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2 =head1 LICENSE
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3
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4 Copyright (c) 1999-2011 The European Bioinformatics Institute and
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5 Genome Research Limited. All rights reserved.
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6
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7 This software is distributed under a modified Apache license.
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8 For license details, please see
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9
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10 http://www.ensembl.org/info/about/code_licence.html
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11
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12 =head1 CONTACT
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13
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14 Please email comments or questions to the public Ensembl
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15 developers list at <ensembl-dev@ebi.ac.uk>.
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16
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17 Questions may also be sent to the Ensembl help desk at
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18 <helpdesk@ensembl.org>.
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19
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::Funcgen::Experiment
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24
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25 =head1 SYNOPSIS
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26
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27 use Bio::EnsEMBL::Funcgen::Experiment;
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28
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29 my $exp = Bio::EnsEMBL::Funcgen::Experiment->new
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30 (
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31 -ADAPTOR => $self,
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32 -NAME => $name,
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33 -EXPERIMENTAL_GROUP => $experimental_group,
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34 -DATE => $date,
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35 -PRIMARY_DESIGN_TYPE => 'binding_site_indentification',
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36 -DESCRIPTION => $description,
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37 -ARCHIVE_ID => $archive_id,
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38 );
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39
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40 my $db_adaptor = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(...);
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41 my $exp_adaptor = $db_adaptor->get_ExperimentAdaptor();
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42 my $exp = $exp_adaptor->fetch_by_name($exp_name)
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43
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44 =head1 DESCRIPTION
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45
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46 The Experiment class represents an instance of an experiment i.e. a discrete set of data
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47
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48 =cut
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49
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50
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51 ################################################################################
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52
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53 package Bio::EnsEMBL::Funcgen::Experiment;
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54
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55 use warnings;
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56 use strict;
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57
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58 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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59 use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate );
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60 use Bio::EnsEMBL::Funcgen::Storable;
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61 use vars qw(@ISA);
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62
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63 @ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
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64
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65
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66
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67 =head2 new
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68
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69 Arg [-NAME] : String - experiment name
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70 Arg [-EXPERIMENTAL_GROUP] : Bio::EnsEMBL::Funcgen ExperimentalGroup associated with this experiment
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71 Arg [-DATE] : String - Date of the experiment (YYYY-MM-DD)
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72 Arg [-PRIMARY_DESIGN_TYPE] : String - MGED term for the primary design of teh experiment e.g. binding_site_identification
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73 Arg [-DESCRIPTION] : String
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74
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75 Example : my $array = Bio::EnsEMBL::Funcgen::Experiment->new
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76 (
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77 -NAME => $name,
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78 -EXPERIMENTAL_GROUP => $group,
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79 -DATE => $date,
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80 -PRIMARY_DESIGN_TYPE => $p_design_type,
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81 -DESCRIPTION => $description,
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82 );
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83
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84 Description: Creates a new Bio::EnsEMBL::Funcgen::Experiment object.
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85 Returntype : Bio::EnsEMBL::Funcgen::Experiment
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86 Exceptions : Throws if name not defined
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87 Throws if ExperimentalGroup not valid
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88 Caller : General
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89 Status : Medium Risk
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90
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91 =cut
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92
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93 sub new {
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94 my $caller = shift;
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95
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96 my $class = ref($caller) || $caller;
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97
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98 my $self = $class->SUPER::new(@_);
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99
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100 my ($name, $group, $date, $p_dtype, $desc, $archive_id, $data_url, $xml_id, $xml)
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101 = rearrange( ['NAME', 'EXPERIMENTAL_GROUP', 'DATE', 'PRIMARY_DESIGN_TYPE',
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102 'DESCRIPTION','ARCHIVE_ID', 'DATA_URL', 'MAGE_XML', 'MAGE_XML_ID'], @_ );
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103
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104
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105 #Added in v68
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106 #Remove in v69
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107 if($data_url || $archive_id){
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108 throw('The -data_url and -archive_id parameters have been moved to the InputSubSet class');
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109 }
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110
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111
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112 #Mandatory attr checks
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113
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114 if(ref($group) ne 'Bio::EnsEMBL::Funcgen::ExperimentalGroup'){
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115 throw("Must pass a valid stored Bio::EnsEMBL::Funcgen::ExperimentalGroup object");
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116 }
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117
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118 if(! defined $name){
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119 throw('You must provide a name parameter');
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120 }
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121
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122 #test date format here?
