taxonomy/taxonomy.hpp

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#ifndef GENESIS_TAXONOMY_TAXONOMY_H_
#define GENESIS_TAXONOMY_TAXONOMY_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2018 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 <string>
#include <list>
 
namespace genesis {
namespace taxonomy {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
class Taxon;
class Taxonomy;
void swap( Taxonomy& lhs, Taxonomy& rhs );
 
// =================================================================================================
//     Taxonomy
// =================================================================================================
 
class Taxonomy
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs and Enums
    // -------------------------------------------------------------------------
 
    typedef std::list<Taxon>::iterator             iterator;
    typedef std::list<Taxon>::const_iterator const_iterator;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    Taxonomy()          = default;
    virtual ~Taxonomy() = default;
 
    Taxonomy( Taxonomy const& );
 
    Taxonomy( Taxonomy&& );
 
    Taxonomy& operator= ( Taxonomy const& );
 
    Taxonomy& operator= ( Taxonomy&& );
 
    friend void swap( Taxonomy& lhs, Taxonomy& rhs );
 
    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------
 
    size_t size() const;
 
    bool has_child ( std::string name ) const;
 
    Taxon const& get_child ( std::string name ) const;
 
    Taxon&       get_child ( std::string name );
 
    Taxon const& operator [] ( std::string name ) const;
 
    Taxon&       operator [] ( std::string name );
 
    Taxon const& at ( size_t index  ) const;
 
    Taxon&       at ( size_t index  );
 
    Taxon const& operator [] ( size_t index ) const;
 
    Taxon&       operator [] ( size_t index );
 
    size_t index_of( std::string const& name ) const;
 
    // -------------------------------------------------------------------------
    //     Modifiers
    // -------------------------------------------------------------------------
 
    Taxon& add_child( Taxon const&       child, bool merge_duplicates = true );
 
    Taxon& add_child( std::string const& name, bool merge_duplicates = true );
 
    void remove_child( std::string const& name );
 
    void remove_at( size_t index );
 
    void clear_children();
 
    template <class Compare>
    void sort( Compare comp )
    {
        children_.sort( comp );
    }
 
    // -------------------------------------------------------------------------
    //     Iterators
    // -------------------------------------------------------------------------
 
    iterator begin();
 
    iterator end();
 
    const_iterator begin() const;
 
    const_iterator end() const;
 
    const_iterator cbegin() const;
 
    const_iterator cend() const;
 
    // -------------------------------------------------------------------------
    //     Internal Implementation Details
    // -------------------------------------------------------------------------
 
protected:
 
    virtual Taxon& add_child_( Taxon const& child, bool merge_duplicates );
 
    void reset_parent_pointers_( Taxon* parent );
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    std::list<Taxon> children_;
};
 
} // namespace taxonomy
} // namespace genesis
 
#endif // include guard