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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::MergedAdaptor
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24
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25 =head1 SYNOPSIS
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26
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27 $merged_adaptor = new Bio::EnsEMBL::DBSQL::MergedAdaptor(
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28 -species => "human",
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29 -type => "Population"
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30 );
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31
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32 =head1 DESCRIPTION
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33
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34 The MergedAdaptor object is merely a list of adaptors. AUTOLOAD is used
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35 to call a subroutine on each adaptor and merge the results.
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36
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37 =head1 METHODS
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38
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39 =cut
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40
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41
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42 package Bio::EnsEMBL::DBSQL::MergedAdaptor;
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43
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44
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45 use vars qw(@ISA);
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46 use strict;
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47
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48 use Bio::EnsEMBL::Utils::Exception qw(throw warning deprecate);
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49 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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50 use Bio::EnsEMBL::Registry;
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51 my $reg = "Bio::EnsEMBL::Registry";
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52
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53
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54 =head2 new
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55
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56 Arg [SPECIES]: (optional) string
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57 species name to get adaptors for
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58 Arg [TYPE] : (optional) string
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59 type to get adaptors for
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60 Arg [GROUPS] : (optional) ref to list
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61 Example : $MergedAdaptor = new
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62 : Bio::EnsEMBL::DBSQL::MergedAdaptor(-species=> 'human', -type =>'Population', -groups => ['Sanger','Ensembl']);
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63
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64 Description: Creates a new MergedAdaptor
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65 Returntype : Bio::EnsEMBL::DBSQL::MergedAdaptor
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66 Exceptions : throws if species or type not specified
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67 Caller : general
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68 Status : At Risk
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69 : Under development
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70
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71 =cut
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72
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73 sub new {
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74 my ($class,@args) = @_;
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75
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76 my $self ={};
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77 bless $self,$class;
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78
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79 my ($species, $type, $groups) =
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80 rearrange([qw(SPECIES TYPE GROUPS)], @args);
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81
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82 if(!defined($species)|| !defined($type)){
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83 die "Species and Type must be specified\n";
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84 }
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85
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86 my @adaps;
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87 if (!defined ($groups)){
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88 #get all adaptors for that species and type
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89 @adaps = @{$reg->get_all_adaptors(-species => $species, -type => $type)};
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90 }
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91 else{
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92 #get only specified adaptors for the particular groups
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93 foreach my $group (@{$groups}){
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94 push @adaps, $reg->get_adaptor($species,$group,$type);
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95 }
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96 }
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97
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98 my @list =();
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99 push(@list,@adaps);
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100 $self->{'list'}= \@list;
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101
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102 return $self;
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103 }
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104
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105 =head2 add_list
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106
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107 Example : $MergedAdaptor->add_list(@adaptors);
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108 Description: adds a list of adaptors to the Merged adaptor list.
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109 Returntype : none
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110 Exceptions : none
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111 Status : At Risk
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112 : Under development
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113
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114 =cut
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115
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116 sub add_list{
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117 my ($self, @arr) = @_;
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118
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119 foreach my $adap (@arr){
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120 $self->add_adaptor($adap);
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121 }
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122 }
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123
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124 =head2 add_adaptor
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125
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126 Example : $MergedAdaptor->add_adaptor(@adaptors);
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127 Description: adds an adaptor to the Merged adaptor list.
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128 Returntype : none
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129 Exceptions : none
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130 Status : At Risk
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131 : Under development
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132
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133 =cut
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134
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135 sub add_adaptor{
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136 my ($self,$adaptor)=@_;
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137
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138 if(!defined ($self->{'list'})){
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139 my @list =();
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140 push(@list,$adaptor);
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141 $self->{'list'}= \@list;
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142 }
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143 else{
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144 push(@{$self->{'list'}},$adaptor);
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145 }
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146 }
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147
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148
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149 sub printit{
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150 my ($self)=@_;
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151
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152 foreach my $adaptor (@{$self->{'list'}}){
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153 print "printit $adaptor\t".$adaptor->db->group()."\n";
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154 }
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155 }
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156
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157
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158 use vars '$AUTOLOAD';
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159
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160 sub AUTOLOAD {
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161 my ($self,@args) = @_;
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162 my @array_return=();
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163 my $ref_return = undef;
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164 $AUTOLOAD =~ /^.*::(\w+)+$/ ;
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165
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166 my $sub = $1;
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167
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168 foreach my $adaptor (@{$self->{'list'}}) {
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169 my $ref;
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170 if($adaptor->can($sub)){
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171 $ref = $adaptor->$sub(@args);
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172 if( ref($ref) eq 'ARRAY' ) {
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173 push @array_return, @{$ref};
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174 } else {
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175 push @array_return, $ref;
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176 }
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177 }
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178 else{ # end of can
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179 warn("In Merged Adaptor $adaptor cannot call sub $sub");
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180 }
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181 }
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182 return \@array_return;
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183 }
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184
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185 sub DESTROY{
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186 }
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187
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188 1;
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