TransitionPQPFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger, Hannes Roest $
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#pragma once

#include <OpenMS/ANALYSIS/OPENSWATH/TransitionTSVFile.h>

#include <boost/range/algorithm.hpp>
#include <boost/range/algorithm_ext/erase.hpp>
#include <sqlite3.h>
#include <iostream>

namespace OpenMS
{

  class OPENMS_DLLAPI TransitionPQPFile :
    public TransitionTSVFile
  {

private:

    void readPQPInput_(const char* filename, std::vector<TSVTransition>& transition_list, bool legacy_traml_id = false);

    void writePQPOutput_(const char* filename, OpenMS::TargetedExperiment& targeted_exp);

public:

    TransitionPQPFile();

    ~TransitionPQPFile() override;

    void convertTargetedExperimentToPQP(const char* filename, OpenMS::TargetedExperiment& targeted_exp);

    void convertPQPToTargetedExperiment(const char* filename, OpenMS::TargetedExperiment& targeted_exp, bool legacy_traml_id = false);

    void convertPQPToTargetedExperiment(const char* filename, OpenSwath::LightTargetedExperiment& targeted_exp, bool legacy_traml_id = false);

  };
}