/ 
Bio-NEXUS-0.76
River stage one • 1 direct dependent • 1 total dependent
/ Bio::NEXUS::Block

NAME

Bio::NEXUS::Block - 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 don't create a new Bio::NEXUS::Block object. Other modules, like AssumptionsBlock, simply inherit subroutines from this module.

DESCRIPTION

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

COMMENTS

FEEDBACK

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

AUTHORS

Chengzhi Liang (liangc@umbi.umd.edu)
Weigang Qiu (weigang@genectr.hunter.cuny.edu)
Eugene Melamud (melamud@carb.nist.gov)
Peter Yang (pyang@rice.edu)
Thomas Hladish (tjhladish at yahoo)

VERSION

$Revision: 1.49 $

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

add_otu_clone

Title   : add_otu_clone
Usage   : ...
Function: ...
Returns : ...
Args    : ...

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'