// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, 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: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
// ==========================================================================
// Simple matrices;  Used in many alignment algorithms.
// ==========================================================================

#ifndef SEQAN_HEADER_MATRIX_BASE_H
#define SEQAN_HEADER_MATRIX_BASE_H

namespace seqan2
{

//////////////////////////////////////////////////////////////////////////////

struct NDimensional;


template <typename TValue, unsigned DIMENSION = 0/*typename TSpec = NDimensional*/, typename THost = String<TValue> >
class Matrix;

//////////////////////////////////////////////////////////////////////////////
template <typename T> struct SizeArr_;

template <typename TValue, unsigned DIMENSION, typename THost>
struct SizeArr_<Matrix<TValue, DIMENSION, THost> >
{
    typedef Matrix<TValue, DIMENSION, THost> TMatrix_;
    typedef typename Size<TMatrix_>::Type TSize_;
    typedef String<TSize_> Type;
};

//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost>
struct Host<Matrix<TValue, DIMENSION, THost> >
{
    typedef THost Type;
};

template <typename TValue, unsigned DIMENSION, typename THost>
struct Host<Matrix<TValue, DIMENSION, THost> const>
{
    typedef THost const Type;
};

//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////

// TODO(holtgrew): Add more comprehensive documentation!

/*!
 * @class Matrix
 * @headerfile <seqan/align.h>
 * @brief A simple n-dimensional matrix type.
 *
 * @signature template <typename TValue[, unsigned DIMENSION]>
 *            class Matrix;
 *
 * @tparam TValue    Type of matrix entries.
 * @tparam DIMENSION Dimension of the matrix.  Use 0 for n-dimensional, values &gt; 0 for a matrix with
 *                   <tt>DIMENSION</tt> dimensions.  Defaults to 0.
 */


template <typename TValue, typename THost>
class Matrix<TValue, 0, THost>
{
//____________________________________________________________________________

public:
    typedef typename Size<Matrix>::Type TSize;
    typedef String<TSize> TSizeArr;

    TSizeArr data_lengths;        //Length of every dimension
    TSizeArr data_factors;        //used for positions of dimensions in host ("size of jumps" to get to next entry of specified dimension)

    Holder<THost> data_host;
//____________________________________________________________________________

public:
    Matrix()
    {
        create(data_host);
    }
    Matrix(Matrix const & other_):
        data_lengths(other_.data_lengths),
        data_factors(other_.data_factors),
        data_host(other_.data_host)
    {
    }
    inline Matrix const &
    operator = (Matrix const & other_)
    {
        data_lengths = other_.data_lengths;
        data_factors = other_.data_factors;
        data_host = other_.data_host;

        return *this;
    }
    ~Matrix()
    {
    }
//____________________________________________________________________________


//____________________________________________________________________________

    inline TValue &
    operator () (TSize x1, TSize x2)
    {
        return value(*this, x1, x2);
    }
    inline TValue &
    operator () (TSize x1, TSize x2, TSize x3)
    {
        return value(*this, x1, x2, x3);
    }
    inline TValue &
    operator () (TSize x1, TSize x2, TSize x3, TSize x4)
    {
        return value(*this, x1, x2, x3, x4);
    }

//____________________________________________________________________________
};


template <typename TValue, typename THost>
class Matrix<TValue, 2, THost>
{
//____________________________________________________________________________

public:
    typedef typename Size<Matrix>::Type TSize;
    typedef String<TSize> TSizeArr;

    TSizeArr data_lengths;
    TSizeArr data_factors;

    Holder<THost> data_host;


//____________________________________________________________________________

public:
    Matrix()
    {
        create(data_host);

        //setDimension to 2
        resize(data_lengths, 2, 0);
        resize(data_factors, 2, 0);
        data_factors[0] = 1;
    }
    Matrix(Matrix const & other_):
        data_lengths(other_.data_lengths),
        data_factors(other_.data_factors),
        data_host(other_.data_host)
    {
    }
    inline Matrix const &
    operator = (Matrix const & other_)
    {
        data_lengths = other_.data_lengths;
        data_factors = other_.data_factors;
        data_host = other_.data_host;

        return *this;
    }

    ~Matrix()
    {
    }
//____________________________________________________________________________


