OpenSwathTSVWriter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
// Interfaces
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
#include <OpenMS/KERNEL/FeatureMap.h>
 
#include <fstream>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI OpenSwathTSVWriter
  {
    std::ofstream ofs;
    String input_filename_;
    bool doWrite_;
    bool use_ms1_traces_;
    bool sonar_;
 
  public:
 
    OpenSwathTSVWriter(const String& output_filename,
                       const String& input_filename = "inputfile",
                       bool ms1_scores = false,
                       bool sonar = false);
 
    bool isActive() const;
 
    void writeHeader();
 
    String prepareLine(const OpenSwath::LightCompound& pep,
        const OpenSwath::LightTransition * transition,
        const FeatureMap& output, const String& id) const;
 
    void writeLines(const std::vector<String>& to_output);
 
  };
 
}