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

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NAME

Bio::NEXUS::TaxaBlock - Represents TAXA block of a NEXUS file

CONTENTS

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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perl v5.20.3 BIO::NEXUS::TAXABLOCK (3) 2012-02-10

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