//____________________________________________________________________________

    inline TValue &
    operator () (TSize x1, TSize x2)
    {
        return value(*this, x1, x2);
    }

//____________________________________________________________________________
};

template <typename TValue, typename THost>
class Matrix<TValue, 3, THost>
{
//____________________________________________________________________________

public:
    typedef typename Size<Matrix>::Type TSize;
    typedef String<TSize> TSizeArr;

    TSizeArr data_lengths;
    TSizeArr data_factors;

    Holder<THost> data_host;


//____________________________________________________________________________

public:
    Matrix()
    {
        create(data_host);

        //setDimension to 3
        resize(data_lengths, 3, 0);
        resize(data_factors, 3);
        data_factors[0] = 1;
    }
    Matrix(Matrix const & other_):
        data_lengths(other_.data_lengths),
        data_factors(other_.data_factors),
        data_host(other_.data_host)
    {
    }
    inline Matrix const &
    operator = (Matrix const & other_)
    {
        data_lengths = other_.data_lengths;
        data_factors = other_.data_factors;
        data_host = other_.data_host;

        return *this;
    }

    ~Matrix()
    {
    }
//____________________________________________________________________________


//____________________________________________________________________________

    inline TValue &
    operator () (TSize x1, TSize x2, TSize x3)
    {
        return value(*this, x1, x2, x3);
    }

//____________________________________________________________________________
};

template <typename TValue, unsigned DIMENSION, typename THost>
inline typename SizeArr_<Matrix<TValue, DIMENSION, THost> >::Type &
_dataLengths(Matrix<TValue, DIMENSION, THost> & me)
{
    return me.data_lengths;
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline typename SizeArr_<Matrix<TValue, DIMENSION, THost> >::Type const &
_dataLengths(Matrix<TValue, DIMENSION, THost> const & me)
{
    return me.data_lengths;
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline typename SizeArr_<Matrix<TValue, DIMENSION, THost> >::Type &
_dataFactors(Matrix<TValue, DIMENSION, THost> & me)
{
    return me.data_factors;
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline typename SizeArr_<Matrix<TValue, DIMENSION, THost> >::Type const &
_dataFactors(Matrix<TValue, DIMENSION, THost> const & me)
{
    return me.data_factors;
}

//____________________________________________________________________________


template <typename TValue, unsigned DIMENSION, typename THost>
inline bool
dependent(Matrix<TValue, DIMENSION, THost> & me)
{
    return dependent(me.data_host);
}

//____________________________________________________________________________

template <typename TValue, unsigned DIMENSION, typename THost>
inline Holder<typename Host<Matrix<TValue, DIMENSION, THost> >::Type> &
_dataHost(Matrix<TValue, DIMENSION, THost> & matrix)
{
    return matrix.data_host;
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline Holder<typename Host<Matrix<TValue, DIMENSION, THost> >::Type> const &
_dataHost(Matrix<TValue, DIMENSION, THost> const & matrix)
{
    return matrix.data_host;
}

//____________________________________________________________________________

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
assignHost(Matrix<TValue, DIMENSION, THost> & me, THost const & value_)
{
    assignValue(me.data_host, value_);
}

//____________________________________________________________________________

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
moveHost(Matrix<TValue, DIMENSION, THost> & me, THost const & value_)
{
    moveValue(me.data_host, value_);
}
//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost>
struct Value< Matrix<TValue, DIMENSION, THost> >
{
    typedef TValue Type;
};

//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost, typename TIteratorSpec>
struct Iterator< Matrix<TValue, DIMENSION, THost>, TIteratorSpec >
{
    typedef Iter<Matrix<TValue, DIMENSION, THost>, PositionIterator> Type;
};

template <typename TValue, unsigned DIMENSION, typename THost, typename TIteratorSpec>
struct Iterator< Matrix<TValue, DIMENSION, THost> const, TIteratorSpec >
{
    typedef Iter<Matrix<TValue, DIMENSION, THost> const, PositionIterator> Type;
};

