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OpenSwathTSVWriter.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: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 // Interfaces
38 #include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
39
40 #include <OpenMS/KERNEL/FeatureMap.h>
41
42 #include <fstream>
43
44 namespace OpenMS
45 {
46
129 class OPENMS_DLLAPI OpenSwathTSVWriter
130 {
131 std::ofstream ofs;
132 String input_filename_;
133 bool doWrite_;
134 bool use_ms1_traces_;
135 bool sonar_;
136
137 public:
138
139 OpenSwathTSVWriter(const String& output_filename,
140 const String& input_filename = "inputfile",
141 bool ms1_scores = false,
142 bool sonar = false);
143
144 bool isActive() const;
145
150 void writeHeader();
151
166 String prepareLine(const OpenSwath::LightCompound& pep,
167 const OpenSwath::LightTransition * transition,
168 const FeatureMap& output, const String id) const;
169
180 void writeLines(const std::vector<String>& to_output);
181
182 };
183
184 }
185
186
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenSwath::LightCompound
Definition: TransitionExperiment.h:149
OpenMS::OpenSwathTSVWriter::doWrite_
bool doWrite_
Definition: OpenSwathTSVWriter.h:133
FeatureMap.h
OpenMS::OpenSwathTSVWriter::use_ms1_traces_
bool use_ms1_traces_
Definition: OpenSwathTSVWriter.h:134
OpenMS::OpenSwathTSVWriter::sonar_
bool sonar_
Definition: OpenSwathTSVWriter.h:135
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::OpenSwathTSVWriter
Class to write out an OpenSwath TSV output (mProphet input).
Definition: OpenSwathTSVWriter.h:129
OpenMS::OpenSwathTSVWriter::ofs
std::ofstream ofs
Definition: OpenSwathTSVWriter.h:131
OpenSwath::LightTransition
Definition: TransitionExperiment.h:46
TransitionExperiment.h
OpenMS::OpenSwathTSVWriter::input_filename_
String input_filename_
Definition: OpenSwathTSVWriter.h:132