openms/include/OpenMS/INTERFACES/DataStructures.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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