jplace_writer.hpp

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#ifndef GENESIS_PLACEMENT_FORMATS_JPLACE_WRITER_H_
#define GENESIS_PLACEMENT_FORMATS_JPLACE_WRITER_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2020 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/io/output_target.hpp"
 
#include <iosfwd>
#include <string>
#include <vector>
 
namespace genesis {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
namespace utils {
    class JsonDocument;
}
 
namespace placement {
    class Sample;
    class SampleSet;
}
 
// =================================================================================================
//     Jplace Writer
// =================================================================================================
 
namespace placement {
 
class JplaceWriter
{
public:
 
    // ---------------------------------------------------------------------
    //     Constructor and Rule of Five
    // ---------------------------------------------------------------------
 
    JplaceWriter();
    ~JplaceWriter() = default;
 
    JplaceWriter( JplaceWriter const& ) = default;
    JplaceWriter( JplaceWriter&& )      = default;
 
    JplaceWriter& operator= ( JplaceWriter const& ) = default;
    JplaceWriter& operator= ( JplaceWriter&& )      = default;
 
    // ---------------------------------------------------------------------
    //     Printing
    // ---------------------------------------------------------------------
 
    void write( Sample const& sample, std::shared_ptr<utils::BaseOutputTarget> target ) const;
 
    utils::JsonDocument to_document( Sample const& sample ) const;
 
    // -------------------------------------------------------------------------
    //     Settings
    // -------------------------------------------------------------------------
 
public:
 
    size_t branch_length_precision() const
    {
        return branch_length_precision_;
    }
 
    JplaceWriter& branch_length_precision( size_t value )
    {
        branch_length_precision_ = value;
        return *this;
    }
 
    std::string const& program() const
    {
        return program_;
    }
 
    JplaceWriter& program( std::string const& program )
    {
        program_ = program;
        return *this;
    }
 
    std::string const& invocation() const
    {
        return invocation_;
    }
 
    JplaceWriter& invocation( std::string const& invocation )
    {
        invocation_ = invocation;
        return *this;
    }
 
private:
 
    size_t branch_length_precision_ = 6;
    std::string program_;
    std::string invocation_;
};
 
} // namespace placement
} // namespace genesis
 
#endif // include guard