OpenMS
MzIdentMLHandler Member List

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

ActionMode enum nameXMLHandler
actual_peptide_MzIdentMLHandlerprivate
actual_protein_MzIdentMLHandlerprivate
asBool_(const String &in) constXMLHandlerinlineprotected
asDateTime_(String date_string) constXMLHandlerinlineprotected
asDouble_(const String &in) constXMLHandlerinlineprotected
asFloat_(const String &in) constXMLHandlerinlineprotected
asInt_(const String &in) constXMLHandlerinlineprotected
asInt_(const XMLCh *in) constXMLHandlerinlineprotected
asUInt_(const String &in) constXMLHandlerinlineprotected
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) overrideMzIdentMLHandler
checkUniqueIdentifiers_(const std::vector< ProteinIdentification > &prot_ids) constXMLHandler
cid_MzIdentMLHandlerprotected
cpep_id_MzIdentMLHandlerprotected
cpro_id_MzIdentMLHandlerprotected
current_id_hit_MzIdentMLHandlerprotected
current_mod_location_MzIdentMLHandlerprivate
current_spectrum_id_MzIdentMLHandlerprotected
cv_MzIdentMLHandlerprotected
cv_terms_XMLHandlerprotected
cvParamToValue(const ControlledVocabulary &cv, const String &parent_tag, const String &accession, const String &name, const String &value, const String &unit_accession) constXMLHandler
cvParamToValue(const ControlledVocabulary &cv, const CVTerm &raw_term) constXMLHandler
cvStringToEnum_(const Size section, const String &term, const char *message, const SignedSize result_on_error=0)XMLHandlerprotected
endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) overrideMzIdentMLHandler
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
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
fromXSDString(const String &type, const String &value)XMLHandlerinlinestatic
getChildWithName_(const String &parent_accession, const String &name) constMzIdentMLHandlerprotected
getLoadDetail() constXMLHandlervirtual
handleCVParam_(const String &parent_parent_tag, const String &parent_tag, const String &accession, const xercesc::Attributes &attributes, const String &cv_ref)MzIdentMLHandlerprotected
handleUserParam_(const String &parent_parent_tag, const String &parent_tag, const String &name, const String &type, const String &value)MzIdentMLHandlerprotected
id_MzIdentMLHandlerprotected
LD_ALLDATA enum valueXMLHandler
LD_COUNTS_WITHOPTIONS enum valueXMLHandler
LD_RAWCOUNTS enum valueXMLHandler
LOAD enum valueXMLHandler
load_detail_XMLHandlerprotected
LOADDETAIL enum nameXMLHandler
logger_MzIdentMLHandlerprotected
MzIdentMLHandler(const std::vector< ProteinIdentification > &pro_id, const std::vector< PeptideIdentification > &pep_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()MzIdentMLHandlerprivate
MzIdentMLHandler(const MzIdentMLHandler &rhs)MzIdentMLHandlerprivate
open_tags_XMLHandlerprotected
operator=(const MzIdentMLHandler &rhs)MzIdentMLHandlerprivate
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
pep_id_MzIdentMLHandlerprotected
pep_sequences_MzIdentMLHandlerprivate
ph_2_sdat_MzIdentMLHandlerprivate
pp_identifier_2_sil_MzIdentMLHandlerprivate
pro_id_MzIdentMLHandlerprotected
reset()XMLHandler
setLoadDetail(const LOADDETAIL d)XMLHandlervirtual
sil_2_sdat_MzIdentMLHandlerprivate
sil_2_sdb_MzIdentMLHandlerprivate
sil_2_sip_MzIdentMLHandlerprivate
sm_XMLHandlerprotected
startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) overrideMzIdentMLHandler
STORE enum valueXMLHandler
tag_MzIdentMLHandlerprotected
trimOpenMSfileURI(const String &file) constMzIdentMLHandlerprotected
unimod_MzIdentMLHandlerprotected
version_XMLHandlerprotected
warning(const xercesc::SAXParseException &exception) overrideXMLHandler
warning(ActionMode mode, const String &msg, UInt line=0, UInt column=0) constXMLHandler
writeEnzyme_(String &s, const DigestionEnzymeProtein &enzy, UInt miss, UInt indent) constMzIdentMLHandlerprotected
writeFragmentAnnotations_(String &s, const std::vector< PeptideHit::PeakAnnotation > &annotations, UInt indent, bool is_ppxl) constMzIdentMLHandlerprotected
writeMetaInfos_(String &s, const MetaInfoInterface &meta, UInt indent) constMzIdentMLHandlerprotected
writeModParam_(String &s, const std::vector< String > &mod_names, bool fixed, UInt indent) constMzIdentMLHandlerprotected
writePeptideHit(const PeptideHit &hit, std::vector< PeptideIdentification >::const_iterator &it, std::map< String, String > &pep_ids, const 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)MzIdentMLHandlerprotected
writeTo(std::ostream &os) overrideMzIdentMLHandlervirtual
writeUserParam_(const String &tag_name, std::ostream &os, const MetaInfoInterface &meta, UInt indent) constXMLHandlerprotected
writeXLMSPeptideHit(const PeptideHit &hit, std::vector< PeptideIdentification >::const_iterator &it, const String &ppxl_linkid, std::map< String, String > &pep_ids, const 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)MzIdentMLHandlerprotected
writeXMLEscape(const String &to_escape)XMLHandlerinlinestatic
XMLHandler(const String &filename, const String &version)XMLHandler
XMLHandler()XMLHandlerprivate
~MzIdentMLHandler() overrideMzIdentMLHandler
~XMLHandler() overrideXMLHandler