/ 
Bio-NEXUS-0.72
River stage one • 1 direct dependent • 1 total dependent
/ Bio::NEXUS::TaxUnitSet

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