C++ autoarray::AutoArray类代码示例

			MultiRankCacheLF ( iterator BWT, uint64_t const rn, uint64_t const rmaxval = 0)
			: n(rn)
			{
				if ( n )
				{
					uint64_t maxval = rmaxval;
					for ( uint64_t i = 0; i < n; ++i )
						maxval = std::max ( maxval, static_cast<uint64_t>(BWT[i]) );
						
					rank_dictionaries = ::libmaus2::autoarray::AutoArray < rank_ptr_type >(maxval+1);
					
					for ( uint64_t i = 0; i < rank_dictionaries.size(); ++i )
					{
						rank_ptr_type trank_dictionariesi(new rank_type(n+1));
						rank_dictionaries[i] = UNIQUE_PTR_MOVE(trank_dictionariesi);
						writer_type writer = rank_dictionaries[i]->getWriteContext();
						
						for ( uint64_t j = 0; j < n; ++j )
							writer.writeBit(BWT[j] == i);
						// write additional bit to make rankm1 defined for n
						writer.writeBit(0);
						
						writer.flush();
					}
					
					D = ::libmaus2::autoarray::AutoArray < uint64_t >(rank_dictionaries.size()+1);
					for ( uint64_t i = 0; i < rank_dictionaries.size(); ++i )
						D [ i ] = rank_dictionaries[i]->rank1(n-1);
					D.prefixSums();
				}
			}

::libmaus2::util::Histogram::unique_ptr_type libmaus2::util::Utf8String::getHistogram(::libmaus2::autoarray::AutoArray<uint8_t> const & A)
{
	#if defined(_OPENMP)
	uint64_t const numthreads = omp_get_max_threads();
	#else
	uint64_t const numthreads = 1;
	#endif
	
	::libmaus2::autoarray::AutoArray<uint64_t> const partstarts = computePartStarts(A,numthreads);
	uint64_t const numparts = partstarts.size()-1;
	
	::libmaus2::util::Histogram::unique_ptr_type hist(new ::libmaus2::util::Histogram);
	::libmaus2::parallel::OMPLock lock;
	
	#if defined(_OPENMP)
	#pragma omp parallel for
	#endif
	for ( int64_t t = 0; t < static_cast<int64_t>(numparts); ++t )
	{
		::libmaus2::util::Histogram::unique_ptr_type lhist(new ::libmaus2::util::Histogram);
	
		uint64_t codelen = 0;
		uint64_t const tcodelen = partstarts[t+1]-partstarts[t];
		::libmaus2::util::GetObject<uint8_t const *> G(A.begin()+partstarts[t]);
		
		while ( codelen != tcodelen )
			(*lhist)(::libmaus2::util::UTF8::decodeUTF8(G,codelen));
			
		lock.lock();
		hist->merge(*lhist);
		lock.unlock();
	}
	
	return UNIQUE_PTR_MOVE(hist);
}

			::libmaus2::autoarray::AutoArray < std::pair<uint64_t,uint64_t> > computeSymAccu() const
			{
				uint64_t numint = 0;
				for ( uint64_t i = 0; i < index.size(); ++i )
					numint += index[i].size();
				::libmaus2::autoarray::AutoArray<uint64_t> preaccu(numint+1);
				uint64_t outptr = 0;
				for ( uint64_t i = 0; i < index.size(); ++i )
					for ( uint64_t j = 0; j < index[i].size(); ++j )
						preaccu[outptr++] = index[i][j].vcnt;
				preaccu.prefixSums();
				::libmaus2::autoarray::AutoArray < std::pair<uint64_t,uint64_t> > symaccu(numint);
				for ( uint64_t i = 1; i < preaccu.size(); ++i )
					symaccu[i-1] = std::pair<uint64_t,uint64_t>(preaccu[i-1],preaccu[i]);
	
				#if 0
				std::cerr << "presymaccu:" << std::endl;
				for ( uint64_t i = 0; i < preaccu.size(); ++i )
					std::cerr << preaccu[i] << std::endl;

				std::cerr << "symaccu:" << std::endl;
				for ( uint64_t i = 0; i < symaccu.size(); ++i )
					std::cerr << "[" << i << "]=[" << symaccu[i].first << "," << symaccu[i].second << ")" << std::endl;
				#endif
					
				return symaccu;
			}

			/**
			 * constructor from hash intervals and file prefix
			 *
			 * @param rHI hash intervals
			 * @param fileprefix prefix for files
			 **/
			SynchronousOutputFile8ArrayTemplate(
				::libmaus2::autoarray::AutoArray< std::pair<uint64_t,uint64_t> > const & rHI, 
				std::string const & fileprefix
			)
			: HI(&rHI), buffers(HI->size()), IT(new ::libmaus2::util::IntervalTree(*HI,0,HI->size()))
			{
				init ( HI->size(), fileprefix );
			}

			ExternalMemoryIndexGenerator(std::string const & filename)
			: Pstream(libmaus2::aio::InputOutputStreamFactoryContainer::constructUnique(filename,std::ios::in|std::ios::out|std::ios::trunc|std::ios::binary)), stream(*Pstream), 
			  ic(0), flushed(false), writeCache(1024),
			  wa(writeCache.begin()), wc(wa), we(writeCache.end())
			{
			
