| OpenMS 2.5.0

XTandemXMLFile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/METADATA/PeptideIdentification.h>
38 #include <OpenMS/FORMAT/XMLFile.h>
39 #include <OpenMS/FORMAT/HANDLERS/XMLHandler.h>
40 #include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
41 #include <stack>
42
43 namespace OpenMS
44 {
45 class String;
46 class ProteinIdentification;
47
56 class OPENMS_DLLAPI XTandemXMLFile :
57 protected Internal::XMLHandler,
58 public Internal::XMLFile
59 {
60 public:
61
63 XTandemXMLFile();
64
66 ~XTandemXMLFile() override;
80 void load(const String& filename, ProteinIdentification& protein_identification, std::vector<PeptideIdentification>& id_data, ModificationDefinitionsSet& mod_def_set);
81
82
83 protected:
84
85 // Docu in base class
86 void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
87
88 // Docu in base class
89 void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
90
91 // Docu in base class
92 void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;
93
94 XTandemXMLFile(const XTandemXMLFile& rhs);
95
96 XTandemXMLFile& operator=(const XTandemXMLFile& rhs);
97
98 private:
99
100 ProteinIdentification* protein_identification_;
101
102 // true during "note" element containing protein accession
103 bool is_protein_note_;
104
105 // true during "note" element containing spectrum ID
106 bool is_spectrum_note_;
107
108 // true after non-new protein entries, so that with the next "protein note" the
109 // accession will not be updated again
110 bool skip_protein_acc_update_;
111
112 // peptide hits per spectrum
113 std::map<UInt, std::vector<PeptideHit> > peptide_hits_;
114
115 // protein hits
116 std::vector<ProteinHit> protein_hits_;
117
118 // protein unique IDs (assigned by X! Tandem), to keep track of which proteins were already seen
119 std::set<UInt> protein_uids_;
120
121 // accession of the current protein
122 String current_protein_;
123
124 // charge of current peptide
125 Int current_charge_;
126
127 // X! Tandem ID of current peptide
128 UInt current_id_;
129
130 // tag
131 String tag_;
132
133 // start position of current peptide in protein sequence
134 UInt current_start_;
135
136 // stop position of current peptide in protein sequence
137 UInt current_stop_;
138
139 // previous peptide sequence
140 String previous_seq_;
141
142 // mapping from X! Tandem ID to spectrum ID
143 std::map<UInt, String> spectrum_ids_;
144
145 // modification definitions
146 ModificationDefinitionsSet mod_def_set_;
147
148 // modifications used by X! Tandem by default
149 ModificationDefinitionsSet default_nterm_mods_;
150
151 // the possible type attributes of the group tag elements
152 enum class GroupType
153 {
154 MODEL,
155 PARAMETERS,
156 SUPPORT
157 };
158
159 // stack of types of the group elements
160 // they can be nested (e.g. a support group in a model group)
161 // parsing of child elements sometimes depends on the group type
162 std::stack<GroupType> group_type_stack_;
163
164 };
165
166 } // namespace OpenMS
167
OpenMS::XTandemXMLFile::current_id_
UInt current_id_
Definition: XTandemXMLFile.h:128
OpenMS::XTandemXMLFile::current_charge_
Int current_charge_
Definition: XTandemXMLFile.h:125
OpenMS::String
A more convenient string class.
Definition: String.h:58
XMLFile.h
OpenMS::XTandemXMLFile::is_spectrum_note_
bool is_spectrum_note_
Definition: XTandemXMLFile.h:106
OpenMS::XTandemXMLFile::current_start_
UInt current_start_
Definition: XTandemXMLFile.h:134
OpenMS::XTandemXMLFile::is_protein_note_
bool is_protein_note_
Definition: XTandemXMLFile.h:103
XMLHandler.h
OpenMS::XTandemXMLFile::group_type_stack_
std::stack< GroupType > group_type_stack_
Definition: XTandemXMLFile.h:162
OpenMS::XTandemXMLFile::GroupType
GroupType
Definition: XTandemXMLFile.h:152
OpenMS::XTandemXMLFile::mod_def_set_
ModificationDefinitionsSet mod_def_set_
Definition: XTandemXMLFile.h:146
OpenMS::XTandemXMLFile::tag_
String tag_
Definition: XTandemXMLFile.h:131
OpenMS::XTandemXMLFile
Used to load XTandemXML files.
Definition: XTandemXMLFile.h:56
OpenMS::XTandemXMLFile::current_protein_
String current_protein_
Definition: XTandemXMLFile.h:122
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::XTandemXMLFile::spectrum_ids_
std::map< UInt, String > spectrum_ids_
Definition: XTandemXMLFile.h:143
OpenMS::XTandemXMLFile::current_stop_
UInt current_stop_
Definition: XTandemXMLFile.h:137
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::XTandemXMLFile::protein_uids_
std::set< UInt > protein_uids_
Definition: XTandemXMLFile.h:119
OpenMS::XTandemXMLFile::protein_identification_
ProteinIdentification * protein_identification_
Definition: XTandemXMLFile.h:100
ModificationDefinitionsSet.h
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::XTandemXMLFile::previous_seq_
String previous_seq_
Definition: XTandemXMLFile.h:140
OpenMS::XTandemXMLFile::skip_protein_acc_update_
bool skip_protein_acc_update_
Definition: XTandemXMLFile.h:110
OpenMS::XTandemXMLFile::peptide_hits_
std::map< UInt, std::vector< PeptideHit > > peptide_hits_
Definition: XTandemXMLFile.h:113
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::ModificationDefinitionsSet
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
int
OpenMS::XTandemXMLFile::default_nterm_mods_
ModificationDefinitionsSet default_nterm_mods_
Definition: XTandemXMLFile.h:149
OpenMS::XTandemXMLFile::protein_hits_
std::vector< ProteinHit > protein_hits_
Definition: XTandemXMLFile.h:116
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151