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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::DBSQL::ProxySNPAdaptor
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24
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25 =head1 SYNOPSIS
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26
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27 Designed as an abstraction over the database specific SNPAdaptors. This
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28 is written right now to serve as a replacement for a core SNPadaptor
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29 which doesn''t even exist yet and probably never will since SNPs are
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30 taken from external databases. In the future some sort of DBRegistry may
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31 remove the need for this class.
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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::DBSQL::ProxySNPAdaptor;
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38
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39 use strict;
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40
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41 use Bio::EnsEMBL::DBSQL::BaseAdaptor;
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42 use Bio::EnsEMBL::Utils::Exception qw(throw);
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43
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44 use vars ('@ISA', '$AUTOLOAD');
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45
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46 @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
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47
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48 =head2 fetch_attributes_only
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49
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50 Arg [1] : int refsnp_id
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51 Arg [2] : (optional) string source
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52 Example : none
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53 Description: Retrieves a snp objcet from the SNP database but does not
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54 populate the location information. This is necessary given
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55 the current state of the snp database because location
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56 information has to be retrieved differently for different
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57 species!
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58 Returntype : Bio::EnsEMBL::SNP
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59 Exceptions : none
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60 Caller : snpview
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61
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62 =cut
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63
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64
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65
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66 sub fetch_attributes_only{
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67 my ( $self, @args ) = @_;
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68
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69 my $lite_db = Bio::EnsEMBL::Registry->get_db($self->db(),'lite');
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70 my $snp_db = Bio::EnsEMBL::Registry->get_db($self->db(),'SNP');
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71
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72 if( defined $snp_db ) {
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73 my $snp_adaptor = $snp_db->get_SNPAdaptor();
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74 return $snp_adaptor->fetch_attributes_only( @args );
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75 }
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76
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77 if( defined $lite_db ) {
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78 my $snp_adaptor = $lite_db->get_SNPAdaptor();
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79 return $snp_adaptor->fetch_attributes_only( @args );
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80 }
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81
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82 }
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83
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84
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85
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86
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87 =head2 AUTOLOAD
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88
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89 Arg [1] : list of arbitrary values @args
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90 a list of arguments to pass to the request method
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91 Example : -
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92 Description: AUTOLOAD method should not be called directly. It is called
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93 implicitly when a method requested from this class cannot be
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94 found. This method first tries to execute the requested method
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95 in the primary adaptor. If the method cannot be found then
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96 it searches the other attached databases for equivalent adaptors
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97 and tries then one at a time.
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98 Returntype : arbitrary
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99 Exceptions : thrown if the requested method cannot be found on the primary
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100 adaptor or on any of the attached databases.
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101 Caller : called implicitly by perl
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102
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103 =cut
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104
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105 sub AUTOLOAD {
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106 my ($self, @args) = @_;
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107
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108 #determine the method which was called
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109 my $method = $AUTOLOAD;
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110
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111 #strip out fully qualified method name
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112 $method =~ s/.*:://;
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113
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114 my $lite_db = Bio::EnsEMBL::Registry->get_db($self->db(),'lite');
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115 my $snp_db = Bio::EnsEMBL::Registry->get_db($self->db(),'SNP');
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116
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117 if( defined $lite_db ) {
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118 my $snp_adaptor = $lite_db->get_SNPAdaptor();
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119 if($snp_adaptor->can($method)) {
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120 return $snp_adaptor->$method(@args);
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121 }
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122 }
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123
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124 if( defined $snp_db ) {
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125 my $snp_adaptor = $snp_db->get_SNPAdaptor();
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126 if($snp_adaptor->can($method)) {
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127 return $snp_adaptor->$method(@args);
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128 }
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129 }
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130
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131
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132
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133 throw("The requested method $method could not be found in lite or snp" );
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134 }
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135
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136 sub DESTROY {
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137 }
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138
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139 1;
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140
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141 __END__
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