openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/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 2002-2022.
//
// 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/OPENSWATHALGO/OpenSwathAlgoConfig.h>

namespace OpenSwath
{
  struct OPENSWATHALGO_DLLAPI OSBinaryDataArray
  {
    //DataProcessingPtr dataProcessingPtr;

    std::vector<double> data;

    std::string description;
  };
  typedef OSBinaryDataArray BinaryDataArray;
  typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr;

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

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

  struct OPENSWATHALGO_DLLAPI OSChromatogram
  {
private:
    std::size_t defaultArrayLength;

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

    std::vector<BinaryDataArrayPtr> binaryDataArrayPtrs;
public:

    OSChromatogram() :
      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];
    }

    void setTimeArray(BinaryDataArrayPtr data)
    {
      binaryDataArrayPtrs[0] = data;
    }

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

    void setIntensityArray(BinaryDataArrayPtr data)
    {
      binaryDataArrayPtrs[1] = data;
    }

    const std::vector<BinaryDataArrayPtr> & getDataArrays() const
    {
      return binaryDataArrayPtrs;
    }

    std::vector<BinaryDataArrayPtr> & getDataArrays()
    {
      return binaryDataArrayPtrs;
    }

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

  struct OPENSWATHALGO_DLLAPI OSSpectrumMeta
  {
    size_t index;

    std::string id;

    double RT;

    int ms_level;

    OSSpectrumMeta() :
      index(0)
    {
    }

    struct RTLess
    {
      inline bool operator()(const OSSpectrumMeta& a, const OSSpectrumMeta& b) const
      {
        return a.RT < b.RT;
      }
    };

  };
  typedef OSSpectrumMeta SpectrumMeta;
  typedef boost::shared_ptr<SpectrumMeta> SpectrumMetaPtr;

  struct OPENSWATHALGO_DLLAPI OSSpectrum
  {
private:
    std::size_t defaultArrayLength;

    std::vector<BinaryDataArrayPtr> binaryDataArrayPtrs;

public:
    OSSpectrum() :
      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;
    }

    BinaryDataArrayPtr getDriftTimeArray() const
    {
      // The array name starts with "Ion Mobility", but may carry additional
      // information such as the actual unit in which it was measured (seconds,
      // milliseconds, volt-second per square centimeter). We currently ignore
      // the unit but return the correct array.
      // For diaPASEF data converted with proteowizard ion mobility arrays are stored in "inverse reduced ion mobility"
      for (auto & bda : binaryDataArrayPtrs)
      {
        if (bda->description.find("Ion Mobility") == 0)
        {
          return bda;
        }
        else if (bda->description.find("mean inverse reduced ion mobility array") == 0)
        {
          return bda;
        }
      }
      return BinaryDataArrayPtr(); // return null
    }

    const std::vector<BinaryDataArrayPtr> & getDataArrays() const
    {
      return binaryDataArrayPtrs;
    }

    std::vector<BinaryDataArrayPtr> & getDataArrays()
    {
      return binaryDataArrayPtrs;
    }

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