tree/tree.hpp

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#ifndef GENESIS_TREE_TREE_H_
#define GENESIS_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/node.hpp"
#include "genesis/tree/tree/edge.hpp"
#include "genesis/tree/tree/link.hpp"
#include "genesis/tree/tree/node_data.hpp"
#include "genesis/tree/tree/edge_data.hpp"
 
#include "genesis/utils/containers/range.hpp"
#include "genesis/utils/containers/deref_iterator.hpp"
 
#include <cassert>
#include <memory>
#include <vector>
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
class Tree;
bool validate_topology( Tree const& tree );
 
// =================================================================================================
//     Tree
// =================================================================================================
 
class Tree
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs
    // -------------------------------------------------------------------------
 
    template< class T >
    using ContainerType      = std::vector< std::unique_ptr< T >>;
 
    using LinkContainerType  = ContainerType< TreeLink >;
 
    using NodeContainerType  = ContainerType< TreeNode >;
 
    using EdgeContainerType  = ContainerType< TreeEdge >;
 
    using      IteratorLinks = utils::DereferenceIterator< ContainerType<TreeLink>::iterator >;
    using ConstIteratorLinks = utils::DereferenceIterator< ContainerType<TreeLink>::const_iterator >;
 
    using      IteratorNodes = utils::DereferenceIterator< ContainerType<TreeNode>::iterator >;
    using ConstIteratorNodes = utils::DereferenceIterator< ContainerType<TreeNode>::const_iterator >;
 
    using      IteratorEdges = utils::DereferenceIterator< ContainerType<TreeEdge>::iterator >;
    using ConstIteratorEdges = utils::DereferenceIterator< ContainerType<TreeEdge>::const_iterator >;
 
    // -------------------------------------------------------------------------
    //     Construction and Rule of Five
    // -------------------------------------------------------------------------
 
    Tree()  = default;
    ~Tree() = default;
 
    Tree( Tree const& other );
    Tree( Tree&& ) = default;
 
    Tree& operator= ( Tree const& other );
    Tree& operator= ( Tree&& ) = default;
 
    Tree clone_topology() const;
 
    void swap( Tree& other );
 
    void clear();
 
    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------
 
    bool empty() const
    {
        return links_.empty() && nodes_.empty() && edges_.empty();
    }
 
    TreeLink& link_at(size_t index)
    {
        assert( index < links_.size() );
        return *links_[ index ].get();
    }
 
    TreeLink const& link_at(size_t index) const
    {
        assert( index < links_.size() );
        return *links_[ index ].get();
    }
 
    TreeNode& node_at(size_t index)
    {
        assert( index < nodes_.size() );
        return *nodes_[ index ].get();
    }
 
    TreeNode const& node_at(size_t index) const
    {
        assert( index < nodes_.size() );
        return *nodes_[ index ].get();
    }
 
    TreeEdge& edge_at(size_t index)
    {
        assert( index < edges_.size() );
        return *edges_[ index ].get();
    }
 
    TreeEdge const& edge_at(size_t index) const
    {
        assert( index < edges_.size() );
        return *edges_[ index ].get();
    }
 
    size_t link_count() const
    {
        return links_.size();
    }
 
    size_t node_count() const
    {
        return nodes_.size();
    }
 
    size_t edge_count() const
    {
        return edges_.size();
    }
 
    // -------------------------------------------------------------------------
    //     Root
    // -------------------------------------------------------------------------
 
    TreeLink& root_link()
    {
        return *root_link_;
    }
 
    TreeLink const& root_link() const
    {
        return *root_link_;
    }
 
    TreeNode& root_node()
    {
        return root_link_->node();
    }
 
    TreeNode const& root_node() const
    {
        return root_link_->node();
    }
 
    // -------------------------------------------------------------------------
    //     Data Accessors
    // -------------------------------------------------------------------------
 
    Tree& reset_root_link( TreeLink* root_link );
 
    LinkContainerType& expose_link_container();
 
    NodeContainerType& expose_node_container();
 
    EdgeContainerType& expose_edge_container();
 
    // -------------------------------------------------------------------------
    //     Iterators
    // -------------------------------------------------------------------------
 
    // -----------------------------------------------------
    //     Links
    // -----------------------------------------------------
 
    IteratorLinks begin_links()
    {
        return links_.begin();
    }
 
    ConstIteratorLinks begin_links() const
    {
        return links_.cbegin();
    }
 
    IteratorLinks end_links()
    {
        return links_.end();
    }
 
    ConstIteratorLinks end_links() const
    {
        return links_.cend();
    }
 
    utils::Range<IteratorLinks> links()
    {
        return { links_ };
    }
 
    utils::Range<ConstIteratorLinks> links() const
    {
        return { links_ };
    }
 
    // -----------------------------------------------------
    //     Nodes
    // -----------------------------------------------------
 
    IteratorNodes begin_nodes()
    {
        return nodes_.begin();
    }
 
    ConstIteratorNodes begin_nodes() const
    {
        return nodes_.cbegin();
    }
 
    IteratorNodes end_nodes()
    {
        return nodes_.end();
    }
 
    ConstIteratorNodes end_nodes() const
    {
        return nodes_.cend();
    }
 
    utils::Range<IteratorNodes> nodes()
    {
        return { nodes_ };
    }
 
    utils::Range<ConstIteratorNodes> nodes() const
    {
        return { nodes_ };
    }
 
    // -----------------------------------------------------
    //     Edges
    // -----------------------------------------------------
 
    IteratorEdges begin_edges()
    {
        return edges_.begin();
    }
 
    ConstIteratorEdges begin_edges() const
    {
        return edges_.cbegin();
    }
 
    IteratorEdges end_edges()
    {
        return edges_.end();
    }
 
    ConstIteratorEdges end_edges() const
    {
        return edges_.cend();
    }
 
    utils::Range<IteratorEdges> edges()
    {
        return { edges_ };
    }
 
    utils::Range<ConstIteratorEdges> edges() const
    {
        return { edges_ };
    }
 
    // -------------------------------------------------------------------------
    //     Debug and Dump
    // -------------------------------------------------------------------------
 
    friend bool validate_topology( Tree const& tree );
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    TreeLink* root_link_ = nullptr;
 
    LinkContainerType links_;
    NodeContainerType nodes_;
    EdgeContainerType edges_;
 
};
 
} // namespace tree
} // namespace genesis
 
#endif // include guard