//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost>
inline typename Size<Matrix<TValue, DIMENSION, THost> const>::Type
dimension(Matrix<TValue, DIMENSION, THost> const & me)
{
    return length(_dataLengths(me));
}

//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
setDimension(Matrix<TValue, DIMENSION, THost> & me,
             unsigned int dim_)
{

    SEQAN_ASSERT_GT(dim_, 0u);
//std::cout<<"\npress enter1\n";
//std::cin.get();
    resize(_dataLengths(me), dim_, 0);

    resize(_dataFactors(me), dim_);
    _dataFactors(me)[0] = 1;
}

//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost>
inline typename Size<Matrix<TValue, DIMENSION, THost> >::Type
length(Matrix<TValue, DIMENSION, THost> const & me,
       unsigned int dim_)
{
    return me.data_lengths[dim_];
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline typename Size<Matrix <TValue, DIMENSION, THost> >::Type
length(Matrix<TValue, DIMENSION, THost> const & me)
{
    return length(host(me));
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline bool empty(Matrix<TValue, DIMENSION, THost> const & me)
{
    return empty(host(me));
}

//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost, typename TLength>
inline void
setLength(Matrix<TValue, DIMENSION, THost> & me,
          unsigned int dim_,
          TLength length_)
{
    SEQAN_ASSERT_GT(length_, static_cast<TLength>(0));
    SEQAN_ASSERT_LT(dim_, dimension(me));

    typedef typename SizeArr_<Matrix<TValue, DIMENSION, THost> >::TSize_ TSize_;

    _dataLengths(me)[dim_] = static_cast<TSize_>(length_);
}

//////////////////////////////////////////////////////////////////////////////

/*!
 * @fn Matrix#resize
 * @brief Resize the matrix and fill it with a given value or zeroes.
 *
 * @signature void resize(matrix[, val]);
 *
 * @param[in,out] matrix The Matrix to fill.
 * @param[in]     val    The optional value to fill the matrix with.
 */


template <typename TValue, unsigned DIMENSION, typename THost>
inline void
resize(Matrix<TValue, DIMENSION, THost> & me)
{
    typedef Matrix<TValue, DIMENSION, THost> TMatrix;
    typedef typename Size<TMatrix>::Type TSize;

    unsigned int dimension_ = dimension(me);

    SEQAN_ASSERT_GT(dimension_, 0u);

    TSize factor_ = _dataFactors(me)[0] * length(me, 0);
    for (unsigned int i = 1; (factor_ > 0) && (i < dimension_); ++i)
    {
        _dataFactors(me)[i] = factor_;
        factor_ *= length(me, i);
    }

    if (factor_ > 0)
    {
        resize(host(me), factor_);
    }
}

//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost, typename TFillValue>
inline void
resize(Matrix<TValue, DIMENSION, THost> & me, TFillValue myValue)    //resize the matrix and fill with value
{
    typedef Matrix<TValue, DIMENSION, THost> TMatrix;
    typedef typename Size<TMatrix>::Type TSize;

    unsigned int dimension_ = dimension(me);

    SEQAN_ASSERT_GT(dimension_, 0u);

