OpenMS  3.0.0
OSWFile.h
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31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger, Chris Bielow $
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34 
35 #pragma once
36 
42 
43 #include <array>
44 #include <map>
45 
46 namespace OpenMS
47 {
66  class OPENMS_DLLAPI OSWFile
67  {
68  public:
69 
71  static constexpr Size ALL_PROTEINS = -1;
72 
75  OSWFile(const String& filename);
76  OSWFile(const OSWFile& rhs) = default;
77  OSWFile& operator=(const OSWFile& rhs) = default;
78 
82  void read(OSWData& swath_result);
83 
88  void readMinimal(OSWData& swath_result);
89 
99  void readProtein(OSWData& swath_result, const Size index);
100 
102  enum class OSWLevel
103  {
104  MS1,
105  MS2,
106  TRANSITION,
107  SIZE_OF_OSWLEVEL
108  };
109  static const std::array<std::string, (Size)OSWLevel::SIZE_OF_OSWLEVEL> names_of_oswlevel;
110 
112  {
113  PercolatorFeature(double score, double qvalue, double pep)
114  : score(score), qvalue(qvalue), posterior_error_prob(pep)
115  {}
116  PercolatorFeature(const PercolatorFeature& rhs) = default;
117 
118  double score;
119  double qvalue;
121  };
122 
127  static void readToPIN(const std::string& filename, const OSWFile::OSWLevel osw_level, std::ostream& pin_output,
128  const double ipf_max_peakgroup_pep, const double ipf_max_transition_isotope_overlap, const double ipf_min_transition_sn);
129 
133  static void writeFromPercolator(const std::string& osw_filename, const OSWFile::OSWLevel osw_level, const std::map< std::string, PercolatorFeature >& features);
134 
137  UInt64 getRunID() const;
138 
139  protected:
144  void readTransitions_(OSWData& swath_result);
145 
153  void getFullProteins_(OSWData& swath_result, Size prot_index = ALL_PROTEINS);
154 
156  void readMeta_(OSWData& data);
157 
158  private:
162  };
163 
164 } // namespace OpenMS
165 
OpenMS::UInt64
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
OpenMS::OSWFile::OSWLevel
OSWLevel
for Percolator data read/write operations
Definition: OSWFile.h:102
OpenMS::SqliteConnector
File adapter for Sqlite files.
Definition: SqliteConnector.h:56
OpenMS::OSWFile::filename_
String filename_
sql file to open/write to
Definition: OSWFile.h:159
OpenMS::OSWFile
This class serves for reading in and writing OpenSWATH OSW files.
Definition: OSWFile.h:66
OpenMS::OSWFile::has_SCOREMS2_
bool has_SCOREMS2_
database contains pyProphet's score_MS2 table with qvalues
Definition: OSWFile.h:161
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
SqliteConnector.h
OpenMS::OSWFile::PercolatorFeature::qvalue
double qvalue
Definition: OSWFile.h:119
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Exception.h
OpenMS::OSWFile::PercolatorFeature::score
double score
Definition: OSWFile.h:118
OSWData.h
OpenMS::OSWFile::PercolatorFeature::PercolatorFeature
PercolatorFeature(double score, double qvalue, double pep)
Definition: OSWFile.h:113
OpenMS::OSWFile::conn_
SqliteConnector conn_
SQL connection. Stays open as long as this object lives.
Definition: OSWFile.h:160
OpenMS::OSWFile::PercolatorFeature
Definition: OSWFile.h:111
String.h
OpenMS::OSWData
Holds all or partial information from an OSW file.
Definition: OSWData.h:304
OpenMS::OSWFile::PercolatorFeature::posterior_error_prob
double posterior_error_prob
Definition: OSWFile.h:120
StandardTypes.h