Summary

Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags

Package variables

Included modules

Inherit

Bio::Tree::Node

Synopsis

    use Bio::Tree::NodeNHX;
    my $nodeA = new Bio::Tree::NodeNHX();
    my $nodeL = new Bio::Tree::NodeNHX();
    my $nodeR = new Bio::Tree::NodeNHX();

    my $node = new Bio::Tree::NodeNHX();
    $node->add_Descendents($nodeL);
    $node->add_Descendents($nodeR);

    print "node is not a leaf \n" if( $node->is_leaf);

Description

Makes a Tree Node with NHX tags, suitable for building a Tree. See
Bio::Tree::Node for a full list of functionality.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Tree::NodeNHX();
 Function: Builds a new Bio::Tree::NodeNHX object
 Returns : Bio::Tree::NodeNHX
 Args    : -left          => pointer to Left descendent (optional)
           -right         => pointer to Right descenent (optional)
	   -branch_length => branch length [integer] (optional)
           -bootstrap     => value   bootstrap value (string)
           -description   => description of node
           -id            => unique id for node
           -nhx           => hashref of NHX tags and values

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($nhx) = $self->_rearrange([qw(NHX)], @args);

  $self->nhx_tag($nhx);

  return $self;

}

sub DESTROY {

    my ($self) = @_;
    # try to insure that everything is cleaned up
    $self->SUPER::DESTROY();
    if( defined $self->{'_desc'} &&
	ref($self->{'_desc'}) =~ /ARRAY/i ) {
	while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) {
	    $node->{'_ancestor'} = undef; # insure no circular references
	    $node->DESTROY();
	    $node = undef;
	}
	$self->{'_desc'} = {};
    }

}

sub to_string {

   my ($self) = @_;
   return sprintf("%s%s%s",
		  defined $self->id ? $self->id : '',
		  defined $self->branch_length ? ':' . $self->branch_length : ' ',
		  '[' . join(":", "&&NHX", map { "$_=" . $self->nhx_tag($_) } keys %{$self->nhx_tag || {}}) . ']'
		 );

}

sub nhx_tag {

    my ($self, $tags) = @_;

    if (defined $self->bootstrap) {
	$self->{'_nhx_tag'}->{'B'} = $self->bootstrap;
    }

    if (defined $tags && (ref $tags eq 'HASH')) {
	$self->{'_nhx_tag'} = $tags;
	if (exists $self->{'_nhx_tag'}->{'B'}) {
	    if (defined $self->bootstrap &&
		($self->bootstrap != $self->{'_nhx_tag'}) ) {
		$self->warn("bootstrap value (" . $self->bootstrap . ") being overwritten by NHX B: value ($self->{'_nhx_tag'}->{'B'})!");
	    }
	    $self->bootstrap($self->{'_nhx_tag'}->{'B'});
	}
    } elsif (defined $tags and ! ref $tags) {
	return $self->{'_nhx_tag'}->{$tags};
    }
        return $self->{'_nhx_tag'};

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  http://bugzilla.bioperl.org/

Email amackey@virginia.edu

The NHX (New Hampshire eXtended) format was created by Chris Zmasek,
and is described at:

  http://www.genetics.wustl.edu/eddy/forester/NHX.html

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _