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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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Provides functions for working with Placements and Pqueries.
Definition in file placement/function/functions.hpp.
#include "genesis/placement/sample.hpp"#include "genesis/placement/sample_set.hpp"#include "genesis/utils/containers/matrix.hpp"#include <string>#include <unordered_map>#include <unordered_set>#include <utility>#include <vector>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 | |
| void | adjust_branch_lengths (Sample &sample, tree::Tree const &source) |
Take the branch lengths of the source Tree and use them as the new branch lengths of the sample. More... | |
| std::unordered_set< std::string > | all_pquery_names (Sample const &sample) |
| Return a set of all unique PqueryNames of the Pqueries of the given sample. More... | |
| std::vector< int > | closest_leaf_depth_histogram (Sample const &smp) |
| Return a histogram representing how many placements have which depth with respect to their closest leaf node. More... | |
| std::vector< int > | closest_leaf_distance_histogram (Sample const &smp, const double min, const double max, const int bins=10) |
| Returns a histogram counting the number of placements that have a certain distance to their closest leaf node, divided into equally large intervals between a min and a max distance. More... | |
| std::vector< int > | closest_leaf_distance_histogram_auto (Sample const &smp, double &min, double &max, const int bins=10) |
| Returns the same type of histogram as closest_leaf_distance_histogram(), but automatically determines the needed boundaries. More... | |
| std::vector< double > | closest_leaf_weight_distribution (Sample const &sample) |
| void | collect_duplicate_pqueries (Sample &smp) |
| Find all Pqueries that share a common name and combine them into a single Pquery containing all their collective PqueryPlacements and PqueryNames. More... | |
| void | copy_pqueries (Sample const &source, Sample &target) |
| Copy all Pqueries from the source Sample (left parameter) to the target Sample (right parameter). More... | |
| void | filter_max_pendant_length (Pquery &pquery, double threshold) |
Remove all PqueryPlacements that have a pendant_length above the given threshold. More... | |
| void | filter_max_pendant_length (Sample &sample, double threshold) |
Remove all PqueryPlacements that have a pendant_length above the given threshold from all Pqueries of the Sample. More... | |
| void | filter_min_accumulated_weight (Pquery &pquery, double threshold=0.99) |
Remove the PqueryPlacements with the lowest like_weight_ratio, while keeping the accumulated weight (sum of all remaining like_weight_ratios) above a given threshold. More... | |
| void | filter_min_accumulated_weight (Sample &smp, double threshold=0.99) |
Remove the PqueryPlacements with the lowest like_weight_ratio, while keeping the accumulated weight (sum of all remaining like_weight_ratios) above a given threshold. More... | |
| void | filter_min_pendant_length (Pquery &pquery, double threshold) |
Remove all PqueryPlacements that have a pendant_length below the given threshold. More... | |
| void | filter_min_pendant_length (Sample &sample, double threshold) |
Remove all PqueryPlacements that have a pendant_length below the given threshold from all Pqueries of the Sample. More... | |
| void | filter_min_weight_threshold (Pquery &pquery, double threshold=0.01) |
Remove all PqueryPlacements that have a like_weight_ratio below the given threshold. More... | |
| void | filter_min_weight_threshold (Sample &smp, double threshold=0.01) |
Remove all PqueryPlacements that have a like_weight_ratio below the given threshold from all Pqueries of the Sample. More... | |
| void | filter_n_max_weight_placements (Pquery &pquery, size_t n=1) |
Remove all PqueryPlacements but the n most likely ones from the Pquery. More... | |
| void | filter_n_max_weight_placements (Sample &smp, size_t n=1) |
Remove all PqueryPlacements but the n most likely ones from all Pqueries in the Sample. More... | |
| void | filter_pqueries_differing_names (Sample &sample_1, Sample &sample_2, bool remove_empty_name_pqueries=true) |
| Remove all PqueryNames from the two Samples that occur in both of them. More... | |
