simple_tree.hpp

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#ifndef GENESIS_TREE_FORMATS_NEWICK_SIMPLE_TREE_H_
#define GENESIS_TREE_FORMATS_NEWICK_SIMPLE_TREE_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2022 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 <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include "genesis/tree/tree.hpp"
#include "genesis/tree/common_tree/tree.hpp"
#include "genesis/tree/function/operators.hpp"
 
#include <string>
#include <vector>
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Typedefs
// =================================================================================================
 
using SimpleNewickTree = Tree;
 
using SimpleNewickTreeEdge = TreeEdge;
 
using SimpleNewickTreeLink = TreeLink;
 
using SimpleNewickTreeNode = TreeNode;
 
// =================================================================================================
//     Simple Newick Tree Node Data
// =================================================================================================
 
class SimpleNewickNodeData : public CommonNodeData
{
public:
 
    // -------------------------------------------------------------------
    //     Constructor and Rule of Five
    // -------------------------------------------------------------------
 
    virtual ~SimpleNewickNodeData() override = default;
 
    // Move ctor and assignment.
    SimpleNewickNodeData( SimpleNewickNodeData&& )             = delete;
    SimpleNewickNodeData& operator= ( SimpleNewickNodeData&& ) = delete;
 
protected:
 
    SimpleNewickNodeData() = default;
 
    // Copy ctor and assignment.
    SimpleNewickNodeData( SimpleNewickNodeData const& )             = default;
    SimpleNewickNodeData& operator= ( SimpleNewickNodeData const& ) = default;
 
public:
 
    static std::unique_ptr< SimpleNewickNodeData > create()
    {
        return std::unique_ptr< SimpleNewickNodeData >( new SimpleNewickNodeData() );
    }
 
    virtual std::unique_ptr< BaseNodeData > recreate() const override
    {
        return std::unique_ptr< SimpleNewickNodeData >( new SimpleNewickNodeData() );
    }
 
    virtual std::unique_ptr< BaseNodeData > clone() const override
    {
        return std::unique_ptr< SimpleNewickNodeData >( new SimpleNewickNodeData( *this ));
    }
 
    // -----------------------------------------------------
    //     Data Members
    // -----------------------------------------------------
 
    std::vector<std::string> comments;
 
};
 
// =================================================================================================
//     SimpleNewick Tree Edge Data
// =================================================================================================
 
class SimpleNewickEdgeData : public CommonEdgeData
{
public:
 
    // -------------------------------------------------------------------
    //     Constructor and Rule of Five
    // -------------------------------------------------------------------
 
    virtual ~SimpleNewickEdgeData() override = default;
 
    // Move ctor and assignment.
    SimpleNewickEdgeData( SimpleNewickEdgeData&& )             = delete;
    SimpleNewickEdgeData& operator= ( SimpleNewickEdgeData&& ) = delete;
 
protected:
 
    SimpleNewickEdgeData() = default;
 
    // Copy ctor and assignment.
    SimpleNewickEdgeData( SimpleNewickEdgeData const& )             = default;
    SimpleNewickEdgeData& operator= ( SimpleNewickEdgeData const& ) = default;
 
public:
 
    static std::unique_ptr< SimpleNewickEdgeData > create()
    {
        return std::unique_ptr< SimpleNewickEdgeData >( new SimpleNewickEdgeData() );
    }
 
    virtual std::unique_ptr< BaseEdgeData > recreate() const override
    {
        return std::unique_ptr< SimpleNewickEdgeData >( new SimpleNewickEdgeData() );
    }
 
    virtual std::unique_ptr< BaseEdgeData > clone() const override
    {
        return std::unique_ptr< SimpleNewickEdgeData >( new SimpleNewickEdgeData( *this ));
    }
 
    // -----------------------------------------------------
    //     Data Members
    // -----------------------------------------------------
 
    std::vector<std::string> values;
 
    std::vector<std::string> tags;
 
};
 
// =================================================================================================
//     Common Converter
// =================================================================================================
 
inline SimpleNewickTree convert_common_tree_to_simple_newick_tree( CommonTree const& source )
{
    return convert(
        source,
        [] ( tree::BaseNodeData const& node_data ) {
            auto attr_node = tree::SimpleNewickNodeData::create();
            auto const& orig_node = dynamic_cast< CommonNodeData const& >( node_data );
            attr_node->name = orig_node.name;
 
            return attr_node;
        },
        [] ( tree::BaseEdgeData const& edge_data ) {
            auto attr_edge = tree::SimpleNewickEdgeData::create();
            auto const& orig_edge = dynamic_cast< CommonEdgeData const& >( edge_data );
            attr_edge->branch_length = orig_edge.branch_length;
 
            return attr_edge;
        }
    );
}
 
} // namespace tree
} // namespace genesis
 
#endif // include guard