Arlin Stoltzfus > Bio-NEXUS > Bio::NEXUS::TaxUnit

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Bio-NEXUS-0.78.tar.gz

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NAME ^

Bio::NEXUS::TaxUnit - Represents a taxon unit in a NEXUS file

SYNOPSIS ^

$tu = new Bio::NEXUS::TaxUnit($name, $seq);

DESCRIPTION ^

This module represents a taxon unit in a NEXUS file (in characters block or History block)

COMMENTS ^

FEEDBACK ^

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

AUTHORS ^

 Chengzhi Liang (liangc@umbi.umd.edu)
 Thomas Hladish (tjhladish at yahoo)

VERSION ^

$Revision: 1.23 $

METHODS ^

new

 Title   : new
 Usage   : $otu = new Bio::NEXUS::TaxUnit($name, $seq);
 Function: Creates a new Bio::NEXUS::TaxUnit object 
 Returns : Bio::NEXUS::TaxUnit object
 Args    : name and sequence of TaxUnit object

clone

 Title   : clone
 Usage   : my $newtu = $set->clone();
 Function: clone an TaxUnit object 
 Returns : TaxUnit object
 Args    : none

set_name

 Title   : set_name
 Usage   : $tu->set_name($name);
 Function: sets the name of OTU 
 Returns : none
 Args    : name

get_name

 Title   : get_name
 Usage   : $tu->get_name();
 Function: Returns name
 Returns : name
 Args    : none

set_seq

 Title   : set_seq
 Usage   : $tu->set_seq($seq);
 Function: sets the sequence of OTU 
 Returns : none
 Args    : sequence

get_seq

 Title   : get_seq
 Usage   : $tu->get_seq();
 Function: Returns sequence
 Returns : sequence (an array of characters or tokens)
 Args    : none

get_seq_string

 Title   : get_seq_string
 Usage   : $taxunit->get_seq_string($tokens_flag);
 Function: Returns sequence
 Returns : sequence (a string, wherein tokens or characters are space-delimited 
           if a true value has been passed in for $tokens)
 Args    : boolean tokens argument (optional)
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