Bio::Tree NodeNHX
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Summary
Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags
Package variables
No package variables defined.
Inherit
Bio::Tree::Node
Synopsis
    use Bio::Tree::NodeNHX;
my $nodeA = Bio::Tree::NodeNHX->new();
my $nodeL = Bio::Tree::NodeNHX->new();
my $nodeR = Bio::Tree::NodeNHX->new();
my $node = Bio::Tree::NodeNHX->new(); $node->add_Descendents($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
newDescriptionCode
DESTROY
No description
Code
to_string
No description
Code
nhx_tagDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tree::NodeNHX->new();
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 => bootstrap value (string)
-description => description of node
-id => unique id for node
-nhx => hashref of NHX tags and values
nhx_tagcodeprevnextTop
 Title   : nhx_tag
Usage : my $tag = $nodenhx->nhx_tag(%tags);
Function: Set tag-value pairs for NHX nodes
Returns : none
Args : hashref to update the tags/value pairs
OR
with a scalar value update the bootstrap value by default
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($nhx) = $self->_rearrange([qw(NHX)], @args);
  $self->nhx_tag($nhx);
  return $self;
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my ($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; } $self->{'_desc'} = {}; }
}
to_stringdescriptionprevnextTop
sub to_string {
   my ($self) = @_;
   my @tags = $self->get_all_tags;
   my $tagstr = '';
   if( scalar(@tags) > 0 ) {
       $tagstr = '[' . join(":", "&&NHX", 
			    map { "$_=" .join(',',
					      $self->get_tag_values($_))}
			    @tags ) . ']';
   }
   return sprintf("%s%s%s",
		  defined $self->id ? $self->id : '',
		  defined $self->branch_length ? ':' . 
		  $self->branch_length : ' ',
		  $tagstr);
}
nhx_tagdescriptionprevnextTop
sub nhx_tag {
    my ($self, $tags) = @_;
    if (defined $tags && (ref($tags) =~ /HASH/i)) {
	while( my ($tag,$val) = each %$tags ) {
	    if( ref($val) =~ /ARRAY/i ) {
		for my $v ( @$val ) {
		    $self->add_tag_value($tag,$v);
		}
	    } else {
		$self->add_tag_value($tag,$val);
	    }
	}
	if (exists $tags->{'B'}) {
	    $self->bootstrap($tags->{'B'});
	}
    } elsif (defined $tags and ! ref ($tags)) {
	$self->debug( "here with $tags\n");
        # bootstrap by default
$self->bootstrap($tags); } } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Aaron MackeyTop
Email amackey@virginia.edu
CONTRIBUTORSTop
The NHX (New Hampshire eXtended) format was created by Chris Zmasek,
and is described at:
  http://sourceforge.net/projects/forester-atv/
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _