OpenMS  2.8.0
MascotXMLHandler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Nico Pfeifer, Chris Bielow $
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34 
35 #pragma once
36 
45 
46 #include <vector>
47 
48 namespace OpenMS
49 {
50  namespace Internal
51  {
55  class OPENMS_DLLAPI MascotXMLHandler :
56  public XMLHandler
57  {
58 public:
60  MascotXMLHandler(ProteinIdentification& protein_identification,
61  std::vector<PeptideIdentification>& identifications,
62  const String& filename,
63  std::map<String, std::vector<AASequence> >& peptides,
64  const SpectrumMetaDataLookup& lookup);
65 
67  ~MascotXMLHandler() override;
68 
69  // Docu in base class
70  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
71 
72  // Docu in base class
73  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
74 
75  // Docu in base class
76  void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;
77 
79  static std::vector<String> splitModificationBySpecifiedAA(String mod);
80 
81 private:
82 
84  std::vector<PeptideIdentification>& id_data_;
96  std::map<String, std::vector<AASequence> >& modified_peptides_;
97 
102 
103  // list of modifications, which cannot be set as fixed and needs
104  // to be removed, because added from mascot as variable modification
105  std::vector<String> remove_fixed_mods_;
106 
109 
112  };
113 
114  } // namespace Internal
115 } // namespace OpenMS
116 
DateTime Class.
Definition: DateTime.h:55
Handler that is used for parsing MascotXML data.
Definition: MascotXMLHandler.h:57
String minor_version_
Definition: MascotXMLHandler.h:101
UInt actual_query_
Definition: MascotXMLHandler.h:92
PeptideEvidence actual_peptide_evidence_
Definition: MascotXMLHandler.h:87
String major_version_
Definition: MascotXMLHandler.h:100
std::map< String, std::vector< AASequence > > & modified_peptides_
Definition: MascotXMLHandler.h:96
PeptideHit actual_peptide_hit_
Definition: MascotXMLHandler.h:86
ProteinIdentification::SearchParameters search_parameters_
Definition: MascotXMLHandler.h:93
bool no_rt_error_
Error for missing RT information already reported?
Definition: MascotXMLHandler.h:111
String tag_
Definition: MascotXMLHandler.h:89
static std::vector< String > splitModificationBySpecifiedAA(String mod)
Split modification search parameter if for more than one amino acid specified e.g....
String date_time_string_
Definition: MascotXMLHandler.h:91
String actual_title_
Definition: MascotXMLHandler.h:95
StringList tags_open_
tracking the current XML tree
Definition: MascotXMLHandler.h:98
std::vector< PeptideIdentification > & id_data_
the identifications (storing the peptide hits)
Definition: MascotXMLHandler.h:84
ProteinHit actual_protein_hit_
Definition: MascotXMLHandler.h:85
MascotXMLHandler(ProteinIdentification &protein_identification, std::vector< PeptideIdentification > &identifications, const String &filename, std::map< String, std::vector< AASequence > > &peptides, const SpectrumMetaDataLookup &lookup)
Constructor.
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
DateTime date_
Definition: MascotXMLHandler.h:90
UInt peptide_identification_index_
Definition: MascotXMLHandler.h:88
const SpectrumMetaDataLookup & lookup_
Helper object for looking up RT information.
Definition: MascotXMLHandler.h:108
void characters(const XMLCh *const chars, const XMLSize_t) override
String character_buffer_
filled by MascotXMLHandler::characters
Definition: MascotXMLHandler.h:99
~MascotXMLHandler() override
Destructor.
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
ProteinIdentification & protein_identification_
the protein identifications
Definition: MascotXMLHandler.h:83
std::vector< String > remove_fixed_mods_
Definition: MascotXMLHandler.h:105
String identifier_
Definition: MascotXMLHandler.h:94
Base class for XML handlers.
Definition: XMLHandler.h:325
Representation of a peptide evidence.
Definition: PeptideEvidence.h:51
Representation of a peptide hit.
Definition: PeptideHit.h:57
Representation of a protein hit.
Definition: ProteinHit.h:60
Representation of a protein identification run.
Definition: ProteinIdentification.h:72
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:143
A more convenient string class.
Definition: String.h:60
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Search parameters of the DB search.
Definition: ProteinIdentification.h:260