/**
 ** Copyright (c) 2007-2009 Illumina, Inc.
 **
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 ** \file FilteringStreams.cpp
 **
 ** \brief Implementation of the I/O API for sequence data type (qseq files).
 **
 ** \author Come Raczy
 **/

#include "common/FilteringStreams.hh"

#include <boost/iostreams/device/file.hpp>
#ifdef HAVE_ZLIB
#  include <boost/iostreams/filter/gzip.hpp>
#endif

namespace casava
{
namespace common
{

Ifstream::Ifstream(const std::string &filePath, const Filter &decompress)
{
    decompress(*this);
    push(boost::iostreams::file_source(filePath));
}

bool Ifstream::is_open()
{
    using boost::iostreams::file_source;
    return (size() > 0) && component<file_source> (size() - 1) && component<
            file_source> (size() - 1)->is_open();
}

/**
 * \brief Starting with boost 1.44, there is an optimization which skips writing anything into the
 * chain if the size of it is 0 bytes. Since the gzip_compressor needs the write to be executed at
 * least once, the proper header and crcs are not written and the empty files don't form a valid gzip
 *
 */
void Ofstream::preventCorruptGzipFiles()
{
#ifdef HAVE_ZLIB
    boost::iostreams::gzip_compressor *pgzComp(component<boost::iostreams::gzip_compressor>(0));
    if (pgzComp)
    {
        boost::iostreams::file_sink *pfs(component<boost::iostreams::file_sink>(1));
        // second component is expected to be a file_sink. If it is not, someone has put more
        // stuff in the chain. Please have a check if this approach is still valid.
        BOOST_ASSERT(pfs);
        pgzComp->write(*pfs, "", 0);
    }
#endif
}

Ofstream::Ofstream(const std::string &filePath, const Filter &compress,
        ios_base::openmode mode)
{
    compress(*this);
    push(boost::iostreams::file_sink(filePath, mode));
    preventCorruptGzipFiles();
}

Ofstream::Ofstream(const Filter &compress)
{
    compress(*this);
}

void Ofstream::open(const std::string &filePath, ios_base::openmode mode)
{
    push(boost::iostreams::file_sink(filePath, mode));
    preventCorruptGzipFiles();
}

void Ofstream::close()
{
    pop();
}

bool Ofstream::is_open()
{
    using boost::iostreams::file_sink;
    return (size() > 0) && component<file_sink> (size() - 1) && component<
            file_sink> (size() - 1)->is_open();
}

} // namespace common
} // namespace casava