taxonomy/functions/entropy.hpp

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#ifndef GENESIS_TAXONOMY_FUNCTIONS_ENTROPY_H_
#define GENESIS_TAXONOMY_FUNCTIONS_ENTROPY_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/taxonomy/functions/entropy_data.hpp"
 
#include <string>
 
namespace genesis {
namespace taxonomy {
 
// =================================================================================================
//     Forwad Declarations
// =================================================================================================
 
class Taxon;
class Taxonomy;
 
// =================================================================================================
//     Prune Settings
// =================================================================================================
 
struct PruneByEntropySettings
{
    size_t min_subtaxonomy_size = 0;
 
    size_t max_subtaxonomy_size = 0;
 
    size_t min_border_level = 0;
 
    bool   allow_approximation  = false;
};
 
// =================================================================================================
//     Prune Functions
// =================================================================================================
 
void prune_by_entropy(
    Taxonomy&              taxonomy,
    size_t                 target_taxonomy_size,
    PruneByEntropySettings settings = {}
);
 
void expand_small_subtaxonomies(
    Taxonomy& taxonomy,
    size_t    min_subtaxonomy_size
);
 
size_t count_taxa_with_prune_status(
    Taxonomy const&               taxonomy,
    EntropyTaxonData::PruneStatus status
);
 
void remove_pruned_taxonomy_children( Taxonomy& taxonomy );
 
std::string print_pruned_taxonomy(    Taxonomy const& taxonomy );
 
bool        validate_pruned_taxonomy( Taxonomy const& taxonomy );
 
} // namespace taxonomy
} // namespace genesis
 
#endif // include guard