Bio-Phylo/lib/Bio/Phylo/Unparsers/Html.pm
package Bio::Phylo::Unparsers::Html;
use strict;
use warnings;
use base 'Bio::Phylo::Unparsers::Abstract';
use Bio::Phylo::Util::CONSTANT qw'/looks_like/ :objecttypes';
use Bio::Phylo::Util::Exceptions 'throw';
use Bio::Phylo::Util::Dependency qw'Template';
=head1 NAME
Bio::Phylo::Unparsers::Html - Serializer used by Bio::Phylo::IO, no serviceable
parts inside
=head1 DESCRIPTION
This module creates an HTML representation of the provided project
=begin comment
Type : Wrapper
Title : _to_string
Usage : my $json_string = $obj->_to_string;
Function: Stringifies a Bio::Phylo object into an HTML string
Alias :
Returns : SCALAR
Args : Bio::Phylo::* object
=end comment
=cut
sub _to_string {
my $self = shift;
my $obj = $self->{'PHYLO'};
if ( $obj->_type == _PROJECT_ ) {
my $result;
my $template = $self->{'TEMPLATE'} || \*DATA;
my $tt = Template->new;
$tt->process($template,{'proj' => $obj},\$result);
return $result;
}
else {
throw 'ObjectMismatch' => "Can't make HTML string out of $obj";
}
}
# podinherit_insert_token
=head1 SEE ALSO
There is a mailing list at L<https://groups.google.com/forum/#!forum/bio-phylo>
for any user or developer questions and discussions.
=over
=item L<Bio::Phylo::IO>
The html unparser is called by the L<Bio::Phylo::IO> object.
Look there to learn how to unparse objects.
=item L<Bio::Phylo::Manual>
Also see the manual: L<Bio::Phylo::Manual> and L<http://rutgervos.blogspot.com>.
=back
=head1 CITATION
If you use Bio::Phylo in published research, please cite it:
B<Rutger A Vos>, B<Jason Caravas>, B<Klaas Hartmann>, B<Mark A Jensen>
and B<Chase Miller>, 2011. Bio::Phylo - phyloinformatic analysis using Perl.
I<BMC Bioinformatics> B<12>:63.
L<http://dx.doi.org/10.1186/1471-2105-12-63>
=cut
1;
__DATA__
<html>
<head>
<title>
[% IF proj.get_name %]
[% proj.get_name %]
[% END %]
</title>
</head>
<body>
<img src="http://www.evoio.org/wg/evoio/images/f/f1/Phylotastic_logo.png"/>
<h1>Document</h1>
[% PROCESS identifiable obj = proj, tag = "h2" %]
<!-- process taxa blocks, if any -->
[% IF proj.get_taxa.size > 0 %]
<h1>Taxa</h1>
<!-- iterate over each taxa block -->
<ul>
[% FOREACH taxa = proj.get_taxa %]
<li>
<!-- write taxa block metadata -->
[% PROCESS identifiable obj = taxa, tag = "h2" %]
<h3>Number of taxa: [% taxa.get_ntax %]</h3>
<!-- write taxon contents -->
<ul>
[% FOREACH taxon = taxa.get_entities %]
[% PROCESS identifiable obj = taxon, tag = "li" %]
[% END %]
</ul>
</li>
[% END %]
</ul>
[% END %]
<!-- process characters blocks, if any -->
[% IF proj.get_matrices.size > 0 %]
<h1>Characters</h1>
<!-- iterate over each characters block -->
[% FOREACH matrix = proj.get_matrices %]
<!-- write characters block metadata -->
[% PROCESS identifiable obj = matrix, tag = "h2" %]
<ul>
<li>Data type: [% matrix.get_type %]</li>
<li>Number of taxa: [% matrix.get_ntax %]</li>
<li>Number of characters: [% matrix.get_nchar %]</li>
<li>Taxa block:
<a href="#[% matrix.get_taxa.get_xml_id %]">
[% matrix.get_taxa.get_internal_name %]
</a>
<li>
</ul>
<!-- write datum contents -->
<table>
[% FOREACH datum = matrix.get_entities %]
<tr>
<td>
[% PROCESS identifiable obj = datum, tag = "h3" %]
</td>
<td>
<pre>[% datum.get_char %]</pre>
</td>
</tr>
[% END %]
<table>
[% END %]
[% END %]
<!-- process trees blocks, if any -->
[% IF proj.get_forests.size > 0 %]
<h1>Trees</h1>
<!-- iterate over each trees block -->
[% FOREACH forest = proj.get_forests %]
<!-- write trees block metadata -->
[% PROCESS identifiable obj = forest, tag = "h2" %]
<!-- write trees block contents -->
[% FOREACH tree = forest.get_entities %]
[% PROCESS identifiable obj = tree, tag = "h3" %]
<pre>[% tree.to_newick %]</pre>
[% END %]
[% END %]
[% END %]
</body>
</html>
[% BLOCK identifiable %]
<[% tag %] id="[% obj.get_xml_id %]" class="[% obj.get_tag %]">
<a name="[% obj.get_xml_id %]">
[% IF obj.get_name %]
[% obj.get_name %]
[% END %]
</a>
</[% tag %]>
[% PROCESS annotatable %]
[% END %]
[% BLOCK annotatable %]
[% IF obj.get_meta.size > 0 %]
<ul>
[% FOREACH meta = obj.get_meta %]
<li id="[% meta.get_xml_id %]" class="[% meta.get_tag %]">
<a href="[% meta.get_predicate_namespace %][% meta.get_predicate_local %]" class="predicate">
[% meta.get_predicate %]
</a> =
[% IF meta.is_resource %]
[% IF meta.is_xml_literal %]
<pre class="xml_literal">[% meta.get_object %]</pre>
[% ELSE %]
<a href="[% meta.get_object %]" rel="[% meta.get_predicate %]" class="resource">
[% meta.get_object %]
</a>
[% END %]
[% ELSE %]
<span class="[% meta.get_object_type %]">[% meta.get_object %]</span>
[% END %]
[% PROCESS annotatable obj = meta %]
</li>
[% END %]
</ul>
[% END %]
[% END %]