ed_utils.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
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 *      notice, this list of conditions and the following disclaimer.
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 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
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#pragma once

#include <nvbio/basic/types.h>
#include <nvbio/basic/numbers.h>

namespace nvbio {
namespace aln {

namespace priv {


struct EditDistanceSWScheme
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 match(const uint8 q = 0)      const { return  0; };
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 mismatch(const uint8 q = 0)   const { return -1; };
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 mismatch(const uint8 a, const uint8 b, const uint8 q = 0)   const { return -1; };
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 deletion()                    const { return -1; };
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 insertion()                   const { return -1; };
};


} // namespace priv

} // namespace aln
} // namespace nvbio