SimTypes.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Stephan Aiche$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------

#ifndef OPENMS_SIMULATION_SIMTYPES_H
#define OPENMS_SIMULATION_SIMTYPES_H

#include <vector>
#include <utility>
#include <map>
#include <utility>

#include <OpenMS/KERNEL/Peak2D.h>
#include <OpenMS/KERNEL/RichPeak1D.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/ANALYSIS/QUANTITATION/ItraqConstants.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>

// GSL includes (random number generation)
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>

namespace OpenMS
{
  typedef Peak2D::CoordinateType SimCoordinateType;

  typedef Peak2D::IntensityType SimIntensityType;

  typedef Feature::ChargeType SimChargeType;

  typedef Peak1D SimPointType;

  typedef std::vector<std::pair<FASTAFile::FASTAEntry, MetaInfoInterface> > SampleProteins;

  typedef std::vector<SampleProteins> SampleChannels;

  typedef FeatureMap<> FeatureMapSim;

  typedef std::vector<FeatureMapSim> FeatureMapSimVector;

  typedef MSExperiment<SimPointType> MSSimExperiment;

  struct SimRandomNumberGenerator
  {
    gsl_rng * biological_rng;
    gsl_rng * technical_rng;

    SimRandomNumberGenerator() :
      biological_rng(NULL),
      technical_rng(NULL)
    {
    }


    SimRandomNumberGenerator(const SimRandomNumberGenerator & other) :
      biological_rng(other.biological_rng),
      technical_rng(other.technical_rng)
    {
    }

    ~SimRandomNumberGenerator()
    {
      if (biological_rng != 0)
      {
        gsl_rng_free(biological_rng);
      }

      if (technical_rng != 0)
      {
        gsl_rng_free(technical_rng);
      }
    }


    SimRandomNumberGenerator & operator=(const SimRandomNumberGenerator & source)
    {
      this->biological_rng = source.biological_rng;
      this->technical_rng = source.technical_rng;

      return *this;
    }

  };

}

#endif