Thomas Hladish > Bio-NEXUS-0.69b > Bio::NEXUS::Matrix

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Source   Latest Release: Bio-NEXUS-0.78

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
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