squash_clustering.hpp

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#ifndef GENESIS_TREE_MASS_TREE_SQUASH_CLUSTERING_H_
#define GENESIS_TREE_MASS_TREE_SQUASH_CLUSTERING_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2019 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/mass_tree/tree.hpp"
 
#include <cstddef>
#include <functional>
#include <string>
#include <utility>
#include <vector>
 
namespace genesis {
namespace tree {
 
// =================================================================================================
//     Squash Clustering
// =================================================================================================
 
class SquashClustering
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs and Constants
    // -------------------------------------------------------------------------
 
    struct Cluster
    {
        MassTree tree;
 
        size_t count;
 
        bool active;
 
        std::vector<double> distances;
    };
 
    struct Merger
    {
        size_t index_a;
 
        double distance_a;
 
        size_t index_b;
 
        double distance_b;
    };
 
    // -------------------------------------------------------------------------
    //     Constructor and Rule of Five
    // -------------------------------------------------------------------------
 
    SquashClustering() = default;
    ~SquashClustering() = default;
 
    SquashClustering( SquashClustering const& ) = default;
    SquashClustering( SquashClustering&& )      = default;
 
    SquashClustering& operator= ( SquashClustering const& ) = default;
    SquashClustering& operator= ( SquashClustering&& )      = default;
 
    // -------------------------------------------------------------------------
    //     Public Functions
    // -------------------------------------------------------------------------
 
    void run( std::vector<MassTree>&& trees );
 
    std::string tree_string( std::vector<std::string> const& labels ) const;
 
    SquashClustering& p( double value )
    {
        p_ = value;
        return *this;
    }
 
    double p() const
    {
        return p_;
    }
 
    std::vector<Cluster> const& clusters() const
    {
        return clusters_;
    }
 
    std::vector<Merger> const& mergers() const
    {
        return mergers_;
    }
 
    void clear();
 
    // -------------------------------------------------------------------------
    //     Progress Report & Output
    // -------------------------------------------------------------------------
 
    std::function<void( void )>                   report_initialization;
    std::function<void( size_t i, size_t total )> report_step;
 
    std::function<void( MassTree const& cluster_tree, size_t index )> write_cluster_tree;
 
    // -------------------------------------------------------------------------
    //     Private Functions
    // -------------------------------------------------------------------------
 
private:
 
    void init_( std::vector<MassTree>&& trees );
    std::pair<size_t, size_t> min_entry_() const;
    void merge_clusters_( size_t i, size_t j );
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    double p_ = 1.0;
 
    std::vector<Cluster> clusters_;
    std::vector<Merger>  mergers_;
};
 
} // namespace tree
} // namespace genesis
 
#endif // include guard