jade::basic_nwk2cov< TValue > Class Template Reference

A template for a class that converts Newick-formatted trees to covariance matrices. More...

#include <jade.nwk2cov.hpp>

Collaboration diagram for jade::basic_nwk2cov< TValue >:

Public Types
typedef TValue	value_type
	The value type. More...
typedef basic_newick_node< value_type >	newick_node_type
	The Newick node type. More...
typedef basic_matrix< value_type >	matrix_type
	The matrix type. More...
typedef basic_rerooted_tree< value_type >	rerooted_tree_type
	The rerooted tree 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_nwk2cov< TValue >

A template for a class that converts Newick-formatted trees to covariance matrices.

Definition at line 20 of file jade.nwk2cov.hpp.

Member Typedef Documentation

matrix_type

template<typename TValue >

typedef basic_matrix<value_type> jade::basic_nwk2cov< TValue >::matrix_type

The matrix type.

Definition at line 30 of file jade.nwk2cov.hpp.

newick_node_type

template<typename TValue >

typedef basic_newick_node<value_type> jade::basic_nwk2cov< TValue >::newick_node_type

The Newick node type.

Definition at line 27 of file jade.nwk2cov.hpp.

rerooted_tree_type

template<typename TValue >

typedef basic_rerooted_tree<value_type> jade::basic_nwk2cov< TValue >::rerooted_tree_type

The rerooted tree type.

Definition at line 33 of file jade.nwk2cov.hpp.

value_type

template<typename TValue >

typedef TValue jade::basic_nwk2cov< TValue >::value_type

The value type.

Definition at line 24 of file jade.nwk2cov.hpp.

Member Function Documentation

execute()

template<typename TValue >

static void jade::basic_nwk2cov< 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 38 of file jade.nwk2cov.hpp.

        {
            const newick_node_type   node (in);
            const rerooted_tree_type tree (node);
 
            const auto rk = tree.get_rk();
            matrix_type c (rk, rk);
 
            for (size_t i = 0; i < rk; i++)
                for (size_t j = 0; j <= i; j++)
                    c(i, j) = tree.get_overlap(i, j).get_length();
 
            c.copy_lower_to_upper();
 
            matrix_type::set_high_precision(out);
            out << c;
        }

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

• jade.nwk2cov.hpp