utils/io/serializer.hpp

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#ifndef GENESIS_UTILS_IO_SERIALIZER_H_
#define GENESIS_UTILS_IO_SERIALIZER_H_

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2017 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/core/std.hpp"
#include "genesis/utils/io/input_buffer.hpp"
#include "genesis/utils/io/input_reader.hpp"
#include "genesis/utils/io/input_source.hpp"
#include "genesis/utils/io/output_stream.hpp"

#include <algorithm>
#include <cstring>
#include <fstream>
#include <iostream>
#include <stdexcept>
#include <string>

namespace genesis {
namespace utils {

// =================================================================================================
//     Serializer
// =================================================================================================

class Serializer
{
public:

    // -------------------------------------------------------------------------
    //     Constructor and Destructor
    // -------------------------------------------------------------------------

    Serializer (const std::string& filename) :
        outstream (outfile)
    {
        utils::file_output_stream( filename, outfile, std::ofstream::out | std::ofstream::binary );
    };

    Serializer (std::ostream& outstream) :
        outstream (outstream)
    {};

    ~Serializer()
    {
        outfile.close();
    }

    // -------------------------------------------------------------------------
    //     Stream Status
    // -------------------------------------------------------------------------

    inline operator bool() const
    {
        return !outstream.fail();
    }

    inline bool good() const
    {
        return outstream.good();
    }

    inline bool eof() const
    {
        return outstream.eof();
    }

    inline bool fail() const
    {
        return outstream.fail();
    }

    inline bool bad() const
    {
        return outstream.bad();
    }

    // -------------------------------------------------------------------------
    //     File Status
    // -------------------------------------------------------------------------

    inline bool is_open() const
    {
        return outfile.is_open();
    }

    inline void flush()
    {
        outfile.flush();
    }

    inline void close()
    {
        outfile.close();
    }

    // -------------------------------------------------------------------------
    //     Serialization
    // -------------------------------------------------------------------------

    void put_null (const size_t n)
    {
        char* buffer = new char[n];
        std::fill(buffer, buffer+n, '\0');
        outstream.write (buffer, n);
        delete[] buffer;
    }

    void put_raw( char const* data, size_t n )
    {
        outstream.write (data, n);
    }

    void put_raw_string (const std::string& v)
    {
        outstream.write (v.c_str(), v.length());
    }

    void put_string (const std::string& v)
    {
        size_t len = v.length();
        put_int(len);
        put_raw_string(v);
    }

    template<typename T>
    void put_plain (const T v)
    {
        outstream.write((char*)(&v), sizeof(v));
    }

    template<typename T>
    void put_int (const T v)
    {
        put_plain(v);
    }

    template<typename T>
    void put_float (const T v)
    {
        put_plain(v);
    }

    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------

protected:
    std::ofstream outfile;
    std::ostream& outstream;
};

// =================================================================================================
//     Deserializer
// =================================================================================================

class Deserializer
{
public:

    // -------------------------------------------------------------------------
    //     Constructor and Destructor
    // -------------------------------------------------------------------------

    Deserializer( std::string const& file_name )
        : buffer_( utils::make_unique< FileInputSource >( file_name ) )
    {
        if( ! buffer_ ) {
            throw std::runtime_error("Creating Deserializer from file failed.");
        }
    }

    Deserializer( std::istream& instream )
        : buffer_( utils::make_unique< StreamInputSource >( instream ) )
    {
        if( ! buffer_ ) {
            throw std::runtime_error("Creating Deserializer from stream failed.");
        }
    }

    // -------------------------------------------------------------------------
    //     Stream Status
    // -------------------------------------------------------------------------

    inline operator bool() const
    {
        return buffer_;
    }

    // inline bool good() const
    // {
    //     return instream.good();
    // }
    //
    // inline bool eof() const
    // {
    //     return instream.eof();
    // }
    //
    // inline bool fail() const
    // {
    //     return instream.fail();
    // }
    //
    // inline bool bad() const
    // {
    //     return instream.bad();
    // }
    //
    // inline bool succeeded() const
    // {
    //     return !instream.eof() && instream.peek() == EOF;
    // }

    inline bool finished() const
    {
        return ! buffer_;
    }

    // -------------------------------------------------------------------------
    //     File Status
    // -------------------------------------------------------------------------

    // inline bool is_open() const
    // {
    //     return infile.is_open();
    // }
    //
    // inline void close()
    // {
    //     infile.close();
    // }

    // -------------------------------------------------------------------------
    //     Deserialization
    // -------------------------------------------------------------------------

    void get_raw(char* buffer, size_t n)
    {
        size_t const got = buffer_.read(buffer, n);
        if( got != n ) {
            throw std::runtime_error(
                "Could only read " + std::to_string(got)  + " bytes instead of n=" +
                std::to_string( n ) + " bytes from Deserializer input."
            );
        }
    }

    bool get_null (size_t n)
    {
        char* buffer = new char[n];
        get_raw( buffer, n );

        bool ret = true;
        for (size_t i = 0; i < n; ++i) {
            ret &= (buffer[i] == '\0');
        }

        delete[] buffer;
        return ret;
    }

    std::string get_raw_string(size_t n)
    {
        char* buffer = new char[n];
        get_raw( buffer, n );

        std::string str (buffer, n);
        delete[] buffer;
        return str;
    }

    std::string get_string ()
    {
        size_t len = get_int<size_t>();
        return get_raw_string(len);
    }

    // TODO maybe trailing return types is a solution to make this work without having to specify the template parameters? (also for the othter, similar methods in this class)
    template<typename T>
    T get_plain ()
    {
        T res;
        get_raw( (char*)(&res), sizeof(T) );
        return res;
    }

    template<typename T>
    void get_plain (T& res)
    {
        get_raw( (char*)(&res), sizeof(T) );
    }

    template<typename T>
    T get_int ()
    {
        return get_plain<T>();
    }

    template<typename T>
    void get_int (T& res)
    {
        res = get_plain<T>();
    }

    template<typename T>
    T get_float ()
    {
        return get_plain<T>();
    }

    template<typename T>
    void get_float (T& res)
    {
        res = get_plain<T>();
    }

    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------

private:

    InputBuffer buffer_;

};

} // namespace utils
} // namespace genesis

#endif // include guard