placement/pquery/placement.hpp

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#ifndef GENESIS_PLACEMENT_PQUERY_PLACEMENT_H_
#define GENESIS_PLACEMENT_PQUERY_PLACEMENT_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/placement/placement_tree.hpp"
 
namespace genesis {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
namespace tree {
 
    class TreeEdge;
 
}
 
namespace placement {
 
    using PlacementTreeEdge = tree::TreeEdge;
 
    class PlacementEdgeData;
    class PlacementNodeData;
    class Pquery;
 
}
 
// =================================================================================================
//     Pquery Placement
// =================================================================================================
 
namespace placement {
 
class PqueryPlacement
{
public:
 
    // -------------------------------------------------------------------
    //     Constructor and Rule of Five
    // -------------------------------------------------------------------
 
    PqueryPlacement ()
        : likelihood(0.0)
        , like_weight_ratio(0.0)
        , proximal_length(0.0)
        , pendant_length(0.0)
        , edge_(nullptr)
    {}
 
    explicit PqueryPlacement( PlacementTreeEdge& edge )
        : likelihood(0.0)
        , like_weight_ratio(0.0)
        , proximal_length(0.0)
        , pendant_length(0.0)
        , edge_(&edge)
    {}
 
    ~PqueryPlacement() = default;
 
    PqueryPlacement( PqueryPlacement const& ) = default;
    PqueryPlacement( PqueryPlacement&& )      = default;
 
    PqueryPlacement& operator= ( PqueryPlacement const& ) = default;
    PqueryPlacement& operator= ( PqueryPlacement&& )      = default;
 
    // -------------------------------------------------------------------
    //     Public Property Data Members
    // -------------------------------------------------------------------
 
    // Yes, the following members are public data members. It's neither nice nor consistent,
    // but makes life so much easier for the moment. Maybe we'll fix that in the future...
 
    double likelihood;
 
    double like_weight_ratio;
 
    double proximal_length;
 
    double pendant_length;
 
    // Additional properties that are defined by the `jplace` standard. They are currently not used
    // by any genesis function, so we completely ignore them in order to save memory.
    // double parsimony;
    // double post_prob;
    // double marginal_like; // or marginal_prob in jplace version 1
    // std::string classification;
    // double map_ratio;
    // double map_overlap;
 
    // -------------------------------------------------------------------
    //     Properties
    // -------------------------------------------------------------------
 
    PlacementEdgeData::EdgeNumType edge_num() const
    {
        return edge_->data<PlacementEdgeData>().edge_num();
    }
 
    PlacementTreeEdge const& edge() const
    {
        return *edge_;
    }
 
    PlacementTreeEdge& edge()
    {
        return *edge_;
    }
 
    void reset_edge( PlacementTreeEdge& edge )
    {
        edge_ = &edge;
    }
 
    // -------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------
 
private:
 
    PlacementTreeEdge* edge_;
};
 
} // namespace placement
} // namespace genesis
 
#endif // include guard