OpenMS  2.5.0
IdXMLFile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
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34 
35 #pragma once
36 
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  public ProgressLogger
67  {
68 public:
69  // both ConsensusXMLFile and FeatureXMLFile use some protected IdXML helper functions to parse identifications without code duplication
70  friend class ConsensusXMLFile;
71  friend class FeatureXMLFile;
72 
74  IdXMLFile();
75 
85  void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids);
86 
96  void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, String& document_id);
97 
105  void store(const String& filename, const std::vector<ProteinIdentification>& protein_ids, const std::vector<PeptideIdentification>& peptide_ids, const String& document_id = "");
106 
107 
108 protected:
109  // Docu in base class
110  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
111 
112  // Docu in base class
113  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
114 
118  void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups,
119  const String& group_name, const std::unordered_map<std::string, UInt>& accession_to_id, XMLHandler::ActionMode mode);
120 
122  void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name);
123 
128  static std::ostream& createFlankingAAXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);
129 
134  static std::ostream& createPositionXMLString_(const std::vector<PeptideEvidence> & pes, std::ostream& os);
135 
136 
140  static void writeFragmentAnnotations_(const String & tag_name, std::ostream & os,
141  const std::vector<PeptideHit::PeakAnnotation>& annotations, UInt indent);
142 
146  static void parseFragmentAnnotation_(const String& s, std::vector<PeptideHit::PeakAnnotation> & annotations);
147 
148 
150 
151  std::vector<ProteinIdentification>* prot_ids_;
154  std::vector<PeptideIdentification>* pep_ids_;
158  std::map<String, ProteinIdentification::SearchParameters> parameters_;
174  std::vector<PeptideEvidence> peptide_evidences_;
176  std::unordered_map<std::string, String> proteinid_to_accession_;
182  };
183 
184 } // namespace OpenMS
185 
std::vector< PeptideEvidence > peptide_evidences_
Temporary peptide evidences.
Definition: IdXMLFile.h:174
std::unordered_map< std::string, String > proteinid_to_accession_
Map from protein id to accession.
Definition: IdXMLFile.h:176
Analysis Result (containing search engine / prophet results)
Definition: PeptideHit.h:210
Base class for XML handlers.
Definition: XMLHandler.h:151
PeptideHit::PepXMLAnalysisResult current_analysis_result_
Temporary analysis result instance.
Definition: IdXMLFile.h:172
Used to load and store idXML files.
Definition: IdXMLFile.h:63
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
ProteinHit prot_hit_
Temporary protein hit.
Definition: IdXMLFile.h:168
Representation of a protein hit.
Definition: ProteinHit.h:57
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
bool prot_id_in_run_
true if a prot id is contained in the current run
Definition: IdXMLFile.h:180
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
String * document_id_
Document identifier.
Definition: IdXMLFile.h:178
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
std::vector< PeptideIdentification > * pep_ids_
Pointer to fill in peptide identifications.
Definition: IdXMLFile.h:154
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
ActionMode
Action to set the current mode (for error messages)
Definition: XMLHandler.h:169
Search parameters of the DB search.
Definition: ProteinIdentification.h:221
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
std::map< String, ProteinIdentification::SearchParameters > parameters_
Search parameters map (key is the "id")
Definition: IdXMLFile.h:158
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: IdXMLFile.h:166
Representation of a peptide hit.
Definition: PeptideHit.h:54
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
String id_
Temporary id.
Definition: IdXMLFile.h:162
A more convenient string class.
Definition: String.h:58
ProteinIdentification::SearchParameters param_
Temporary search parameters variable.
Definition: IdXMLFile.h:160
MetaInfoInterface * last_meta_
Pointer to last read object with MetaInfoInterface.
Definition: IdXMLFile.h:156
PeptideHit pep_hit_
Temporary peptide hit.
Definition: IdXMLFile.h:170
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: IdXMLFile.h:164
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46