/ 
Bio-NEXUS-0.66
River stage one • 1 direct dependent • 1 total dependent
/ Bio::NEXUS::CharactersBlock

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: 1.63 $

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 : Has 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

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