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A library for working with phylogenetic and population genetic data.
v0.32.0 |
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A library for working with phylogenetic and population genetic data.
v0.32.0 |
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Implementation of the Placement Functions.
Definition in file placement/function/helper.cpp.
#include "genesis/placement/function/helper.hpp"#include "genesis/placement/function/functions.hpp"#include "genesis/placement/function/masses.hpp"#include "genesis/placement/pquery/plain.hpp"#include "genesis/tree/function/operators.hpp"#include "genesis/tree/iterator/postorder.hpp"#include "genesis/utils/core/logging.hpp"#include <algorithm>#include <cassert>#include <limits>Go to the source code of this file.
Namespaces | |
| genesis | |
| Container namespace for all symbols of genesis in order to keep them separate when used as a library. | |
| genesis::placement | |
Functions | |
| std::unordered_map< int, PlacementTreeEdge * > | edge_num_to_edge_map (PlacementTree const &tree) |
Return a mapping of edge_num integers to the corresponding PlacementTreeEdge object. More... | |
| std::unordered_map< int, PlacementTreeEdge * > | edge_num_to_edge_map (Sample const &smp) |
| Return a mapping of edge_num integers to the corresponding PlacementTreeEdge object. More... | |
| bool | has_consecutive_edge_nums (PlacementTree const &tree) |
Verify that the PlacementTree has no duplicate edge_nums and that they form consecutive numbers starting from 0. More... | |
| bool | has_correct_edge_nums (PlacementTree const &tree) |
| Verify that the tree has correctly set edge nums. More... | |
| std::vector< size_t > | placement_count_per_edge (Sample const &sample) |
| Return a vector that contains the number of PqueryPlacements per edge of the tree of the Sample. More... | |
| utils::Matrix< size_t > | placement_count_per_edge (SampleSet const &sample_set) |
| std::vector< std::vector< PqueryPlacement const * > > | placements_per_edge (Sample const &smp, bool only_max_lwr_placements=false) |
| Return a mapping from each PlacementTreeEdges to the PqueryPlacements that are placed on that edge. More... | |
| std::vector< PqueryPlacement const * > | placements_per_edge (Sample const &smp, PlacementTreeEdge const &edge) |
| Return a vector of all PqueryPlacements that are placed on the given PlacementTreeEdge. More... | |
| std::vector< PqueryPlain > | plain_queries (Sample const &smp) |
| Return a plain representation of all pqueries of this map. More... | |
| std::vector< std::vector< Pquery const * > > | pqueries_per_edge (Sample const &sample, bool only_max_lwr_placements=false) |
| Return a mapping from each edge to the Pqueries on that edge. More... | |
| void | rectify_values (Sample &sample) |
| Correct invalid values of the PqueryPlacements and PqueryNames as good as possible. More... | |
| void | rectify_values (SampleSet &sset) |
| Correct invalid values of the PqueryPlacements and PqueryNames as good as possible. More... | |
| void | reset_edge_nums (PlacementTree &tree) |
| Reset all edge nums of a PlacementTree. More... | |
| bool | validate (Sample const &smp, bool check_values=false, bool break_on_values=false) |
| Validate the integrity of the pointers, references and data in a Sample object. More... | |
1.8.17