placement/function/operators.hpp

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#ifndef GENESIS_PLACEMENT_FUNCTION_OPERATORS_H_
#define GENESIS_PLACEMENT_FUNCTION_OPERATORS_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 "genesis/placement/placement_tree.hpp"
 
#include <iosfwd>
#include <string>
 
namespace genesis {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
namespace tree {
 
    class Tree;
    class TreeSet;
 
    class CommonNodeData;
    class CommonEdgeData;
 
    using CommonTree = Tree;
    using MassTree = Tree;
}
 
namespace placement {
    class PlacementEdgeData;
    class PlacementNodeData;
 
    class Sample;
    class SampleSet;
}
 
namespace placement {
 
// =================================================================================================
//     Comparision and Equality
// =================================================================================================
 
bool compatible_trees( PlacementTree const& lhs, PlacementTree const& rhs );
 
bool compatible_trees( Sample        const& lhs, Sample        const& rhs );
 
// =================================================================================================
//     Conversion
// =================================================================================================
 
PlacementTree convert_common_tree_to_placement_tree( tree::CommonTree const& source_tree );
 
double add_sample_to_mass_tree(
    Sample const& smp, double const sign, double const scaler, tree::MassTree& target
);
 
std::pair< tree::MassTree, double > convert_sample_to_mass_tree( Sample const& sample, bool normalize );
 
std::pair< tree::TreeSet, std::vector<double> >
convert_sample_set_to_mass_trees( SampleSet const& sample_set, bool normalize );
 
// =================================================================================================
//     Output
// =================================================================================================
 
std::ostream& operator << ( std::ostream& out, Sample const& smp );
 
std::string print_tree( Sample const& smp );
 
} // namespace placement
} // namespace genesis
 
#endif // include guard