nexus/document.hpp

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#ifndef GENESIS_UTILS_FORMATS_NEXUS_DOCUMENT_H_
#define GENESIS_UTILS_FORMATS_NEXUS_DOCUMENT_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/formats/nexus/block.hpp"
#include "genesis/utils/formats/nexus/taxa.hpp"
#include "genesis/utils/formats/nexus/trees.hpp"
 
#include "genesis/utils/core/std.hpp"
 
#include <memory>
#include <string>
#include <vector>
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     Nexus Document
// =================================================================================================
 
class NexusDocument
{
public:
 
    // ---------------------------------------------------------------------
    //     Constructor and Rule of Five
    // ---------------------------------------------------------------------
 
    NexusDocument()  = default;
    ~NexusDocument() = default;
 
    // NexusDocument( NexusDocument const& ) = default;
    NexusDocument( NexusDocument&& )      = default;
 
    NexusDocument& operator= ( NexusDocument const& ) = default;
    NexusDocument& operator= ( NexusDocument&& )      = default;
 
    // ---------------------------------------------------------------------
    //     Member Types
    // ---------------------------------------------------------------------
 
    using container      = std::vector<std::unique_ptr<NexusBlock>>;
    using const_iterator = container::const_iterator;
 
    // ---------------------------------------------------------------------
    //     Accessors
    // ---------------------------------------------------------------------
 
    bool has_block( std::string block_name ) const;
 
    NexusBlock const* get_block( std::string block_name ) const;
    NexusBlock*       get_block( std::string block_name );
 
    // ---------------------------------------------------------------------
    //     Modifiers
    // ---------------------------------------------------------------------
 
    // void push_back_block(NexusBlock const& block)
    // {
    //     data_.push_back( utils::make_unique<NexusBlock>(block) );
    // }
 
    // void set_block_trees( Trees const& trees );
    // void set_block_taxa( Taxa const& taxa );
 
    NexusBlock* set_block( std::unique_ptr<NexusBlock> block );
 
    // ---------------------------------------------------------------------
    //     Iterators
    // ---------------------------------------------------------------------
 
public:
 
    const_iterator begin() const
    {
        return data_.cbegin();
    }
 
    const_iterator end() const
    {
        return data_.cend();
    }
 
    // ---------------------------------------------------------------------
    //     Data Members
    // ---------------------------------------------------------------------
 
private:
 
    container data_;
 
};
 
} // namespace utils
} // namespace genesis
 
#endif // include guard