packedstream_loader.h

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/*
 * 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.
 * 
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#pragma once

#include <nvbio/basic/packedstream.h>
#include <nvbio/basic/types.h>
#include <nvbio/basic/numbers.h>
#include <nvbio/basic/strided_iterator.h>
#include <nvbio/basic/cuda/arch.h>
#include <nvbio/basic/iterator.h>

namespace nvbio {

template <uint32 CACHE_SIZE> struct lmem_cache_tag {};

struct uncached_tag  {};





template <typename StorageIterator, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename Tag = uncached_tag>
struct PackedStringLoader {};

template <typename StorageIterator, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, uint32 CACHE_SIZE>
struct PackedStringLoader<StorageIterator,SYMBOL_SIZE_T,BIG_ENDIAN_T,lmem_cache_tag<CACHE_SIZE> >
{
    typedef PackedStream<StorageIterator,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T>                                                  input_stream;
    typedef input_stream                                                                                                    input_iterator;
    typedef typename std::iterator_traits<StorageIterator>::value_type                                                      storage_type;
    typedef typename PackedStream<const_cached_iterator<const storage_type*>,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T>::iterator    iterator;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    iterator load(const input_stream stream, const uint32 length);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    iterator load(
        const input_stream      stream,
        const uint32            length,
        const uint2             loaded_range,
        const uint32            rev_flag);

    storage_type lmem[CACHE_SIZE];
};

template <typename StorageIterator, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T>
struct PackedStringLoader<StorageIterator,SYMBOL_SIZE_T,BIG_ENDIAN_T,uncached_tag>
{
    typedef typename std::iterator_traits<StorageIterator>::value_type                           storage_type;
    typedef PackedStream<StorageIterator,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T>                       input_stream;
    typedef input_stream                                                                         input_iterator;
    typedef typename PackedStream<StorageIterator,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T>::iterator    iterator;

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    iterator load(const input_stream stream, const uint32 length);

    NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
    iterator load(
        const input_stream      stream,
        const uint32            length,
        const uint2             substring_range,
        const uint32            rev_flag);
};


} // namespace nvbio

#include <nvbio/basic/packedstream_loader_inl.h>