QcMLFile Member List

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

ActionMode enum name	XMLHandler
addRunAttachment(String r, Attachment at)	QcMLFile
addRunQualityParameter(String r, QualityParameter qp)	QcMLFile
addSetAttachment(String r, Attachment at)	QcMLFile
addSetQualityParameter(String r, QualityParameter qp)	QcMLFile
asBool_(const String &in) const	XMLHandler	inlineprotected
asDateTime_(String date_string) const	XMLHandler	inlineprotected
asDouble_(const String &in) const	XMLHandler	inlineprotected
asFloat_(const String &in) const	XMLHandler	inlineprotected
asInt_(const String &in) const	XMLHandler	inlineprotected
asInt_(const XMLCh *in) const	XMLHandler	inlineprotected
asUInt_(const 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, std::vector< PeptideIdentification > &pep_ids, const FeatureMap &feature_map, const ConsensusMap &consensus_map, const String &inputfile_raw, const bool remove_duplicate_features, const MSExperiment &exp)	QcMLFile
collectSetParameter(const String setname, const String qp, std::vector< String > &ret)	QcMLFile
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	protected
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override	QcMLFile	protected
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) override	XMLHandler
error(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const	XMLHandler
error_message_	XMLHandler	mutableprotected
errorString()	XMLHandler
existsRun(const String filename, bool checkname=false) const	QcMLFile
existsRunQualityParameter(const String filename, const String qpname, std::vector< String > &ids) const	QcMLFile
existsSet(const String filename, bool checkname=false) const	QcMLFile
existsSetQualityParameter(const String filename, const String qpname, std::vector< String > &ids) const	QcMLFile
expectList_(const String &str) const	XMLHandler	inlineprivate
exportAttachment(const String filename, const String qpname) const	QcMLFile
exportIDstats(const String &filename) const	QcMLFile
exportQP(const String filename, const String qpname) const	QcMLFile
exportQPs(const String filename, const StringList qpnames) const	QcMLFile
fatalError(const xercesc::SAXParseException &exception) override	XMLHandler
fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const	XMLHandler
file_	XMLHandler	protected
getLoadDetail() const	XMLHandler	virtual
getLogType() const	ProgressLogger
getRunIDs(std::vector< String > &ids) const	QcMLFile
getRunNames(std::vector< String > &ids) const	QcMLFile
getVersion() const	XMLFile
GUI enum value	ProgressLogger
header_	QcMLFile	protected
isValid(const 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 String &filename)	QcMLFile
load_detail_	XMLHandler	protected
LOADDETAIL enum name	XMLHandler
LogType enum name	ProgressLogger
logTypeToFactoryName_(LogType type)	ProgressLogger	protectedstatic
map2csv(const std::map< String, std::map< String, String > > &cvs_table, const String &separator) const	QcMLFile
merge(const QcMLFile &addendum, 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_(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
parse_(const 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 String id, const String name)	QcMLFile
registerSet(const String id, const String name, const std::set< String > &names)	QcMLFile
removeAllAttachments(String at)	QcMLFile
removeAttachment(String r, std::vector< String > &ids, String at="")	QcMLFile
removeAttachment(String r, String at)	QcMLFile
removeQualityParameter(String r, std::vector< 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 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
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 String &label) const	ProgressLogger
STORE enum value	XMLHandler
store(const String &filename) const	QcMLFile
tag_	QcMLFile	protected
type_	ProgressLogger	mutableprotected
version_	XMLHandler	protected
warning(const xercesc::SAXParseException &exception) override	XMLHandler
warning(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const	XMLHandler
writeTo(std::ostream &)	XMLHandler	virtual
writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const	XMLHandler	protected
writeXMLEscape(const String &to_escape)	XMLHandler	inlinestatic
XMLFile()	XMLFile
XMLFile(const String &schema_location, const String &version)	XMLFile
XMLHandler(const String &filename, const String &version)	XMLHandler
XMLHandler()	XMLHandler	private
~ProgressLogger()	ProgressLogger	virtual
~QcMLFile() override	QcMLFile
~XMLFile()	XMLFile	virtual
~XMLHandler() override	XMLHandler