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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 # Ensembl module for Bio::EnsEMBL::Variation::Study
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22 #
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23 # Copyright (c) 2011 Ensembl
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24 #
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25
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26
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27 =head1 NAME
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28
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29 Bio::EnsEMBL::Variation::Study - Ensembl representation of a study.
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30
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31 =head1 SYNOPSIS
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32
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33 # Study
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34 $study = Bio::EnsEMBL::Variation::Study->new
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35 (-name => 'EGAS00000000001',
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36 -external_reference => 'pubmed/17554300',
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37 -url => 'http://www.ebi.ac.uk/ega/page.php?page=study&study=EGAS00000000001&cat=www.wtccc.studies.xml.ega&subcat=BD'
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38 );
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39 ...
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40
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41
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42 =head1 DESCRIPTION
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43
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44 This is a class representing a study from the ensembl-variation database.
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45
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46 =head1 METHODS
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47
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48 =cut
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49
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50 use strict;
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51 use warnings;
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52
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53 package Bio::EnsEMBL::Variation::Study;
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54
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55 use Bio::EnsEMBL::Storable;
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56 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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57 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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58
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59 our @ISA = ('Bio::EnsEMBL::Storable');
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60
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61
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62 =head2 new
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63
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64 Arg [-dbID] :
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65 see superclass constructor
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66 Arg [-ADAPTOR] :
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67 see superclass constructor
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68 Arg [-NAME] :
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69 name of the study
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70 Arg [-DESCRIPTION] :
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71 study description
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72 Arg [-URL] :
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73 string - url of the database/file where the data are stored
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74 Arg [-EXTERNAL_REFERENCE] :
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75 string - the pubmed/ids or project/study names
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76 Arg [-TYPE] :
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77 string - type of the study (e.g. GWAS)
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78 Arg [-SOURCE] :
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79 string - name of the source
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80 Arg [-ASSOCIATE] :
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81 array ref - list of the study objects associated with the current study
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82
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83 Example :
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84
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85 $study = Bio::EnsEMBL::Variation::Study->new
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86 (-name => 'EGAS00000000001',
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87 -external_reference => 'pubmed/17554300',
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88 -url => 'http://www.ebi.ac.uk/ega/page.php?page=study&study=EGAS00000000001&cat=www.wtccc.studies.xml.ega&subcat=BD'
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89 );
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90
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91 Description: Constructor. Instantiates a new Study object.
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92 Returntype : Bio::EnsEMBL::Variation::Study
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93 Exceptions : none
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94 Caller : general
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95 Status : At Risk
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96
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97 =cut
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98
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99 sub new {
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100 my $caller = shift;
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101 my $class = ref($caller) || $caller;
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102
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103 my $self = $class->SUPER::new(@_);
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104 my ($dbID,$adaptor,$study_name,$study_description,$study_url,$external_reference,
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105 $study_type,$source_name,$associate) =
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106 rearrange([qw(dbID ADAPTOR NAME DESCRIPTION URL EXTERNAL_REFERENCE TYPE SOURCE ASSOCIATE)], @_);
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107
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108 $self = {
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109 'dbID' => $dbID,
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110 'adaptor' => $adaptor,
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111 'name' => $study_name,
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112 'description' => $study_description,
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113 'url' => $study_url,
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114 'external_reference' => $external_reference,
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115 'type' => $study_type,
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116 'source' => $source_name,
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117 'associate' => $associate
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118 };
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119
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120 return bless $self, $class;
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121 }
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122
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123
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124 =head2 name
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125
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126 Arg [1] : string $newval (optional)
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127 The new value to set the name attribute to
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128 Example : $name = $obj->name()
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129 Description: Getter/Setter for the name attribute
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130 Returntype : string
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131 Exceptions : none
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132 Caller : general
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133 Status : At Risk
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134
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135 =cut
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136
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137 sub name{
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138 my $self = shift;
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139 return $self->{'name'} = shift if(@_);
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140 return $self->{'name'};
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141 }
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142
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143
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144 =head2 description
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145
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146 Arg [1] : string $newval (optional)
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147 The new value to set the description attribute to
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148 Example : $name = $obj->description()
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149 Description: Getter/Setter for the description attribute
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150 Returntype : string
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151 Exceptions : none
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152 Caller : general
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153 Status : At Risk
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154
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155 =cut
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156
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157 sub description{
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158 my $self = shift;
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159 return $self->{'description'} = shift if(@_);
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160 return $self->{'description'};
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161 }
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162
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163
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164 =head2 url
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165
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166 Arg [1] : string $newval (optional)
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167 The new value to set the url attribute to
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168 Example : $name = $obj->url()
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169 Description: Getter/Setter for the url attribute
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170 Returntype : string
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171 Exceptions : none
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172 Caller : general
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173 Status : At Risk
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174
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175 =cut
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176
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177 sub url{
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178 my $self = shift;
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179 return $self->{'url'} = shift if(@_);
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180 return $self->{'url'};
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181 }
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182
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183
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184 =head2 external_reference
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185
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186 Arg [1] : string $newval (optional)
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187 The new value to set the external_reference attribute to
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188 Example : $name = $obj->external_reference()
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189 Description: Getter/Setter for the external_reference attribute
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190 Returntype : string
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191 Exceptions : none
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192 Caller : general
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193 Status : At Risk
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194
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195 =cut
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196
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197 sub external_reference{
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198 my $self = shift;
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199 return $self->{'external_reference'} = shift if(@_);
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200 return $self->{'external_reference'};
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201 }
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202
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203
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204 =head2 type
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205
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206 Arg [1] : string $newval (optional)
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207 The new value to set the type attribute to
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208 Example : $name = $obj->type()
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209 Description: Getter/Setter for the type attribute
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210 Returntype : string
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211 Exceptions : none
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212 Caller : general
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213 Status : At Risk
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214
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215 =cut
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216
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217 sub type{
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218 my $self = shift;
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219 return $self->{'type'} = shift if(@_);
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220 return $self->{'type'};
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221 }
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222
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223
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224 =head2 source
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225
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226 Arg [1] : string $newval (optional)
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227 The new value to set the source attribute to
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228 Example : $name = $obj->source()
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229 Description: Getter/Setter for the source attribute
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230 Returntype : string
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231 Exceptions : none
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232 Caller : general
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233 Status : At Risk
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234
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235 =cut
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236
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237 sub source{
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238 my $self = shift;
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239 return $self->{'source'} = shift if(@_);
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240 return $self->{'source'};
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241 }
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242
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243
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244 =head2 associated_studies
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245 Example : $name = $obj->associate_studies()
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246 Description: Getter/Setter for the associated_studies attribute
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247 Returntype : reference to list of Bio::EnsEMBL::Variation::Study
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248 Exceptions : none
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249 Caller : general
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250 Status : At Risk
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251
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252 =cut
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253
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254 sub associated_studies{
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255 my $self = shift;
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256
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257 my $results;
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258
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259 if (defined($self->{'associate'}) && defined($self->{'adaptor'})) {
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260 my $studya = $self->{'adaptor'}->db()->get_StudyAdaptor();
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261 return $studya->fetch_all_by_dbID_list($self->{'associate'});
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262 }
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263 else {
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264 return [];
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265 }
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266 }
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