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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, 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>
// ==========================================================================
// Implements the context that can be passed to the dp functions in order
// to reuse memory blocks in mutliple calls of the same function.
// ==========================================================================
#ifndef INCLUDE_SEQAN_ALIGN_DP_CONTEXT_H_
#define INCLUDE_SEQAN_ALIGN_DP_CONTEXT_H_
namespace seqan
{
// ============================================================================
// Forwards
// ============================================================================
template <typename T>
struct GetDPScoreMatrix
{};
template <typename T>
struct GetDPTraceMatrix
{};
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
template <typename TScoreValue, typename TGapCosts>
struct DPContext
{
typedef typename GetDPScoreMatrix<DPContext>::Type TScoreMatrixHost;
typedef typename GetDPTraceMatrix<DPContext>::Type TTraceMatrixHost;
TScoreMatrixHost _scoreMatrix;
TTraceMatrixHost _traceMatrix;
DPContext() : _scoreMatrix(), _traceMatrix()
{}
};
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction GetDPScoreMatrix
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TGapCosts>
struct GetDPScoreMatrix<DPContext<TScoreValue, TGapCosts> >
{
typedef DPCell_<TScoreValue, TGapCosts> TDPScoreValue_;
typedef DPMatrix_<TDPScoreValue_, FullDPMatrix> TDPScoreMatrix_;
typedef typename Host<TDPScoreMatrix_>::Type Type;
};
template <typename TScoreValue, typename TGapCosts>
struct GetDPScoreMatrix<DPContext<TScoreValue, TGapCosts> const >
{
typedef DPCell_<TScoreValue, TGapCosts> TDPScoreValue_;
typedef DPMatrix_<TDPScoreValue_, FullDPMatrix> TDPScoreMatrix_;
typedef typename Host<TDPScoreMatrix_>::Type const Type;
};
// ----------------------------------------------------------------------------
// Metafunction GetDPTraceMatrix
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TGapCosts>
struct GetDPTraceMatrix<DPContext<TScoreValue, TGapCosts> >
{
typedef typename TraceBitMap_<TScoreValue>::Type TTraceValue_;
typedef DPMatrix_<TTraceValue_, FullDPMatrix> TDPScoreMatrix_;
typedef typename Host<TDPScoreMatrix_>::Type Type;
};
template <typename TScoreValue, typename TGapCosts>
struct GetDPTraceMatrix<DPContext<TScoreValue, TGapCosts> const >
{
typedef typename TraceBitMap_<TScoreValue>::Type TTraceValue_;
typedef DPMatrix_<TTraceValue_, FullDPMatrix> TDPScoreMatrix_;
typedef typename Host<TDPScoreMatrix_>::Type const Type;
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function dpScoreMatrix()
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TGapCosts>
inline typename GetDPScoreMatrix<DPContext<TScoreValue, TGapCosts> >::Type &
getDpScoreMatrix(DPContext<TScoreValue, TGapCosts> & dpContext)
{
return dpContext._scoreMatrix;
}
template <typename TScoreValue, typename TGapCosts>
inline typename GetDPScoreMatrix<DPContext<TScoreValue, TGapCosts> const >::Type &
getDpScoreMatrix(DPContext<TScoreValue, TGapCosts> const & dpContext)
{
return dpContext._scoreMatrix;
}
// ----------------------------------------------------------------------------
// Function dpTraceMatrix()
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TGapCosts>
inline typename GetDPTraceMatrix<DPContext<TScoreValue, TGapCosts> >::Type &
getDpTraceMatrix(DPContext<TScoreValue, TGapCosts> & dpContext)
{
return dpContext._traceMatrix;
}
template <typename TScoreValue, typename TGapCosts>
inline typename GetDPTraceMatrix<DPContext<TScoreValue, TGapCosts> const >::Type &
getDpTraceMatrix(DPContext<TScoreValue, TGapCosts> const & dpContext)
{
return dpContext._traceMatrix;
}
// ----------------------------------------------------------------------------
// Function setDpScoreMatrix()
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TGapCosts>
inline void
setDpTraceMatrix(DPContext<TScoreValue, TGapCosts> & dpContext,
typename GetDPScoreMatrix<DPContext<TScoreValue, TGapCosts> >::Type const & scoreMatrix)
{
dpContext._scoreMatrix = scoreMatrix;
}
// ----------------------------------------------------------------------------
// Function setDpTraceMatrix()
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TGapCosts>
inline void
setDpTraceMatrix(DPContext<TScoreValue, TGapCosts> & dpContext,
typename GetDPTraceMatrix<DPContext<TScoreValue, TGapCosts> >::Type const & traceMatrix)
{
dpContext._tarceMatrix = traceMatrix;
}
}
#endif // INCLUDE_SEQAN_ALIGN_DP_CONTEXT_H_
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