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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::UnconventionalTranscriptAssociationAdaptor
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24
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25 =head1 SYNOPSIS
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26
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27 $utaa = $registry->get_adaptor( 'Human', 'Core',
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28 'UnconventionalTranscriptAssociation' );
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29
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30 my $uta = $utaa->fetch_all_by_type('antisense');
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31
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32 =head1 DESCRIPTION
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33
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34 This is an adaptor for the retrieval and storage of
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35 UnconventionalTranscriptAssociation objects from the database. Most of
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36 the implementation is in the superclass BaseFeatureAdaptor.
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37
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38 =head1 METHODS
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39
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40 =cut
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41
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42 package Bio::EnsEMBL::DBSQL::UnconventionalTranscriptAssociationAdaptor;
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43
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44 use strict;
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45 use Bio::EnsEMBL::DBSQL::BaseAdaptor;
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46 use Bio::EnsEMBL::UnconventionalTranscriptAssociation;
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47
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48 use vars qw(@ISA);
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49
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50 @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
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51
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52
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53
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54
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55 =head2 fetch_all_by_interaction_type
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56
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57 Arg [1] : String type
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58 the type of associations to obtain
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59 Example : $utas = $utaa->fetch_all_by_type('antisense');
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60 Description: Obtains all unconventional transcript associations that
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61 have a particular interaction type.
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62 NOTE: In a multi-species database, this method will
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63 return all the entries matching the search criteria, not
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64 just the ones associated with the current species.
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65 Returntype : listREF of Bio::EnsEMBL::UnconventionalTranscriptAssociations
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66 Exceptions : none
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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 fetch_all_by_interaction_type {
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74
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75 my( $self, $type) = @_;
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76
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77 my $sth = $self->prepare("SELECT transcript_id, gene_id, interaction_type " .
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78 "FROM unconventional_transcript_association " .
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79 "WHERE interaction_type = ?");
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80
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81 $sth->bind_param(1, $type, SQL_VARCHAR);
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82 $sth->execute();
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83
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84 my $results = $self->_objs_from_sth($sth);
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85
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86 $sth->finish();
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87
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88 return $results;
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89
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90 }
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91
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92
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93 =head2 fetch_all_by_gene
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94
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95 Arg [1] : String gene the gene of associations to obtain
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96 Arg [2] : (optional) An interaction type; if set, only associations of this type will be returned.
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97 Example : $utas = $utaa->fetch_all_by_gene($gene, 'antisense');
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98 Description: Obtains all unconventional transcript associations that involve
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99 a particular gene.
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100 Returntype : listREF of Bio::EnsEMBL::UnconventionalTranscriptAssociations
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101 Exceptions : none
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102 Caller : general
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103 Status : At Risk
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104 : under development
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105
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106 =cut
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107
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108 sub fetch_all_by_gene {
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109
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110 my( $self, $gene, $type) = @_;
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111
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112 if(!ref($gene) || !$gene->isa('Bio::EnsEMBL::Gene')) {
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113 throw('$gene must be a Bio::EnsEMBL::Gene');
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114 }
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115
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116 my $sql = "SELECT transcript_id, gene_id, interaction_type FROM unconventional_transcript_association WHERE gene_id = ?";
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117 $sql .= " AND interaction_type = ?" if ($type);
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118
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119 my $sth = $self->prepare($sql);
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120
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121 $sth->bind_param(1, $gene->dbID(), SQL_INTEGER);
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122 $sth->bind_param(2, $type, SQL_VARCHAR) if ($type);
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123
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124 $sth->execute();
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125
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126 my $results = $self->_objs_from_sth($sth);
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127
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128 $sth->finish();
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129
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130 return $results;
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131
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132 }
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133
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134
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135 =head2 fetch_all_by_transcript
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136
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137 Arg [1] : String transcript the transcript of associations to obtain
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138 Arg [2] : (optional) An interaction type; if set, only associations of this type will be returned.
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139 Example : $utas = $utaa->fetch_all_by_transcript($transcript, 'antisense');
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140 Description: Obtains all unconventional transcript associations that involve
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141 a particular transcript.
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142 Returntype : listREF of Bio::EnsEMBL::UnconventionalTranscriptAssociations
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143 Exceptions : none
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144 Caller : general
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145 Status : At Risk
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146 : under development
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147
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148 =cut
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149
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150 sub fetch_all_by_transcript {
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151
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152 my( $self, $transcript, $type) = @_;
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153
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154 if(!ref($transcript) || !$transcript->isa('Bio::EnsEMBL::Transcript')) {
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155 throw('$transcript must be a Bio::EnsEMBL::Transcript');
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156 }
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157
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158 my $sql = "SELECT transcript_id, gene_id, interaction_type FROM unconventional_transcript_association WHERE transcript_id = ?";
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159 $sql .= " AND interaction_type = ?" if ($type);
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160
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161 my $sth = $self->prepare($sql);
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162
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163 $sth->bind_param(1, $transcript->dbID(), SQL_INTEGER);
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164 $sth->bind_param(2, $type, SQL_VARCHAR) if ($type);
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165
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166 $sth->execute();
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167
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168 my $results = $self->_objs_from_sth($sth);
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169
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170 $sth->finish();
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171
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172 return $results;
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173
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174 }
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175
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176
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177 =head2 store
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178
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179 Arg [1] : Bio::EnsEMBL::UnconventionalTranscriptAssociation
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180 the unconventional transcript association to store in the database
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181 Example : $utaa_adaptor->store($uta);
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182 Description: stores unconventional transcript associations in the database
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183 Returntype : none
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184 Exceptions :
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185 Caller : general
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186 Status : At Risk
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187 : under development
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188
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189 =cut
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190
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191 sub store {
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192
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193 my( $self, $uta ) = @_;
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194
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195 if(!ref($uta) || !$uta->isa('Bio::EnsEMBL::UnconventionalTranscriptAssociation')) {
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196 throw('$uta must be a Bio::EnsEMBL::UnconventionalTranscriptAssociation');
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197 }
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198
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199 my $sth = $self->prepare(qq {INSERT into unconventional_transcript_association
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200 (transcript_id, gene_id, interaction_type) VALUES (?,?,?)});
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201
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202 $sth->bind_param(1, $uta->transcript()->dbID(), SQL_INTEGER);
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203 $sth->bind_param(2, $uta->gene()->dbID, SQL_INTEGER);
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204 $sth->bind_param(3, $uta->interaction_type(), SQL_VARCHAR);
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205
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206 $sth->execute();
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207
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208 }
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209
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210
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211
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212 sub _objs_from_sth {
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213
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214 my ($self, $sth) = @_;
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215
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216 my $transcript_adaptor = $self->db()->get_TranscriptAdaptor();
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217 my $gene_adaptor = $self->db()->get_GeneAdaptor();
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218
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219 my ($gene_id, $transcript_id, $type);
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220 $sth->bind_columns(\$transcript_id, \$gene_id, \$type);
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221
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222 my @results;
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223
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224 while($sth->fetch()) {
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225
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226 my $gene = $gene_adaptor->fetch_by_dbID($gene_id);
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227 my $transcript = $transcript_adaptor->fetch_by_dbID($transcript_id);
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228
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229 my $obj = Bio::EnsEMBL::UnconventionalTranscriptAssociation->new($transcript, $gene, $type);
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230 push @results, $obj;
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231
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232 }
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233
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234 return \@results;
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235 }
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236
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237 1;
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238
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239
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