Arlin Stoltzfus > Bio-NEXUS > Bio::NEXUS::DistancesBlock

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NAME ^

Bio::NEXUS::DistancesBlock - Represents DISTANCES block in NEXUS file

SYNOPSIS ^

DESCRIPTION ^

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.

COMMENTS ^

FEEDBACK ^

All feedback (bugs, feature enhancements, etc.) are greatly appreciated.

AUTHORS ^

 Tom Hladish (tjhladish at yahoo)

VERSION ^

$Revision: 1.18 $

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.
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