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OpenSwathOSWWriter.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
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30 // --------------------------------------------------------------------------
31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 // Interfaces
38 #include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
39
40 #include <OpenMS/CONCEPT/UniqueIdGenerator.h>
41
42 #include <OpenMS/KERNEL/FeatureMap.h>
43
44 #include <fstream>
45
46 namespace OpenMS
47 {
48
115 class OPENMS_DLLAPI OpenSwathOSWWriter
116 {
117 String output_filename_;
118 String input_filename_;
119 OpenMS::UInt64 run_id_;
120 bool doWrite_;
121 bool use_ms1_traces_;
122 bool sonar_;
123 bool enable_uis_scoring_;
124
125 public:
126
127 OpenSwathOSWWriter(const String& output_filename,
128 const String& input_filename = "inputfile",
129 bool ms1_scores = false,
130 bool sonar = false,
131 bool uis_scores = false) :
132 output_filename_(output_filename),
133 input_filename_(input_filename),
134 run_id_(OpenMS::UniqueIdGenerator::getUniqueId()),
135 doWrite_(!output_filename.empty()),
136 use_ms1_traces_(ms1_scores),
137 sonar_(sonar),
138 enable_uis_scoring_(uis_scores)
139 {}
140
141 bool isActive() const;
142
147 void writeHeader();
148
160 String getScore(const Feature& feature, std::string score_name) const;
161
173 std::vector<String> getSeparateScore(const Feature& feature, std::string score_name) const;
174
189 String prepareLine(const OpenSwath::LightCompound& /* pep */,
190 const OpenSwath::LightTransition* /* transition */,
191 FeatureMap& output, String id) const;
192
206 void writeLines(const std::vector<String>& to_osw_output);
207
208 };
209
210 }
211
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::OpenSwathOSWWriter::run_id_
OpenMS::UInt64 run_id_
Definition: OpenSwathOSWWriter.h:119
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::OpenSwathOSWWriter::OpenSwathOSWWriter
OpenSwathOSWWriter(const String &output_filename, const String &input_filename="inputfile", bool ms1_scores=false, bool sonar=false, bool uis_scores=false)
Definition: OpenSwathOSWWriter.h:127
UniqueIdGenerator.h
OpenMS::UInt64
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenSwath::LightCompound
Definition: TransitionExperiment.h:149
OpenMS::OpenSwathOSWWriter::enable_uis_scoring_
bool enable_uis_scoring_
Definition: OpenSwathOSWWriter.h:123
OpenMS::OpenSwathOSWWriter::use_ms1_traces_
bool use_ms1_traces_
Definition: OpenSwathOSWWriter.h:121
OpenMS::UniqueIdGenerator
A generator for unique ids.
Definition: UniqueIdGenerator.h:59
FeatureMap.h
OpenMS::OpenSwathOSWWriter::doWrite_
bool doWrite_
Definition: OpenSwathOSWWriter.h:120
OpenMS::OpenSwathOSWWriter
Class to write out an OpenSwath OSW SQLite output (PyProphet input).
Definition: OpenSwathOSWWriter.h:115
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::OpenSwathOSWWriter::sonar_
bool sonar_
Definition: OpenSwathOSWWriter.h:122
OpenMS::OpenSwathOSWWriter::output_filename_
String output_filename_
Definition: OpenSwathOSWWriter.h:117
OpenSwath::LightTransition
Definition: TransitionExperiment.h:46
OpenMS::OpenSwathOSWWriter::input_filename_
String input_filename_
Definition: OpenSwathOSWWriter.h:118
TransitionExperiment.h