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123
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124
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125 #Direct assignment here so we avoid setter test in methods
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126 $self->{name} = $name;
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127 $self->{group} = $group;
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128 $self->{date} = $date if defined $date;
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129 $self->{primary_design_type} = $p_dtype if defined $p_dtype; #MGED term for primary design type
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130 $self->{description} = $desc if defined $desc;
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131
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132 #Maintain setter funcs here as these are populated after initialisation
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133 $self->mage_xml_id($xml_id) if defined $xml_id;
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134 $self->mage_xml($xml) if defined $xml;
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135
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136 return $self;
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137 }
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138
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139
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140 ### ACCESSOR METHODS ###
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141
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142 =head2 name
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143
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144 Example : my $exp_name = $exp->name;
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145 Description : Getter for the experiment name
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146 Returntype : String
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147 Exceptions : None
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148 Caller : General
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149 Status : Stable
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150
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151 =cut
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152
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153 sub name{
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154 return $_[0]->{'name'};
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155 }
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156
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157
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158 =head2 experimental_group
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159
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160 Example : my $exp_group_name = $exp->experimental_group()->name();
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161 Description : Getter for the experimental group
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162 Returntype : Bio::EnsEMBL::Funcgen::ExperimentalGroup
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163 Exceptions : None
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164 Caller : General
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165 Status : At risk
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166
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167 =cut
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168
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169 sub experimental_group{
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170 return $_[0]->{'group'};
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171 }
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172
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173
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174 =head2 date
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175
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176 Example : my $exp_date = $exp->date;
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177 Description : Getter for the date
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178 Returntype : String
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179 Exceptions : None
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180 Caller : General
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181 Status : Stable
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182
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183 =cut
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184
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185 sub date{
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186 return $_[0]->{'date'};
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187 }
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188
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189
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190 =head2 description
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191
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192 Example : my $exp_desc = $exp->description
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193 Description : Getter for the experiment description
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194 Returntype : String
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195 Exceptions : None
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196 Caller : General
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197 Status : At risk - Not used, was stable until v64
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198
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199 =cut
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200
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201 sub description{
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202 return $_[0]->{'description'};
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203 }
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204
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205
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206
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207
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208
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209 =head2 primary_design_type
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210
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211 Example : my $pdt = $exp->primary_design_type;
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212 Description : Getter for the primary design type
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213 Returntype : String - MGED term
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214 Exceptions : None
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215 Caller : General
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216 Status : At risk
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217
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218 =cut
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219
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220 sub primary_design_type{
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221 return $_[0]->{'primary_design_type'};
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222 }
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223
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224
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225 # Accessor/Setter methods
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226
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227 =head2 mage_xml
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228
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229 Arg [1] : string(optional) - MAGE XML
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230 Example : my $xml = $exp->mage_xml();
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231 Description : Getter/Setter for the mage_xml attribute
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232 Returntype : String
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233 Exceptions : None
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234 Caller : General
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235 Status : at risk
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236
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237 =cut
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238
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239 sub mage_xml{
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240 my ($self) = shift;
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241
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242 $self->{'mage_xml'} = shift if(@_);
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243
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244 #use fetch_attrs?
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245 if(! exists $self->{'mage_xml'} && $self->mage_xml_id()){
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246 $self->{'mage_xml'} = $self->adaptor->fetch_mage_xml_by_Experiment($self);
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247 }
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248
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249 return (exists $self->{'mage_xml'}) ? $self->{'mage_xml'} : undef;
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250 }
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251
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252
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253 =head2 mage_xml_id
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254
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255 Arg [1] : int (optional) - mage_xml_id
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256 Example : $exp->group_db_id('1');
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257 Description : Getter/Setter for the mage_xml attribute
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258 Returntype : String
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259 Exceptions : None
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260 Caller : General
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261 Status : at risk
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262
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263 =cut
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264
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265 sub mage_xml_id{
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266 my $self = shift;
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267
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268 $self->{'mage_xml_id'} = shift if @_;
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269
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270 return $self->{'mage_xml_id'};
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271 }
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272
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273
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274
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275
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276
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277
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278 #These convenience methods are to provide a registry for the experimental chips of the experiment
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279
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280 =head2 get_ExperimentalChips
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281
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282 Example : my $exp_chips = @{$exp->get_ExperimentalChips()}
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283 Description : Retrieves all ExperiemntalChips
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284 Returntype : Listref of ExperimentalChips
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285 Exceptions : None
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286 Caller : General
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287 Status : At risk
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288
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289 =cut
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290
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291 sub get_ExperimentalChips{
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292 my ($self) = shift;
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293
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294 #should this also store echips?
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295
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296 #Need to retrieve all from DB if not defined, then check whether already present and add and store if not
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297 #what about immediate access to dbID
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298 #should we separate and have add_ExperimentalChip?
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299
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300
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301
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302 if(! exists $self->{'experimental_chips'}){
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303 $self->{'experimental_chips'} = {};
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304
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305 #need to warn about DBAdaptor here?
