deserializer.hpp

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#ifndef GENESIS_UTILS_IO_DESERIALIZER_H_
#define GENESIS_UTILS_IO_DESERIALIZER_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2019 Lucas Czech and HITS gGmbH
 
    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 {
 
// =================================================================================================
//     Deserializer
// =================================================================================================
 
class Deserializer
{
public:
 
    // -------------------------------------------------------------------------
    //     Constructor and Destructor
    // -------------------------------------------------------------------------
 
    explicit Deserializer( std::string const& file_name )
        : buffer_( std::make_shared< FileInputSource >( file_name ) )
    {
        if( ! buffer_ ) {
            throw std::runtime_error("Creating Deserializer from file failed.");
        }
    }
 
    explicit Deserializer( std::istream& instream )
        : buffer_( std::make_shared< 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( reinterpret_cast<char*>( &res ), sizeof(T) );
        return res;
    }
 
    template<typename T>
    void get_plain (T& res)
    {
        get_raw( reinterpret_cast<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