Bio::TreeIO::svggraph - A simple output format that converts a Tree object to an SVG output

  use Bio::TreeIO;
  my $in = Bio::TreeIO->new(-file => 'input', -format => 'newick');
  my $out = Bio::TreeIO->new(-file => '>output', -format => 'svggraph');

  while( my $tree = $in->next_tree ) {
      my $svg_xml = $out->write_tree($tree);
  }

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  https://redmine.open-bio.org/projects/bioperl/

 Title   : new
 Usage   : my $obj = Bio::TreeIO::svggraph->new();
 Function: Builds a new Bio::TreeIO::svggraph object 
 Returns : Bio::TreeIO::svggraph
 Args    :-width    => image width (default 1600)
          -height   => image height (default 1000)
          -margin   => margin (default 30)
          -stroke   => stroke color (default 'black')
          -stroke_width=> stroke width (default 2)
          -font_size=> font size (default '10px')
          -nomalize => undef or 'log' (default is undef)

 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

 Title   : _decorateRoot
 Usage   : internal methods
 Function:
 Example :
 Returns :
 Args    :

 Title   : next_tree
 Usage   : 
 Function: Sorry not possible with this format
 Returns : none
 Args    : none

#
# BioPerl module for Bio::TreeIO::svg-graph
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Allen Day <allenday@ucla.edu>
#
# Copyright Brian O'Connor
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

# Let the code begin...


package Bio::TreeIO::svggraph;
use strict;

# Object preamble - inherits from Bio::Root::Root

use SVG::Graph;
use SVG::Graph::Data;
use SVG::Graph::Data::Tree;
use SVG::Graph::Data::Node;
use Bio::Tree::TreeI;
use Bio::Tree::Node;
use Tree::DAG_Node;


use base qw(Bio::TreeIO);

sub _initialize {
    my $self = shift;
    my ($width,$height,$margin,$stroke,
	$stroke_width,$font_size,
	$normalize) = $self->_rearrange([qw
					 (WIDTH
					  HEIGHT
					  MARGIN
					  STROKE
					  STROKE_WIDTH
					  FONT_SIZE
					  NORMALIZE)],
					@_);
    $self->{_width}        = $width || 1600;
    $self->{_height}       = $height || 1000;
    $self->{_margin}       = defined $margin ? $margin : 30;
    $self->{_stroke}       = $stroke || 'black';
    $self->{_stroke_width} = $stroke_width || 2;
    $self->{_font_size}    = $font_size || '10px';
    $self->{_normalize}    = $normalize || '';
    $self->SUPER::_initialize(@_);
}

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

sub _write_tree_Helper {
   my ($self,$node) = @_;

   my $graph = SVG::Graph->new
       ('width'   => $self->{'_width'},
	'height'  => $self->{'_height'},
	'margin'  => $self->{'_margin'});
   
   my $group0 = $graph->add_frame;
   my $tree = SVG::Graph::Data::Tree->new;
   my $root = SVG::Graph::Data::Node->new;
   $root->name($node->id);
   $self->_decorateRoot($root, $node->each_Descendent());
   $tree->root($root);
   $group0->add_data($tree);

   $group0->add_glyph('tree', 
		      'stroke'      =>$self->{'_stroke'},
		      'stroke-width'=>$self->{'_stroke_width'},
		      'font-size'   =>$self->{'_font_size'});

   return($graph->draw);
}

sub _decorateRoot {
    my ($self,$previousNode,@children) = @_;
    for my $child (@children) {
	my $currNode = SVG::Graph::Data::Node->new;
	$currNode->branch_label($child->id);
	my $length = $child->branch_length;
      CASE: 
	{  # is this right? copies from Guillame
	    if ($self->{_normalize} eq 'log') {
		$length = log($length + 1);
		last CASE;
	    }
	}
	$currNode->branch_length($length);
	$previousNode->add_daughter($currNode);
	$self->_decorateRoot($currNode, $child->each_Descendent());
    }
}

sub next_tree{
    $_[0]->throw("Sorry the format 'svggraph' can only be used as an output format");
}

1;