openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h

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// Copyright (c) 2002-present, OpenMS Inc. -- 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 <memory>
 
#include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
 
namespace OpenSwath
{
  struct OPENSWATHALGO_DLLAPI OSBinaryDataArray
  {
    //DataProcessingPtr dataProcessingPtr;
 
    std::vector<double> data;
 
    std::string description;
  };
  typedef OSBinaryDataArray BinaryDataArray;
  typedef std::shared_ptr<BinaryDataArray> BinaryDataArrayPtr;
 
  struct OPENSWATHALGO_DLLAPI OSChromatogramMeta
  {
    std::size_t index;
    std::string id;
    OSChromatogramMeta() :
      index()
    {
    }
 
  };
  typedef OSChromatogramMeta ChromatogramMeta;
  typedef std::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;
    }
 
    void setDataArrays(std::vector<BinaryDataArrayPtr>& val)
    {
      binaryDataArrayPtrs = val;
    }
 
  };
  typedef OSChromatogram Chromatogram;
  typedef std::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 std::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;
    }
 
    void setDriftTimeArray(BinaryDataArrayPtr data)
    {
      data->description = "Ion Mobility";
      binaryDataArrayPtrs.push_back(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;
    }
 
    void setDataArrays(std::vector<BinaryDataArrayPtr>& val)
    {
      binaryDataArrayPtrs = val;
    }
 
  };
  typedef OSSpectrum Spectrum;
  typedef std::shared_ptr<Spectrum> SpectrumPtr;
} //end Namespace OpenSwath