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 2002-2018.
//
// 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 $
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#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_;
    bool enable_uis_scoring_;

  public:

    OpenSwathTSVWriter(const String& output_filename, 
                       const String& input_filename = "inputfile",
                       bool ms1_scores = false, 
                       bool sonar = false, 
                       bool uis_scores = 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(std::vector<String> to_output);

  };

}