sink.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. 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 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
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 */

#pragma once

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

namespace nvbio {
namespace aln {



struct NullSink
{
    template <typename ScoreType>
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void report(const ScoreType _score, const uint2 _sink) {}
};

template <typename ScoreType>
struct BestSink
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    BestSink();

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void invalidate();

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void report(const ScoreType _score, const uint2 _sink);

    ScoreType score;
    uint2     sink;
};

template <>
struct BestSink<simd4u8>
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    BestSink() : score( uint32(0) ) {}

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void report(const simd4u8 _score) { score = nvbio::max( score, _score ); }

    simd4u8 score;
};

template <typename ScoreType>
struct Best2Sink
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    Best2Sink(const uint32 distinct_dist = 0);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void invalidate();

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void report(const ScoreType score, const uint2 sink);

    ScoreType score1;
    ScoreType score2;
    uint2     sink1;
    uint2     sink2;

private:
    uint32    m_distinct_dist;
};

template <typename ScoreType, uint32 N = 16>
struct BestColumnSink
{
    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    BestColumnSink(const uint32 column_width = 50, const ScoreType min_score = Field_traits<ScoreType>::min());

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void set_column_width(const uint32 column_width) { m_column_width = column_width; }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void set_min_score(const uint32 min_score) { m_min_score = min_score; }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void invalidate();

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void report(const ScoreType score, const uint2 sink);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    void best2(uint32& i1, uint32& i2, const uint32 min_dist) const;

    ScoreType scores[N+1];
    uint2     sinks[N+1];

private:
    uint32    m_column_width;
    ScoreType m_min_score;
};



} // namespace aln
} // namespace nvbio

#include <nvbio/alignment/sink_inl.h>