package Bio::Phylo::Unparsers::Nexus;
use strict;
use base 'Bio::Phylo::Unparsers::Abstract';
use Bio::Phylo::Util::CONSTANT ':objecttypes';
use Bio::Phylo::Util::Exceptions 'throw';
=head1 NAME
Bio::Phylo::Unparsers::Nexus - Serializer used by Bio::Phylo::IO, no serviceable parts inside
=head1 DESCRIPTION
This module turns a L<Bio::Phylo::Matrices::Matrix> object into a nexus
formatted matrix. It is called by the L<Bio::Phylo::IO> facade, don't call it
directly. You can pass the following additional arguments to the unparse call:
# an array reference of matrix, forest and taxa objects:
-phylo => [ $block1, $block2 ]
# the arguments that can be passed for matrix objects,
# refer to Bio::Phylo::Matrices::Matrix::to_nexus:
-matrix_args => {}
# the arguments that can be passed for forest objects,
# refer to Bio::Phylo::Forest::to_nexus:
-forest_args => {}
# the arguments that can be passed for taxa objects,
# refer to Bio::Phylo::Taxa::to_nexus:
-taxa_args => {}
OR:
# for backward compatibility:
-phylo => $matrix
=begin comment
Type : Wrapper
Title : _to_string($matrix)
Usage : $nexus->_to_string($matrix);
Function: Stringifies a matrix object into
a nexus formatted table.
Alias :
Returns : SCALAR
Args : Bio::Phylo::Matrices::Matrix;
=end comment
=cut
sub _to_string {
my $self = shift;
my $blocks = $self->{'PHYLO'};
my $nexus = "#NEXUS\n";
my $type;
eval { $type = $blocks->_type };
# array?
if ($@) {
for my $block (@$blocks) {
eval { $type = $block->_type };
my %args;
if ( $type == _FOREST_ ) {
if ( exists $self->{'FOREST_ARGS'} ) {
%args = %{ $self->{'FOREST_ARGS'} };
}
}
elsif ( $type == _TAXA_ ) {
if ( exists $self->{'TAXA_ARGS'} ) {
%args = %{ $self->{'TAXA_ARGS'} };
}
}
elsif ( $type == _MATRIX_ ) {
if ( exists $self->{'MATRIX_ARGS'} ) {
%args = %{ $self->{'MATRIX_ARGS'} };
}
}
elsif ($@) {
throw 'ObjectMismatch' => "Can't unparse this object: $blocks";
}
$nexus .= $block->to_nexus(%args);
}
}
# matrix?
elsif ( defined $type and $type == _MATRIX_ ) {
$nexus .= $blocks->to_nexus;
}
# project?
elsif ( defined $type and $type == _PROJECT_ ) {
$nexus = $blocks->to_nexus;
}
# wrong!
else {
throw 'ObjectMismatch' => "Can't unparse this object: $blocks";
}
return $nexus;
}
# 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 nexus serializer is called by the L<Bio::Phylo::IO> object.
=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;