DataAccessHelper.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#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 OpenSwath::ChromatogramPtr convertToChromatogramPtr(const 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