    TSize factor_ = _dataFactors(me)[0] * length(me, 0);
    for (unsigned int i = 1; (factor_ > 0) && (i < dimension_); ++i)
    {
        _dataFactors(me)[i] = factor_;
        factor_ *= length(me, i);
    }

    if (factor_ > 0)
        resize(host(me), factor_, myValue);
}


//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition>
inline typename Position<Matrix <TValue, DIMENSION, THost> >::Type
nextPosition(Matrix<TValue, DIMENSION, THost> & me,
             TPosition position_,
             unsigned int dimension_)
{
    return position_ + _dataFactors(me)[dimension_];
}

template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition>
inline typename Position<Matrix <TValue, DIMENSION, THost> >::Type
nextPosition(Matrix<TValue, DIMENSION, THost> const & me,
             TPosition position_,
             unsigned int dimension_)
{
    return position_ + _dataFactors(me)[dimension_];
}

template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition>
inline typename Position<Matrix <TValue, DIMENSION, THost> >::Type
previousPosition(Matrix<TValue, DIMENSION, THost> & me,
                 TPosition position_,
                 unsigned int dimension_)
{
    return position_ - _dataFactors(me)[dimension_];
}

template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition>
inline typename Position<Matrix <TValue, DIMENSION, THost> >::Type
previousPosition(Matrix<TValue, DIMENSION, THost> const & me,
                 TPosition position_,
                 unsigned int dimension_)
{
    return position_ - _dataFactors(me)[dimension_];
}

//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition>
inline typename Size< Matrix <TValue, DIMENSION, THost> >::Type
coordinate(Matrix<TValue, DIMENSION, THost> const & me,
           TPosition position_,
           unsigned int dimension_)
{
    SEQAN_ASSERT_LT(dimension_, dimension(me));

    if (dimension_ < dimension(me) - 1)
    {
        return (position_ / _dataFactors(me)[dimension_]) % _dataFactors(me)[dimension_ + 1];
    }
    else
    {
        return position_ / _dataFactors(me)[dimension_];
    }
}

//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost, typename TTag>
inline typename Iterator<Matrix <TValue, DIMENSION, THost>, Tag<TTag> const>::Type
begin(Matrix<TValue, DIMENSION, THost> & me,
      Tag<TTag> const)
{
    return typename Iterator<Matrix <TValue, DIMENSION, THost>, Tag<TTag> const >::Type(me, 0);
}
template <typename TValue, unsigned DIMENSION, typename THost, typename TTag>
inline typename Iterator<Matrix <TValue, DIMENSION, THost> const, Tag<TTag> const>::Type
begin(Matrix<TValue, DIMENSION, THost> const & me,
      Tag<TTag> const)
{
    return typename Iterator<Matrix <TValue, DIMENSION, THost> const, Tag<TTag> const >::Type(me, 0);
}

//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost, typename TTag>
inline typename Iterator<Matrix <TValue, DIMENSION, THost>, Tag<TTag> const >::Type
end(Matrix<TValue, DIMENSION, THost> & me,
      Tag<TTag> const)
{
    return typename Iterator<Matrix <TValue, DIMENSION, THost>, Tag<TTag> const >::Type(me, length(host(me)));
}
template <typename TValue, unsigned DIMENSION, typename THost, typename TTag>
inline typename Iterator<Matrix <TValue, DIMENSION, THost> const, Tag<TTag> const >::Type
end(Matrix<TValue, DIMENSION, THost> const & me,
      Tag<TTag> const)
{
    return typename Iterator<Matrix <TValue, DIMENSION, THost>, Tag<TTag> const >::Type(me, length(host(me)));
}

//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition>
inline typename Reference<Matrix<TValue, DIMENSION, THost> >::Type
value(Matrix<TValue, DIMENSION, THost> & me,
      TPosition position_)
{
    return value(host(me), position_);
}

template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition>
inline typename Reference<Matrix<TValue, DIMENSION, THost> const>::Type
value(Matrix<TValue, DIMENSION, THost> const & me,
      TPosition position_)
{
    return value(host(me), position_);
}

//____________________________________________________________________________

//two dimensional value access
template <typename TValue, unsigned DIMENSION, typename THost, typename TOrdinate1, typename TOrdinate2>
inline typename Reference<Matrix<TValue, DIMENSION, THost> >::Type
value(Matrix<TValue, DIMENSION, THost> & me,
      TOrdinate1 i1,
      TOrdinate2 i2)
{
    return value(host(me), i1 + i2 * _dataFactors(me)[1]);
}

template <typename TValue, unsigned DIMENSION, typename THost, typename TOrdinate1, typename TOrdinate2>
inline typename Reference<Matrix<TValue, DIMENSION, THost> const>::Type
value(Matrix<TValue, DIMENSION, THost> const & me,
      TOrdinate1 i1,
      TOrdinate2 i2)
{
    return value(host(me), i1 + i2 * _dataFactors(me)[1]);
}

