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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/FORMAT/genericMolFile.h>
#include <BALL/KERNEL/system.h>
#include <BALL/KERNEL/molecule.h>
#include <boost/iostreams/filtering_streambuf.hpp>
#include <boost/iostreams/copy.hpp>
#include <boost/iostreams/filter/gzip.hpp>
namespace BALL
{
GenericMolFile::GenericMolFile()
: LineBasedFile(),
input_is_temporary_(false),
compress_output_(false),
gmf_is_closed_(false)
{
}
GenericMolFile::GenericMolFile(const String& filename, File::OpenMode open_mode)
: LineBasedFile(filename, open_mode),
input_is_temporary_(false),
compress_output_(false),
gmf_is_closed_(false)
{
}
GenericMolFile::~GenericMolFile()
{
GenericMolFile::close();
}
void GenericMolFile::close()
{
LineBasedFile::close();
if (gmf_is_closed_) return;
if (getOpenMode() == std::ios::in)
{
if (input_is_temporary_)
{
File::remove(name_);
}
}
else if(compress_output_)
{
std::fstream::close();
std::ifstream unzipped_file(name_.c_str(), ios_base::in);
boost::iostreams::filtering_streambuf<boost::iostreams::input> in;
in.push(boost::iostreams::gzip_compressor());
in.push(unzipped_file);
std::ofstream zipped_file(zipped_filename_.c_str(), std::ios::out | std::ios_base::binary);
boost::iostreams::copy(in, zipped_file);
File::remove(name_);
}
gmf_is_closed_ = true;
}
void GenericMolFile::defineInputAsTemporary(bool b)
{
input_is_temporary_ = b;
}
void GenericMolFile::enableOutputCompression(String zipped_filename)
{
compress_output_ = true;
zipped_filename_ = zipped_filename;
}
bool GenericMolFile::isCompressedFile()
{
if (getOpenMode() == std::ios::in)
{
return input_is_temporary_;
}
else
{
return compress_output_;
}
}
const GenericMolFile& GenericMolFile::operator = (const GenericMolFile& rhs)
{
LineBasedFile::operator = (rhs);
return *this;
}
bool GenericMolFile::read(System& system)
{
if (!isOpen())
{
return false;
}
initRead_();
bool read_anything = false;
Molecule* molecule = 0;
while ((molecule = read()) != 0)
{
system.append(*molecule);
read_anything = true;
}
return read_anything;
}
Molecule* GenericMolFile::read()
{
return 0;
}
bool GenericMolFile::write(const Molecule& /* molecule */)
{
if (!isOpen() || getOpenMode() != std::ios::out)
{
throw (File::CannotWrite(__FILE__, __LINE__, name_));
}
return true;
}
bool GenericMolFile::write(const System& system)
{
if (!isOpen() || getOpenMode() != std::ios::out)
{
throw (File::CannotWrite(__FILE__, __LINE__, name_));
}
initWrite_();
MoleculeConstIterator molecule = system.beginMolecule();
for (; +molecule; ++molecule)
{
if (!write(*molecule)) return false;
}
return true;
}
GenericMolFile& GenericMolFile::operator >> (System& system)
{
read(system);
return *this;
}
GenericMolFile& GenericMolFile::operator << (const System& system)
{
write(system);
return *this;
}
GenericMolFile& GenericMolFile::operator >> (Molecule& molecule)
{
molecule.clear();
Molecule* new_mol = read();
if (new_mol != 0)
{
molecule = *new_mol; // copy the Molecule
}
delete new_mol;
return *this;
}
GenericMolFile& GenericMolFile::operator << (const Molecule& molecule)
{
write(molecule);
return *this;
}
void GenericMolFile::initRead_()
{
}
void GenericMolFile::initWrite_()
{
}
} // namespace BALL
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