package Bio::Phylo::Unparsers::Mrp;
use strict;
use base 'Bio::Phylo::Unparsers::Abstract';
use Bio::Phylo::Util::CONSTANT qw'/looks_like/ :objecttypes';
use Bio::Phylo::Util::Exceptions 'throw';
use Bio::Phylo::Factory;
my $factory = Bio::Phylo::Factory->new;
=head1 NAME
Bio::Phylo::Unparsers::Mrp - Serializer used by Bio::Phylo::IO, no serviceable parts inside
=head1 DESCRIPTION
This module turns a L<Bio::Phylo::Forest> object into an MRP nexus
formatted matrix. It is called by the L<Bio::Phylo::IO> facade, don't call it
directly.
=begin comment
Type : Wrapper
Title : _to_string
Usage : my $mrp_string = $mrp->_to_string;
Function: Stringifies a matrix object into
an MRP nexus formatted table.
Alias :
Returns : SCALAR
Args : Bio::Phylo::Matrices::Matrix;
=end comment
=cut
sub _to_string {
my $self = shift;
my $forest = $self->{'PHYLO'};
if ( looks_like_implementor $forest, 'get_forests' ) {
($forest) = @{ $forest->get_forests };
}
if ( looks_like_implementor $forest, 'make_matrix' ) {
my $proj = $factory->create_project;
my $matrix = $forest->make_matrix;
$proj->insert( $matrix->get_taxa, $matrix );
return $proj->to_nexus( '-charstatelabels' => 1 );
}
else {
throw 'ObjectMismatch' => "Can't make MRP matrix out of $forest";
}
}
# 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 mrp unparser is called by the L<Bio::Phylo::IO> object.
Look there to learn how to create mrp matrices.
=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;