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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 INCLUDE_SEQAN_ALIGN_PARALLEL_DP_TRAITS_H_
#define INCLUDE_SEQAN_ALIGN_PARALLEL_DP_TRAITS_H_
namespace seqan2
{
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// Traits for DP configuration. Currently used only internally.
struct DPTraits
{
// Gocal alignment with linear gap costs.
struct GlobalLinear
{
// The algorithm to choose.
using TAlgorithmType = GlobalAlignment_<>;
// The Gaps to choos
using TGapType = LinearGaps;
// The Band to choose.
using TBandType = BandOff;
// The traceback.
using TTracebackType = TracebackOn<TracebackConfig_<SingleTrace, GapsLeft>>;
// The output to choose.
using TFormat = ArrayGaps;
};
// Global alignment with affine gap costs.
struct GlobalAffine : public GlobalLinear
{
using TGapType = AffineGaps;
};
// Global alignment with affine gap costs.
struct SemiGlobalLinear : public GlobalLinear
{
using TAlgorithmType = GlobalAlignment_<FreeEndGaps_<True, False, True, False>>;
};
// Global alignment with affine gap costs.
struct SemiGlobalAffine : public GlobalAffine
{
using TAlgorithmType = GlobalAlignment_<FreeEndGaps_<True, False, True, False>>;
};
// Banded global alignment with linear gap costs.
struct BandedGlobalLinear : public GlobalLinear
{
using TBandType = BandOn;
};
// Banded global alignment with affine gap costs.
struct BandedGlobalAffine : public BandedGlobalLinear
{
using TGapType = AffineGaps;
};
// Local alignment with linear gap costs.
struct LocalLinear : public GlobalLinear
{
using TAlgorithmType = LocalAlignment_<>;
};
// Local alignment with affine gap costs.
struct LocalAffine : public LocalLinear
{
using TGapType = AffineGaps;
};
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
} // namespace seqan2
#endif // INCLUDE_SEQAN_ALIGN_PARALLEL_DP_TRAITS_H_
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