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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::RepeatConsensusAdaptor
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24
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25 =head1 SYNOPSIS
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26
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27 $rca = $database_adaptor->get_RepeatConsensusAdaptor();
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28
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29 $repeat_consensus = $rca->fetch_by_dbID(132);
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30 $repeat_consensus = $rca->fetch_by_name_class( 'AluSx', 'SINE/Alu' );
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31
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32 $rca->store( $rc1, $rc2, $rc3 );
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33
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34 =head1 DESCRIPTION
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35
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36 This is an adaptor for the retrieval and storage of RepeatConsensus
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37 objects.
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38
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39 =head1 METHODS
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40
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41 =cut
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42
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43 package Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor;
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44
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45 use strict;
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46 use warnings;
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47 use Bio::EnsEMBL::DBSQL::BaseAdaptor;
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48 use Bio::EnsEMBL::RepeatConsensus;
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49 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
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50
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51 use base qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
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52
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53 =head2 fetch_all_repeat_types
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54
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55 Example : my $types = $rca->fetch_all_repeat_types();
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56 Description : Returns the distinct repeat types available from a database
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57 Returntype : Array
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58 Exceptions : -
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59
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60 =cut
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61
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62
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63 sub fetch_all_repeat_types {
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64 my ($self) = @_;
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65 return $self->dbc()->sql_helper()->execute_simple(
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66 -SQL => 'SELECT DISTINCT repeat_type FROM repeat_consensus');
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67 }
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68
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69
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70 =head2 fetch_by_dbID
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71
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72 Arg [1] : int $db_id
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73 The database identifier for the RepeatConsensus to obtain
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74 Example : $repeat_consensus = $repeat_consensus_adaptor->fetch_by_dbID(4);
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75 Description: Obtains a RepeatConsensus object from the database via its
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76 primary key.
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77 Returntype : Bio::EnsEMBL::RepeatConsensus
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78 Exceptions : none
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79 Caller : general, Bio::EnsEMBL::RepeatFeatureAdaptor
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80 Status : Stable
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81
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82 =cut
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83
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84 sub fetch_by_dbID {
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85 my( $self, $db_id ) = @_;
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86
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87 my ($rc) = @{$self->_generic_fetch("repeat_consensus_id = $db_id")};
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88
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89 return $rc;
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90 }
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91
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92
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93
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94 =head2 fetch_by_name
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95
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96 Arg [1] : string $name
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97 the name of the repeat consensus to obtain
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98 Example : $rc = $repeat_consensus_adaptor->fetch_by_name('AluSx');
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99 Description: Obtains a repeat consensus from the database via its name
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100 Returntype : Bio::EnsEMBL::RepeatConsensus
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101 Exceptions : none
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102 Caller : general
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103 Status : Stable
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104
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105 =cut
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106
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107 sub fetch_by_name {
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108 my( $self, $name ) = @_;
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109
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110 my ($rc) = @{$self->_generic_fetch("repeat_name = '$name'")};
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111
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112 return $rc;
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113 }
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114
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115
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116 =head2 fetch_by_name_class
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117
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118 Arg [1] : string $name
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119 the name of the repeat consensus to obtain
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120 Arg [2] : string $class
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121 the class of the repeat consensus to obtain
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122 Example : $rc = $repeat_consensus_adaptor->
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123 fetch_by_name_class('AluSx', 'SINE/Alu');
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124 Description: Obtains a repeat consensus from the database
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125 via its name and class
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126 Returntype : Bio::EnsEMBL::RepeatConsensus
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127 Exceptions : none
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128 Caller : general
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129 Status : Stable
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130
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131 =cut
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132
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133 sub fetch_by_name_class {
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134 my( $self, $name, $class ) = @_;
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135
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136
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137 my ($rc) = @{$self->_generic_fetch(qq{
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138 repeat_name = '$name'
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139 AND repeat_class = '$class'
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140 })};
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141
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142 return $rc;
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143 }
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144
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145
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146 =head2 fetch_all_by_class_seq
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147
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148 Arg [1] : string $class
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149 the class of the repeat consensus to obtain
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150 Arg [2] : string $seq
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151 the sequence of the repeat consensus to obtain
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152 Example : $rc = $repeat_consensus_adaptor->
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153 fetch_all_by_class_seq('trf', 'ATGGTGTCA');
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154 Description: Obtains a repeat consensus from the database
