Bio::TreeIO
svggraph
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
SVG::Graph
SVG::Graph::Data
SVG::Graph::Data::Node
SVG::Graph::Data::Tree
Tree::DAG_Node
Inherit
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
Methods description
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 : next_tree
Usage :
Function: Sorry not possible with this format
Returns : none
Args : none |
Methods code
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 = $child->branch_length;
CASE:
{
if ($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");} | 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/wiki/Mailing_lists - 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.open-bio.org/
| AUTHOR - Brian OConnor | Top |
Email brian.oconnor-at-excite.com
Allen Day
Guillaume Rousse, Guillaume-dot-Rousse-at-inria-dot-fr
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : new
Usage : my $obj = new Bio::TreeIO::svggraph();
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 : _decorateRoot
Usage : internal methods
Function:
Example :
Returns :
Args :