NAME

Bio::NEXUS::TaxaBlock - parses and reads in the taxa block of a NEXUS file

SYNOPSIS

if ( $type =~ /taxa/i ) {
    $block_object = new Bio::NEXUS::TaxaBlock($type, $block, $verbose);
}

DESCRIPTION

If a NEXUS block is a taxa block, this module parses the block and stores the taxonomic data.

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: 1.36 $

METHODS

new

Title   : new
Usage   : block_object = new Bio::NEXUS::TaxaBlock($block_type, $commands, $verbose);
Function: Creates a new Bio::NEXUS::TaxaBlock object 
Returns : Bio::NEXUS::TaxaBlock object
Args    : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1; optional)

is_taxon

Title   : is_taxon
Usage   : $block->is_taxon($query_taxonlabel);
Function: Validates OTU names/taxlabels
Returns : Returns taxlabel if true, undef if false
Args    : Query taxon label

get_ntax

Title   : get_ntax
Usage   : $block->get_ntax();
Function: Returns the dimensions (that is, ntax) of the block
Returns : dimensions (integer)
Args    : none

rename_otus

Title   : rename_otus
Usage   : $block->rename_otus(\%translation);
Function: Renames all the OTUs to something else
Returns : none
Args    : hash containing translation

equals

Name    : equals
Usage   : $taxa->equals($another);
Function: compare if two Bio::NEXUS::TaxaBlock objects are equal
Returns : boolean 
Args    : a Bio::NEXUS::TaxaBlock object