Bio::TreeIO svggraph
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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
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 = 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); }
Description
This outputs a tree as an SVG graphic using the SVG::Graph API
Methods
_initialize
No description
Code
write_treeDescriptionCode
_write_tree_Helper
No description
Code
_decorateRoot
No description
Code
next_treeDescriptionCode
Methods description
write_treecode    nextTop
 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
_initializedescriptionprevnextTop
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 || '';
    $self->SUPER::_initialize(@_);
}
write_treedescriptionprevnextTop
sub write_tree {
   my ($self,$tree) = @_;
   my $line = $self->_write_tree_Helper($tree->get_root_node);
   $self->_print($line. "\n");
   $self->flush if $self->_flush_on_write && defined $self->_fh;
   return;
}
_write_tree_HelperdescriptionprevnextTop
sub _write_tree_Helper {
   my ($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($graph->draw);
}
_decorateRootdescriptionprevnextTop
sub _decorateRoot {
    my ($self,$previousNode,@children) = @_;
    for my $child (@children) {
        my $currNode = SVG::Graph::Data::Node->new;

        # if no ID is set, the branch label is intentionally set blank (bug in SVG::Graph)
my $id = $child->id || ''; $currNode->branch_label($id); my $length = $child->branch_length; if ($self->{_normalize} eq 'log') { $length = log($length + 1); } $currNode->branch_length($length); $previousNode->add_daughter($currNode); $self->_decorateRoot($currNode, $child->each_Descendent()); }
}
next_treedescriptionprevnextTop
sub next_tree {
    $_[0]->throw("Sorry the format 'svggraph' can only be used as an output format");
}

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
SupportTop
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 - Brian OConnorTop
Email brian.oconnor-at-excite.com
CONTRIBUTORSTop
Allen Day
Guillaume Rousse, Guillaume-dot-Rousse-at-inria-dot-fr
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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)
decorateRootTop
 Title   : _decorateRoot
Usage : internal methods
Function:
Example :
Returns :
Args :