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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;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * 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/packedstream.h>
- #include <nvbio/basic/cached_iterator.h>
- #include <nvbio/basic/vector_view.h>
- namespace nvbio {
- template <typename StringType>
- struct lmem_selector {};
- template <typename StreamType,
- typename SymbolType,
- uint32 SYMBOL_SIZE_T,
- bool BIG_ENDIAN_T>
- struct lmem_selector< vector_view< PackedStream<StreamType,SymbolType,SYMBOL_SIZE_T,BIG_ENDIAN_T> > >
- {
- typedef typename std::iterator_traits<StreamType>::value_type type;
- static const uint32 SYMBOLS_PER_WORD = (sizeof(type)*8)/SYMBOL_SIZE_T;
- static const uint32 WORDS = 512 / SYMBOLS_PER_WORD;
- };
- template <typename StreamType,
- typename SymbolType,
- uint32 SYMBOL_SIZE_T,
- bool BIG_ENDIAN_T,
- typename W>
- NVBIO_FORCEINLINE NVBIO_HOST_DEVICE
- vector_view< typename PackedStream<const_cached_iterator<const W*>,SymbolType,SYMBOL_SIZE_T,BIG_ENDIAN_T>::iterator >
- make_local_string(
- vector_view< PackedStream<StreamType,SymbolType,SYMBOL_SIZE_T,BIG_ENDIAN_T> > string,
- W* lmem)
- {
- const StreamType in_stream = string.begin().stream();
- const uint32 in_offset = string.begin().index();
- const uint32 N = string.length();
- typedef typename std::iterator_traits<StreamType>::value_type word_type;
- const uint32 SYMBOLS_PER_WORD = (sizeof(word_type)*8) / SYMBOL_SIZE_T;
- uint32 word_offset = in_offset & (SYMBOLS_PER_WORD-1);
- uint32 begin_word = in_offset / SYMBOLS_PER_WORD;
- uint32 end_word = (in_offset + N + SYMBOLS_PER_WORD-1) / SYMBOLS_PER_WORD;
- for (uint32 word = begin_word; word < end_word; ++word)
- lmem[word - begin_word] = in_stream[ word ];
- typedef PackedStream<const_cached_iterator<const W*>,uint8,SYMBOL_SIZE_T,BIG_ENDIAN_T> const_stream_type;
- const_stream_type clmem_stream( lmem );
- return vector_view<const_stream_type>( N, clmem_stream + word_offset );
- }
- } // namespace nvbio
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