tree/common_tree/tree.hpp

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#ifndef GENESIS_TREE_COMMON_TREE_TREE_H_
#define GENESIS_TREE_COMMON_TREE_TREE_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/tree/tree.hpp"
 
#include <string>
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Typedefs
// =================================================================================================
 
using CommonTree     = Tree;
 
using CommonTreeEdge = TreeEdge;
 
using CommonTreeLink = TreeLink;
 
using CommonTreeNode = TreeNode;
 
// =================================================================================================
//     Common Tree Node Data
// =================================================================================================
 
class CommonNodeData : public BaseNodeData
{
    // -------------------------------------------------------------------
    //     Constructor and Rule of Five
    // -------------------------------------------------------------------
 
public:
 
    virtual ~CommonNodeData() override = default;
 
    // Move ctor and assignment.
    CommonNodeData( CommonNodeData&& )             = delete;
    CommonNodeData& operator= ( CommonNodeData&& ) = delete;
 
protected:
 
    CommonNodeData() = default;
 
    // Copy ctor and assignment.
    CommonNodeData( CommonNodeData const& )             = default;
    CommonNodeData& operator= ( CommonNodeData const& ) = default;
 
public:
 
    static std::unique_ptr< CommonNodeData > create()
    {
        return std::unique_ptr< CommonNodeData >( new CommonNodeData() );
    }
 
    virtual std::unique_ptr< BaseNodeData > recreate() const override
    {
        return std::unique_ptr< CommonNodeData >( new CommonNodeData() );
    }
 
    virtual std::unique_ptr< BaseNodeData > clone() const override
    {
        return std::unique_ptr< CommonNodeData >( new CommonNodeData( *this ));
    }
 
    // -----------------------------------------------------
    //     Data Members
    // -----------------------------------------------------
 
    std::string name;
 
};
 
// =================================================================================================
//     Common Tree Edge Data
// =================================================================================================
 
class CommonEdgeData : public BaseEdgeData
{
    // -------------------------------------------------------------------
    //     Constructor and Rule of Five
    // -------------------------------------------------------------------
 
public:
 
    virtual ~CommonEdgeData() override = default;
 
    // Move ctor and assignment.
    CommonEdgeData( CommonEdgeData&& )             = delete;
    CommonEdgeData& operator= ( CommonEdgeData&& ) = delete;
 
protected:
 
    CommonEdgeData() = default;
 
    // Copy ctor and assignment.
    CommonEdgeData( CommonEdgeData const& )             = default;
    CommonEdgeData& operator= ( CommonEdgeData const& ) = default;
 
public:
 
    static std::unique_ptr< CommonEdgeData > create()
    {
        return std::unique_ptr< CommonEdgeData >( new CommonEdgeData() );
    }
 
    virtual std::unique_ptr< BaseEdgeData > recreate() const override
    {
        return std::unique_ptr< CommonEdgeData >( new CommonEdgeData() );
    }
 
    virtual std::unique_ptr< BaseEdgeData > clone() const override
    {
        return std::unique_ptr< CommonEdgeData >( new CommonEdgeData( *this ));
    }
 
    // -----------------------------------------------------
    //     Data Members
    // -----------------------------------------------------
 
    double branch_length = 0.0;
 
};
 
} // namespace tree
} // namespace genesis
 
#endif // include guard