/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
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 * 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 the NVIDIA CORPORATION 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 NVIDIA CORPORATION BE LIABLE FOR ANY
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 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#include <nvBowtie/bowtie2/cuda/score.h>
#include <nvBowtie/bowtie2/cuda/score_opposite_impl.h>
#include <nvBowtie/bowtie2/cuda/scoring.h>
#include <nvBowtie/bowtie2/cuda/params.h>
#include <nvbio/io/utils.h>

namespace nvbio {
namespace bowtie2 {
namespace cuda {

//
// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping
//
template <typename scheme_type>
void ungapped_opposite_score_best_t(
    const BestApproxScoringPipelineState<scheme_type>&  pipeline,
    const ParamsPOD                                     params)
{
    if (params.alignment_type == LocalAlignment)
    {
        detail::opposite_score_best(
            pipeline,
            pipeline.scoring_scheme.ungapped_local_aligner(),
            params );
    }
    else
    {
        detail::opposite_score_best(
            pipeline,
            pipeline.scoring_scheme.ungapped_end_to_end_aligner(),
            params );
    }
}

//
// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping
//
// \b inputs:
//  - HitQueues::seed
//  - HitQueues::loc
//  - HitQueues::score
//  - HitQueues::sink
//
// \b outputs:
//  - HitQueues::opposite_score
//  - HitQueues::opposite_loc
//  - HitQueues::opposite_sink
//
void ungapped_opposite_score_best(
    const BestApproxScoringPipelineState<EditDistanceScoringScheme>&    pipeline,
    const ParamsPOD&                                                    params)
{
    ungapped_opposite_score_best_t( pipeline, params );
}

//
// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping
//
// \b inputs:
//  - HitQueues::seed
//  - HitQueues::loc
//  - HitQueues::score
//  - HitQueues::sink
//
// \b outputs:
//  - HitQueues::opposite_score
//  - HitQueues::opposite_loc
//  - HitQueues::opposite_sink
//
void ungapped_opposite_score_best(
    const BestApproxScoringPipelineState<SmithWatermanScoringScheme<> >&    pipeline,
    const ParamsPOD&                                                        params)
{
    ungapped_opposite_score_best_t( pipeline, params );
}

//
// execute a batch of full-DP alignment score calculations for the opposite mates, best mapping
//
// \b inputs:
//  - HitQueues::seed
//  - HitQueues::loc
//  - HitQueues::score
//  - HitQueues::sink
//
// \b outputs:
//  - HitQueues::opposite_score
//  - HitQueues::opposite_loc
//  - HitQueues::opposite_sink
//
void ungapped_opposite_score_best(
    const BestApproxScoringPipelineState<WfaScoringScheme<> >&              pipeline,
    const ParamsPOD&                                                        params)
{
    ungapped_opposite_score_best_t( pipeline, params );
}

} // namespace cuda
} // namespace bowtie2
} // namespace nvbio
