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Man Pages


Manual Reference Pages  -  BIO::NEXUS::BLOCK (3)

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NAME

Bio::NEXUS::Block - Provides useful functions for blocks in NEXUS file (parent class).

CONTENTS

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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