gzip_stream.hpp

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#ifndef GENESIS_UTILS_IO_GZIP_STREAM_H_
#define GENESIS_UTILS_IO_GZIP_STREAM_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2020 Lucas Czech
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/
 
/*
    The code in this file as well as the according header file lib/utils/io/gzip_stream.hpp are
    adapted from the excellent zstr library (C++ header-only ZLib wrapper" classes) by Matei David,
    see https://github.com/mateidavid/zstr
 
    We adapted the original code by renaming all classes and variables to our standards,
    moving much of the implementation into a source file (so that the header does not clutter
    its callers with zlib-internal symbols), and refining some functionality.
 
    For this and the according source file, we need to include the following original license:
 
    The MIT License (MIT)
 
    Copyright (c) 2015 Matei David, Ontario Institute for Cancer Research
 
    Permission is hereby granted, free of charge, to any person obtaining a copy
    of this software and associated documentation files (the "Software"), to deal
    in the Software without restriction, including without limitation the rights
    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
    copies of the Software, and to permit persons to whom the Software is
    furnished to do so, subject to the following conditions:
 
    The above copyright notice and this permission notice shall be included in all
    copies or substantial portions of the Software.
 
    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
    SOFTWARE.
 */
 
#include "genesis/utils/io/gzip.hpp"
 
#include "genesis/utils/io/strict_fstream.hpp"
 
#include <cassert>
#include <fstream>
#include <sstream>
#include <string>
 
namespace genesis {
namespace utils {
 
// ================================================================================================
//     Gzip Settings
// ================================================================================================
 
enum class GzipCompressionLevel : int
{
    kDefaultCompression = -1,
    kNoCompression      =  0,
    kBestSpeed          =  1,
    kBestCompression    =  9
};
 
static const std::size_t GZIP_DEFAULT_BUFFER_SIZE = (std::size_t) 1 << 20;
 
// ================================================================================================
//     Gzip Input Stream
// ================================================================================================
 
class GzipIStream
    : public std::istream
{
public:
 
    GzipIStream(
        std::istream& is,
        bool auto_detect = true,
        std::size_t buffer_size = GZIP_DEFAULT_BUFFER_SIZE
    );
 
    explicit GzipIStream(
        std::streambuf * sbuf_p,
        bool auto_detect = true,
        std::size_t buffer_size = GZIP_DEFAULT_BUFFER_SIZE
    );
 
    virtual ~GzipIStream();
};
 
// ================================================================================================
//     Gzip Output Stream
// ================================================================================================
 
class GzipOStream
    : public std::ostream
{
public:
 
    GzipOStream(
        std::ostream& os,
        GzipCompressionLevel level = GzipCompressionLevel::kDefaultCompression,
        std::size_t buffer_size = GZIP_DEFAULT_BUFFER_SIZE
    );
 
    explicit GzipOStream(
        std::streambuf* sbuf_p,
        GzipCompressionLevel level = GzipCompressionLevel::kDefaultCompression,
        std::size_t buffer_size = GZIP_DEFAULT_BUFFER_SIZE
    );
 
    virtual ~GzipOStream();
};
 
// ================================================================================================
//     Strict File Stream Holder
// ================================================================================================
 
template < typename FStreamType >
struct StrictFStreamHolder
{
    StrictFStreamHolder( std::string const& filename, std::ios_base::openmode mode = std::ios_base::in )
        : file_stream_(filename, mode)
    {}
 
    FStreamType file_stream_;
};
 
// ================================================================================================
//     Gzip Input File Stream
// ================================================================================================
 
class GzipIFStream
    : private StrictFStreamHolder<StrictIFStream>
    , public std::istream
{
public:
 
    explicit GzipIFStream(
        std::string const& filename,
        std::ios_base::openmode mode = std::ios_base::in,
        bool auto_detect = true,
        std::size_t buffer_size = GZIP_DEFAULT_BUFFER_SIZE
    );
 
    virtual ~GzipIFStream();
};
 
// ================================================================================================
//     Gzip Output File Stream
// ================================================================================================
 
class GzipOFStream
    : private StrictFStreamHolder<StrictOFStream>
    , public std::ostream
{
public:
 
    explicit GzipOFStream(
        std::string const& filename,
        std::ios_base::openmode mode = std::ios_base::out,
        GzipCompressionLevel level = GzipCompressionLevel::kDefaultCompression,
        std::size_t buffer_size = GZIP_DEFAULT_BUFFER_SIZE
    );
 
    virtual ~GzipOFStream();
 
    GzipOFStream& flush();
};
 
} // namespace utils
} // namespace genesis
 
#endif // include guard