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// ==========================================================================
// 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: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Class DPMatrix [SparseDPMatrix]
// ----------------------------------------------------------------------------
template <typename TValue, typename THost>
class DPMatrix_<TValue, SparseDPMatrix, THost>
{
public:
typedef typename Member<DPMatrix_, DPMatrixMember>::Type TMatrix;
Holder<TMatrix> data_host; // The host containing the actual matrix.
DPMatrix_() :
data_host()
{
create(data_host);
}
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function resize()
// ----------------------------------------------------------------------------
template <typename TValue, typename THost>
inline void
resize(DPMatrix_<TValue, SparseDPMatrix, THost> & dpMatrix)
{
typedef DPMatrix_<TValue, SparseDPMatrix, THost> TDPMatrix;
typedef typename Size<TDPMatrix>::Type TSize;
TSize _dimVertical = length(dpMatrix, DPMatrixDimension_::VERTICAL);
if (_dimVertical >= length(dpMatrix))
resize(host(dpMatrix), _dimVertical, Exact());
}
template <typename TValue, typename THost>
inline void
resize(DPMatrix_<TValue, SparseDPMatrix, THost> & dpMatrix,
TValue const & fillValue)
{
typedef DPMatrix_<TValue, SparseDPMatrix, THost> TDPMatrix;
typedef typename Size<TDPMatrix>::Type TSize;
TSize _dimVertical = length(dpMatrix, DPMatrixDimension_::VERTICAL);
if (_dimVertical > length(dpMatrix))
resize(host(dpMatrix), _dimVertical, fillValue, Exact());
}
// ----------------------------------------------------------------------------
// Function value()
// ----------------------------------------------------------------------------
template <typename TValue, typename THost, typename TPositionV, typename TPositionH>
inline typename Reference<DPMatrix_<TValue, SparseDPMatrix, THost> >::Type
value(DPMatrix_<TValue, SparseDPMatrix, THost> & dpMatrix,
TPositionV const & posV,
TPositionH const &)
{
return value(dpMatrix, posV);
}
template <typename TValue, typename THost, typename TPositionV, typename TPositionH>
inline typename Reference<DPMatrix_<TValue, SparseDPMatrix, THost> const>::Type
value(DPMatrix_<TValue, SparseDPMatrix, THost> const & dpMatrix,
TPositionV const & posV,
TPositionH const &)
{
return value(dpMatrix, posV);
}
// ----------------------------------------------------------------------------
// Function coordinate()
// ----------------------------------------------------------------------------
template <typename TValue, typename THost, typename TPosition>
inline typename Position<DPMatrix_<TValue, SparseDPMatrix, THost> >::Type
coordinate(DPMatrix_<TValue, SparseDPMatrix, THost> const & /*dpMatrix*/,
TPosition hostPos,
typename DPMatrixDimension_::TValue dimension)
{
SEQAN_ASSERT(_checkCorrectDimension(dimension));
if (dimension == DPMatrixDimension_::VERTICAL)
return hostPos;
return 0u;
}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_SPARSE_H_
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