gzip_input_source.hpp

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#ifndef GENESIS_UTILS_IO_GZIP_INPUT_SOURCE_H_
#define GENESIS_UTILS_IO_GZIP_INPUT_SOURCE_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2024 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
*/
 
#include "genesis/utils/io/base_input_source.hpp"
 
#include <memory>
#include <string>
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     Gzip Input Source
// =================================================================================================
 
class GzipInputSource final : public BaseInputSource
{
public:
 
    // -------------------------------------------------------------
    //     Typedefs and Enums
    // -------------------------------------------------------------
 
    enum class Format
    {
        kAutomatic,
 
        kGzip,
 
        kZlib,
 
        kDeflate
    };
 
    // -------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------
 
    explicit GzipInputSource(
        std::shared_ptr<BaseInputSource> input_source,
        Format format = Format::kAutomatic
    );
 
    GzipInputSource( GzipInputSource const& ) = delete;
    GzipInputSource( GzipInputSource&& )      = default;
 
    GzipInputSource& operator= ( GzipInputSource const& ) = delete;
    GzipInputSource& operator= ( GzipInputSource&& )      = default;
 
    ~GzipInputSource() override;
 
    // -------------------------------------------------------------
    //     Overloaded Internal Members
    // -------------------------------------------------------------
 
private:
 
    static const size_t BlockLength = 1 << 20;
 
    void create_zstream_();
 
    void destroy_zstream_();
 
    size_t read_( char* buffer, size_t size ) override;
 
    std::string source_name_() const override
    {
        return format_name_ + "-compressed " + input_source_->source_name();
    }
 
    std::string source_string_() const override;
 
    bool is_trivial_() const override
    {
        return false;
    }
 
    int get_format_( Format format ) const;
 
    std::string translate_format_( Format format ) const;
 
    // -------------------------------------------------------------
    //     Member Variables
    // -------------------------------------------------------------
 
    std::shared_ptr<BaseInputSource> input_source_;
 
    Format format_;
    std::string format_name_;
 
    // We want to avoid including the zlib header in this header,
    // because it totally pollutes everything.
    // So, we use a PIMPL-like data hiding technique for the zlib related members.
    struct ZlibData;
 
    // Store the implementation and the implementation's deleter as well.
    // Deleter is a pointer to a function with signature `void func(ZlibData *)`.
    // This way, we can use the default move constructor and default move assignment
    // for this class without implementing them on our own.
    std::unique_ptr<ZlibData, void (*)(ZlibData *)> zlib_data_;
 
};
 
} // namespace utils
} // namespace genesis
 
#endif // include guard