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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// 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.
//
// --------------------------------------------------------------------------
// $Maintainer: Stephan Aiche$
// $Authors: Stephan Aiche, Chris Bielow$
// --------------------------------------------------------------------------
#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
{
/// Coordinate type in mz and rt dimension
typedef Peak2D::CoordinateType SimCoordinateType;
/// Abundance of proteins/peptides
typedef Peak2D::IntensityType SimIntensityType;
/// Charge of a peptide
typedef Feature::ChargeType SimChargeType;
/// Raw data point
typedef Peak1D SimPointType;
/// Container for FASTAEntry & abundance information
class OPENMS_DLLAPI SampleProteins : public std::vector<std::pair<FASTAFile::FASTAEntry, MetaInfoInterface> > { };
/// Container for multiple channels of SampleProteins
class OPENMS_DLLAPI SampleChannels : public std::vector<SampleProteins> { };
/// Sim FeatureMap
typedef FeatureMap<> FeatureMapSim;
/// Sim FeatureMap Vector
typedef std::vector<FeatureMapSim> FeatureMapSimVector;
/// Sim MSExperiment type
typedef MSExperiment<SimPointType> MSSimExperiment;
/**
@brief Wrapper class for random number generators used by the simulation classes
The random numbers are separated two sources of randomness:
<ul>
<li><em>technical random numbers</em> which should represent technical
sources of variability like instrument noise and </li>
<li><em>biological random numbers</em> which should represent biological
sources of variability (e.g. between two samples of the same composition)</li>
</ul>
@ingroup Simulation
*/
struct SimRandomNumberGenerator
{
/// GSL random number generator for biological variability
gsl_rng * biological_rng;
/// GSL random number generator for technical variability
gsl_rng * technical_rng;
/// Default constructor
SimRandomNumberGenerator() :
biological_rng(NULL),
technical_rng(NULL)
{
}
/** @name Constructors and Destructors
*/
//@{
/// Copy constructor
SimRandomNumberGenerator(const SimRandomNumberGenerator & other) :
biological_rng(other.biological_rng),
technical_rng(other.technical_rng)
{
}
/// Destructor
~SimRandomNumberGenerator()
{
if (biological_rng != 0)
{
gsl_rng_free(biological_rng);
}
if (technical_rng != 0)
{
gsl_rng_free(technical_rng);
}
}
//@}
/// Assignment operator
SimRandomNumberGenerator & operator=(const SimRandomNumberGenerator & source)
{
this->biological_rng = source.biological_rng;
this->technical_rng = source.technical_rng;
return *this;
}
/// Initialize the RNGs
void initialize(bool biological_random, bool technical_random)
{
biological_rng = gsl_rng_alloc(gsl_rng_mt19937);
if (biological_random)
{
gsl_rng_set(biological_rng, time(0));
}
else // use gsl default seed to get reproducible experiments
{
gsl_rng_set(biological_rng, 0);
}
technical_rng = gsl_rng_alloc(gsl_rng_mt19937);
if (technical_random)
{
gsl_rng_set(technical_rng, time(0));
}
else // use gsl default seed to get reproducible experiments
{
gsl_rng_set(technical_rng, 0);
}
}
};
}
#endif
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