//____________________________________________________________________________

//3 dimensional value access

template <typename TValue, unsigned DIMENSION, typename THost, typename TOrdinate1, typename TOrdinate2, typename TOrdinate3>
inline typename Reference<Matrix<TValue, DIMENSION, THost> >::Type
value(Matrix<TValue, DIMENSION, THost> & me,
      TOrdinate1 i1,
      TOrdinate2 i2,
      TOrdinate3 i3)
{
    return value(host(me), i1 + i2 * _dataFactors(me)[1] + i3 * _dataFactors(me)[2]);
}

//____________________________________________________________________________

//4 dimensional value access

template <typename TValue, unsigned DIMENSION, typename THost, typename TOrdinate1, typename TOrdinate2, typename TOrdinate3, typename TOrdinate4>
inline typename Reference<Matrix<TValue, DIMENSION, THost> >::Type
value(Matrix<TValue, DIMENSION, THost> & me,
      TOrdinate1 i1,
      TOrdinate2 i2,
      TOrdinate3 i3,
      TOrdinate4 i4)
{
    return value(host(me), i1 + i2 * _dataFactors(me)[1] + i3 * _dataFactors(me)[2] + i4 * _dataFactors(me)[3]);
}

//////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////
// Iterator: goNext
//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
goNext(Iter<Matrix<TValue, DIMENSION, THost>, PositionIterator> & me,
       unsigned int dimension_)
{
    setPosition(me, nextPosition(container(me), position(me), dimension_));
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
goNext(Iter<Matrix<TValue, DIMENSION, THost> const, PositionIterator> & me,
       unsigned int dimension_)
{
    setPosition(me, nextPosition(container(me), position(me), dimension_));
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
goNext(Iter<Matrix<TValue, DIMENSION, THost>, PositionIterator> & me)
{
    goNext(me, 0);
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
goNext(Iter<Matrix<TValue, DIMENSION, THost> const, PositionIterator> & me)
{
    goNext(me, 0);
}

//////////////////////////////////////////////////////////////////////////////
// Iterator: goPrevious
//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
goPrevious(Iter< Matrix<TValue, DIMENSION, THost>, PositionIterator > & me,
           unsigned int dimension_)
{
    setPosition(me, previousPosition(container(me), position(me), dimension_));
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
goPrevious(Iter< Matrix<TValue, DIMENSION, THost> const, PositionIterator > & me,
           unsigned int dimension_)
{
    setPosition(me, previousPosition(container(me), position(me), dimension_));
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
goPrevious(Iter< Matrix<TValue, DIMENSION, THost>, PositionIterator > & me)
{
    goPrevious(me, 0);
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline void
goPrevious(Iter< Matrix<TValue, DIMENSION, THost> const, PositionIterator > & me)
{
    goPrevious(me, 0);
}

//////////////////////////////////////////////////////////////////////////////
// goTo
//////////////////////////////////////////////////////////////////////////////

template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition0, typename TPosition1>
inline void
goTo(Iter<Matrix<TValue, DIMENSION, THost>, PositionIterator> & me, TPosition0 pos0, TPosition1 pos1)
{
    setPosition(me, pos0 + pos1 * _dataFactors(container(me))[1]);
}


template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition0, typename TPosition1>
inline void
goTo(Iter<Matrix<TValue, DIMENSION, THost> const, PositionIterator> & me, TPosition0 pos0, TPosition1 pos1)
{
    setPosition(me, pos0 + pos1 * _dataFactors(container(me))[1]);
}


