Bio::NEXUS::Block 0.67

Bio::NEXUS::Block is a Perl module that provides useful functions for blocks in NEXUS file (parent class).

SYNOPSIS

This module is the super class of all NEXUS block classes. It is not used specifically from a program; in other words, you dont create a new Bio::NEXUS::Block object. Other modules, like AssumptionsBlock, simply inherit subroutines from this module.

Provides a few useful functions for general blocks (to be used by sub-classes).

METHODS

clone

Title : clone
Usage : my $newblock = $block->clone();
Function: clone a block object (shallow)
Returns : Block object
Args : none

get_type

Title : get_type
Usage : print $block->get_type();
Function: Returns a string containing the block type
Returns : type (string)
Args : none

set_ntax

Title : set_ntax
Usage : print $block->set_ntax();
Function: Sets the value of Dimensions:ntax
Returns : none
Args : number of taxa (scalar)

set_dimensions

Title : set_dimensions
Usage : $block->set_dimensions($dimensions);
Function: set a dimensions command
Returns : none
Args : hash content of dimensions command

get_dimensions

Title : get_dimensions
Usage : $block->get_dimensions($attribute);
Function: get a dimensions command
Returns : hash content of dimensions command, or the value for a particular attribute if specified
Args : none, or a string

set_command

Title : set_command
Usage : $block->set_command($command, $content);
Function: Set a command
Returns : none
Args : comand name, and content (string)

set_title

Title : set_title
Usage : $block->set_title($name);
Function: Set the block name
Returns : none
Args : block name (string)

get_title

Title : get_title
Usage : $block->get_title();
Function: Returns a string containing the block title
Returns : name (string)
Args : none

set_link

Title : set_link
Usage : $block->set_link($link_hashref);
Function: Set the block link commands
Returns : none
Args : block link (hash)

add_link

Title : add_link
Usage : $block->add_link($linkname, $title);
Function: add a link command
Returns : none
Args : $link, $title (of another block)

get_link

Title : get_link
Usage : $block->get_link();
Function: Returns a hash containing the block links
Returns : link (hash)
Args : none

set_taxlabels

Title : set_taxlabels
Usage : $block->set_taxlabels($labels);
Function: Set the taxa names
Returns : none
Args : array of taxa names

add_taxlabel

Title : add_taxlabel
Usage : $block->add_taxlabel($label);
Function: add a taxon name
Returns : none
Args : a taxon name

get_taxlabels

Title : get_taxlabels
Usage : $block->get_taxlabels();
Function: Returns an array of taxa labels
Returns : taxa names
Args : none

set_otus

Title : set_otus
Usage : $block->set_otus($otus);
Function: sets the list of OTUs
Returns : none
Args : array of OTUs

get_otus

Title : get_otus
Usage : $block->get_otus();
Function: Returns array of otus
Returns : all otus
Args : none

set_otuset

Title : set_otuset
Usage : $block->set_otuset($otuset);
Function: Set the otus
Returns : none
Args : TaxUnitSet object

get_otuset

Title : get_otuset
Usage : $block->get_otuset();
Function: get the OTUs
Returns : TaxUnitSet object
Args : none

select_otus

Title : select_otus
Usage : $block->select_otus($names);
Function: select a subset of OTUs
Returns : array of OTUs
Args : OTU names

rename_otus

Title : rename_otus
Usage : $block->rename_otus($names);
Function: rename all OTUs
Returns : none
Args : hash of OTU names

set_comments

Title : set_comments
Usage : $block->set_comments($comments);
Function: Set the block comments
Returns : none
Args : block comments (array of strings)

get_comments

Title : get_comments
Usage : $block->get_comments();
Function: Returns block comments
Returns : comments (array of strings)
Args : none

add_comment

Title : add_comment
Usage : $block->add_comment($comment);
Function: add a comment
Returns : none
Args : comment (string)

equals

Name : equals
Usage : $block->equals($another);
Function: compare if two Block objects are equal
Returns : boolean
Args : a Block object