Bio::NEXUS::TaxaBlock 0.67

Bio::NEXUS::TaxaBlock is a Perl module that represents TAXA block of a NEXUS file.

SYNOPSIS

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

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

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

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Requirements:

· Perl