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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::SeqRegionSynonym -
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24 Object representing an alternatice name.
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25
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26 =head1 SYNOPSIS
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27
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28 =head1 DESCRIPTION
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29
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30 This object holds information about alternative name to
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31 Ensembl seq regions.
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32
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33 =head1 METHODS
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34
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35 =cut
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36
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37 package Bio::EnsEMBL::SeqRegionSynonym;
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38
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39 use strict;
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40 use warnings;
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41 no warnings qw(uninitialized);
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42
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43 use Bio::EnsEMBL::Storable;
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44 use Bio::Annotation::DBLink;
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45
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46 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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47 use Bio::EnsEMBL::Utils::Exception qw(deprecate);
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48
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49 our @ISA = qw(Bio::EnsEMBL::Storable);
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50
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51 =head2 new
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52
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53 Args [...] : list of named parameters
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54 Example : my $srs = new Bio::EnsEMBL::SeqRegionSynonym(
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55 -adaptor => $adaptor,
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56 -synonym => $alt_name,
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57 -external_db_id => 1234
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58 -seq_region_id => 12);
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59 Description: Creates a new SeqRegionSynonym object
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60 Returntype : Bio::EnsEMBL::SeqRegionSynonym
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61 Exceptions : none
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62 Caller : Bio::EnsEMBL::SeqRegionSynonymAdaptor
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63 Status : At Risk
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64 =cut
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65
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66 sub new {
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67 my ($class, @args) = @_;
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68
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69 my $self = bless {},$class;
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70
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71 my ( $adaptor, $synonym, $ex_db, $seq_region_id, $dbid) =
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72 rearrange ( ['ADAPTOR','SYNONYM','EXTERNAL_DB_ID','SEQ_REGION_ID','DBID'], @args );
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73
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74 $self->adaptor($adaptor);
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75
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76 if( defined $ex_db ) { $self->external_db_id( $ex_db ) }
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77 if( defined $seq_region_id ) { $self->seq_region_id( $seq_region_id ) }
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78 if (defined $dbid) { $self->{'dbID'} = $dbid}
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79
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80 if( defined $synonym ) {
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81 $self->name( $synonym ) ;
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82 } else {
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83 warn "No alternative name given\n";
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84 return undef;
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85 }
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86
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87 return $self;
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88 }
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89
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90 sub name{
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91 my $self = shift;
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92 $self->{'name'} = shift if(@_);
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93 return $self->{'name'};
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94 }
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95
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96 sub external_db_id{
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97 my $self = shift;
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98 $self->{'ex_db'} = shift if(@_);
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99 return $self->{'ex_db'};
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100 }
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101
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102 sub seq_region_id{
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103 my $self = shift;
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104 $self->{'seq_region_id'} = shift if(@_);
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105 return $self->{'seq_region_id'};
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106 }
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107
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108 1;
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