Bio::NEXUS::DistancesBlock 0.67

Bio::NEXUS::DistancesBlock is a Perl module that represents DISTANCES block in NEXUS file.

The DistancesBlock class represents a NEXUS Distances Block and provides methods for reading, writing, and accessing data within these blocks. Distances Blocks contain distance matrices, or a table of calculated distances between each possible pair of taxa.

METHODS

new

Title : new
Usage : block_object = new Bio::NEXUS::DistancesBlock($block_type, $commands, $verbose, $taxa);
Function: Creates a new Bio::NEXUS::DistancesBlock object
Returns : Bio::NEXUS::DistancesBlock object
Args : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1)

get_matrix

Title : get_matrix
Usage : $matrix = $self->get_matrix();
Function: Retrieves the entire distance matrix
Returns : a hashref of hashrefs
Args : none
Note : Distance values may be retrieved by specifying the row and column keys, e.g. $dist = $matrix->{$row_taxon}{$col_taxon}

get_distances_for

Title : get_distances_for
Usage : %taxon1_distances = %{ $self->get_distances_for($first_taxon) };
Function: Retrieves a row of the distance matrix
Returns :
Args : the row label (a taxlabel) for the row desired (string)

get_distance_between

Title : get_distance_between
Usage : $distance = $self->get_distance_between($row_taxon, $column_taxon);
Function: Retrieves a cell from the matrix
Returns : A scalar (number)
Args : the row and column labels (both taxa) for the cell desired
Note : Generally get_distance_between($A, $B) == get_distance_between($B, $A); however, this need not be true if the distance matrix is not symmetric. Make sure you are asking for the distance you want.