// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2024, 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"
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// 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_
