QcMLFile Member List

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

ActionMode enum name	XMLHandler
addRunAttachment(const std::string &r, const Attachment &at)	QcMLFile
addRunQualityParameter(const std::string &r, const QualityParameter &qp)	QcMLFile
addSetAttachment(const std::string &r, const Attachment &at)	QcMLFile
addSetQualityParameter(const std::string &r, const QualityParameter &qp)	QcMLFile
asBool_(const std::string &in) const	XMLHandler	inlineprotected
asDateTime_(std::string date_string) const	XMLHandler	inlineprotected
asDouble_(const std::string &in) const	XMLHandler	inlineprotected
asFloat_(const std::string &in) const	XMLHandler	inlineprotected
asInt_(const std::string &in) const	XMLHandler	inlineprotected
asInt_(const XMLCh *in) const	XMLHandler	inlineprotected
asUInt_(const std::string &in) const	XMLHandler	inlineprotected
at_	QcMLFile	protected
ats_	QcMLFile	protected
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) override	QcMLFile	protected
checkUniqueIdentifiers_(const std::vector< ProteinIdentification > &prot_ids) const	XMLHandler
CMD enum value	ProgressLogger
collectQCData(std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids, const FeatureMap &feature_map, const ConsensusMap &consensus_map, const std::string &inputfile_raw, const bool remove_duplicate_features, const MSExperiment &exp)	QcMLFile
collectSetParameter(const std::string &setname, const std::string &qp, std::vector< std::string > &ret)	QcMLFile
current_logger_	ProgressLogger	mutableprotected
cv_terms_	XMLHandler	protected
cvParamToValue(const ControlledVocabulary &cv, const std::string &parent_tag, const std::string &accession, const std::string &name, const std::string &value, const std::string &unit_accession) const	XMLHandler
cvParamToValue(const ControlledVocabulary &cv, const CVTerm &raw_term) const	XMLHandler
cvStringToEnum_(const Size section, const std::string &term, const char *message, const SignedSize result_on_error=0)	XMLHandler	protected
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override	QcMLFile	protected
endProgress(UInt64 bytes_processed=0) const	ProgressLogger
enforced_encoding_	XMLFile	protected
enforceEncoding_(const std::string &encoding)	XMLFile	protected
equal_(const XMLCh *a, const XMLCh *b) const	XMLHandler	inlineprotected
error(const xercesc::SAXParseException &exception) override	XMLHandler
error(ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const	XMLHandler
existsRun(const std::string &filename, bool checkname=false) const	QcMLFile
existsRunQualityParameter(const std::string &filename, const std::string &qpname, std::vector< std::string > &ids) const	QcMLFile
existsSet(const std::string &filename, bool checkname=false) const	QcMLFile
existsSetQualityParameter(const std::string &filename, const std::string &qpname, std::vector< std::string > &ids) const	QcMLFile
expectList_(const std::string &str) const	XMLHandler	inlineprivate
exportAttachment(const std::string &filename, const std::string &qpname) const	QcMLFile
exportIDstats(const std::string &filename) const	QcMLFile
exportQP(const std::string &filename, const std::string &qpname) const	QcMLFile
exportQPs(const std::string &filename, const StringList &qpnames) const	QcMLFile
fatalError(const xercesc::SAXParseException &exception) override	XMLHandler
fatalError(ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const	XMLHandler
file_	XMLHandler	protected
fromXSDString(const std::string &type, const std::string &value)	XMLHandler	inlinestatic
getLoadDetail() const	XMLHandler	virtual
getLogType() const	ProgressLogger
getRunIDs(std::vector< std::string > &ids) const	QcMLFile
getRunNames(std::vector< std::string > &ids) const	QcMLFile
