Bio::TreeIO svggraph
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output
Package variables
No package variables defined.
Included modules
Bio::Tree::Node
Bio::Tree::TreeI
Bio::TreeIO
SVG::Graph
SVG::Graph::Data
SVG::Graph::Data::Node
SVG::Graph::Data::Tree
Tree::DAG_Node
Inherit
Bio::TreeIO
Synopsis
  use Bio::TreeIO;
  my $in = new Bio::TreeIO(-file => 'input', -format => 'newick');
  my $out = new Bio::TreeIO(-file => '>output', -format => 'svggraph');

  while( my $tree = $in->next_tree ) {
      my $svg_xml = $out->write_tree($tree);
  }
Description
This outputs a tree as an SVG graphic using the SVG::Graph API
Methods
newDescriptionCode
write_treeDescriptionCode
_write_tree_Helper
No description
Code
_decorateRoot
No description
Code
next_treeDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $obj = new Bio::TreeIO::svggraph();
 Function: Builds a new Bio::TreeIO::svggraph object 
 Returns : Bio::TreeIO::svggraph
 Args    :
write_treecodeprevnextTop
 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Write a tree out to data stream in newick/phylip format
 Returns : none
 Args    : Bio::Tree::TreeI object
next_treecodeprevnextTop
 Title   : next_tree
 Usage   : 
 Function: Sorry not possible with this format
 Returns : none
 Args    : none
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
}
write_treedescriptionprevnextTop
sub write_tree {
   my ($self,$tree) = @_;
   my $line = _write_tree_Helper($tree->get_root_node);
   $self->_print($line. "\n");
   $self->flush if $self->_flush_on_write && defined $self->_fh;
   return;
}
_write_tree_HelperdescriptionprevnextTop
sub _write_tree_Helper {
   my ($node) = @_;

   #this needs to be parameterized
   my $graph = SVG::Graph->new(width=>1600,height=>1000,margin=>30);

   my $group0 = $graph->add_frame;
   my $tree = SVG::Graph::Data::Tree->new;
   my $root = SVG::Graph::Data::Node->new;
   $root->name($node->id);
   _decorateRoot($root, $node->each_Descendent());
   $tree->root($root);
   $group0->add_data($tree);

   #this needs to be parameterized
   $group0->add_glyph('tree', stroke=>'black','stroke-width'=>2,'font-size'=>'10px');

   return($graph->draw);
}
_decorateRootdescriptionprevnextTop
sub _decorateRoot {
  my $previousNode = shift;
  my @children = @_;
   foreach my $child (@children)
	 {
	   my $currNode = SVG::Graph::Data::Node->new;
	   $currNode->branch_label($child->id);
	   $currNode->branch_length($child->branch_length);
	   $previousNode->add_daughter($currNode);
	   _decorateRoot($currNode, $child->each_Descendent());
	 }
}
next_treedescriptionprevnextTop
sub next_tree {
    $_[0]->throw("Sorry the format 'svggraph' can only be used as an output format");
}
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/MailList.shtml  - About the mailing lists
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
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Brian OConnorTop
Email brian.oconnor@excite.com
Describe contact details here
CONTRIBUTORSTop
Allen Day
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
decorateRootTop
 Title   : _decorateRoot
 Usage   : internal methods
 Function:
 Example :
 Returns :
 Args    :