| void | filter_pqueries_intersecting_names (Sample &sample_1, Sample &sample_2, bool remove_empty_name_pqueries=true) |
| Remove all PqueryNames from the two Samples that are unique to each of them. More... | |
| void | filter_pqueries_keeping_names (Sample &smp, std::string const ®ex, bool remove_empty_name_pqueries=true) |
Remove all PqueryNames which do not match the given regex. More... | |
| void | filter_pqueries_keeping_names (Sample &smp, std::unordered_set< std::string > const &keep_list, bool remove_empty_name_pqueries=true) |
Remove all PqueryNames which do not occur in the given keep_list. More... | |
| void | filter_pqueries_removing_names (Sample &smp, std::string const ®ex, bool remove_empty_name_pqueries=true) |
Remove all PqueryNames which match the given regex. More... | |
| void | filter_pqueries_removing_names (Sample &smp, std::unordered_set< std::string > const &remove_list, bool remove_empty_name_pqueries=true) |
Remove all PqueryNames which occur in the given remove_list. More... | |
| Pquery * | find_pquery (Sample &smp, std::string const &name) |
| Return the first Pquery that has a particular name, or nullptr of none has. More... | |
| Pquery const * | find_pquery (Sample const &smp, std::string const &name) |
| Return the first Pquery that has a particular name, or nullptr of none has. More... | |
| bool | has_name (Pquery const &pquery, std::string const &name) |
| Return true iff the given Pquery contains a particular name. More... | |
| bool | has_name (Sample const &smp, std::string const &name) |
| Return true iff the given Sample contains a Pquery with a particular name, i.e., a PqueryName whose name member equals the given name. More... | |
| void | merge_duplicate_names (Pquery &pquery) |
Merge all PqueryNames that have the same name property into one, while adding up their multiplicity. More... | |
| void | merge_duplicate_names (Sample &smp) |
Call merge_duplicate_names() for each Pquery of the Sample. More... | |
| void | merge_duplicate_placements (Pquery &pquery) |
| Merge all PqueryPlacements of a Pquery that are on the same TreeEdge into one averaged PqueryPlacement. More... | |
| void | merge_duplicate_placements (Sample &smp) |
| Call merge_duplicate_placements( Pquery& ) for each Pquery of a Sample. More... | |
| void | merge_duplicates (Sample &smp) |
| Look for Pqueries with the same name and merge them. More... | |
| void | normalize_weight_ratios (Pquery &pquery) |
Recalculate the like_weight_ratio of the PqueryPlacement&s of a Pquery, so that their sum is 1.0, while maintaining their ratio to each other. More... | |
| void | normalize_weight_ratios (Sample &smp) |
Recalculate the like_weight_ratio of the PqueryPlacement&s of each Pquery in the Sample, so that their sum is 1.0, while maintaining their ratio to each other. More... | |
| std::pair< PlacementTreeEdge const *, size_t > | placement_count_max_edge (Sample const &smp) |
| Get the number of placements on the edge with the most placements, and a pointer to this edge. More... | |
| std::pair< PlacementTreeEdge const *, double > | placement_mass_max_edge (Sample const &smp) |
Get the summed mass of the placements on the heaviest edge, measured by their like_weight_ratio, and a pointer to this edge. More... | |
| size_t | remove_empty_name_pqueries (Sample &sample) |
| Remove all Pqueries from the Sample that have no PqueryNames. More... | |
| size_t | remove_empty_placement_pqueries (Sample &sample) |
| Remove all Pqueries from the Sample that have no PqueryPlacements. More... | |
| void | scale_all_branch_lengths (Sample &smp, double factor=1.0) |
| Scale all branch lengths of the Tree and the position of the PqueryPlacements by a given factor. More... | |
| void | sort_placements_by_weight (Pquery &pquery) |
Sort the PqueryPlacements of a Pquery by their like_weight_ratio, in descending order (most likely first). More... | |
| void | sort_placements_by_weight (Sample &smp) |
Sort the PqueryPlacements of all Pqueries by their like_weight_ratio, in descending order (most likely first). More... | |
| size_t | total_name_count (Sample const &smp) |
| Get the total number of PqueryNames in all Pqueries of the given Sample. More... | |
| size_t | total_placement_count (Sample const &smp) |
| Get the total number of PqueryPlacements in all Pqueries of the given Sample. More... | |
1.8.17