template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition0, typename TPosition1, typename TPosition2>
inline void
goTo(Iter<Matrix<TValue, DIMENSION, THost>, PositionIterator> & me, TPosition0 pos0, TPosition1 pos1, TPosition2 pos2)
{
    setPosition(me, pos0 + pos1 * _dataFactors(container(me))[1] + pos2 * _dataFactors(container(me))[2]);
}


template <typename TValue, unsigned DIMENSION, typename THost, typename TPosition0, typename TPosition1, typename TPosition2>
inline void
goTo(Iter<Matrix<TValue, DIMENSION, THost> const, PositionIterator> & me, TPosition0 pos0, TPosition1 pos1, TPosition2 pos2)
{
    setPosition(me, pos0 + pos1 * _dataFactors(container(me))[1] + pos2 * _dataFactors(container(me))[2]);
}

//////////////////////////////////////////////////////////////////////////////
// Iterator: coordinate

template <typename TValue, unsigned DIMENSION, typename THost>
inline typename Size< Matrix<TValue, DIMENSION, THost> >::Type
coordinate(Iter<Matrix<TValue, DIMENSION, THost>, PositionIterator > & me,
           unsigned int dimension_)
{
    return coordinate(container(me), position(me), dimension_);
}

template <typename TValue, unsigned DIMENSION, typename THost>
inline typename Size< Matrix<TValue, DIMENSION, THost> >::Type
coordinate(Iter<Matrix<TValue, DIMENSION, THost> const, PositionIterator > & me,
           unsigned int dimension_)
{
    return coordinate(container(me), position(me), dimension_);
}

/*!
 * @fn Matrix::operator+
 * @brief Sum operator for the Matrix type.
 *
 * @signature TMatrix Matrix::operator+(lhs, rhs);
 *
 * @param[in] lhs First summand.
 * @param[in] rhs Second summand.
 *
 * @return TMatrix The resulting matrix of same type as <tt>lhs</tt> and <tt>rhs</tt>.
 */

template <typename TValue,unsigned DIMENSION, typename THost1, typename THost2>
Matrix<TValue,DIMENSION>
operator + (Matrix<TValue,DIMENSION, THost1> const & matrix1, Matrix<TValue,DIMENSION, THost2> const & matrix2)
{
    //the two matrices must have same dimension
    SEQAN_ASSERT(_dataLengths(matrix1) == _dataLengths(matrix2));

    Matrix<TValue,DIMENSION> result;
    //copy the first matrix
    setDimension(result,length(_dataLengths(matrix1)));
    _dataLengths(result) = _dataLengths(matrix1);
    resize(result);

    //add the matrices
    for(unsigned int i = 0;i< length(host(result));++i)
    {
        value(host(result), i)=value(host(matrix1), i)+value(host(matrix2), i);
    }
    //Return matrix sum
    return result;
}

template <typename TValue,unsigned DIMENSION, typename THost1, typename THost2>
Matrix<TValue,DIMENSION>
operator - (Matrix<TValue,DIMENSION, THost1> const & matrix1,Matrix<TValue,DIMENSION, THost2> const & matrix2)
{
    //the two matrices must have same dimension
    SEQAN_ASSERT(_dataLengths(matrix1) == _dataLengths(matrix2));

    Matrix<TValue,DIMENSION> result;
    //resize the matrix
    setDimension(result,length(_dataLengths(matrix1)));
    _dataLengths(result) = _dataLengths(matrix1);
    resize(result);

    //subtract the matrices
    for(unsigned int i = 0;i< length(host(result));++i)
    {
        value(host(result), i)=value(host(matrix1), i)-value(host(matrix2), i);
    }
    //Return matrix difference
    return result;
}

template <typename TValue, typename THost1, typename THost2>
Matrix<TValue, 2>
operator * (Matrix<TValue, 2, THost1> const & matrix1, Matrix<TValue, 2, THost2> const & matrix2)
{
    SEQAN_ASSERT_EQ(length(matrix1,1), length(matrix2,0));

    unsigned int nrow1=length(matrix1,0);
    unsigned int ncol2=length(matrix2,1);
    Matrix<TValue, 2> result;
    //resize the matrix
    setLength(result, 0, nrow1);
    setLength(result, 1, ncol2);
    resize(result,(TValue) 0);

