void testUtf8String(std::string const & fn)
{
::libmaus::util::Utf8String::shared_ptr_type us = ::libmaus::util::Utf8String::constructRaw(fn);
::libmaus::util::Utf8StringPairAdapter usp(us);
::libmaus::util::Utf8DecoderWrapper decwr(fn);
uint64_t const numsyms = ::libmaus::util::GetFileSize::getFileSize(decwr);
assert ( us->size() == numsyms );
for ( uint64_t i = 0; i < numsyms; ++i )
{
assert ( static_cast<wchar_t>(decwr.get()) == us->get(i) );
assert (
us->get(i) ==
((usp[2*i] << 12) | (usp[2*i+1]))
);
}
::std::map<int64_t,uint64_t> const chist = us->getHistogramAsMap();
::libmaus::huffman::HuffmanTreeNode::shared_ptr_type htree = ::libmaus::huffman::HuffmanBase::createTree(chist);
::libmaus::huffman::EncodeTable<1> ET(htree.get());
for ( ::std::map<int64_t,uint64_t>::const_iterator ita = chist.begin(); ita != chist.end(); ++ita )
{
::libmaus::util::UTF8::encodeUTF8(ita->first,std::cerr);
std::cerr << "\t" << ita->second << "\t" << ET.printCode(ita->first) << std::endl;
}
}
Species format_species(const Species& sp)
{
unit_species_comparerator comp(sp);
std::vector<unit_species_comparerator::index_type> units;
for (unit_species_comparerator::index_type i(0); i < sp.num_units(); ++i)
{
units.push_back(i);
}
std::sort(units.begin(), units.end(), comp);
std::vector<unit_species_comparerator::index_type>
next(sp.num_units(), sp.num_units());
unsigned int stride(0);
for (unit_species_comparerator::index_type i(0); i < sp.num_units(); ++i)
{
const unit_species_comparerator::index_type idx(units[i]);
comp.reorder_units(next, idx, stride);
}
for (unsigned int i(0); i < sp.num_units(); ++i)
{
units[next[i]] = i;
}
Species newsp;
utils::get_mapper_mf<std::string, std::string>::type cache;
stride = 1;
std::stringstream ss;
for (std::vector<unit_species_comparerator::index_type>::const_iterator
i(units.begin()); i != units.end(); ++i)
{
UnitSpecies usp(sp.at(*i));
for (UnitSpecies::container_type::size_type j(0);
j < static_cast<UnitSpecies::container_type::size_type>(usp.num_sites()); ++j)
{
UnitSpecies::container_type::value_type& site(usp.at(j));
if (site.second.second == "" || is_wildcard(site.second.second))
{
continue;
}
utils::get_mapper_mf<std::string, std::string>::type::const_iterator
it(cache.find(site.second.second));
if (it == cache.end())
{
ss << stride;
cache.insert(std::make_pair(site.second.second, ss.str()));
site.second.second = ss.str();
++stride;
ss.clear();
ss.str("");
}
else
{
site.second.second = (*it).second;
}
}
newsp.add_unit(usp);
}
return newsp;
}
