DataAccessHelper.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#pragma once

#include <fstream>

#include <boost/numeric/conversion/cast.hpp>

#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>

namespace OpenMS
{
  class OPENMS_DLLAPI OpenSwathDataAccessHelper
  {
public:
    static void convertToOpenMSSpectrum(const OpenSwath::SpectrumPtr sptr, OpenMS::MSSpectrum & spectrum);

    static OpenSwath::SpectrumPtr convertToSpectrumPtr(const OpenMS::MSSpectrum & spectrum);

    static void convertToOpenMSChromatogram(const OpenSwath::ChromatogramPtr cptr, OpenMS::MSChromatogram & chromatogram);

    static void convertToOpenMSChromatogramFilter(OpenMS::MSChromatogram & chromatogram, const OpenSwath::ChromatogramPtr cptr,
                                                  double rt_min, double rt_max);

    static void convertTargetedExp(const OpenMS::TargetedExperiment & transition_exp_, OpenSwath::LightTargetedExperiment & transition_exp);

    static void convertTargetedCompound(const TargetedExperiment::Peptide& pep, OpenSwath::LightCompound& comp);

    static void convertTargetedCompound(const TargetedExperiment::Compound& compound, OpenSwath::LightCompound& comp);

    static void convertPeptideToAASequence(const OpenSwath::LightCompound & peptide, AASequence & aa_sequence);

  };

} //end namespace OpenMS