| OpenMS 2.5.0

MascotXMLHandler.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Nico Pfeifer, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CHEMISTRY/AASequence.h>
38 #include <OpenMS/CHEMISTRY/ModificationsDB.h>
39 #include <OpenMS/DATASTRUCTURES/Map.h>
40 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
41 #include <OpenMS/METADATA/PeptideIdentification.h>
42 #include <OpenMS/METADATA/PeptideEvidence.h>
43 #include <OpenMS/METADATA/ProteinIdentification.h>
44 #include <OpenMS/METADATA/SpectrumMetaDataLookup.h>
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
83 ProteinIdentification& protein_identification_;
84 std::vector<PeptideIdentification>& id_data_;
85 ProteinHit actual_protein_hit_;
86 PeptideHit actual_peptide_hit_;
87 PeptideEvidence actual_peptide_evidence_;
88 UInt peptide_identification_index_;
89 String tag_;
90 DateTime date_;
91 String date_time_string_;
92 UInt actual_query_;
93 ProteinIdentification::SearchParameters search_parameters_;
94 String identifier_;
95 String actual_title_;
96 std::map<String, std::vector<AASequence> >& modified_peptides_;
97
98 StringList tags_open_;
99 String character_buffer_;
100 String major_version_;
101 String minor_version_;
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
108 const SpectrumMetaDataLookup& lookup_;
109
111 bool no_rt_error_;
112 };
113
114 } // namespace Internal
115 } // namespace OpenMS
116
OpenMS::Internal::MascotXMLHandler::remove_fixed_mods_
std::vector< String > remove_fixed_mods_
Definition: MascotXMLHandler.h:105
ProteinIdentification.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::MascotXMLHandler::protein_identification_
ProteinIdentification & protein_identification_
the protein identifications
Definition: MascotXMLHandler.h:83
OpenMS::Internal::MascotXMLHandler::peptide_identification_index_
UInt peptide_identification_index_
Definition: MascotXMLHandler.h:88
OpenMS::Internal::MascotXMLHandler::tags_open_
StringList tags_open_
tracking the current XML tree
Definition: MascotXMLHandler.h:98
XMLHandler.h
AASequence.h
OpenMS::Internal::MascotXMLHandler::actual_peptide_evidence_
PeptideEvidence actual_peptide_evidence_
Definition: MascotXMLHandler.h:87
OpenMS::Internal::MascotXMLHandler::no_rt_error_
bool no_rt_error_
Error for missing RT information already reported?
Definition: MascotXMLHandler.h:111
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:57
OpenMS::Internal::MascotXMLHandler::id_data_
std::vector< PeptideIdentification > & id_data_
the identifications (storing the peptide hits)
Definition: MascotXMLHandler.h:84
OpenMS::PeptideEvidence
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
PeptideEvidence.h
OpenMS::Internal::MascotXMLHandler::actual_query_
UInt actual_query_
Definition: MascotXMLHandler.h:92
OpenMS::Internal::MascotXMLHandler::actual_protein_hit_
ProteinHit actual_protein_hit_
Definition: MascotXMLHandler.h:85
OpenMS::Internal::MascotXMLHandler::identifier_
String identifier_
Definition: MascotXMLHandler.h:94
OpenMS::Internal::MascotXMLHandler::minor_version_
String minor_version_
Definition: MascotXMLHandler.h:101
PeptideIdentification.h
OpenMS::Internal::MascotXMLHandler::date_time_string_
String date_time_string_
Definition: MascotXMLHandler.h:91
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
SpectrumMetaDataLookup.h
OpenMS::SpectrumMetaDataLookup
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:142
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
OpenMS::DateTime
DateTime Class.
Definition: DateTime.h:54
ModificationsDB.h
Map.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Internal::MascotXMLHandler
Handler that is used for parsing MascotXML data.
Definition: MascotXMLHandler.h:55
OpenMS::Internal::MascotXMLHandler::tag_
String tag_
Definition: MascotXMLHandler.h:89
OpenMS::Internal::MascotXMLHandler::actual_peptide_hit_
PeptideHit actual_peptide_hit_
Definition: MascotXMLHandler.h:86
OpenMS::Internal::MascotXMLHandler::character_buffer_
String character_buffer_
filled by MascotXMLHandler::characters
Definition: MascotXMLHandler.h:99
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::Internal::MascotXMLHandler::major_version_
String major_version_
Definition: MascotXMLHandler.h:100
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151
OpenMS::Internal::MascotXMLHandler::actual_title_
String actual_title_
Definition: MascotXMLHandler.h:95
OpenMS::Internal::MascotXMLHandler::lookup_
const SpectrumMetaDataLookup & lookup_
Helper object for looking up RT information.
Definition: MascotXMLHandler.h:108
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
OpenMS::Internal::MascotXMLHandler::modified_peptides_
std::map< String, std::vector< AASequence > > & modified_peptides_
Definition: MascotXMLHandler.h:96
OpenMS::Internal::MascotXMLHandler::search_parameters_
ProteinIdentification::SearchParameters search_parameters_
Definition: MascotXMLHandler.h:93
OpenMS::Internal::MascotXMLHandler::date_
DateTime date_
Definition: MascotXMLHandler.h:90