measures.cpp File Reference

Detailed Description

Implementation of PlacementMeasures class.

Definition in file measures.cpp.

#include "genesis/placement/function/measures.hpp"
#include "genesis/placement/function/distances.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/placement_tree.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/operators.hpp"
#include "genesis/tree/function/tree_set.hpp"
#include "genesis/tree/iterator/node_links.hpp"
#include "genesis/tree/iterator/postorder.hpp"
#include "genesis/tree/mass_tree/functions.hpp"
#include "genesis/tree/mass_tree/tree.hpp"
#include "genesis/tree/tree_set.hpp"
#include "genesis/tree/tree.hpp"
#include "genesis/utils/core/logging.hpp"
#include "genesis/utils/core/options.hpp"
#include "genesis/utils/containers/matrix.hpp"
#include "genesis/utils/containers/matrix/operators.hpp"
#include <algorithm>
#include <cassert>
#include <map>
#include <stdexcept>
#include <thread>

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
double	edpl (Pquery const &pquery, utils::Matrix< double > const &node_distances)
	Calculate the EDPL uncertainty values for a Pquery. More...
std::vector< double >	edpl (Sample const &sample)
	Calculate the expected distance between placement locations (EDPL) for all Pqueries in a Sample. More...
double	edpl (Sample const &sample, Pquery const &pquery)
	Calculate the EDPL uncertainty values for a Pquery. More...
std::vector< double >	edpl (Sample const &sample, utils::Matrix< double > const &node_distances)
	Calculate the edpl() for all Pqueries in the Sample. More...
double	pairwise_distance (const Sample &smp_a, const Sample &smp_b, bool with_pendant_length=false)
	Calculate the normalized pairwise distance between all placements of the two Samples. More...
double	variance (const Sample &smp, bool with_pendant_length=false)
	Calculate the variance of the placements on a tree. More...
static double	variance_partial_ (const PqueryPlain &pqry_a, const std::vector< PqueryPlain > &pqrys_b, const utils::Matrix< double > &node_distances, bool with_pendant_length)
	Internal function that calculates the sum of distances contributed by one pquery for the variance. See variance() for more information. More...
static void	variance_thread_ (const int offset, const int incr, const std::vector< PqueryPlain > *pqrys, const utils::Matrix< double > *node_distances, double *partial, bool with_pendant_length)
	Internal function that calculates the sum of distances for the variance that is contributed by a subset of the pqueries. See variance() for more information. More...