OpenMS  3.0.0
XTandemXMLFile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
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34 
35 #pragma once
36 
38 #include <OpenMS/FORMAT/XMLFile.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 
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 
101 
102  // true during "note" element containing protein accession
104 
105  // true during "note" element containing spectrum ID
107 
108  // true after non-new protein entries, so that with the next "protein note" the
109  // accession will not be updated again
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
123 
124  // charge of current peptide
126 
127  // X! Tandem ID of current peptide
129 
130  // tag
132 
133  // start position of current peptide in protein sequence
135 
136  // stop position of current peptide in protein sequence
138 
139  // previous peptide sequence
141 
142  // mapping from X! Tandem ID to spectrum ID
143  std::map<UInt, String> spectrum_ids_;
144 
145  // modification definitions
147 
148  // modifications used by X! Tandem by default
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 
XMLFile.h
OpenMS::XTandemXMLFile::default_nterm_mods_
ModificationDefinitionsSet default_nterm_mods_
Definition: XTandemXMLFile.h:149
OpenMS::XTandemXMLFile::group_type_stack_
std::stack< GroupType > group_type_stack_
Definition: XTandemXMLFile.h:162
OpenMS::XTandemXMLFile::current_start_
UInt current_start_
Definition: XTandemXMLFile.h:134
OpenMS::XTandemXMLFile::GroupType
GroupType
Definition: XTandemXMLFile.h:152
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::XTandemXMLFile::mod_def_set_
ModificationDefinitionsSet mod_def_set_
Definition: XTandemXMLFile.h:146
OpenMS::ModificationDefinitionsSet
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
OpenMS::XTandemXMLFile::is_spectrum_note_
bool is_spectrum_note_
Definition: XTandemXMLFile.h:106
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::XTandemXMLFile::is_protein_note_
bool is_protein_note_
Definition: XTandemXMLFile.h:103
OpenMS::XTandemXMLFile::tag_
String tag_
Definition: XTandemXMLFile.h:131
XMLHandler.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::XTandemXMLFile::spectrum_ids_
std::map< UInt, String > spectrum_ids_
Definition: XTandemXMLFile.h:143
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::XTandemXMLFile::current_protein_
String current_protein_
Definition: XTandemXMLFile.h:122
OpenMS::XTandemXMLFile::peptide_hits_
std::map< UInt, std::vector< PeptideHit > > peptide_hits_
Definition: XTandemXMLFile.h:113
ModificationDefinitionsSet.h
OpenMS::XTandemXMLFile::protein_uids_
std::set< UInt > protein_uids_
Definition: XTandemXMLFile.h:119
OpenMS::XTandemXMLFile::current_charge_
Int current_charge_
Definition: XTandemXMLFile.h:125
OpenMS::XTandemXMLFile::current_stop_
UInt current_stop_
Definition: XTandemXMLFile.h:137
OpenMS::XTandemXMLFile::protein_identification_
ProteinIdentification * protein_identification_
Definition: XTandemXMLFile.h:100
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::XTandemXMLFile::current_id_
UInt current_id_
Definition: XTandemXMLFile.h:128
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::XTandemXMLFile::skip_protein_acc_update_
bool skip_protein_acc_update_
Definition: XTandemXMLFile.h:110
OpenMS::XTandemXMLFile::previous_seq_
String previous_seq_
Definition: XTandemXMLFile.h:140
OpenMS::XTandemXMLFile::protein_hits_
std::vector< ProteinHit > protein_hits_
Definition: XTandemXMLFile.h:116
OpenMS::XTandemXMLFile
Used to load XTandemXML files.
Definition: XTandemXMLFile.h:56
PeptideIdentification.h