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155 via its class and sequence
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156 Returntype : listREF of Bio::EnsEMBL::RepeatConsensus
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157 Exceptions : none
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158 Caller : general
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159 Status : Stable
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160
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161 =cut
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162
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163 sub fetch_all_by_class_seq {
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164 my( $self, $class, $seq ) = @_;
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165
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166 return $self->_generic_fetch(qq{
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167 repeat_class = '$class'
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168 AND repeat_consensus = '$seq'
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169 });
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170 }
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171
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172
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173 sub fetch_by_class_seq {
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174 deprecate('Use fetch_all_by_class_seq instead');
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175 fetch_all_by_class_seq(@_);
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176 }
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177
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178
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179 =head2 _generic_fetch
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180
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181 Arg [1] : string $where_clause
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182 Example : none
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183 Description: PRIVATE used to create RepeatConsensus features from an
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184 SQL constraint
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185 Returntype : listref of Bio::EnsEMBL::RepeatConsensus objects
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186 Exceptions : none
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187 Caller : internal
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188 Status : Stable
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189
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190 =cut
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191
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192 sub _generic_fetch {
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193 my( $self, $where_clause ) = @_;
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194
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195 my( $repeat_consensus_id, $repeat_name, $repeat_class,$repeat_length,
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196 $repeat_consensus, $repeat_type );
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197
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198 my $sth = $self->prepare(qq{
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199 SELECT repeat_consensus_id
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200 , repeat_name
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201 , repeat_class
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202 , repeat_type
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203 , repeat_consensus
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204 FROM repeat_consensus
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205 WHERE }. $where_clause);
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206
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207 $sth->execute;
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208 $sth->bind_columns(
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209 \$repeat_consensus_id,
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210 \$repeat_name,
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211 \$repeat_class,
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212 \$repeat_type,
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213 \$repeat_consensus
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214 );
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215
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216
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217 my @consensi;
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218 while ($sth->fetch) {
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219 if ($repeat_consensus =~ /^(\d+)\(N\)$/) {
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220 $repeat_length = $1;
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221 } else {
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222 $repeat_length = CORE::length($repeat_consensus);
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223 }
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224
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225 push @consensi, Bio::EnsEMBL::RepeatConsensus->new
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226 (-DBID => $repeat_consensus_id,
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227 -NAME => $repeat_name,
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228 -REPEAT_CLASS => $repeat_class,
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229 -REPEAT_TYPE => $repeat_type,
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230 -LENGTH => $repeat_length,
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231 -ADAPTOR => $self,
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232 -REPEAT_CONSENSUS => $repeat_consensus);
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233 }
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234 return \@consensi;
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235 }
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236
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237
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238 =head2 store
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239
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240 Arg [1] : list of Bio::EnsEMBL::RepeatConsensus @consensi
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241 Example : $repeat_consensus_adaptor->store(@consensi);
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242 Description: stores a list of RepeatConsensus objects in the database
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243 Returntype : none
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244 Exceptions : none
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245 Caller : ?
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246 Status : Stable
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247
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248 =cut
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249
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250 sub store {
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251 my( $self, @consensi ) = @_;
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252
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253 my $sth = $self->prepare(q{
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254 INSERT into repeat_consensus( repeat_consensus_id
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255 , repeat_name
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256 , repeat_class
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257 , repeat_type
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258 , repeat_consensus )
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259 VALUES (NULL, ?,?,?,?)
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260 });
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261
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262 foreach my $rc (@consensi) {
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263 my $name = $rc->name
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264 or throw("name not set");
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265 my $class = $rc->repeat_class
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266 or throw("repeat_class not set");
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267 my $type = $rc->repeat_type();
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268 $type = "" unless defined $type;
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269 my $seq = $rc->repeat_consensus
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270 or throw("repeat_consensus not set");
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271
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272 $sth->bind_param(1,$name,SQL_VARCHAR);
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273 $sth->bind_param(2,$class,SQL_VARCHAR);
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274 $sth->bind_param(3,$type,SQL_VARCHAR);
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275 $sth->bind_param(4,$seq,SQL_LONGVARCHAR);
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276
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277 $sth->execute();
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278
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279 my $db_id = $sth->{'mysql_insertid'}
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280 or throw("Didn't get an insertid from the INSERT statement");
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281
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282 $rc->dbID($db_id);
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283 $rc->adaptor($self);
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284 }
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285 }
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286
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287 1;
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288
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289 __END__
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290
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