prefetcher.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
 * 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
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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 * 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.
 */

#pragma once

#include <nvbio/basic/types.h>
#include <nvbio/basic/packedstream.h>
#include <nvbio/basic/packedstream_loader.h>
#include <nvbio/basic/vector_view.h>
#include <nvbio/strings/infix.h>


namespace nvbio {



template <typename StringType, typename CacheTag>
struct StringPrefetcher
{
    typedef StringType  input_string_type;
    typedef StringType        string_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    const string_type& load(const input_string_type& string) { return string; }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    const string_type& load(
        const input_string_type& string,
        const uint2              range) { return string; }
};

template <typename StorageIterator, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, uint32 CACHE_SIZE>
struct StringPrefetcher<
    vector_view< PackedStream<StorageIterator,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T> >,
    lmem_cache_tag<CACHE_SIZE> >
{
    typedef vector_view< PackedStream<StorageIterator,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T> >                           input_string_type;
    typedef PackedStringLoader<StorageIterator,SYMBOL_SIZE_T,BIG_ENDIAN_T,lmem_cache_tag<CACHE_SIZE> >              loader_type;
    typedef vector_view<typename loader_type::iterator>                                                             string_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    string_type load(const input_string_type& string)
    {
        return string_type(
            string.size(),
            loader.load( string.base(),
                         string.size() ) );
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    string_type load(
        const input_string_type& string,
        const uint2              range)
    {
        return string_type(
            string.size(),
            loader.load( string.base(),
                         string.size(),
                         range,
                         false ) );
    }

    loader_type loader;
};

template <typename InfixCoordType, typename StorageIterator, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, uint32 CACHE_SIZE>
struct StringPrefetcher<
    Infix< PackedStream<StorageIterator,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T>,
           InfixCoordType >,
    lmem_cache_tag<CACHE_SIZE> >
{
    typedef Infix< PackedStream<StorageIterator,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T>,
                   InfixCoordType>                                                                                  input_string_type;
    typedef PackedStringLoader<StorageIterator,SYMBOL_SIZE_T,BIG_ENDIAN_T,lmem_cache_tag<CACHE_SIZE> >              loader_type;
    typedef vector_view<typename loader_type::iterator>                                                             string_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    string_type load(const input_string_type& string)
    {
        return string_type(
            string.size(),
            loader.load( string.m_string + string.range().x,
                         string.size() ) );
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    string_type load(
        const input_string_type& string,
        const uint2              range)
    {
        return string_type(
            string.size(),
            loader.load( string.m_string + string.range().x,
                         string.size(),
                         range,
                         false ) );
    }

    loader_type loader;
};

template <typename InfixCoordType, typename StorageIterator, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, uint32 CACHE_SIZE>
struct StringPrefetcher<
    Infix< vector_view< PackedStream<StorageIterator,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T> >,
           InfixCoordType >,
    lmem_cache_tag<CACHE_SIZE> >
{
    typedef Infix< vector_view< PackedStream<StorageIterator,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T> >,
                   InfixCoordType>                                                                                  input_string_type;
    typedef PackedStringLoader<StorageIterator,SYMBOL_SIZE_T,BIG_ENDIAN_T,lmem_cache_tag<CACHE_SIZE> >              loader_type;
    typedef vector_view<typename loader_type::iterator>                                                             string_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    string_type load(const input_string_type& string)
    {
        return string_type(
            string.size(),
            loader.load( string.m_string.base() + string.range().x,
                         string.size() ) );
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    string_type load(
        const input_string_type& string,
        const uint2              range)
    {
        return string_type(
            string.size(),
            loader.load( string.m_string.base() + string.range().x,
                         string.size(),
                         range,
                         false ) );
    }

    loader_type loader;
};

template <typename T, uint32 CACHE_SIZE>
struct StringPrefetcher<
    vector_view<const T*>,
    lmem_cache_tag<CACHE_SIZE> >
{
    static const uint32 CACHE_BYTES = CACHE_SIZE * sizeof(uint32);
    static const uint32 CACHE_ITEMS = CACHE_BYTES / sizeof(T);

    typedef vector_view<const T*>   input_string_type;
    typedef vector_view<const T*>   string_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    string_type load(const input_string_type& string)
    {
        const uint32 L = string.size();

        // check whether the cache is too small
        if (L > CACHE_ITEMS)
            return string;

        for (uint32 i = 0; i < L; ++i)
            cache[i] = string[i];

        return string_type( L, cache );
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    string_type load(
        const input_string_type& string,
        const uint2              range)
    {
        // check whether the cache is too small, to prevent overflows
        if (range.y - range.x > CACHE_ITEMS)
            return string;

        for (uint32 i = range.x; i < range.y; ++i)
            cache[i - range.x] = string[i];

        return string_type( string.size(), cache - range.x );
    }

    T cache[CACHE_ITEMS];
};

template <typename T, uint32 CACHE_SIZE>
struct StringPrefetcher<
    vector_view<T*>,
    lmem_cache_tag<CACHE_SIZE> >
{
    static const uint32 CACHE_BYTES = CACHE_SIZE * sizeof(uint32);
    static const uint32 CACHE_ITEMS = CACHE_BYTES / sizeof(T);

    typedef vector_view<T*>         input_string_type;
    typedef vector_view<const T*>   string_type;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    string_type load(const input_string_type& string)
    {
        const uint32 L = string.size();

        // check whether the cache is too small
        if (L > CACHE_ITEMS)
            return string_type( L, string.base() );

        for (uint32 i = 0; i < L; ++i)
            cache[i] = string[i];

        return string_type( L, cache );
    }

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    string_type load(
        const input_string_type& string,
        const uint2              range)
    {
        // check whether the cache is too small, to prevent overflows
        if (range.y - range.x > CACHE_ITEMS)
            return string_type( string.size(), string.base() );

        for (uint32 i = range.x; i < range.y; ++i)
            cache[i - range.x] = string[i];

        return string_type( string.size(), cache - range.x );
    }

    T cache[CACHE_ITEMS];
};


} // namespace nvbio