Bio::NEXUS::UnalignedBlock 0.67

Bio::NEXUS::UnalignedBlock is a Perl module that represents an UNALIGNED block of a NEXUS file.

SYNOPSIS

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

This is a class representing an unaligned block in NEXUS file

METHODS

new

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

find_taxon

Title : find_taxon
Usage : my $is_taxon_present = $self->find_taxon($taxon_name);
Function: Finds whether the input taxon name is present in the taxon label.
Returns : 0 (not present) or 1 (if present).
Args : taxon label (as string)

set_format

Title : set_format
Usage : $block->set_format(%format);
Function: set the format of the characters
Returns : none
Args : hash of format values

get_format

Title : get_format
Usage : $block->get_format();
Function: Returns the format of the characters
Returns : hash of format values
Args : none

set_otuset

Title : set_otuset
Usage : $block->set_otuset($otuset);
Function: Set the otus
Returns : none
Args : TaxUnitSet object

set_charstatelabels

Title : set_charstatelabels
Usage : $block->set_charstatelabels($labels);
Function: Set the character names and states
Returns : none
Args : array of character states

get_charstatelabels

Title : get_charstatelabels
Usage : $set->get_charstatelabels();
Function: Returns an array of character states
Returns : character states
Args : none

get_ntax

Title : get_ntax
Usage : $block->get_ntax();
Function: Returns the number of taxa of the block
Returns : # taxa
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 : $block->equals($another);
Function: compare if two Bio::NEXUS::UnalignedBlock objects are equal
Returns : boolean
Args : a Bio::NEXUS::CharactersBlock object