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 2002-2020.
//
// 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.
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// 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
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <vector>
#include <utility>
#include <map>
#include <utility>
#include <boost/shared_ptr.hpp>
 
#include <boost/random/mersenne_twister.hpp>
 
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/Peak2D.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
 
namespace OpenMS
{
 
  namespace SimTypes
  {
    typedef Peak2D::CoordinateType SimCoordinateType;
 
    typedef Peak2D::IntensityType SimIntensityType;
 
    typedef Feature::ChargeType SimChargeType;
 
    typedef Peak1D SimPointType;
 
    struct SimProtein
    {
      FASTAFile::FASTAEntry entry;
      MetaInfoInterface meta;
 
      SimProtein(FASTAFile::FASTAEntry& e, MetaInfoInterface& m) :
       entry(e),
       meta(m)
      {}
    };
 
    typedef std::vector<SimProtein> SampleProteins;
 
    typedef std::vector<SampleProteins> SampleChannels;
 
    typedef FeatureMap FeatureMapSim;
 
    typedef std::vector<FeatureMapSim> FeatureMapSimVector;
 
    typedef PeakMap MSSimExperiment;
 
    class SimRandomNumberGenerator
    {
public:
 
      boost::random::mt19937_64& getBiologicalRng()
      {
        return biological_rng_;
      }
 
      boost::random::mt19937_64& getTechnicalRng()
      {
        return technical_rng_;
      }
 
      void setBiologicalRngSeed(unsigned long int seed)
      {
        biological_rng_.seed(seed);
      }
 
      void setTechnicalRngSeed(unsigned long int seed)
      {
        technical_rng_.seed(seed);
      }
 
      void initialize(bool biological_random, bool technical_random)
      {
        // use 0 as default seed to get reproducible experiments
        if (biological_random)
        {
          biological_rng_ = boost::random::mt19937_64(std::time(nullptr));
        }
        else
        {
          biological_rng_ = boost::random::mt19937_64(0);
        }
 
        if (technical_random)
        {
          technical_rng_ = boost::random::mt19937_64(std::time(nullptr));
        }
        else
        {
          technical_rng_ = boost::random::mt19937_64(0);
        }
      }
 
private:
      boost::random::mt19937_64 biological_rng_;
      boost::random::mt19937_64 technical_rng_;
 
    };
 
    //Sim Shared Pointer type
    typedef boost::shared_ptr<SimRandomNumberGenerator> MutableSimRandomNumberGeneratorPtr;
 
  }
 
}