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OpenMS
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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) 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 |
| 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 | |
| checkUniqueIdentifiers_(const std::vector< ProteinIdentification > &prot_ids) const | 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 |
| cvParamToValue(const ControlledVocabulary &cv, const String &parent_tag, const String &accession, const String &name, const String &value, const String &unit_accession) const | XMLHandler | |
| cvParamToValue(const ControlledVocabulary &cv, const CVTerm &raw_term) const | XMLHandler | |
| 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 | 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 | |
| expectList_(const String &str) const | XMLHandler | inlineprivate |
| fatalError(const xercesc::SAXParseException &exception) override | XMLHandler | |
| fatalError(ActionMode mode, const String &msg, UInt line=0, UInt column=0) const | XMLHandler | |
| file_ | XMLHandler | protected |
| fromXSDString(const String &type, const String &value) | XMLHandler | inlinestatic |
| 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 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() | 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, const 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, 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) | 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, 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) | MzIdentMLHandler | protected |
| writeXMLEscape(const String &to_escape) | XMLHandler | inlinestatic |
| XMLHandler(const String &filename, const String &version) | XMLHandler | |
| XMLHandler() | XMLHandler | private |
| ~MzIdentMLHandler() override | MzIdentMLHandler | |
| ~XMLHandler() override | XMLHandler |
1.9.1 
