/ 
Bio-NEXUS-0.78
River stage one • 1 direct dependent • 1 total dependent
/ Bio::NEXUS::UnalignedBlock

NAME

Bio::NEXUS::UnalignedBlock - Represents an UNALIGNED block of a NEXUS file

SYNOPSIS

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

DESCRIPTION

This is a class representing an unaligned block in NEXUS file

FEEDBACK

All feedback (bugs, feature enhancements, etc.) is greatly appreciated.

AUTHORS

Thomas Hladish (tjhladish at yahoo)

VERSION

$Id: UnalignedBlock.pm,v 1.25 2012/02/10 13:28:28 astoltzfus Exp $

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

add_otu_clone

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

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