Bio::NEXUS::TaxUnitSet - Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file
$otuset = new Bio::NEXUS::TaxUnitSet(\@otus);
This module represents a set of OTUs (Bio::NEXUS::TaxUnit objects) in a NEXUS file (in characters block or History block)
All feedback (bugs, feature enhancements, etc.) are greatly appreciated.
Chengzhi Liang (liangc@umbi.umd.edu) Peter Yang (pyang@rice.edu) Thomas Hladish (tjhladish at yahoo)
$Revision: 1.30 $
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
Title : clone Usage : my $newset = $set->clone(); Function: clone an TaxUnitSet object Returns : TaxUnitSet object Args : none
Title : add_otu Usage : $block->add_otu($otu); Function: add a taxon Returns : none Args : a taxon
Title : set_otus Usage : $set->set_otus($otus); Function: sets the list of OTUs Returns : none Args : array of OTUs
Title : get_otus Usage : $set->get_otus(); Function: Returns array of otus Returns : all otus Args : none
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
Title : get_otu_names Usage : $set->get_otu_names(); Function: Returns array of OTU names Returns : all OTU names Args : none
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
Title : get_seq_array_hash Usage : $set->get_seq_array_hash(); Function: gets sequences as arrays Returns : hashref Args : scalar
Title : rename_otus Usage : $set->rename_otus($names); Function: rename all OTUs Returns : none Args : hash of OTU names
Title : subset Usage : $block->subset($otunames); Function: select a subset of OTUs Returns : new TaxUnitSet object Args : OTU names
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
Title : select_chars Usage : $set->select_chars($columns); Function: select a subset of characters Returns : new self with subset of characters Args : column numbers
Title : set_charlabels Usage : $set->set_charlabels($labels); Function: Set the character names Returns : none Args : array of character names
Title : get_charlabels Usage : $set->get_charlabels(); Function: Returns an array of character labels Returns : character names Args : none
Title : set_statelabels Usage : $set->set_statelabels($labels); Function: Set the state names Returns : none Args : array of state names
Title : get_statelabels Usage : $set->get_statelabels(); Function: Returns an array of state labels Returns : state names Args : none
Title : set_charstatelabels Usage : $set->set_charstatelabels($labels); Function: Set the character names and states Returns : none Args : array of character states
Title : get_charstatelabels Usage : $set->get_charstatelabels(); Function: Returns an array of character states Returns : character states Args : none
Title : get_ntax Usage : $set->get_ntax(); Function: Returns the number of taxa of the block Returns : # taxa Args : none
Title : get_nchar Usage : $set->get_nchar(); Function: Returns the number of characters of the block Returns : # charaters Args : none
Title : select_charlabels Usage : $set->select_charlabels($columns); Function: select a subset of charlabels Returns : new self with subset of charlabels Args : column numbers
Title : select_charstatelabels Usage : $set->select_charstatelabels($columns); Function: select a subset of charstates Returns : new self with subset of charstates Args : column numbers
Name : equals Usage : $set->equals($another); Function: compare if two TaxUnitSet objects are equal Returns : boolean Args : an TaxUnitSet object
To install Bio::NEXUS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::NEXUS
CPAN shell
perl -MCPAN -e shell install Bio::NEXUS
For more information on module installation, please visit the detailed CPAN module installation guide.