placement/function/helper.hpp

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#ifndef GENESIS_PLACEMENT_FUNCTION_HELPER_H_
#define GENESIS_PLACEMENT_FUNCTION_HELPER_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/sample.hpp"
#include "genesis/placement/sample_set.hpp"
#include "genesis/utils/containers/matrix.hpp"
 
#include <unordered_map>
#include <vector>
 
namespace genesis {
namespace placement {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
struct PqueryPlain;
 
// =================================================================================================
//     Helper Functions
// =================================================================================================
 
std::unordered_map<int, PlacementTreeEdge*> edge_num_to_edge_map( PlacementTree const& tree );
 
std::unordered_map<int, PlacementTreeEdge*> edge_num_to_edge_map( Sample const& smp );
 
std::vector<std::vector< Pquery const* >> pqueries_per_edge(
    Sample const& sample,
    bool only_max_lwr_placements = false
);
 
std::vector< std::vector< PqueryPlacement const* >> placements_per_edge(
    Sample const& smp,
    bool only_max_lwr_placements = false
);
 
std::vector<PqueryPlacement const*> placements_per_edge(
    Sample            const& smp,
    PlacementTreeEdge const& edge
);
 
std::vector<size_t> placement_count_per_edge( Sample const& sample );
 
utils::Matrix<size_t> placement_count_per_edge( SampleSet const& sample_set );
 
std::vector<PqueryPlain> plain_queries( Sample const & smp );
 
// =================================================================================================
//     Verification
// =================================================================================================
 
void rectify_values( Sample& sample );
 
void rectify_values( SampleSet& sset );
 
void reset_edge_nums( PlacementTree& tree );
 
bool has_consecutive_edge_nums( PlacementTree const& tree );
 
bool has_correct_edge_nums( PlacementTree const& tree );
 
bool validate( Sample const& smp, bool check_values = false, bool break_on_values = false );
 
} // namespace placement
} // namespace genesis
 
#endif // include guard