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ConsensusXMLFile.h
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31 // $Maintainer: Clemens Groepl $
32 // $Authors: Clemens Groepl, Marc Sturm $
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34 
35 #ifndef OPENMS_FORMAT_CONSENSUSXMLFILE_H
36 #define OPENMS_FORMAT_CONSENSUSXMLFILE_H
37 
41 #include <OpenMS/FORMAT/XMLFile.h>
43 
44 namespace OpenMS
45 {
59  class OPENMS_DLLAPI ConsensusXMLFile :
60  public Internal::XMLHandler,
61  public Internal::XMLFile,
62  public ProgressLogger
63  {
64 public:
69 
70 
78  void load(const String & filename, ConsensusMap & map);
79 
87  void store(const String & filename, const ConsensusMap & consensus_map);
88 
90  PeakFileOptions & getOptions();
91 
93  const PeakFileOptions & getOptions() const;
94 
95 protected:
96 
97  // Docu in base class
98  virtual void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname);
99 
100  // Docu in base class
101  virtual void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes);
102 
103  // Docu in base class
104  virtual void characters(const XMLCh * const chars, const XMLSize_t length);
105 
106 
108  void writePeptideIdentification_(const String & filename, std::ostream & os, const PeptideIdentification & id, const String & tag_name, UInt indentation_level);
109 
110 
113 
115 
121 
142 
144 
145  };
146 } // namespace OpenMS
147 
148 #endif // OPENMS_FOMAT_CONSENSUSXMLFILE_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
ConsensusMap * consensus_map_
Definition: ConsensusXMLFile.h:116
A more convenient string class.
Definition: String.h:56
Map< String, String > id_identifier_
Map from file xs:id to identification run identifier (for linking peptide identifications to the corr...
Definition: ConsensusXMLFile.h:139
PeakFileOptions options_
Options that can be set.
Definition: ConsensusXMLFile.h:112
ProteinIdentification::SearchParameters search_param_
Temporary search parameters file.
Definition: ConsensusXMLFile.h:141
ConsensusFeature act_cons_element_
Definition: ConsensusXMLFile.h:117
ProteinHit prot_hit_
Temporary protein hit.
Definition: ConsensusXMLFile.h:129
ProteinIdentification prot_id_
Temporary protein ProteinIdentification.
Definition: ConsensusXMLFile.h:125
A container for consensus elements.
Definition: ConsensusMap.h:60
Base class for XML handlers.
Definition: XMLHandler.h:89
PeptideHit pep_hit_
Temporary peptide hit.
Definition: ConsensusXMLFile.h:131
Search parameters of the DB search.
Definition: ProteinIdentification.h:115
PeptideIdentification pep_id_
Temporary peptide ProteinIdentification.
Definition: ConsensusXMLFile.h:127
Map< String, Size > accession_to_id_
Map from search identifier concatenated with protein accession to id.
Definition: ConsensusXMLFile.h:135
Map< String, String > identifier_id_
Map from identification run identifier to file xs:id (for linking peptide identifications to the corr...
Definition: ConsensusXMLFile.h:137
UInt progress_
Definition: ConsensusXMLFile.h:143
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:59
Representation of a peptide hit.
Definition: PeptideHit.h:54
Map< String, String > proteinid_to_accession_
Map from protein id to accession.
Definition: ConsensusXMLFile.h:133
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
Representation of a protein hit.
Definition: ProteinHit.h:54
DoubleReal it_
Definition: ConsensusXMLFile.h:119
Base class for all classes that want to report their progess.
Definition: ProgressLogger.h:56
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 as a MetaInfoInterface, or null.
Definition: ConsensusXMLFile.h:123
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
DPosition< 2 > pos_
Definition: ConsensusXMLFile.h:118
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
A 2-dimensional consensus feature.
Definition: ConsensusFeature.h:59
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:12 using doxygen 1.8.5