getVersion() const	XMLFile
GUI enum value	ProgressLogger
header_	QcMLFile	protected
isValid(const std::string &filename, std::ostream &os)	XMLFile
last_invoke_	ProgressLogger	mutableprotected
LD_ALLDATA enum value	XMLHandler
LD_COUNTS_WITHOPTIONS enum value	XMLHandler
LD_RAWCOUNTS enum value	XMLHandler
LOAD enum value	XMLHandler
load(const std::string &filename)	QcMLFile
load_detail_	XMLHandler	protected
LOADDETAIL enum name	XMLHandler
LogType enum name	ProgressLogger
map2csv(const std::map< std::string, std::map< std::string, std::string > > &cvs_table, const std::string &separator) const	QcMLFile
merge(const QcMLFile &addendum, const std::string &setname="")	QcMLFile
name_	QcMLFile	protected
names_	QcMLFile	protected
nextProgress() const	ProgressLogger
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_(std::string &value, const xercesc::Attributes &a, const char *name) const	XMLHandler	inlineprotected
optionalAttributeAsString_(std::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
parse_(const std::string &filename, XMLHandler *handler)	XMLFile	protected
parseBuffer_(const std::string &buffer, XMLHandler *handler)	XMLFile	protected
progress_	QcMLFile	protected
ProgressLogger()	ProgressLogger
ProgressLogger(const ProgressLogger &other)	ProgressLogger
QcMLFile()	QcMLFile
qp_	QcMLFile	protected
qps_	QcMLFile	protected
recursion_depth_	ProgressLogger	protectedstatic
registerRun(const std::string &id, const std::string &name)	QcMLFile
registerSet(const std::string &id, const std::string &name, const std::set< std::string > &names)	QcMLFile
removeAllAttachments(const std::string &at)	QcMLFile
removeAttachment(const std::string &r, std::vector< std::string > &ids, const std::string &at="")	QcMLFile
removeAttachment(const std::string &r, const std::string &at)	QcMLFile
removeQualityParameter(const std::string &r, std::vector< std::string > &ids)	QcMLFile
reset()	XMLHandler
row_	QcMLFile	protected
run_id_	QcMLFile	protected
run_Name_ID_map_	QcMLFile	protected
runQualityAts_	QcMLFile	protected
runQualityQPs_	QcMLFile	protected
save_(const std::string &filename, XMLHandler *handler) const	XMLFile	protected
schema_location_	XMLFile	protected
schema_version_	XMLFile	protected
set_Name_ID_map_	QcMLFile	protected
setLoadDetail(const LOADDETAIL d)	XMLHandler	virtual
setLogger(ProgressLoggerImpl *logger)	ProgressLogger
setLogType(LogType type) const	ProgressLogger
setProgress(SignedSize value) const	ProgressLogger
setQualityAts_	QcMLFile	protected
setQualityQPs_	QcMLFile	protected
setQualityQPs_members_	QcMLFile	protected
sm_	XMLHandler	protected
startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override	QcMLFile	protected
startProgress(SignedSize begin, SignedSize end, const std::string &label) const	ProgressLogger
STORE enum value	XMLHandler
store(const std::string &filename) const	QcMLFile
tag_	QcMLFile	protected
type_	ProgressLogger	mutableprotected
version_	XMLHandler	protected
warning(const xercesc::SAXParseException &exception) override	XMLHandler
warning(ActionMode mode, const std::string &msg, UInt line=0, UInt column=0) const	XMLHandler
writeTo(std::ostream &)	XMLHandler	virtual
writeUserParam_(const std::string &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const	XMLHandler	protected
writeXMLEscape(const std::string &to_escape)	XMLHandler	inlinestatic
XMLFile()	XMLFile
XMLFile(const std::string &schema_location, const std::string &version)	XMLFile
XMLHandler(const std::string &filename, const std::string &version)	XMLHandler
XMLHandler()	XMLHandler	private
~ProgressLogger()	ProgressLogger	virtual
~QcMLFile() override	QcMLFile
~XMLFile()	XMLFile	virtual
~XMLHandler() override	XMLHandler