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PercolatorOutfile.h
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34 
35 #ifndef OPENMS_FORMAT_PERCOLATOROUTFILE_H
36 #define OPENMS_FORMAT_PERCOLATOROUTFILE_H
37 
41 
42 #include <boost/regex.hpp>
43 
44 #include <map>
45 #include <vector>
46 
47 namespace OpenMS
48 {
54  class OPENMS_DLLAPI PercolatorOutfile
55  {
56 
57  public:
58 
60  enum ScoreType { QVALUE, POSTERRPROB, SCORE, SIZE_OF_SCORETYPE };
61 
63  static const std::string score_type_names[SIZE_OF_SCORETYPE];
64 
66  static enum ScoreType getScoreType(String score_type_name);
67 
70 
72  void load(const String& filename, ProteinIdentification& proteins,
73  std::vector<PeptideIdentification>& peptides,
74  enum ScoreType output_score = QVALUE,
75  const String& psm_regex = "", bool count_from_zero = false,
76  const MSExperiment<>* experiment_p = 0);
77 
78  private:
79 
81  struct ScanInfo
82  {
84  double rt, mz;
85  };
86 
88  typedef std::map<Size, struct ScanInfo> ScanInfoMap;
89 
92  {
93  boost::regex re; // regular expression for meta data extraction
94  bool count_from_zero; // start counting scans at 0 or 1?
95  };
96 
98  std::vector<struct PSMInfoExtractor> extractors_;
99 
105  bool getPSMInfo_(const String& PSM_ID,
106  const std::vector<struct PSMInfoExtractor>& extractors,
107  Int& scan_number, Int& charge, double& rt, double& mz);
108 
110  void getPeptideSequence_(String peptide, AASequence& seq) const;
111 
113  void preprocessExperiment_(const MSExperiment<>& experiment,
114  ScanInfoMap& scan_map);
115  };
116 
117 } // namespace OpenMS
118 
119 #endif // OPENMS_FORMAT_PERCOLATOROUTFILE_H
Representation of a protein identification run.
Definition: ProteinIdentification.h:61
ScoreType
Types of Percolator scores.
Definition: PercolatorOutfile.h:60
A more convenient string class.
Definition: String.h:57
Int charge
Definition: PercolatorOutfile.h:83
bool count_from_zero
Definition: PercolatorOutfile.h:94
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Description of how to extract information from PSM IDs.
Definition: PercolatorOutfile.h:91
double rt
Definition: PercolatorOutfile.h:84
boost::regex re
Definition: PercolatorOutfile.h:93
std::vector< struct PSMInfoExtractor > extractors_
List of data extractors to try by default.
Definition: PercolatorOutfile.h:98
Class for reading Percolator tab-delimited output files.
Definition: PercolatorOutfile.h:54
Information about a single fragment spectrum.
Definition: PercolatorOutfile.h:81
std::map< Size, struct ScanInfo > ScanInfoMap
Mapping: spectrum index -> fragment spectrum details.
Definition: PercolatorOutfile.h:88
int Int
Signed integer type.
Definition: Types.h:96

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:27 using doxygen 1.8.9.1