view variant_effect_predictor/Bio/EnsEMBL/Utils/IO/FeatureSerializer.pm @ 0:1f6dce3d34e0

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=pod

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

  http://www.ensembl.org/info/about/code_licence.html

=head1 NAME

FeatureSerializer - An abstract serializer for turning EnsEMBL Features into other formats

=head1 AUTHOR

Kieron Taylor, 2012 - [e-mail]

=head1 SYNOPSIS

my $serializer = new Bio::EnsEMBL::Utils::IO::FeatureSerializer( $filehandle );
$serializer->print_feature_list( \@list_of_features );

=head1 DESCRIPTION

Generic class for serializing features Subclass this class to create a 
format-specific serializer. Be sure to implement print_feature at the 
bare minimum

=cut

package Bio::EnsEMBL::Utils::IO::FeatureSerializer;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Utils::IO::Serializer);

# Majority of methods inherited from Serializer

sub print_feature {
	throw( "print_feature method not implemented.");
}

=head2 print_feature_list

	Arg [1]    : Listref of Features
	Description: Run print_feature on every feature in the list

=cut

sub print_feature_list {
	my $self = shift;
	my $feature_list = shift;
	if (ref($feature_list) eq 'ARRAY') {
		if (scalar(@$feature_list) > 0) {$self->{'achieved_something'} = 1;} 
		foreach my $feature (@{$feature_list}) {
			$self->print_feature($feature);
		}
	}
	else {
		throw( "print_feature_list requires a listref as argument" );
	}
}

=head2 print_feature_Iterator

	Arg [1]    : Bio::EnsEMBL::Utils::Iterator
	Description: Automatically spools through an iterator for convenience
	Returntype : None
=cut

sub print_feature_Iterator {
	my $self = shift;
	my $iterator = shift;
	if ($iterator->can('has_next')) {
		$iterator->each(
			sub {
				$self->print_feature($_); 
				$self->{'achieved_something'} = 1;
			}
		);
	}
	else {
		throw("Supplied iterator does not look like Bio::EnsEMBL::Utils::Iterator");
	}
}

1;