jplace_writer.hpp

Go to the documentation of this file.

#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