    //Matrix product
    for(unsigned int row = 0; row < nrow1; row++)
    {
        for(unsigned int col = 0; col < ncol2; col++)
        {
            for(unsigned int colRes = 0; colRes < length(matrix1,1); colRes++)
            {
                value(result,row,col)+=    value(host(matrix1), row + colRes * matrix1.data_factors[1])*value(host(matrix2), colRes + col * matrix2.data_factors[1]);
            }
        }
    }
    //return the matrix product
    return result;
}


template <typename TValue, typename THost>
Matrix<TValue, 2>
operator * (TValue const & scalar, Matrix<TValue, 2, THost> const & matrix)
{
    Matrix<TValue, 2> result;
    result= matrix;
    //scalar multiplication
    for(unsigned int i = 0;i< length(host(result));++i)
    {
        value(host(result), i)*=scalar;
    }
    //return the matrix product
    return result;
}

template <typename TValue, typename THost>
Matrix<TValue, 2>
operator * (Matrix<TValue, 2, THost> const & matrix, TValue const & scalar)
{
    Matrix<TValue, 2> result;
    result= matrix;
    //scalar multiplication
    for(unsigned int i = 0;i< length(host(result));++i)
    {
        value(host(result), i)*=scalar;
    }
    //return the matrix product
    return result;
}


template <typename TValue, unsigned DIMENSION1, typename THost1, unsigned DIMENSION2, typename THost2>
bool
operator == (Matrix<TValue, DIMENSION1, THost1> const & matrix1, Matrix<TValue, DIMENSION2, THost2> const & matrix2)
{
    bool result;
    result= (matrix1.data_lengths==matrix2.data_lengths)&&(matrix1.data_factors==matrix2.data_factors)&&(value(matrix1.data_host)==value(matrix2.data_host))&&(DIMENSION1==DIMENSION2);
    return result;
}

/*
template <typename TValue>
Matrix<TValue,2>
matricialSum(Matrix<TValue,2> &matrix1,Matrix<TValue,2> &matrix2)
{
    //the two matrices must have same dimension
    if(length(matrix1,0) != length(matrix2,0)||length(matrix1,1) != length(matrix2,1))
    {
        fprintf(stderr,"Error: The two matrices have different dimensions");
    }


    unsigned int nrow=length(matrix1,0);
    unsigned int ncol=length(matrix1,1);

    Matrix<TValue,2> result;
    //resize the matrix
    setLength(result, 0, nrow);
    setLength(result, 1, ncol);
    resize(result);

    //add the matrices
    for(unsigned int i = 0;i< nrow*ncol;++i)
    {
        value(host(result), i)=value(host(matrix1), i)+value(host(matrix2), i);
    }
    //Return matrix difference
    return result;

}
*/
//////////////////////////////////////////////////////////////////////////////
// _matricialDifference
//////////////////////////////////////////////////////////////////////////////

/*
template <typename TValue>
inline Matrix<TValue,2>
matricialDifference(Matrix<TValue,2> & matrix1, Matrix<TValue,2> & matrix2)
{
    //the two matrices must have same dimension
    if(length(matrix1,0) != length(matrix2,0)||length(matrix1,1) != length(matrix2,1))
    {
        fprintf(stderr,"Error: The two matrices have different dimensions");
    }

    unsigned int nrow=length(matrix1,0);
    unsigned int ncol=length(matrix1,1);

    Matrix<TValue,2> result;
    //resize the matrix
    //setDimension(result, 2);
    setLength(result, 0, nrow);
    setLength(result, 1, ncol);
    resize(result);

