Arlin Stoltzfus > Bio-NEXUS > Bio::NEXUS::TaxaBlock

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Bio-NEXUS-0.78.tar.gz

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NAME ^

Bio::NEXUS::TaxaBlock - Represents 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.

VERSION ^

 $Id: TaxaBlock.pm,v 1.45 2012/02/07 21:38:09 astoltzfus Exp $

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

add_otu_clone

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

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
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