sample.hpp

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#ifndef GENESIS_PLACEMENT_SAMPLE_H_
#define GENESIS_PLACEMENT_SAMPLE_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2021 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 <memory>
#include <string>
#include <unordered_map>
#include <utility>
#include <vector>
 
#include "genesis/placement/placement_tree.hpp"
#include "genesis/placement/pquery.hpp"
 
#include "genesis/utils/containers/range.hpp"
 
namespace genesis {
namespace placement {
 
// =================================================================================================
//     Sample
// =================================================================================================
 
class Sample
{
 
public:
 
    // -------------------------------------------------------------------
    //     Typedefs
    // -------------------------------------------------------------------
 
    using       iterator_pqueries = std::vector<Pquery>::iterator;
    using const_iterator_pqueries = std::vector<Pquery>::const_iterator;
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    Sample() = default;
 
    explicit Sample( PlacementTree const& tree );
 
    Sample( Sample const& );
 
    Sample( Sample&& ) = default;
 
    Sample& operator= ( Sample const& );
 
    Sample& operator= ( Sample&& ) = default;
 
    ~Sample() = default;
 
    void swap( Sample& other );
 
    friend void swap( Sample& lhs, Sample& rhs );
 
    // -------------------------------------------------------------------------
    //     Modifiers
    // -------------------------------------------------------------------------
 
    void clear();
 
    // -------------------------------------------------------------------------
    //     Tree Accessors and Modifiers
    // -------------------------------------------------------------------------
 
    PlacementTree& tree();
 
    PlacementTree const& tree() const;
 
    // -------------------------------------------------------------------------
    //     Pquery Accessors and Modifiers
    // -------------------------------------------------------------------------
 
    size_t size() const;
 
    bool empty() const;
 
    Pquery& add();
 
    Pquery& add( Pquery const& other );
 
    Pquery& at( size_t index );
 
    Pquery const& at( size_t index ) const;
 
    void remove( size_t index );
 
    void remove( size_t first_index, size_t last_index );
 
    void remove( iterator_pqueries position );
 
    void remove( iterator_pqueries first, iterator_pqueries last );
 
    void clear_pqueries();
 
    // -------------------------------------------------------------------------
    //     Pquery Iterator
    // -------------------------------------------------------------------------
 
    iterator_pqueries       begin();
 
    const_iterator_pqueries begin() const;
 
    iterator_pqueries       end();
 
    const_iterator_pqueries end() const;
 
    utils::Range<iterator_pqueries>       pqueries();
 
    utils::Range<const_iterator_pqueries> pqueries() const;
 
    // -------------------------------------------------------------------------
    //     Members
    // -------------------------------------------------------------------------
 
private:
 
    std::vector<Pquery> pqueries_;
    PlacementTree       tree_;
 
public:
 
    // There is not much to mess up here for a user, so we can simply make this public.
    // Okay, this is ugly. But for now, it's way easier. We never use the metadata anyway...
    std::unordered_map<std::string, std::string> metadata;
 
};
 
} // namespace placement
} // namespace genesis
 
#endif // include guard