NAME

Bio::NEXUS::Matrix - Provides functions for handling blocks that have matrices

SYNOPSIS

This module is the super class of Characters, Unaligned, and Distances block classes, and indirectly it is a super-class of Data and History blocks, which are both sub-classes of Characters blocks. These sub-classes inherint the methods within this module. There is no constructor, as a Matrix should not exist that is not also one of the sub-class block types.

DESCRIPTION

Provides functions used for handling blocks that have matrices.

COMMENTS

FEEDBACK

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

AUTHORS

Thomas Hladish (tjhladish at yahoo)

VERSION

$Revision: 1.23 $

METHODS

get_ntax

Title   : get_ntax
Usage   : $block->get_ntax();
Function: Returns the number of taxa in the block
Returns : # taxa
Args    : none

set_nchar

Title   : set_nchar
Usage   : print $block->set_nchar();
Function: Sets the value of Dimensions:nchar
Returns : none
Args    : number of char(scalar)

get_nchar

Title   : get_nchar
Usage   : $block->get_nchar();
Function: Returns the number of characters in the block (Note: In Distances Blocks, this is the number of characters used to infer distances.)
Returns : # taxa
Args    : none

set_format

Title   : set_format
Usage   : $block->set_format(\%format);
Function: set the format of the characters
Returns : none
Args    : hash of format values

get_format

Title   : get_format
Usage   : $block->get_format($attribute);
Function: Returns the format of the characters
Returns : hash of format values, or if $attribute (a string) is supplied, the value of that attribute in the hash
Args    : none

add_taxlabels

Title   : add_taxlabels
Usage   : $block->add_taxlabels($new_taxlabels);
Function: Adds new taxa to taxlabels if they aren't already there
Returns : none
Args    : taxa to be added