A template for a class that approximates covariance matrices as Newick-formatted trees. More...

#include <jade.cov2nwk.hpp>

Collaboration diagram for jade::basic_cov2nwk< TValue >:

Public Types
typedef TValue	value_type
	The value type. More...

Static Public Member Functions
static void	execute (std::istream &in, std::ostream &out)
	Executes the program through the specified streams. More...

Detailed Description

template<typename TValue>
class jade::basic_cov2nwk< TValue >

A template for a class that approximates covariance matrices as Newick-formatted trees.

Definition at line 20 of file jade.cov2nwk.hpp.

Member Typedef Documentation

◆ value_type

template<typename TValue >

typedef TValue jade::basic_cov2nwk< TValue >::value_type

The value type.

Definition at line 24 of file jade.cov2nwk.hpp.

Member Function Documentation

◆ execute()

template<typename TValue >

static void jade::basic_cov2nwk< TValue >::execute	(	std::istream &	in,
		std::ostream &	out
	)

inlinestatic

Executes the program through the specified streams.

Parameters

in	The input stream.
out	The output stream.

Definition at line 29 of file jade.cov2nwk.hpp.

         {
             typedef basic_matrix<value_type> matrix_type;
             const matrix_type c (in);
  
             typedef basic_verification<value_type> verification_type;
             verification_type::validate_c(c);
  
             const auto rk = c.get_height();
             const auto k  = rk + 1;
  
             matrix_type padded_c (k, k);
             for (size_t i = 0; i < rk; i++)
                 for (size_t j = 0; j < rk; j++)
                     padded_c(i + 1, j + 1) = c(i, j);
  
             matrix_type distances (k, k);
             for (size_t i = 0; i < k; i++)
             {
                 const auto c_ii = padded_c(i, i);
                 for (size_t j = 0; j < k; j++)
                 {
                     const auto c_jj = padded_c(j, j);
                     const auto c_ij = padded_c(i, j);
                     distances(i, j) = c_ii + c_jj - c_ij - c_ij;
                 }
             }
  
             typedef basic_neighbor_joining<value_type> algorithm_type;
             const algorithm_type algorithm (distances);
  
             algorithm.write(out);
             out << std::endl;
         }

The documentation for this class was generated from the following file:

jade.cov2nwk.hpp

Public Types