OpenMS
OpenSwathOSWWriter.h
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5 // ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger $
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34 
35 #pragma once
36 
37 // Interfaces
39 
41 
43 
44 #include <fstream>
45 
46 namespace OpenMS
47 {
48 
115  class OPENMS_DLLAPI OpenSwathOSWWriter
116  {
120  bool doWrite_;
122  bool sonar_;
124 
125  public:
126 
127  OpenSwathOSWWriter(const String& output_filename,
128  const UInt64 run_id,
129  const String& input_filename = "inputfile",
130  bool ms1_scores = false,
131  bool sonar = false,
132  bool uis_scores = false);
133 
134  bool isActive() const;
135 
140  void writeHeader();
141 
153  String getScore(const Feature& feature, const std::string& score_name) const;
154 
166  std::vector<String> getSeparateScore(const Feature& feature, const std::string& score_name) const;
167 
183  const OpenSwath::LightTransition* /* transition */,
184  const FeatureMap& output, const String& id) const;
185 
199  void writeLines(const std::vector<String>& to_osw_output);
200 
201  };
202 
203 }
204 
A container for features.
Definition: FeatureMap.h:106
An LC-MS feature.
Definition: Feature.h:72
Class to write out an OpenSwath OSW SQLite output (PyProphet input).
Definition: OpenSwathOSWWriter.h:116
String input_filename_
Definition: OpenSwathOSWWriter.h:118
std::vector< String > getSeparateScore(const Feature &feature, const std::string &score_name) const
Prepare concatenated scores for SQLite insertion.
void writeHeader()
Initializes file by generating SQLite tables.
bool sonar_
Definition: OpenSwathOSWWriter.h:122
String output_filename_
Definition: OpenSwathOSWWriter.h:117
bool enable_uis_scoring_
Definition: OpenSwathOSWWriter.h:123
bool use_ms1_traces_
Definition: OpenSwathOSWWriter.h:121
String getScore(const Feature &feature, const std::string &score_name) const
Prepare scores for SQLite insertion.
OpenSwathOSWWriter(const String &output_filename, const UInt64 run_id, const String &input_filename="inputfile", bool ms1_scores=false, bool sonar=false, bool uis_scores=false)
void writeLines(const std::vector< String > &to_osw_output)
Write data to disk.
OpenMS::UInt64 run_id_
Definition: OpenSwathOSWWriter.h:119
String prepareLine(const OpenSwath::LightCompound &, const OpenSwath::LightTransition *, const FeatureMap &output, const String &id) const
Prepare a single line (feature) for output.
bool doWrite_
Definition: OpenSwathOSWWriter.h:120
A more convenient string class.
Definition: String.h:60
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Definition: TransitionExperiment.h:161
Definition: TransitionExperiment.h:46