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