libopenms-dev 1.11.1-5 / usr / include / OpenMS / INTERFACES / DataStructures.h

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// $Maintainer: Hannes Roest, Witold Wolski $
// $Authors: Darren Kessner, Hannes Roest, Witold Wolski$
// --------------------------------------------------------------------------

#ifndef OPENMS_INTERFACES_DATASTRUCTURES_H
#define OPENMS_INTERFACES_DATASTRUCTURES_H

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

#include <OpenMS/config.h>

namespace OpenMS
{
namespace Interfaces
{

  /**
    @brief The datastructures used by the OpenSwath interfaces

    Many of them are closely related to Proteowizard data structures,
    originally written by Darren Kessner and released under the Apache 2.0
    licence and can be found in the file pwiz/data/msdata/MSData.hpp.

    Original author: Darren Kessner <darren@proteowizard.org>

    Copyright 2007 Spielberg Family Center for Applied Proteomics
      Cedars-Sinai Medical Center, Los Angeles, California  90048


    The following datastructures are used :
    - BinaryDataArray : a struct that holds a std::vector<double> with the data
    - ChromatogramMeta : meta information of a chromatogram (index)
    - Chromatogram : chromatogram data. Contains a vector of pointers to BinaryDataArray,
                     the first one is time array (RT), the second one is intensity
    - SpectrumMeta : meta information of a spectrum (index, identifier, RT, ms_level)
    - Spectrum :     spectrum data. Contains a vector of pointers to BinaryDataArray,
                     the first one is mz array, the second one is intensity
  */

  /// The structure into which encoded binary data goes.
  struct BinaryDataArray
  {
    /// this optional attribute may reference the 'id' attribute of the appropiate dataProcessing.
    //DataProcessingPtr dataProcessingPtr;

    /// the binary data.
    std::vector<double> data;
  };
  OPENMS_DLLAPI typedef boost::shared_ptr<BinaryDataArray> BinaryDataArrayPtr;

  /// Identifying information for a chromatogram
  struct ChromatogramMeta
  {
    /// the zero-based, consecutive index of the chromatogram in the ChromatogramList.
    std::size_t index;
    /// a unique identifier for this chromatogram.
    std::string id;
    /// precursor and product m/z
    double precursor_isolation_target;
    double product_isolation_target;

    ChromatogramMeta() :
      index()
    {
    }

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

  /// A single chromatogram.
  struct Chromatogram
  {
    /// default length of binary data arrays contained in this element.
    std::size_t defaultArrayLength;

private:
    /// list of binary data arrays.
    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:
    /// get time array (may be null)
    BinaryDataArrayPtr getTimeArray() const
    {
      return binaryDataArrayPtrs[0];
    }

    /// set time array 
    void setTimeArray(BinaryDataArrayPtr data)
    {
      binaryDataArrayPtrs[0] = data;
    }

    /// get intensity array (may be null)
    BinaryDataArrayPtr getIntensityArray() const
    {
      return binaryDataArrayPtrs[1];
    }

    /// set intensity array 
    void setIntensityArray(BinaryDataArrayPtr data)
    {
      binaryDataArrayPtrs[1] = data;
    }

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

  /// Identifying information for a spectrum
  struct SpectrumMeta
  {
    /// the zero-based, consecutive index of the spectrum in the SpectrumList.
    size_t index;

    /// a unique identifier for this spectrum.
    std::string id;

    /// retention time information
    double RT;

    /// ms level 
    int ms_level;

    SpectrumMeta() :
      index(0)
    {
    }

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

  /// The structure that captures the generation of a peak list (including the underlying acquisitions)
  struct Spectrum
  {
    /// default length of binary data arrays contained in this element.
    std::size_t defaultArrayLength;

private:
    /// list of binary data arrays.
    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:
    /// get m/z array (may be null)
    BinaryDataArrayPtr getMZArray() const
    {
      return binaryDataArrayPtrs[0];
    }

    /// set mz array 
    void setMZArray(BinaryDataArrayPtr data)
    {
      binaryDataArrayPtrs[0] = data;
    }

    /// get intensity array (may be null)
    BinaryDataArrayPtr getIntensityArray() const
    {
      return binaryDataArrayPtrs[1];
    }

    /// set intensity array 
    void setIntensityArray(BinaryDataArrayPtr data)
    {
      binaryDataArrayPtrs[1] = data;
    }

  };
  OPENMS_DLLAPI typedef boost::shared_ptr<Spectrum> SpectrumPtr;

} //end namespace Interfaces
} //end namespace OpenMS
#endif