package Bio::Phylo::Unparsers::Taxlist;
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::Taxlist - Serializer used by Bio::Phylo::IO, no serviceable
parts inside
=head1 DESCRIPTION
This module creates a taxon list/table
=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'};
my $taxa;
if ( $obj->_type == _PROJECT_ ) {
$taxa = $obj->get_items(_TAXON_);
}
elsif ( $obj->_type == _TAXA_ ) {
$taxa = $obj->get_entities;
}
else {
throw 'ObjectMismatch' => "Can't make taxon list string out of $obj";
}
my %predicates;
for my $taxon ( @{ $taxa } ) {
for my $meta ( @{ $taxon->get_meta } ) {
$predicates{$meta->get_predicate} = 1;
}
}
my @predicates = keys %predicates;
my $result = '';
if ( @predicates ) {
$result .= "name\t" . join("\t",@predicates) . "\n";
}
for my $taxon ( @{ $taxa } ) {
$result .= $taxon->get_name;
if ( @predicates ) {
my @values;
for my $predicate ( @predicates ) {
push @values, $taxon->get_meta_object($predicate);
}
$result .= "\t" . join("\t",@values);
}
$result .= "\n";
}
return $result;
}
# 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 taxlist 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;