OpenMS  3.0.0
OMSSAXMLFile.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>
43 
44 #include <vector>
45 
46 namespace OpenMS
47 {
48  class String;
49  class ModificationsDB;
50 
59  class OPENMS_DLLAPI OMSSAXMLFile :
60  protected Internal::XMLHandler,
61  public Internal::XMLFile
62  {
63 public:
64 
66  OMSSAXMLFile();
67 
69  ~OMSSAXMLFile() override;
87  void load(const String& filename,
88  ProteinIdentification& protein_identification,
89  std::vector<PeptideIdentification>& id_data,
90  bool load_proteins = true,
91  bool load_empty_hits = true);
92 
94  void setModificationDefinitionsSet(const ModificationDefinitionsSet& rhs);
95 
96 protected:
97  // Docu in base class
98  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
99 
100  // Docu in base class
101  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
102 
103  // Docu in base class
104  void characters(const XMLCh* const chars, const XMLSize_t /*length*/) override;
105 
106 private:
107 
108  OMSSAXMLFile(const OMSSAXMLFile& rhs);
109 
110  OMSSAXMLFile& operator=(const OMSSAXMLFile& rhs);
111 
113  void readMappingFile_();
114 
116  std::vector<PeptideIdentification>* peptide_identifications_;
117 
119 
121 
123 
124  std::vector<PeptideEvidence> actual_peptide_evidences_;
125 
127 
129 
131 
134 
137 
139  std::vector<std::pair<UInt, String> > modifications_;
140 
143 
146 
148  std::map<UInt, std::vector<const ResidueModification*> > mods_map_;
149 
151  std::map<String, UInt> mods_to_num_;
152 
155  };
156 
157 } // namespace OpenMS
158 
OpenMS::OMSSAXMLFile::actual_peptide_hit_
PeptideHit actual_peptide_hit_
Definition: OMSSAXMLFile.h:120
ModificationsDB
OpenMS::OMSSAXMLFile::tag_
String tag_
Definition: OMSSAXMLFile.h:130
XMLFile.h
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::ModificationDefinitionsSet
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:58
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::OMSSAXMLFile
Used to load OMSSAXML files.
Definition: OMSSAXMLFile.h:59
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:58
OpenMS::OMSSAXMLFile::actual_peptide_evidences_
std::vector< PeptideEvidence > actual_peptide_evidences_
Definition: OMSSAXMLFile.h:124
OpenMS::OMSSAXMLFile::actual_protein_id_
ProteinIdentification actual_protein_id_
Definition: OMSSAXMLFile.h:128
XMLHandler.h
OpenMS::OMSSAXMLFile::mod_def_set_
ModificationDefinitionsSet mod_def_set_
modification definitions set of the search, needed to annotate fixed modifications
Definition: OMSSAXMLFile.h:154
OpenMS::OMSSAXMLFile::mods_to_num_
std::map< String, UInt > mods_to_num_
modification mapping reverse, from the modification to the mod_num
Definition: OMSSAXMLFile.h:151
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::OMSSAXMLFile::peptide_identifications_
std::vector< PeptideIdentification > * peptide_identifications_
the identifications (storing the peptide hits)
Definition: OMSSAXMLFile.h:116
OpenMS::OMSSAXMLFile::modifications_
std::vector< std::pair< UInt, String > > modifications_
modifications of the peptide defined by site and type
Definition: OMSSAXMLFile.h:139
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::OMSSAXMLFile::actual_protein_hit_
ProteinHit actual_protein_hit_
Definition: OMSSAXMLFile.h:118
OpenMS::OMSSAXMLFile::actual_mod_site_
UInt actual_mod_site_
site of the actual modification (simple position in the peptide)
Definition: OMSSAXMLFile.h:133
OpenMS::OMSSAXMLFile::load_proteins_
bool load_proteins_
should protein hits be read from the file?
Definition: OMSSAXMLFile.h:142
ModificationDefinitionsSet.h
ProteinIdentification.h
OpenMS::PeptideEvidence
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
OpenMS::OMSSAXMLFile::mods_map_
std::map< UInt, std::vector< const ResidueModification * > > mods_map_
modifications mapping file from OMSSA mod num to UniMod accession
Definition: OMSSAXMLFile.h:148
OpenMS::OMSSAXMLFile::load_empty_hits_
bool load_empty_hits_
should empty peptide identifications be loaded or skipped?
Definition: OMSSAXMLFile.h:145
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::OMSSAXMLFile::actual_peptide_evidence_
PeptideEvidence actual_peptide_evidence_
Definition: OMSSAXMLFile.h:122
OpenMS::OMSSAXMLFile::actual_peptide_id_
PeptideIdentification actual_peptide_id_
Definition: OMSSAXMLFile.h:126
OpenMS::OMSSAXMLFile::actual_mod_type_
String actual_mod_type_
type of the modification
Definition: OMSSAXMLFile.h:136
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
ResidueModification.h
PeptideIdentification.h
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55