function/sample_set.hpp

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#ifndef GENESIS_PLACEMENT_FUNCTION_SAMPLE_SET_H_
#define GENESIS_PLACEMENT_FUNCTION_SAMPLE_SET_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2017 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 "genesis/placement/sample.hpp"
#include "genesis/placement/sample_set.hpp"
#include "genesis/tree/tree_set.hpp"
 
#include <iosfwd>
#include <string>
 
namespace genesis {
namespace placement {
 
// =================================================================================================
//     Sample Set Functions
// =================================================================================================
 
Sample      * find_sample( SampleSet      & sample_set, std::string const& name );
 
Sample const* find_sample( SampleSet const& sample_set, std::string const& name );
 
Sample merge_all( SampleSet const& sample_set );
 
size_t total_pquery_count( SampleSet const& sample_set );
 
// =================================================================================================
//     Tree Functions
// =================================================================================================
 
tree::Tree average_branch_length_tree( SampleSet const& sample_set );
 
bool all_identical_trees( SampleSet const& sample_set );
 
tree::TreeSet tree_set( SampleSet const& sample_set );
 
void adjust_branch_lengths( SampleSet& sample_set, tree::Tree const& source );
 
void adjust_to_average_branch_lengths( SampleSet& sample_set );
 
// =================================================================================================
//     Output
// =================================================================================================
 
std::ostream& operator << ( std::ostream& out, SampleSet const& sample_set );
 
} // namespace placement
} // namespace genesis
 
#endif // include guard