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1 #
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2 # Ensembl module for Bio::EnsEMBL::Funcgen::InputSubset
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3 #
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4
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5
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6 =head1 LICENSE
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7
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8 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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9 Genome Research Limited. All rights reserved.
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10
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11 This software is distributed under a modified Apache license.
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12 For license details, please see
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13
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14 http://www.ensembl.org/info/about/code_licence.html
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15
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16 =head1 CONTACT
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17
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18 Please email comments or questions to the public Ensembl
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19 developers list at <ensembl-dev@ebi.ac.uk>.
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20
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21 Questions may also be sent to the Ensembl help desk at
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22 <helpdesk@ensembl.org>.
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23
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24
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25 =head1 NAME
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26
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27 Bio::EnsEMBL::InputSubset - A module to represent InputSubset object.
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28
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29
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30 =head1 SYNOPSIS
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31
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32 use Bio::EnsEMBL::Funcgen::InputSubset;
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33
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34 my $input_subset = Bio::EnsEMBL::Funcgen::InputSubset->new
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35 (
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36 -DBID => $dbID,
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37 -ADAPTOR => $self,
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38 -NAME => $name,
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39 -INPUT_SET => $iset,
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40 -archive_id => $archive_id,
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41 -display_url => $display_url,
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42 -replicate => $iss_rep,
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43 -is_control => $is_control,
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44 );
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45
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46
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47
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48 =head1 DESCRIPTION
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49
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50 An InputSubset object represents an individual distinct input within a given InputSet. This
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51 normally translates to single file or replicate. There is no dedicated InputSubsetAdaptor,
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52 store and fetch functionality is embedded within the InputSetAdaptor.
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53
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54 =cut
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55
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56 use strict;
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57 use warnings;
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58
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59 package Bio::EnsEMBL::Funcgen::InputSubset;
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60
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61 use Bio::EnsEMBL::Utils::Argument qw( rearrange );
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62 use Bio::EnsEMBL::Utils::Exception qw( throw );
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63 use Bio::EnsEMBL::Funcgen::Storable;
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64
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65 use vars qw(@ISA);
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66 @ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
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67
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68
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69 =head2 new
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70
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71 Example : my $eset = Bio::EnsEMBL::Funcgen::InputSubset->new
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72 (
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73 -DBID => $dbID,
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74 -ADAPTOR => $self,
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75 -NAME => $name,
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76 -INPUT_SET => $iset,
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77 -archive_id => $archive_id,
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78 -display_url => $display_url,
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79 -replicate => $iss_rep,
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80 -is_control => $is_control,
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81 );
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82
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83
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84 Description: Constructor for InputSubset objects.
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85 Returntype : Bio::EnsEMBL::Funcgen::InputSubset
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86 Exceptions : Throws if no name defined
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87 Caller : InputSetAdaptor
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88 Status : At risk
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89
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90 =cut
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91
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92 sub new {
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93 my $caller = shift;
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94
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95 my $class = ref($caller) || $caller;
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96
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97 my $self = $class->SUPER::new(@_);
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98
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99 #do we need to add $fg_ids to this? Currently maintaining one feature_group focus.(combi exps?)
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100 my ($name, $eset, $archive_id,
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101 $display_url, $rep, $is_control)
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102 = rearrange(['NAME', 'INPUT_SET', 'ARCHIVE_ID',
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103 'DISPLAY_URL', 'REPLICATE', 'IS_CONTROL'], @_);
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104
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105
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106 throw('Must provide a name argument') if ! defined $name;
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107
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108 if(!(ref($eset) &&
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109 $eset->isa('Bio::EnsEMBL::Funcgen::InputSet')
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110 && $eset->dbID())){
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111 throw('Must provide a valid stored input_set argument');
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112 }
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113
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114
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115 $self->{name} = $name;
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116 $self->{input_set} = $eset;
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117 $self->{archive_id} = $archive_id;
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118 $self->{display_url} = $display_url;
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119 $self->{replicate} = $rep;
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120 $self->{is_control} = $is_control;
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121
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122 return $self;
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123 }
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124
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125
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126 =head2 name
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127
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128 Example : my $name = $exp_sset->name();
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129 Description: Getter for the name of this InputSubset.
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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 { return $_[0]->{name}; }
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138
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139
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140 =head2 input_set
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141
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142 Example : my $input_set = $input_sset->input_set;
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143 Description: Getter for the input_set attribute of this InputSubset.
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144 Returntype : Bio::EnsEMBL::Funcgen::InputSet
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145 Exceptions : None
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146 Caller : General
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147 Status : At Risk
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148
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149 =cut
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150
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151 sub input_set { return $_[0]->{input_set}; }
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152
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153
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154 =head2 archive_id
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155
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156 Example : my $archive_id = $inp_sset->archive_id;
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157 Description: Getter for the archive of this InputSubset.
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158 Returntype : String
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159 Exceptions : None
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160 Caller : General
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161 Status : At Risk
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162
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163 =cut
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164
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165 sub archive_id { return $_[0]->{archive_id}; }
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166
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167
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168 =head2 display_url
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169
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170 Example : my $url = $inp_sset->displau_url;
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171 Description: Getter for the display_url of this InputSubset.
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172 Returntype : String
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173 Exceptions : None
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174 Caller : General
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175 Status : At Risk
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176
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177 =cut
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178
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179 sub display_url{ return $_[0]->{display_url}; }
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180
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181
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182 =head2 replicate
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183
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184 Example : my $rep = $inp_sset->replicate;
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185 Description: Getter for the replicate attribute of this InputSubset.
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186 Returntype : Integer
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187 Exceptions : None
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188 Caller : General
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189 Status : At Risk
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190
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191 =cut
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192
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193 sub replicate { return $_[0]->{replicate}; }
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194
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195
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196 =head2 is_control
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197
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198 Example : if($input_sset->is_control){ # Do some control specific stuff here }
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199 Description: Getter for the is_control attribute of this InputSubset.
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200 Returntype : Boolean
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201 Exceptions : None
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202 Caller : General
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203 Status : At Risk
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204
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205 =cut
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206
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207 sub is_control { return $_[0]->{is_control}; }
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208
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209 1;
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210
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