OpenMS  3.0.0
ConsensusXMLHandler.h
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32 // $Authors: Clemens Groepl, Marc Sturm $
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34 
35 #pragma once
36 
44 #include <unordered_map>
45 #include <map>
46 
47 namespace OpenMS
48 {
49 namespace Internal
50 {
64  class OPENMS_DLLAPI ConsensusXMLHandler :
65  public Internal::XMLHandler,
66  public ProgressLogger
67  {
68 public:
70  ConsensusXMLHandler(ConsensusMap& map, const String& filename);
71  ConsensusXMLHandler(const ConsensusMap& map, const String& filename);
73  ~ConsensusXMLHandler() override;
74 
76  PeakFileOptions& getOptions();
77 
78  void setOptions(const PeakFileOptions&);
79 
81  const PeakFileOptions& getOptions() const;
82 
84  void writeTo(std::ostream& os) override;
85 
86 protected:
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 startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
93 
94  // Docu in base class
95  void characters(const XMLCh* const chars, const XMLSize_t length) override;
96 
98  void writePeptideIdentification_(const String& filename, std::ostream& os, const PeptideIdentification& id, const String& tag_name, UInt indentation_level);
99 
103  void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups,
104  const String& group_name, const std::unordered_map<std::string, UInt>& accession_to_id,
105  const String& runid, XMLHandler::ActionMode mode);
106 
108  void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name);
109 
112 
114 
119  double it_;
121 
133  std::vector<PeptideEvidence> peptide_evidences_;
135  std::map<String, String> proteinid_to_accession_;
137  std::unordered_map<std::string, UInt> accession_to_id_;
139  std::map<String, String> identifier_id_;
141  std::map<String, String> id_identifier_;
144 
146  };
147 } // namespace Internal
148 } // namespace OpenMS
149 
OpenMS::Internal::ConsensusXMLHandler::progress_
UInt progress_
Definition: ConsensusXMLHandler.h:145
OpenMS::Internal::ConsensusXMLHandler::pep_id_
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: ConsensusXMLHandler.h:127
OpenMS::Internal::ConsensusXMLHandler::search_param_
ProteinIdentification::SearchParameters search_param_
Temporary search parameters file.
Definition: ConsensusXMLHandler.h:143
OpenMS::Internal::ConsensusXMLHandler
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLHandler.h:64
OpenMS::Internal::ConsensusXMLHandler::last_meta_
MetaInfoInterface * last_meta_
Pointer to last read object as a MetaInfoInterface, or null.
Definition: ConsensusXMLHandler.h:123
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::Internal::ConsensusXMLHandler::options_
PeakFileOptions options_
Options that can be set.
Definition: ConsensusXMLHandler.h:111
OpenMS::Internal::ConsensusXMLHandler::accession_to_id_
std::unordered_map< std::string, UInt > accession_to_id_
Map from search identifier concatenated with protein accession to id.
Definition: ConsensusXMLHandler.h:137
OpenMS::String
A more convenient string class.
Definition: String.h:58
PeptideEvidence.h
ConsensusMap.h
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:58
OpenMS::Internal::ConsensusXMLHandler::cconsensus_map_
const ConsensusMap * cconsensus_map_
Definition: ConsensusXMLHandler.h:116
XMLHandler.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::Internal::ConsensusXMLHandler::proteinid_to_accession_
std::map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: ConsensusXMLHandler.h:135
OpenMS::Internal::ConsensusXMLHandler::prot_id_
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: ConsensusXMLHandler.h:125
OpenMS::Internal::ConsensusXMLHandler::identifier_id_
std::map< String, String > identifier_id_
Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...
Definition: ConsensusXMLHandler.h:139
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Internal::ConsensusXMLHandler::prot_hit_
ProteinHit prot_hit_
Temporary protein hit.
Definition: ConsensusXMLHandler.h:129
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::Internal::ConsensusXMLHandler::pep_hit_
PeptideHit pep_hit_
Temporary peptide hit.
Definition: ConsensusXMLHandler.h:131
ProteinIdentification.h
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::DPosition< 2 >
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
PeakFileOptions.h
OpenMS::Internal::ConsensusXMLHandler::act_cons_element_
ConsensusFeature act_cons_element_
Definition: ConsensusXMLHandler.h:117
OpenMS::Internal::ConsensusXMLHandler::pos_
DPosition< 2 > pos_
Definition: ConsensusXMLHandler.h:118
OpenMS::Internal::ConsensusXMLHandler::id_identifier_
std::map< String, String > id_identifier_
Map from file xs:id to identification run identifier (for linking peptide identifications to the corr...
Definition: ConsensusXMLHandler.h:141
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::Internal::XMLHandler::ActionMode
ActionMode
Action to set the current mode (for error messages)
Definition: XMLHandler.h:341
OpenMS::Internal::ConsensusXMLHandler::consensus_map_
ConsensusMap * consensus_map_
Definition: ConsensusXMLHandler.h:115
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::Internal::ConsensusXMLHandler::it_
double it_
Definition: ConsensusXMLHandler.h:119
OpenMS::Internal::ConsensusXMLHandler::peptide_evidences_
std::vector< PeptideEvidence > peptide_evidences_
Temporary peptide evidences.
Definition: ConsensusXMLHandler.h:133
PeptideIdentification.h
OpenMS::ProteinIdentification::SearchParameters
Search parameters of the DB search.
Definition: ProteinIdentification.h:258
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55