OpenMS  2.8.0
ConsensusXMLHandler.h
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34 
35 #pragma once
36 
44 #include <unordered_map>
45 
46 namespace OpenMS
47 {
48 namespace Internal
49 {
63  class OPENMS_DLLAPI ConsensusXMLHandler :
64  public Internal::XMLHandler,
65  public ProgressLogger
66  {
67 public:
69  ConsensusXMLHandler(ConsensusMap& map, const String& filename);
70  ConsensusXMLHandler(const ConsensusMap& map, const String& filename);
73 
76 
78 
80  const PeakFileOptions& getOptions() const;
81 
83  void writeTo(std::ostream& os) override;
84 
85 protected:
86 
87  // Docu in base class
88  void endElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname) override;
89 
90  // Docu in base class
91  void startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
92 
93  // Docu in base class
94  void characters(const XMLCh* const chars, const XMLSize_t length) override;
95 
97  void writePeptideIdentification_(const String& filename, std::ostream& os, const PeptideIdentification& id, const String& tag_name, UInt indentation_level);
98 
102  void addProteinGroups_(MetaInfoInterface& meta, const std::vector<ProteinIdentification::ProteinGroup>& groups,
103  const String& group_name, const std::unordered_map<std::string, UInt>& accession_to_id,
104  const String& runid, XMLHandler::ActionMode mode);
105 
107  void getProteinGroups_(std::vector<ProteinIdentification::ProteinGroup>& groups, const String& group_name);
108 
111 
113 
118  double it_;
120 
132  std::vector<PeptideEvidence> peptide_evidences_;
136  std::unordered_map<std::string, UInt> accession_to_id_;
143 
145  };
146 } // namespace Internal
147 } // namespace OpenMS
148 
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:71
A container for consensus elements.
Definition: ConsensusMap.h:90
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLHandler.h:66
const ConsensusMap * cconsensus_map_
Definition: ConsensusXMLHandler.h:115
void addProteinGroups_(MetaInfoInterface &meta, const std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name, const std::unordered_map< std::string, UInt > &accession_to_id, const String &runid, XMLHandler::ActionMode mode)
void setOptions(const PeakFileOptions &)
ProteinIdentification::SearchParameters search_param_
Temporary search parameters file.
Definition: ConsensusXMLHandler.h:142
MetaInfoInterface * last_meta_
Pointer to last read object as a MetaInfoInterface, or null.
Definition: ConsensusXMLHandler.h:122
void getProteinGroups_(std::vector< ProteinIdentification::ProteinGroup > &groups, const String &group_name)
Read and store ProteinGroup data.
void writeTo(std::ostream &os) override
Docu in base class XMLHandler::writeTo.
Map< String, String > id_identifier_
Map from file xs:id to identification run identifier (for linking peptide identifications to the corr...
Definition: ConsensusXMLHandler.h:140
DPosition< 2 > pos_
Definition: ConsensusXMLHandler.h:117
const PeakFileOptions & getOptions() const
Non-mutable access to the options for loading/storing.
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: ConsensusXMLHandler.h:124
PeakFileOptions options_
Options that can be set.
Definition: ConsensusXMLHandler.h:110
ConsensusFeature act_cons_element_
Definition: ConsensusXMLHandler.h:116
Map< String, String > identifier_id_
Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...
Definition: ConsensusXMLHandler.h:138
std::unordered_map< std::string, UInt > accession_to_id_
Map from search identifier concatenated with protein accession to id.
Definition: ConsensusXMLHandler.h:136
double it_
Definition: ConsensusXMLHandler.h:118
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
ProteinHit prot_hit_
Temporary protein hit.
Definition: ConsensusXMLHandler.h:128
UInt progress_
Definition: ConsensusXMLHandler.h:144
void writePeptideIdentification_(const String &filename, std::ostream &os, const PeptideIdentification &id, const String &tag_name, UInt indentation_level)
Writes a peptide identification to a stream (for assigned/unassigned peptide identifications)
PeptideHit pep_hit_
Temporary peptide hit.
Definition: ConsensusXMLHandler.h:130
ConsensusMap * consensus_map_
Definition: ConsensusXMLHandler.h:114
std::vector< PeptideEvidence > peptide_evidences_
Temporary peptide evidences.
Definition: ConsensusXMLHandler.h:132
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
ConsensusXMLHandler(ConsensusMap &map, const String &filename)
Constructor.
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: ConsensusXMLHandler.h:126
ConsensusXMLHandler(const ConsensusMap &map, const String &filename)
Map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: ConsensusXMLHandler.h:134
void characters(const XMLCh *const chars, const XMLSize_t length) override
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
~ConsensusXMLHandler() override
Destructor.
Base class for XML handlers.
Definition: XMLHandler.h:325
ActionMode
Action to set the current mode (for error messages)
Definition: XMLHandler.h:342
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:52
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
Options for loading files containing peak data.
Definition: PeakFileOptions.h:48
Representation of a peptide hit.
Definition: PeptideHit.h:57
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:65
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
Representation of a protein hit.
Definition: ProteinHit.h:60
Representation of a protein identification run.
Definition: ProteinIdentification.h:72
A more convenient string class.
Definition: String.h:60
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Search parameters of the DB search.
Definition: ProteinIdentification.h:260