MzIdentMLHandler Member List

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

ActionMode enum name	XMLHandler
actual_peptide_	MzIdentMLHandler	private
actual_protein_	MzIdentMLHandler	private
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) override	MzIdentMLHandler
cid_	MzIdentMLHandler	protected
cpep_id_	MzIdentMLHandler	protected
cpro_id_	MzIdentMLHandler	protected
current_id_hit_	MzIdentMLHandler	protected
current_mod_location_	MzIdentMLHandler	private
current_spectrum_id_	MzIdentMLHandler	protected
cv_	MzIdentMLHandler	protected
cv_terms_	XMLHandler	protected
cvStringToEnum_(const Size section, const String &term, const char *message, const SignedSize result_on_error=0)	XMLHandler	inlineprotected
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override	MzIdentMLHandler
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
fatalError(const xercesc::SAXParseException &exception) override	XMLHandler
fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const	XMLHandler
file_	XMLHandler	protected
getChildWithName_(const String &parent_accession, const String &name) const	MzIdentMLHandler	protected
getLoadDetail() const	XMLHandler	virtual
handleCVParam_(const String &parent_parent_tag, const String &parent_tag, const String &accession, const xercesc::Attributes &attributes, const String &cv_ref)	MzIdentMLHandler	protected
handleUserParam_(const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)	MzIdentMLHandler	protected
id_	MzIdentMLHandler	protected
LD_ALLDATA enum value	XMLHandler
LD_COUNTS_WITHOPTIONS enum value	XMLHandler
LD_RAWCOUNTS enum value	XMLHandler
LOAD enum value	XMLHandler
load_detail_	XMLHandler	protected
LOADDETAIL enum name	XMLHandler
logger_	MzIdentMLHandler	protected
MzIdentMLHandler(const Identification &id, const String &filename, const String &version, const ProgressLogger &logger)	MzIdentMLHandler
MzIdentMLHandler(const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger)	MzIdentMLHandler
MzIdentMLHandler(Identification &id, const String &filename, const String &version, const ProgressLogger &logger)	MzIdentMLHandler
MzIdentMLHandler(std::vector< ProteinIdentification > &pro_id, std::vector< PeptideIdentification > &pep_id, const String &filename, const String &version, const ProgressLogger &logger)	MzIdentMLHandler
MzIdentMLHandler()	MzIdentMLHandler	private
MzIdentMLHandler(const MzIdentMLHandler &rhs)	MzIdentMLHandler	private
open_tags_	XMLHandler	protected
operator=(const MzIdentMLHandler &rhs)	MzIdentMLHandler	private
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
pep_id_	MzIdentMLHandler	protected
pep_sequences_	MzIdentMLHandler	private
ph_2_sdat_	MzIdentMLHandler	private
pp_identifier_2_sil_	MzIdentMLHandler	private
pro_id_	MzIdentMLHandler	protected
reset()	XMLHandler
setLoadDetail(const LOADDETAIL d)	XMLHandler	virtual
sil_2_sdat_	MzIdentMLHandler	private
sil_2_sdb_	MzIdentMLHandler	private
sil_2_sip_	MzIdentMLHandler	private
sm_	XMLHandler	protected
startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override	MzIdentMLHandler
STORE enum value	XMLHandler
tag_	MzIdentMLHandler	protected
trimOpenMSfileURI(const String file) const	MzIdentMLHandler	protected
unimod_	MzIdentMLHandler	protected
version_	XMLHandler	protected
warning(const xercesc::SAXParseException &exception) override	XMLHandler
warning(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const	XMLHandler
writeEnzyme_(String &s, DigestionEnzymeProtein enzy, UInt miss, UInt indent) const	MzIdentMLHandler	protected
writeFragmentAnnotations_(String &s, const std::vector< PeptideHit::PeakAnnotation > &annotations, UInt indent, bool is_ppxl) const	MzIdentMLHandler	protected
writeMetaInfos_(String &s, const MetaInfoInterface &meta, UInt indent) const	MzIdentMLHandler	protected
writeModParam_(String &s, const std::vector< String > &mod_names, bool fixed, UInt indent) const	MzIdentMLHandler	protected
writeTo(std::ostream &os) override	MzIdentMLHandler	virtual
writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) const	XMLHandler	protected
writeXMLEscape(const String &to_escape)	XMLHandler	inlinestatic
XMLHandler(const String &filename, const String &version)	XMLHandler
~MzIdentMLHandler() override	MzIdentMLHandler
~XMLHandler() override	XMLHandler