DataStructures.h

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// $Maintainer: Hannes Roest, Witold Wolski $
// $Authors: Darren Kessner, Hannes Roest, Witold Wolski$
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#ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_DATASTRUCTURES_H
#define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_DATASTRUCTURES_H

#include <string>
#include <vector>
#include <boost/shared_ptr.hpp>

#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h>

namespace OpenSwath
{

  struct BinaryDataArray
  {
    //DataProcessingPtr dataProcessingPtr;

    std::vector<double> data;
  };
  OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr;

  struct ChromatogramMeta
  {
    std::size_t index;
    std::string id;
    ChromatogramMeta() :
      index()
    {
    }

  };
  OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<ChromatogramMeta> ChromatogramMetaPtr;

  struct Chromatogram
  {
    std::size_t defaultArrayLength;

    //DataProcessingPtr dataProcessingPtr;
    //Precursor precursor;
    //Product product;

    std::vector<BinaryDataArrayPtr> binaryDataArrayPtrs;

    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()
    {
      return binaryDataArrayPtrs[0];
    }

    BinaryDataArrayPtr getIntensityArray()
    {
      return binaryDataArrayPtrs[1];
    }

  };
  OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<Chromatogram> ChromatogramPtr;

  struct SpectrumMeta
  {
    size_t index;

    std::string id;

    double RT;

    int ms_level;

    SpectrumMeta() :
      index(0)
    {
    }

  };

  struct 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;
    }

  };
  OPENSWATHALGO_DLLAPI typedef boost::shared_ptr<Spectrum> SpectrumPtr;
} //end Namespace OpenSwath

#endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_DATASTRUCTURES_H