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IdXMLFile.h
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34 
35 #ifndef OPENMS_FORMAT_IDXMLFILE_H
36 #define OPENMS_FORMAT_IDXMLFILE_H
37 
41 #include <OpenMS/FORMAT/XMLFile.h>
42 
43 #include <vector>
44 
45 namespace OpenMS
46 {
63  class OPENMS_DLLAPI IdXMLFile :
64  protected Internal::XMLHandler,
65  public Internal::XMLFile
66  {
67 public:
68 
70  IdXMLFile();
71 
81  void load(const String & filename, std::vector<ProteinIdentification> & protein_ids, std::vector<PeptideIdentification> & peptide_ids);
82 
92  void load(const String & filename, std::vector<ProteinIdentification> & protein_ids, std::vector<PeptideIdentification> & peptide_ids, String & document_id);
93 
101  void store(String filename, const std::vector<ProteinIdentification> & protein_ids, const std::vector<PeptideIdentification> & peptide_ids, const String & document_id = "");
102 
103 protected:
104  // Docu in base class
105  virtual void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);
106 
107  // Docu in base class
108  virtual void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);
109 
111  void addProteinGroups_(MetaInfoInterface & meta, const std::vector<ProteinIdentification::ProteinGroup> & groups, const String & group_name, const std::map<String, UInt> & accession_to_id);
112 
114  void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup> & groups, const String & group_name);
115 
117 
118  std::vector<ProteinIdentification> * prot_ids_;
121  std::vector<PeptideIdentification> * pep_ids_;
125  std::map<String, ProteinIdentification::SearchParameters> parameters_;
139  std::map<String, String> proteinid_to_accession_;
145  };
146 
147 } // namespace OpenMS
148 
149 #endif // OPENMS_FORMAT_IDXMLFILE_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
A more convenient string class.
Definition: String.h:56
PeptideHit pep_hit_
Temporary peptide hit.
Definition: IdXMLFile.h:137
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: IdXMLFile.h:131
std::vector< PeptideIdentification > * pep_ids_
Pointer to fill in peptide identifications.
Definition: IdXMLFile.h:121
bool prot_id_in_run_
true if a prot id is contained in the current run
Definition: IdXMLFile.h:143
String id_
Temporary id.
Definition: IdXMLFile.h:129
Base class for XML handlers.
Definition: XMLHandler.h:89
ProteinHit prot_hit_
Temporary protein hit.
Definition: IdXMLFile.h:135
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: IdXMLFile.h:133
Search parameters of the DB search.
Definition: ProteinIdentification.h:115
ProteinIdentification::SearchParameters param_
Temporary search parameters variable.
Definition: IdXMLFile.h:127
Representation of a peptide hit.
Definition: PeptideHit.h:54
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
std::map< String, ProteinIdentification::SearchParameters > parameters_
Search parameters map (key is the &quot;id&quot;)
Definition: IdXMLFile.h:125
String * document_id_
Document identitifier.
Definition: IdXMLFile.h:141
Representation of a protein hit.
Definition: ProteinHit.h:54
std::map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: IdXMLFile.h:139
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:51
MetaInfoInterface * last_meta_
Pointer to last read object with MetaInfoInterface.
Definition: IdXMLFile.h:123
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
Used to load and store idXML files.
Definition: IdXMLFile.h:63

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:15 using doxygen 1.8.5