			}

			uint64_t operator[](uint64_t const i) const
			{
				for ( uint64_t j = 0; j < rank_dictionaries.size(); ++j )
					if ( (*(rank_dictionaries[j]))[i] )
						return j;
				return rank_dictionaries.size();
			}

			void serialise(stream_type & stream) const
			{
				::libmaus2::util::NumberSerialisation::serialiseNumber(stream,D.size());

				for ( uint64_t i = 0; i < D.size(); ++i )
					::libmaus2::util::NumberSerialisation::serialiseNumber(stream,D[i]);
			}

			::std::streampos seekpos(::std::streampos sp, ::std::ios_base::openmode which = ::std::ios_base::in | ::std::ios_base::out)
			{
				if ( which & ::std::ios_base::in )
				{
					int64_t const cur = symsread-(egptr()-gptr());
					int64_t const curlow = cur - static_cast<int64_t>(gptr()-eback());
					int64_t const curhigh = cur + static_cast<int64_t>(egptr()-gptr());
					
					// call relative seek, if target is in range
					if ( sp >= curlow && sp <= curhigh )
						return seekoff(static_cast<int64_t>(sp) - cur, ::std::ios_base::cur, which);

					// target is out of range, we really need to seek
					uint64_t tsymsread = (sp / buffersize)*buffersize;
					
					symsread = tsymsread;
					stream.clear();
					stream.seekg( (symsread * b) / 8 );
					setg(buffer.end(),buffer.end(),buffer.end());
					underflow();
					setg(eback(),gptr() + (static_cast<int64_t>(sp)-static_cast<int64_t>(tsymsread)), egptr());
				
					return sp;
				}
				
				return -1;
			}

			SocketOutputBufferTemplate(
				::libmaus2::network::SocketBase * rdst, 
				int const rtag,
				uint64_t const bufsize)
			: dst(rdst), tag(rtag), B(bufsize), pa(B.get()), pc(pa), pe(pa+B.getN())
			{
			}

                        /**
                         * constructor by output stream
                         *
                         * @param out output stream
                         * @param bufsize output buffer size
                         **/
                        SynchronousGenericOutput(std::ostream & out, uint64_t const bufsize)
                        : B(bufsize), pa(B.get()), pc(pa), pe(pa+B.getN()), 
                          W(out),
                          datawrittentofile(0)
                        {

                        }

			int_type underflow()
			{
				if ( gptr() < egptr() )
					return static_cast<int_type>(*uptr());
					
				assert ( gptr() == egptr() );
					
				char * midptr = buffer.begin() + pushbackspace;
				uint64_t const copyavail = 
					std::min(
						// previously read
						static_cast<uint64_t>(gptr()-eback()),
						// space we have to copy into
						static_cast<uint64_t>(midptr-buffer.begin())
					);
				::std::memmove(midptr-copyavail,gptr()-copyavail,copyavail);

				stream.read(midptr, buffer.end()-midptr);
				size_t const n = stream.gcount();
				streamreadpos += n;

				setg(midptr-copyavail, midptr, midptr+n);

				if (!n)
					return traits_type::eof();
				
				return static_cast<int_type>(*uptr());
			}

			bool decodeBlock()
			{
				while ( FBO.file < index.Vfn.size() && FBO.block >= index.blocksPerFile[FBO.file] )
				{
					FBO.file++;
					FBO.block = 0;
					FBO.blockoffset = 0; // check this if we change the file format
					FBO.offset = 0;
					openFile();
				}
				if ( FBO.file == index.Vfn.size() )
				{
					PSGI.reset();
					PISI.reset();
					return false;
				}

				libmaus2::gamma::GammaDecoder< libmaus2::aio::SynchronousGenericInput<uint64_t> > GD(*PSGI);
				uint64_t const bs = GD.decode() + 1;
				B.ensureSize(bs);
				for ( uint64_t i = 0; i < bs; ++i )
					B[i] = GD.decode();

				pa = B.begin();
				pc = B.begin();
				pe = B.begin() + bs;

				FBO.block += 1;

				return true;
			}

			void init(bool const repos)
			{
				// set empty buffer
				setgchecked(buffer.end(), buffer.end(), buffer.end());
				// seek
				if ( repos )
					fd->lseek(symsread,SEEK_SET);
			}

			void serialise(std::ostream & out) const
			{
				::libmaus2::fastx::FastInterval::serialise(out,FI);
				designators.serialize(out);
				shortpointers.serialize(out);
				longpointers.serialize(out);
				text.serialize(out);
			}

			StreamWrapperBuffer(stream_type & rstream, ::std::size_t rbuffersize, std::size_t rpushbackspace)
			: stream(rstream), 
			  buffersize(rbuffersize),
			  pushbackspace(rpushbackspace),
			  buffer(buffersize+pushbackspace,false), streamreadpos(0)
			{
				setg(buffer.end(), buffer.end(), buffer.end());	
			}