seqan-dev 1.3-1ubuntu2 / usr / include / seqan / random / random_geometric.h

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// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2010, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
//     * 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 Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
// 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 KNUT REINERT OR THE FU BERLIN 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.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Code for geometrically distributed random number generation, p=0.5.
// ==========================================================================

#ifndef SEQAN_RANDOM_RANDOM_GEOMETRIC_H_
#define SEQAN_RANDOM_RANDOM_GEOMETRIC_H_

namespace seqan {

// ===========================================================================
// Forwards, Tags.
// ===========================================================================

// Specialization Tag for geometric distribution.
struct GeometricFairCoin {};

// ===========================================================================
// Classes
// ===========================================================================

/**
.Spec.Geometric Pdf
..signature:Pdf<GeometricFairCoin>
..general:Class.Pdf
..summary:Geometric probability density function with $p=0.5$.

This can be implemented efficiently not using any floating point arithmetics.
Just bit operations are needed.
..cat:Random
..include:seqan/random.h
*/
template <>
class Pdf<GeometricFairCoin>
{
public:

/**
.Memfunc.Geometric Pdf#Pdf
..class:Spec.Geometric Pdf
..summary:Constructor for geometric Pdf.
..signature:Pdf<Geometric>()
*/
    Pdf() { SEQAN_CHECKPOINT; }
};

// ===========================================================================
// Metafunctions
// ===========================================================================

template <>
struct Value<Pdf<GeometricFairCoin> >
{
    typedef unsigned Type;
};

template <>
struct Value<const Pdf<GeometricFairCoin> > : Value<Pdf<GeometricFairCoin> > {};

// ===========================================================================
// Functions
// ===========================================================================

/*
..summary:Pick a geometricly distributed random number.
*/
template <typename TRNG>
inline
typename Value<Pdf<GeometricFairCoin> >::Type
pickRandomNumber(TRNG & rng, Pdf<GeometricFairCoin> const & /*pdf*/)
{
    SEQAN_CHECKPOINT;

    const int RG_IB1 = 1;
    const int RG_IB2 = 2;
    const int RG_IB5 = 16;
    const int RG_IB18 = 131072;
    const int RG_MASK = RG_IB1 + RG_IB2 + RG_IB5;
    
    typename Value<TRNG>::Type seed = pickRandomNumber(rng);
    typename Value<Pdf<GeometricFairCoin> >::Type value = 0;

    while (true) {
        if ((seed & RG_IB18)) {
            seed = ((seed ^ RG_MASK) << 1) | RG_IB1;
            ++value;
        } else {
            seed <<= 1;
            break;
        }
    }

    return value;
}

}  // namespace seqan

#endif  // SEQAN_RANDOM_RANDOM_GEOMETRIC_H_

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