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