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ConsensusXMLFile Member List

This is the complete list of members for ConsensusXMLFile, including all inherited members.

accession_to_id_ConsensusXMLFileprotected
act_cons_element_ConsensusXMLFileprotected
ActionMode enum nameXMLHandler
addProteinGroups_(MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::unordered_map< std::string, UInt > &accession_to_id, const String &runid, XMLHandler::ActionMode mode)ConsensusXMLFileprotected
asBool_(const String &in)XMLHandlerinlineprotected
asDateTime_(String date_string)XMLHandlerinlineprotected
asDouble_(const String &in)XMLHandlerinlineprotected
asFloat_(const String &in)XMLHandlerinlineprotected
asInt_(const String &in)XMLHandlerinlineprotected
asInt_(const XMLCh *in)XMLHandlerinlineprotected
asUInt_(const String &in)XMLHandlerinlineprotected
attributeAsDouble_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsDouble_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
attributeAsDoubleList_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsDoubleList_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
attributeAsInt_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsInt_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
attributeAsIntList_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsIntList_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
attributeAsString_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsString_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
attributeAsStringList_(const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
attributeAsStringList_(const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
characters(const XMLCh *const chars, const XMLSize_t length) overrideConsensusXMLFileprotected
checkUniqueIdentifiers_(const std::vector< ProteinIdentification > &prot_ids)XMLHandler
CMD enum valueProgressLogger
consensus_map_ConsensusXMLFileprotected
ConsensusXMLFile()ConsensusXMLFile
current_logger_ProgressLoggermutableprotected
cv_terms_XMLHandlerprotected
cvStringToEnum_(const Size section, const String &term, const char *message, const SignedSize result_on_error=0)XMLHandlerinlineprotected
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) overrideConsensusXMLFileprotected
endProgress() constProgressLogger
enforced_encoding_XMLFileprotected
enforceEncoding_(const String &encoding)XMLFileprotected
equal_(const XMLCh *a, const XMLCh *b) constXMLHandlerinlineprotected
error(const xercesc::SAXParseException &exception) overrideXMLHandler
error(ActionMode mode, const String &msg, UInt line=0, UInt column=0) constXMLHandler
error_message_XMLHandlermutableprotected
errorString()XMLHandler
expectList_(const String &str) constXMLHandlerinlineprivate
fatalError(const xercesc::SAXParseException &exception) overrideXMLHandler
fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) constXMLHandler
file_XMLHandlerprotected
getLoadDetail() constXMLHandlervirtual
getLogType() constProgressLogger
getOptions()ConsensusXMLFile
getOptions() constConsensusXMLFile
getProteinGroups_(std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name)ConsensusXMLFileprotected
getVersion() constXMLFile
GUI enum valueProgressLogger
id_identifier_ConsensusXMLFileprotected
identifier_id_ConsensusXMLFileprotected
isValid(const String &filename, std::ostream &os)XMLFile
it_ConsensusXMLFileprotected
last_invoke_ProgressLoggermutableprotected
last_meta_ConsensusXMLFileprotected
LD_ALLDATA enum valueXMLHandler
LD_COUNTS_WITHOPTIONS enum valueXMLHandler
LD_RAWCOUNTS enum valueXMLHandler
load(const String &filename, ConsensusMap &map)ConsensusXMLFile
LOAD enum valueXMLHandler
load_detail_XMLHandlerprotected
LOADDETAIL enum nameXMLHandler
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
nextProgress() constProgressLogger
NONE enum valueProgressLogger
open_tags_XMLHandlerprotected
operator=(const ProgressLogger &other)ProgressLogger
optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const char *name) constXMLHandlerinlineprotected
optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const XMLCh *name) constXMLHandlerinlineprotected
options_ConsensusXMLFileprotected
parse_(const String &filename, XMLHandler *handler)XMLFileprotected
parseBuffer_(const std::string &buffer, XMLHandler *handler)XMLFileprotected
pep_hit_ConsensusXMLFileprotected
pep_id_ConsensusXMLFileprotected
peptide_evidences_ConsensusXMLFileprotected
pos_ConsensusXMLFileprotected
progress_ConsensusXMLFileprotected
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
prot_hit_ConsensusXMLFileprotected
prot_id_ConsensusXMLFileprotected
proteinid_to_accession_ConsensusXMLFileprotected
recursion_depth_ProgressLoggerprotectedstatic
reset()XMLHandler
save_(const String &filename, XMLHandler *handler) constXMLFileprotected
schema_location_XMLFileprotected
schema_version_XMLFileprotected
search_param_ConsensusXMLFileprotected
setLoadDetail(const LOADDETAIL d)XMLHandlervirtual
setLogType(LogType type) constProgressLogger
setProgress(SignedSize value) constProgressLogger
sm_XMLHandlerprotected
startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) overrideConsensusXMLFileprotected
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
STORE enum valueXMLHandler
store(const String &filename, const ConsensusMap &consensus_map)ConsensusXMLFile
type_ProgressLoggermutableprotected
version_XMLHandlerprotected
warning(const xercesc::SAXParseException &exception) overrideXMLHandler
warning(ActionMode mode, const String &msg, UInt line=0, UInt column=0) constXMLHandler
writePeptideIdentification_(const String &filename, std::ostream &os, const PeptideIdentification &id, const String &tag_name, UInt indentation_level)ConsensusXMLFileprotected
writeTo(std::ostream &)XMLHandlervirtual
writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) constXMLHandlerprotected
writeXMLEscape(const String &to_escape)XMLHandlerinlinestatic
XMLFile()XMLFile
XMLFile(const String &schema_location, const String &version)XMLFile
XMLHandler(const String &filename, const String &version)XMLHandler
XMLHandler()XMLHandlerprivate
~ConsensusXMLFile() overrideConsensusXMLFile
~ProgressLogger()ProgressLogger
~XMLFile()XMLFilevirtual
~XMLHandler() overrideXMLHandler
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