Arlin Stoltzfus > Bio-NEXUS > Bio::NEXUS::Block

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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

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

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'
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