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306
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307 foreach my $echip(@{$self->adaptor->db->get_ExperimentalChipAdaptor->fetch_all_by_experiment_dbID($self->dbID())}){
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308 $self->{'experimental_chips'}->{$echip->unique_id()} = $echip;
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309 }
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310 }
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311
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312 #is this returning a list or a listref?
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313 return [values %{$self->{'experimental_chips'}}];
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314 }
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315
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316 =head2 add_ExperimentalChip
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317
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318 Example : $exp_chip = $exp->add_ExperimentalChip($exp_chip)
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319 Description : Adds and stores an ExperiemntalChip for this Experiment
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320 Returntype : Bio::EnsEMBL::Funcgen::ExperimentalChip
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321 Exceptions : Throws is not passed a valid stored Bio::EnsENBML::Funcgen::ExperimentalChip
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322 Caller : General
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323 Status : At risk
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324
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325 =cut
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326
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327 sub add_ExperimentalChip{
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328 my ($self, $echip) = @_;
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329
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330
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331 throw("Must pass a valid stored Bio::EnsEMBL::Funcgen::ExperimentalChip object")
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332 if(! $echip->isa("Bio::EnsEMBL::Funcgen::ExperimentalChip") || ! $echip->dbID());
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333
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334 if(! exists $self->{'experimental_chips'}){
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335 $self->get_ExperimentalChips();
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336 $self->{'experimental_chips'}->{$echip->unique_id()} = $echip;
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337 #do this here without checking to avoid probelm of retrieving first stored chip
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338 }elsif(exists $self->{'experimental_chips'}->{$echip->unique_id()}){
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339 warn("You cannot add the same ExperimentalChip(".$echip->unique_id().")to an Experiment more than once, check your code");
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340 }else{
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341 $self->{'experimental_chips'}->{$echip->unique_id()} = $echip;
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342 }
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343
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344 return;
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345 }
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346
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347 =head2 get_ExperimentalChip_by_unique_id
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348
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349 Example : $exp_chip = $exp->add_ExperimentalChip($exp_chip)
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350 Description : Adds and stores an ExperiemntalChip for this Experiment
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351 Returntype : Bio::EnsEMBL::Funcgen::ExperimentalChip
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352 Exceptions : Throws if no uid supplied
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353 Caller : General
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354 Status : At risk
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355
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356 =cut
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357
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358 sub get_ExperimentalChip_by_unique_id{
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359 my ($self, $uid) = @_;
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360
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361 my ($echip);
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362
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363 throw("Must supply a ExperimentalChip unque_id") if(! defined $uid);
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364
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365 $self->{'experimental_chips'} || $self->get_ExperimentalChips();
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366
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367 if(exists $self->{'experimental_chips'}->{$uid}){
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368 $echip = $self->{'experimental_chips'}->{$uid};
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369 }
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370 #should we warn here if not exists?
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371
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372 return $echip;
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373 }
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374
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375
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376 =head2 get_ExperimentalChip_unique_ids
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377
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378 Example : foreach my $uid(@{$self->experiment->get_ExperimentalChip_unique_ids()}){ ... }
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379 Description : retrieves all ExperimentalChip unique_ids
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380 Returntype : ListRef
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381 Exceptions : None
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382 Caller : General
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383 Status : At risk
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384
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385 =cut
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386
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387 sub get_ExperimentalChip_unique_ids{
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388 my $self = shift;
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389
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390 $self->{'experimental_chips'} || $self->get_ExperimentalChips();
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391
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392 return [keys %{ $self->{'experimental_chips'}}];
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393 }
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394
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395
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396
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397
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398 ### Deprecated methods ###
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399
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400
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401 sub group{
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402 my $self = shift;
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403
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404 deprecate("group is deprecated experimental_group instead");
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405 throw("You are trying to set a experimental group name using a deprecated method") if @_;
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406 return $self->experimental_group()->name;
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407 }
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408
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409
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410
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411 sub group_id{
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412 my ($self) = shift;
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413
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414 deprecate("Experiment->group_id is deprecated. Use exp->experimental_group->dbID instead");
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415 return $self->experimental_group()->dbID;
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416 }
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417
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418
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419
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420 sub archive_id{ #deprecated in v68
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421 #would deprecate, but no easy way of doing this reliably
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422 throw("Use InputSubset->archive_id");
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423 }
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424
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425
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426 sub data_url{ #deprecated in v68
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427 #would deprecate, but no easy way of doing this reliably
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428 throw("Use InputSubset->display_url");
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429 }
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430
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431
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432 sub source_info{ #deprecated in v68
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433 #would deprecate, but no easy way of doing this reliably
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434 throw("Use InputSubset->source_info");
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435 }
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436
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437
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438 1;
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439
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