DArray(std::map<int64_t,uint64_t> const & M, uint64_t const bwtterm)
: D(bwtterm+1)
{
for ( std::map<int64_t,uint64_t>::const_iterator ita = M.begin(); ita != M.end(); ++ita )
D [ ita->first ] += ita->second;
D.prefixSums();
}
ImpWTLF ( iterator BWT, uint64_t const rn, ::libmaus2::util::TempFileNameGenerator & rtmpgen, 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]) );
uint64_t const b = ::libmaus2::math::numbits(maxval);
::libmaus2::wavelet::ImpExternalWaveletGenerator IEWG(b,rtmpgen);
for ( uint64_t i = 0; i < n; ++i )
IEWG.putSymbol(BWT[i]);
std::string const tmpfilename = rtmpgen.getFileName();
IEWG.createFinalStream(tmpfilename);
std::ifstream istr(tmpfilename.c_str(),std::ios::binary);
wt_ptr_type tW(new wt_type(istr));
W = UNIQUE_PTR_MOVE(tW);
istr.close();
remove ( tmpfilename.c_str() );
D = ::libmaus2::autoarray::AutoArray < uint64_t >((1ull<<W->getB())+1);
for ( uint64_t i = 0; i < (1ull<<W->getB()); ++i )
D [ i ] = W->rank(i,n-1);
D.prefixSums();
}
}
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();
}
}
ImpWTLF(std::istream & in)
: n(::libmaus2::util::NumberSerialisation::deserialiseNumber(in)),
W (new wt_type(in))
{
if ( n )
{
D = ::libmaus2::autoarray::AutoArray < uint64_t >((1ull<<W->getB())+1);
for ( uint64_t i = 0; i < (1ull<<W->getB()); ++i )
D [ i ] = W->rank(i,n-1);
D.prefixSums();
}
}
ImpWTLF (::libmaus2::huffman::RLDecoder & decoder, uint64_t const b, ::libmaus2::util::TempFileNameGenerator & rtmpgen)
: n(decoder.getN())
{
if ( n )
{
::libmaus2::wavelet::ImpExternalWaveletGenerator IEWG(b,rtmpgen);
for ( uint64_t i = 0; i < n; ++i )
IEWG.putSymbol(decoder.decode());
std::string const tmpfilename = rtmpgen.getFileName();
IEWG.createFinalStream(tmpfilename);
std::ifstream istr(tmpfilename.c_str(),std::ios::binary);
wt_ptr_type tW(new wt_type(istr));
W = UNIQUE_PTR_MOVE(tW);
istr.close();
remove ( tmpfilename.c_str() );
D = ::libmaus2::autoarray::AutoArray < uint64_t >((1ull<<W->getB())+1);
for ( uint64_t i = 0; i < (1ull<<W->getB()); ++i )
D [ i ] = W->rank(i,n-1);
D.prefixSums();
}
}