openms/include/OpenMS/INTERFACES/DataStructures.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Darren Kessner, Hannes Roest, Witold Wolski$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <string>
#include <vector>
#include <boost/shared_ptr.hpp>
 
#include <OpenMS/config.h>
 
namespace OpenMS
{
namespace Interfaces
{
 
  struct OPENMS_DLLAPI BinaryDataArray
  {
    //DataProcessingPtr dataProcessingPtr;
 
    std::vector<double> data;
  };
  typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr;
 
  struct OPENMS_DLLAPI ChromatogramMeta
  {
    std::size_t index;
    std::string id;
    double precursor_isolation_target;
    double product_isolation_target;
 
    ChromatogramMeta() :
      index()
    {
    }
 
  };
  typedef boost::shared_ptr<ChromatogramMeta> ChromatogramMetaPtr;
 
  struct OPENMS_DLLAPI Chromatogram
  {
    std::size_t defaultArrayLength;
 
private:
    std::vector<BinaryDataArrayPtr> binaryDataArrayPtrs;
 
public:
    Chromatogram() :
      defaultArrayLength(2),
      binaryDataArrayPtrs(defaultArrayLength)
    {
      initvec();
    }
 
private:
 
    void initvec()
    {
      for (std::size_t i = 0; i < defaultArrayLength; ++i)
      {
        BinaryDataArrayPtr empty(new BinaryDataArray);
        binaryDataArrayPtrs[i] = empty;
      }
    }
 
public:
    BinaryDataArrayPtr getTimeArray() const
    {
      return binaryDataArrayPtrs[0];
    }
 
    void setTimeArray(BinaryDataArrayPtr data)
    {
      binaryDataArrayPtrs[0] = data;
    }
 
    BinaryDataArrayPtr getIntensityArray() const
    {
      return binaryDataArrayPtrs[1];
    }
 
    void setIntensityArray(BinaryDataArrayPtr data)
    {
      binaryDataArrayPtrs[1] = data;
    }
 
  };
  typedef boost::shared_ptr<Chromatogram> ChromatogramPtr;
 
  struct OPENMS_DLLAPI SpectrumMeta
  {
    size_t index;
 
    std::string id;
 
    double RT;
 
    int ms_level;
 
    SpectrumMeta() :
      index(0)
    {
    }
 
  };
  typedef boost::shared_ptr<SpectrumMeta> SpectrumMetaPtr;
 
  struct OPENMS_DLLAPI Spectrum
  {
    std::size_t defaultArrayLength;
 
private:
    std::vector<BinaryDataArrayPtr> binaryDataArrayPtrs;
 
public:
    Spectrum() :
      defaultArrayLength(2),
      binaryDataArrayPtrs(defaultArrayLength)
    {
      initvec();
    }
 
private:
 
    void initvec()
    {
      for (std::size_t i = 0; i < defaultArrayLength; ++i)
      {
        BinaryDataArrayPtr empty(new BinaryDataArray);
        binaryDataArrayPtrs[i] = empty;
      }
    }
 
public:
    BinaryDataArrayPtr getMZArray() const
    {
      return binaryDataArrayPtrs[0];
    }
 
    void setMZArray(BinaryDataArrayPtr data)
    {
      binaryDataArrayPtrs[0] = data;
    }
 
    BinaryDataArrayPtr getIntensityArray() const
    {
      return binaryDataArrayPtrs[1];
    }
 
    void setIntensityArray(BinaryDataArrayPtr data)
    {
      binaryDataArrayPtrs[1] = data;
    }
 
  };
  typedef boost::shared_ptr<Spectrum> SpectrumPtr;
 
} //end namespace Interfaces
} //end namespace OpenMS