NAME

Bio::NEXUS::WeightSet

SYNOPSIS

new Bio::NEXUS::WeightSet($name, \@weights, $iswt);

DESCRIPTION

A module representing column weights in alignment (for each character)

FEEDBACK

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

AUTHOR

Chengzhi Liang (liangc@umbi.umd.edu)
Weigang Qiu (weigang@genectr.hunter.cuny.edu)
Thomas Hladish (tjhladish at yahoo)

CONTRIBUTORS

Peter Yang (pyang@rice.edu)

METHODS

new

Title   : new
Usage   : $node = new Bio::NEXUS::WeightSet($name, \@weights);
Function: Creates a new Bio::NEXUS::WeightSet object
Returns : Bio::NEXUS::WeightSet object
Args    : none

set_weights

Title   : set_weights
Usage   : $weight->set_weights(\@weights);
Function: stores it in the list weights
Returns : none
Args    : list of weights

get_weights

Title   : get_weights
Usage   : @wts=@{$weightset->get_weights()};
Function: Returns the weights array
Returns : reference to array containing weights
Args    : none

select_weights

Title   : select_weights
Usage   : $set->select_weights($columns);
Function: select a subset of characters
Returns : new self with subset of weights
Args    : column numbers

is_wt

Title   : is_wt
Usage   : croak unless $weight->is_wt();
Function: Returns if object has weights (1 yes, 0 no)
Returns : weight existence (integer)
Args    : none

set_name

Title   : set_name
Usage   : $weight->set_name($name);
Function: Sets the name of the weightset
Returns : none
Args    : name (string)

get_name

Title   : get_name
Usage   : $name=$weight->get_name();
Function: Returns the name of the weightset
Returns : name (string)
Args    : none

equals

Name    : equals
Usage   : $set->equals($another);
Function: compare if two WeightSet objects are equal
Returns : boolean 
Args    : an WeightSet object