMLFile | protectedvirtual |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| STORE enum value | XMLHandler | protected |
| store(String filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="") | IdXMLFile | |
| type_ | 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 |
| writeFragmentAnnotations_(const String &tag_name, std::ostream &os, std::vector< PeptideHit::PeakAnnotation > annotations, UInt indent) | IdXMLFile | protectedstatic |
| 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 |
| XMLFile() | XMLFile | |
| XMLFile(const String &schema_location, const String &version) | XMLFile | |
| XMLHandler(const String &filename, const String &version) | XMLHandler | protected |
| ~ProgressLogger() | ProgressLogger | |
| ~XMLFile() | XMLFile | virtual |
| ~XMLHandler() | XMLHandler | protectedvirtual |