Bio::NEXUS::CharactersBlock - Represents a CHARACTERS Block (Data or Characters) of a NEXUS file
$block_object = new Bio::NEXUS::CharactersBlock($type, $block, $verbose, $taxlabels_ref);
This is a class representing a Characters Block in a NEXUS file. Characters Blocks generally contain state data for a set of characters for each taxon in the Taxa Block. One common use of a Characters Block is to house multiple sequence alignments.
All feedbacks (bugs, feature enhancements, etc.) are greatly appreciated.
Chengzhi Liang (liangc@umbi.umd.edu) Weigang Qiu (weigang@genectr.hunter.cuny.edu) Eugene Melamud (melamud@carb.nist.gov) Peter Yang (pyang@rice.edu) Thomas Hladish (tjhladish at yahoo)
$Revision: 1.82 $
Title : new Usage : block_object = new Bio::NEXUS::CharactersBlock($block_type, $commands, $verbose, $taxa); Function: Creates a new Bio::NEXUS::CharactersBlock object Returns : Bio::NEXUS::CharactersBlock object Args : type (string), the commands/comments to parse (array ref), and a verbose flag (0 or 1)
Title : add_states_to_charstates Usage : $self->add_states_to_charstates($states); Function: Adds states to the character states Returns : None Args : states
Title : create_charstates Usage : my $char_state_hash = $self->create_charstates($id,$label,$states); Function: Converts the input id, label, states to an hash ref for processing. Returns : Hash reference with (id, charlabel,states as keys) Args : id, label, states
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_otuset Usage : $block->set_otuset($otuset); Function: Set the otus Returns : none Args : TaxUnitSet object
Title : add_otu_clone Usage : ... Function: ... Returns : ... Args : ...
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 : 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 stateacter labels Returns : stateacter names Args : none
Title : get_nchar Usage : $block->get_nchar(); Function: Returns the number of characters of the block Returns : # charaters Args : none
Title : select_columns Usage : $block->select_columns($columns); Function: select a subset of characters Returns : new $self with subset of columns of characters Args : column numbers
Title : rename_otus Usage : $block->rename_otus(\%translation); Function: Renames all the OTUs to something else Returns : none Args : hash containing translation
Name : equals Usage : $block->equals($another); Function: compare if two Bio::NEXUS::CharactersBlock 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.