Arlin Stoltzfus > Bio-NEXUS > Bio::NEXUS::UnalignedBlock

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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
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