NAME

Bio::NEXUS::WeightSet - Represents column weights in alignment ( for each character)

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