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Man Pages


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

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NAME

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

CONTENTS

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

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