NAME

Bio::NEXUS::TaxUnitSet - Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file

SYNOPSIS

$otuset = new Bio::NEXUS::TaxUnitSet(\@otus);

DESCRIPTION

This module represents a set of OTUs (Bio::NEXUS::TaxUnit objects) 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)
 Peter Yang (pyang@rice.edu)
 Thomas Hladish (tjhladish at yahoo)

VERSION

$Revision: 1.30 $

METHODS

new

 Title   : new
 Usage   : $otuset = new Bio::NEXUS::TaxUnitSet(\@otus);
 Function: Creates a new Bio::NEXUS::TaxUnitSet object 
 Returns : Bio::NEXUS::TaxUnitSet object
 Args    : ref to an array of TaxUnit objects

clone

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

add_otu

 Title   : add_otu
 Usage   : $block->add_otu($otu);
 Function: add a taxon
 Returns : none
 Args    : a taxon

set_otus

 Title   : set_otus
 Usage   : $set->set_otus($otus);
 Function: sets the list of OTUs 
 Returns : none
 Args    : array of OTUs

get_otus

 Title   : get_otus
 Usage   : $set->get_otus();
 Function: Returns array of otus
 Returns : all otus
 Args    : none

get_otu

 Title   : get_otu
 Usage   : $set->get_otu(name);
 Function: Returns an OTU with a specified name 
 Returns : an OTU (Bio::NEXUS::TaxUnit)
 Args    : OTU name as scalar string

get_otu_names

 Title   : get_otu_names
 Usage   : $set->get_otu_names();
 Function: Returns array of OTU names
 Returns : all OTU names
 Args    : none

get_seq_string_hash

 Title   : get_seq_string_hash
 Usage   : $set->get_seq_string_hash($delimiter);
 Function: gets sequence string delimited by $delimiter (default is "")
 Returns : hashref
 Args    : scalar

get_seq_array_hash

 Title   : get_seq_array_hash
 Usage   : $set->get_seq_array_hash();
 Function: gets sequences as arrays
 Returns : hashref
 Args    : scalar

rename_otus

 Title   : rename_otus
 Usage   : $set->rename_otus($names);
 Function: rename all OTUs
 Returns : none
 Args    : hash of OTU names

subset

 Title   : subset
 Usage   : $block->subset($otunames);
 Function: select a subset of OTUs
 Returns : new TaxUnitSet object
 Args    : OTU names

select_columns

 Title   : select_columns
 Usage   : $set->select_columns($columns);
 Function: select a subset of characters
 Returns : new $self with subset of columns of characters
 Args    : column numbers

select_chars

 Title   : select_chars
 Usage   : $set->select_chars($columns);
 Function: select a subset of characters
 Returns : new self with subset of characters
 Args    : column numbers

set_charlabels

 Title   : set_charlabels
 Usage   : $set->set_charlabels($labels);
 Function: Set the character names
 Returns : none
 Args    : array of character names

get_charlabels

 Title   : get_charlabels
 Usage   : $set->get_charlabels();
 Function: Returns an array of character labels
 Returns : character names
 Args    : none

set_statelabels

 Title   : set_statelabels
 Usage   : $set->set_statelabels($labels);
 Function: Set the state names
 Returns : none
 Args    : array of state names

get_statelabels

 Title   : get_statelabels
 Usage   : $set->get_statelabels();
 Function: Returns an array of state labels
 Returns : state names
 Args    : none

set_charstatelabels

 Title   : set_charstatelabels
 Usage   : $set->set_charstatelabels($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   : $set->get_ntax();
 Function: Returns the number of taxa of the block
 Returns : # taxa
 Args    : none

get_nchar

 Title   : get_nchar
 Usage   : $set->get_nchar();
 Function: Returns the number of characters of the block
 Returns : # charaters
 Args    : none

select_charlabels

 Title   : select_charlabels
 Usage   : $set->select_charlabels($columns);
 Function: select a subset of charlabels
 Returns : new self with subset of charlabels
 Args    : column numbers

select_charstatelabels

 Title   : select_charstatelabels
 Usage   : $set->select_charstatelabels($columns);
 Function: select a subset of charstates
 Returns : new self with subset of charstates
 Args    : column numbers

equals

 Name    : equals
 Usage   : $set->equals($another);
 Function: compare if two TaxUnitSet objects are equal
 Returns : boolean 
 Args    : an TaxUnitSet object