CPAN::Groonga

package Bio::Phylo::Unparsers::Json;
use strict;
use warnings;
use base 'Bio::Phylo::Unparsers::Abstract';
use Bio::Phylo::Util::CONSTANT qw'/looks_like/';
use Bio::Phylo::Util::Exceptions 'throw';
us

ML::XML2JSON';

=head1 NAME

Bio::Phylo::Unparsers::Json - Serializer used by Bio::Phylo::IO, no serviceable
parts inside

=head1 DESCRIPTION

This module turns the supplied object into a JSON string.

 Type    : Wrapper
 Title   : _to_string
 Usage   : my $json_string = $obj->_to_string;
 Function: Stringifies a Bio::Phylo object into a JSON string
 Alias   :
 Returns : SCALAR
 Args    : Bio::Phyl

ge Bio::Phylo::NeXML::XML2JSON;
use XML::XML2JSON;
use base 'XML::XML2JSON';
use strict;
use warnings;

=head1 NAME

Bio::Phylo::NeXML::XML2JSON - Helps convert NeXML to JSON, no serviceable parts ins

ide

=cut

# As of 2017, the most recent version of XML::XML2JSON seems to have been
# abandoned with a bug in it. It assumes that hash keys are ordered, whereas
# more recent Perl versions randomize 

{ $Self->{attribute_prefix} . 'encoding' } || $Obj->{'encoding'} || 'UTF-8';
	my $Dom = $XML::XML2JSON::XMLPARSER->createDocument( $Version, $Encoding );
	my $GotRoot = 0;

	# patch: first filter out 

package Bio::Phylo::Parsers::Json;
use strict;
use warnings;
use base 'Bio::Phylo::Parsers::Abstract';
use Bio::Phylo::IO 'parse';
use Bio::Phylo::Util::Exceptions 'throw';
use Bio::Phylo::Util::Depen

2JSON';

=head1 NAME

Bio::Phylo::Parsers::Json - Parser used by Bio::Phylo::IO, no serviceable parts inside

=head1 DESCRIPTION

This module is used to import NeXML data that was re-formatted as JSON

, using
the mapping implemented by L<XML::XML2JSON>. This module is experimental in that
complex NeXML-to-JSON mapped strings may fail to yield valid NeXML (and,
consequently, valid Bio::Phylo objects

m can also be written to NeXML (L<http://www.nexml.org>) using
C<to_xml> and to a JSON mapping thereof using C<to_json>.

=back

=head2 Input and output

The L<Bio::Phylo::IO> module is the unified fr

t=UTF-8',
    'phyloxml' => 'application/xml;charset=UTF-8',
    'nexus'    => 'text/plain',
    'json'     => 'text/javascript',
    'newick'   => 'text/plain',
    'fasta'    => 'text/plain',
);
{
 

 to simple JSON. For a conversion to NeXML/JSON, use C<to_json>.

 Type    : Serializer
 Title   : to_js
 Usage   : my $json = $object->to_js;
 Function: Serializes to JSON
 Returns : A JSON string
 A

rgs    : None.
 Comments: 

=cut

	sub to_js {JSON::to_json(shift->_json_data,{'pretty'=>1}) if looks_like_class 'JSON'}    
    
    sub _json_data {
    	my $self = shift;
    	my %data = %{ $self->

eates 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 

ethod
 Title   : _json_data
 Usage   : $node->_json_data;
 Function: Populates a data structure to be serialized as JSON
 Returns : 
 Args    :

=end comment

=cut
    
    sub _json_data {
    	my $s

elf = shift;
    	my %result = %{ $self->SUPER::_json_data };
    	$result{'length'}   = $self->get_branch_length if defined $self->get_branch_length;
    	$result{'rank'}     = $self->get_rank if $se

lf->get_rank;
    	$result{'children'} = [ map { $_->_json_data } @{ $self->get_children } ];
    	return \%result;
    }

=begin comment

 Type    : Internal method
 Title   : _cleanup
 Usage   : $tr

phylo> 
for any user or developer questions and discussions.

=over

=item L<Bio::Phylo::IO>

The json unparser is called by the L<Bio::Phylo::IO> object.
Look there to learn how to unparse objects.

tp://rutgervos.blogspot.com>.

=item L<http://www.json.org>

To learn more about the JavaScript Object Notation (JSON) format, visit
L<http://www.json.org>.

=back

=head1 CITATION

If you use Bio::Ph

rmats
 Returns : [ qw(nexml nexus newick html json phyloxml rss1) ]
 Args    : NONE

=cut

    sub get_supported_formats { [qw(nexml nexus newick html json phyloxml rss1)] }

=item get_authority()

Ge

cy 'JSON';
use Bio::Phylo::Util::Dependency 'URI';

=head1 NAME

Bio::Phylo::Parsers::Tnrs - Parser used by Bio::Phylo::IO, no serviceable parts inside

=head1 DESCRIPTION

This module parses JSON out

taxa = $fac->create_taxa( '-namespaces' => { 'tnrs' => _NS_TNRS_ } );
	my $data_structure = JSON::decode_json( do { local $/; <$fh> } );
	my %authority;
	
	# iterate over all returned names
	for my $n

 of supported formats
 Returns : [ qw(nexml nexus html json) ]
 Args    : NONE

=cut
    
    sub get_supported_formats { [ 'nexml', 'html', 'json', 'nexus', 'rss1' ] }

=item get_redirect()

Gets a r

}
    }
    
=item to_json()

 Serializes object to JSON string

 Type    : Serializer
 Title   : to_json()
 Usage   : print $obj->to_json();
 Function: Serializes object to JSON string
 Returns : Str

 Args    : None
 Comments:

=cut

    sub to_json {
		looks_like_class('Bio::Phylo::NeXML::XML2JSON')->new->convert( shift->to_xml );
    }    

	sub _json_data {
		my $self   = shift;
		my %meta   = 

ap { $_->get_predicate => $_->get_object } @{ $self->get_meta };
		my %result = %{ $self->SUPER::_json_data };
		$result{$_} = $meta{$_} for keys %meta;
		$result{'name'} = $self->get_name if $self->g

 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 

ref of supported formats
 Returns : [ 'nexml', 'json', 'nexus', 'rss1' ]
 Args    : NONE

=cut    
    
    sub get_supported_formats { [ 'nexml', 'json', 'nexus', 'rss1' ] }

=item get_authority()

G