nhd.cpp File Reference

#include "genesis/placement/function/nhd.hpp"
#include "genesis/placement/function/functions.hpp"
#include "genesis/placement/function/helper.hpp"
#include "genesis/placement/function/masses.hpp"
#include "genesis/placement/function/operators.hpp"
#include "genesis/placement/pquery/plain.hpp"
#include "genesis/placement/sample_set.hpp"
#include "genesis/placement/sample.hpp"
#include "genesis/tree/common_tree/distances.hpp"
#include "genesis/tree/function/distances.hpp"
#include "genesis/tree/function/functions.hpp"
#include "genesis/utils/containers/matrix.hpp"
#include "genesis/utils/containers/matrix/operators.hpp"
#include <algorithm>
#include <cassert>
#include <cmath>
#include <stdexcept>

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
static void	fill_node_distance_histogram_set_ (Sample const &sample, utils::Matrix< double > const &node_distances, utils::Matrix< signed char > const &node_sides, NodeDistanceHistogramSet &histogram_set)
	Local helper function to fill the placements of a Sample into Histograms. More...
static NodeDistanceHistogramSet	make_empty_node_distance_histogram_set_ (tree::Tree const &tree, utils::Matrix< double > const &node_distances, utils::Matrix< signed char > const &node_sides, size_t const histogram_bins)
	Local helper function to create a set of Histograms without any weights for a given Tree. More...
NodeDistanceHistogramSet	node_distance_histogram_set (Sample const &sample, utils::Matrix< double > const &node_distances, utils::Matrix< signed char > const &node_sides, size_t const histogram_bins)
	Calculate the NodeDistanceHistogramSet representing a single Sample, given the necessary matrices of this Sample. More...
static NodeDistanceHistogramSet	node_distance_histogram_set (Sample const &sample, size_t const histogram_bins)
static std::vector< NodeDistanceHistogramSet >	node_distance_histogram_set (SampleSet const &sample_set, size_t const histogram_bins)
	Local helper function that calculates all Histograms for all Samples in a SampleSet. More...
static double	node_histogram_distance (NodeDistanceHistogram const &lhs, NodeDistanceHistogram const &rhs)
double	node_histogram_distance (NodeDistanceHistogramSet const &lhs, NodeDistanceHistogramSet const &rhs)
	Given the histogram sets that describe two Samples, calculate their distance. More...
double	node_histogram_distance (Sample const &sample_a, Sample const &sample_b, size_t const histogram_bins=25)
	Calculate the Node Histogram Distance of two Samples. More...
utils::Matrix< double >	node_histogram_distance (SampleSet const &sample_set, size_t const histogram_bins=25)
	Calculate the Node Histogram Distance of every pair of Samples in the SampleSet. More...
utils::Matrix< double >	node_histogram_distance (std::vector< NodeDistanceHistogramSet > const &histogram_sets)
	Given the histogram sets that describe a set of Samples, calculate their pairwise distance matrix. More...