Arlin Stoltzfus > Bio-NEXUS > Bio::NEXUS::CharactersBlock

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NAME ^

Bio::NEXUS::CharactersBlock - Represents a CHARACTERS Block (Data or Characters) of a NEXUS file

SYNOPSIS ^

$block_object = new Bio::NEXUS::CharactersBlock($type, $block, $verbose, $taxlabels_ref);

DESCRIPTION ^

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.

FEEDBACK ^

All feedbacks (bugs, feature enhancements, etc.) are greatly appreciated.

AUTHORS ^

 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)

VERSION ^

$Revision: 1.82 $

METHODS ^

new

 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)

add_states_to_charstates

 Title   : add_states_to_charstates
 Usage   : $self->add_states_to_charstates($states);
 Function: Adds states to the character states
 Returns : None
 Args    : states

create_charstates

 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

find_taxon

 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)

set_otuset

 Title   : set_otuset
 Usage   : $block->set_otuset($otuset);
 Function: Set the otus
 Returns : none
 Args    : TaxUnitSet object

add_otu_clone

 Title   : add_otu_clone
 Usage   : ...
 Function: ...
 Returns : ...
 Args    : ...

set_charstatelabels

 Title   : set_charstatelabels
 Usage   : $block->set_charstatelabels($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

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 stateacter labels
 Returns : stateacter names
 Args    : none

get_nchar

 Title   : get_nchar
 Usage   : $block->get_nchar();
 Function: Returns the number of characters of the block
 Returns : # charaters
 Args    : none

select_columns

 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

rename_otus

 Title   : rename_otus
 Usage   : $block->rename_otus(\%translation);
 Function: Renames all the OTUs to something else
 Returns : none
 Args    : hash containing translation

equals

 Name    : equals
 Usage   : $block->equals($another);
 Function: compare if two Bio::NEXUS::CharactersBlock objects are equal
 Returns : boolean 
 Args    : a Bio::NEXUS::CharactersBlock object
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