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1 =pod
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2
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3 =head1 LICENSE
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4
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5 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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6 Genome Research Limited. All rights reserved.
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7
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8 This software is distributed under a modified Apache license.
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9 For license details, please see
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10
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11 http://www.ensembl.org/info/about/code_licence.html
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12
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13 =head1 NAME
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14
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15 FeatureSerializer - An abstract serializer for turning EnsEMBL Features into other formats
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16
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17 =head1 AUTHOR
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18
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19 Kieron Taylor, 2012 - ktaylor@ebi.ac.uk
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20
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21 =head1 SYNOPSIS
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22
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23 my $serializer = new Bio::EnsEMBL::Utils::IO::FeatureSerializer( $filehandle );
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24 $serializer->print_feature_list( \@list_of_features );
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25
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26 =head1 DESCRIPTION
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27
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28 Generic class for serializing features Subclass this class to create a
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29 format-specific serializer. Be sure to implement print_feature at the
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30 bare minimum
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31
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32 =cut
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33
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34 package Bio::EnsEMBL::Utils::IO::FeatureSerializer;
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35
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36 use strict;
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37 use warnings;
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38
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39 use base qw(Bio::EnsEMBL::Utils::IO::Serializer);
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40
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41 # Majority of methods inherited from Serializer
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42
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43 sub print_feature {
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44 throw( "print_feature method not implemented.");
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45 }
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46
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47 =head2 print_feature_list
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48
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49 Arg [1] : Listref of Features
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50 Description: Run print_feature on every feature in the list
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51
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52 =cut
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53
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54 sub print_feature_list {
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55 my $self = shift;
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56 my $feature_list = shift;
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57 if (ref($feature_list) eq 'ARRAY') {
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58 if (scalar(@$feature_list) > 0) {$self->{'achieved_something'} = 1;}
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59 foreach my $feature (@{$feature_list}) {
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60 $self->print_feature($feature);
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61 }
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62 }
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63 else {
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64 throw( "print_feature_list requires a listref as argument" );
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65 }
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66 }
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67
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68 =head2 print_feature_Iterator
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69
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70 Arg [1] : Bio::EnsEMBL::Utils::Iterator
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71 Description: Automatically spools through an iterator for convenience
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72 Returntype : None
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73 =cut
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74
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75 sub print_feature_Iterator {
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76 my $self = shift;
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77 my $iterator = shift;
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78 if ($iterator->can('has_next')) {
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79 $iterator->each(
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80 sub {
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81 $self->print_feature($_);
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82 $self->{'achieved_something'} = 1;
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83 }
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84 );
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85 }
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86 else {
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87 throw("Supplied iterator does not look like Bio::EnsEMBL::Utils::Iterator");
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88 }
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89 }
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90
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91 1;
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