    //Substract the matrices
    for(unsigned int i1 = 0;i1< nrow;++i1)
        {
            for(unsigned int i2 = 0;i2<ncol;++i2)
            {
                value(host(result), i1 + i2 * _dataFactors(result)[1])=value(host(matrix1), i1 + i2 * _dataFactors(matrix1)[1])-value(host(matrix2), i1 + i2 * _dataFactors(matrix2)[1]);
            }

        }
    //Return matrix difference
    return result;
}
*/

/*
template <typename TValue>
inline Matrix<TValue, 2>
matricialProduct(Matrix<TValue, 2> &matrix1,
        Matrix<TValue, 2> &matrix2)
{
    //SEQAN_ASSERT_LT(dimension_, dimension(me));
    if(length(matrix1,1) != length(matrix2,0))
    {
        fprintf(stderr,"Error: Number of columns of matrix1 is unequal to number of rows of matrix2");
    }

    unsigned int nrow1=length(matrix1,0);
    unsigned int ncol2=length(matrix2,1);
    Matrix<TValue, 2> result;
    //resize the matrix
    setLength(result, 0, nrow1);
    setLength(result, 1, ncol2);
    resize(result,(TValue) 0);

    //Matrix product
    for(unsigned int row = 0; row < nrow1; row++)
    {
        for(unsigned int col = 0; col < ncol2; col++)
        {
            for(unsigned int colRes = 0; colRes < length(matrix1,1); colRes++)
            {
                value(result,row,col)+=value(matrix1, row,colRes)*value(matrix2,colRes,col);
            }
        }
    }
    //return the matrix product
    return result;
}
*/

/*!
 * @fn Matrix#transpose
 * @brief Tranpose a 2D Matrix.
 *
 * @signature TMatrix transpose(matrix);
 *
 * @param[in] matrix The matrix to tranpose.
 * @return TMatrix The resulting tranposed matrix.
 */

template <typename TValue, typename THost>
Matrix<TValue,2>
transpose(Matrix<TValue,2, THost> const & matrix)
{

    unsigned int nrow=length(matrix,0);
    unsigned int ncol=length(matrix,1);

    Matrix<TValue,2> result;
    //resize the matrix
    setLength(result, 0, ncol);
    setLength(result, 1, nrow);
    resize(result);


    for(unsigned int i1 = 0;i1< nrow;++i1)
    {
        for(unsigned int i2 = 0;i2<ncol;++i2)
        {
            value(host(result), i2 + i1 * _dataFactors(result)[1])=value(host(matrix), i1 + i2 * matrix.data_factors[1]);
        }

    }

    //Return transposed matrix
    return result;

}


template < typename TValue , typename THost>
std::ostream& operator<<(std::ostream &out, const Matrix<TValue,2, THost> &matrix)
{
    for(unsigned int i1 = 0;i1< matrix.data_lengths[0];++i1)
    {
            for(unsigned int i2 = 0;i2<(matrix.data_lengths[1]-1);++i2)
            {
                out<<value(host(matrix), i1 + i2 * matrix.data_factors[1])<<"\t";
            }
            //Last line is followd by \n instead of \t
            out<<value(host(matrix), i1 + (matrix.data_lengths[1]-1) *matrix.data_factors[1])<<"\n";
        }

    return out;
}
//////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////
///// READ
/*
 * TODO(goeke) only square matrices of fixed size can be read in...
 */
///////////////////////////////////////////////////////////////
// template < typename TValue >
// void read(FILE *file, Matrix<TValue,2> & matrix)
// {
//     //unsigned int column_size=3;
//     unsigned int column_size=pow(4,5);
//     //read the transition matrix
//     setLength(matrix, 0, column_size);
//     setLength(matrix, 1, column_size);
// resize(matrix,0.0);
//     for(unsigned int row=0; row<column_size; row++)
//     {
//         for(unsigned int col=0; col<column_size; col++)
//         {
//           fscanf(file,"%lf ", & value(matrix, row,col));
//         }
//         fscanf(file,"\n");
//     }
// }

}// namespace seqan2

#endif //#ifndef SEQAN_HEADER_...
