Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Contact Us
Online Help
Domain Status
Man Pages

Virtual Servers

Topology Map

Server Agreement
Year 2038

USA Flag



Man Pages
Bio::NEXUS::DistancesBlock(3) User Contributed Perl Documentation Bio::NEXUS::DistancesBlock(3)

Bio::NEXUS::DistancesBlock - 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.

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

 Tom Hladish (tjhladish at yahoo)

$Revision: 1.18 $

 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)

 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}

 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)

 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.
2007-09-21 perl v5.28.1

Search for    or go to Top of page |  Section 3 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.