Bio::NEXUS::UnalignedBlock - Represents an UNALIGNED block of a NEXUS file
if ( $type =~ /unaligned/i ) { $block_object = new Bio::NEXUS::UnalignedBlock($type, $block, $verbose); }
This is a class representing an unaligned block in NEXUS file
All feedback (bugs, feature enhancements, etc.) is greatly appreciated.
Thomas Hladish (tjhladish at yahoo)
$Id: UnalignedBlock.pm,v 1.25 2012/02/10 13:28:28 astoltzfus Exp $
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)
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)
Title : set_format Usage : $block->set_format(\%format); Function: set the format of the characters Returns : none Args : hash of format values
Title : get_format Usage : $block->get_format(); Function: Returns the format of the characters Returns : hash of format values Args : none
Title : set_otuset Usage : $block->set_otuset($otuset); Function: Set the otus Returns : none Args : TaxUnitSet object
Title : set_charstatelabels Usage : $block->set_charstatelabels($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 : $block->get_ntax(); Function: Returns the number of taxa of the block Returns : # taxa Args : none
Title : rename_otus Usage : $block->rename_otus(\%translation); Function: Renames all the OTUs to something else Returns : none Args : hash containing translation
Title : add_otu_clone Usage : ... Function: ... Returns : ... Args : ...
Name : equals Usage : $block->equals($another); Function: compare if two Bio::NEXUS::UnalignedBlock objects are equal Returns : boolean Args : a Bio::NEXUS::CharactersBlock 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.