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lib/Bio/ViennaNGS/AnnoC.pm  view on Meta::CPAN

# -*-CPerl-*-
# Last changed Time-stamp: <2017-06-10 18:18:45 michl>

package Bio::ViennaNGS::AnnoC;
use Bio::ViennaNGS;
use Bio::ViennaNGS::Util qw(sortbed);
use Bio::Tools::GFF;
use Path::Class;
use Carp;
use Moose;
use namespace::autoclean;
use version; our $VERSION = version->declare(eval($Bio::ViennaNGS::VERSION));

has 'accession' => (
		    is => 'rw',
		    isa => 'Str',
		    predicate => 'has_accession',
		   );

has 'features' => (
		   is => 'ro',
		   isa => 'HashRef',
		   predicate => 'has_features',
		   default => sub { {} },
		  );

has 'nr_features' => (
		     is => 'ro',
		     isa => 'Int',
		     builder => '_get_nr_of_features',
		     lazy => 1,
		     );

has 'featstat' => (
		   is => 'ro',
		   isa => 'HashRef',
		   builder => '_set_featstat',
		   predicate => 'has_featstat',
		   lazy => 1,
		  );

before 'featstat' => sub {
  my $self = shift;
  $self->_get_nr_of_features();
};

sub _set_featstat {
  my $self = shift;
  my $this_function = (caller(0))[3];
  my %fs = ();
  confess "ERROR [$this_function] \$self->features not available"
    unless ($self->has_features);
  $fs{total} = 0;
  $fs{origin} = "$this_function ".$VERSION;
  $fs{count} = $self->nr_features;
  foreach my $uid ( keys %{$self->features} ){
    my $gbkey = ${$self->features}{$uid}->{gbkey};
    $fs{total} += 1;
    unless (exists $fs{$gbkey}){
      $fs{$gbkey} = 0;
    }
    $fs{$gbkey} += 1;
  }
  return \%fs;
}

sub _get_nr_of_features {
  my $self = shift;
  my $this_function = (caller(0))[3];
  confess "ERROR [$this_function] \$self->features not available"
    unless ($self->has_features);