| OpenMS 2.5.0

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 | inline protected
asDateTime_(String date_string) | XMLHandler | inline protected
asDouble_(const String &in) | XMLHandler | inline protected
asFloat_(const String &in) | XMLHandler | inline protected
asInt_(const String &in) | XMLHandler | inline protected
asInt_(const XMLCh *in) | XMLHandler | inline protected
asUInt_(const String &in) | XMLHandler | inline protected
attributeAsDouble_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsDouble_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
attributeAsDoubleList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsDoubleList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
attributeAsInt_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsInt_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
attributeAsIntList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsIntList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
attributeAsString_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsString_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
attributeAsStringList_(const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
attributeAsStringList_(const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
characters(const XMLCh *const chars, const XMLSize_t length) override | MzIdentMLHandler |
checkUniqueIdentifiers_(const std::vector< ProteinIdentification > &prot_ids) | XMLHandler |
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 | inline protected
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override | MzIdentMLHandler |
equal_(const XMLCh *a, const XMLCh *b) const | XMLHandler | inline protected
error(const xercesc::SAXParseException &exception) override | XMLHandler |
error(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | XMLHandler |
error_message_ | XMLHandler | mutable protected
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 | inline protected
optionalAttributeAsDouble_(double &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsDoubleList_(DoubleList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsInt_(Int &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsIntList_(IntList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsString_(String &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsStringList_(StringList &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const char *name) const | XMLHandler | inline protected
optionalAttributeAsUInt_(UInt &value, const xercesc::Attributes &a, const XMLCh *name) const | XMLHandler | inline protected
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
writePeptideHit(const PeptideHit &hit, std::vector< PeptideIdentification >::const_iterator &it, std::map< String, String > &pep_ids, String cv_ns, std::set< String > &sen_set, std::map< String, String > &sen_ids, std::map< String, std::vector< String > > &pep_evis, std::map< String, double > &pp_identifier_2_thresh, String &sidres) | 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
writeXLMSPeptideHit(const PeptideHit &hit, std::vector< PeptideIdentification >::const_iterator &it, String ppxl_linkid, std::map< String, String > &pep_ids, String cv_ns, std::set< String > &sen_set, std::map< String, String > &sen_ids, std::map< String, std::vector< String > > &pep_evis, std::map< String, double > &pp_identifier_2_thresh, double ppxl_crosslink_mass, std::map< String, String > &ppxl_specref_2_element, String &sid, bool alpha_peptide) | MzIdentMLHandler | protected
writeXMLEscape(const String &to_escape) | XMLHandler | inline static
XMLHandler(const String &filename, const String &version) | XMLHandler |
~MzIdentMLHandler() override | MzIdentMLHandler |
~XMLHandler() override | XMLHandler |