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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::SlicingEventFeatureAdaptor - Database adaptor for the retrieval and
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24 storage of SplicingEventFeature objects
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25
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26 =head1 SYNOPSIS
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27
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28 use Bio::EnsEMBL::Registry;
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29
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30 Bio::EnsEMBL::Registry->load_registry_from_db(
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31 -host => 'ensembldb.ensembl.org',
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32 -user => 'anonymous',
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33 );
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34
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35 $se_adaptor =
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36 Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "SplicingEventFeature" );
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37
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38
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39 =head1 DESCRIPTION
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40
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41 This is a database aware adaptor for the retrieval and storage of SlicingEventFeatures
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42 objects.
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43
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44 =head1 METHODS
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45
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46 =cut
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47 package Bio::EnsEMBL::DBSQL::SplicingEventFeatureAdaptor;
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48
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49 use strict;
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50
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51 use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
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52 use Bio::EnsEMBL::DBSQL::SliceAdaptor;
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53 use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
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54 use Bio::EnsEMBL::DBSQL::DBAdaptor;
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55 use Bio::EnsEMBL::SplicingEventFeature;
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56
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57 use vars '@ISA';
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58 @ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
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59
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60
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61
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62 sub fetch_all_by_SplicingEvent{
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63 my ($self, $splicing_event) = @_;
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64
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65
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66 my ($splicing_event_feature_id, $splicing_event_id, $exon_id, $transcript_id, $feature_order, $transcript_association, $type, $start, $end);
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67
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68 $splicing_event_id = $splicing_event->dbID;
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69
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70 my $sql = "select splicing_event_feature_id, exon_id, transcript_id, feature_order, transcript_association, type, start, end from splicing_event_feature where splicing_event_id = $splicing_event_id";
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71
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72 my $sth = $self->prepare($sql);
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73
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74 $sth->execute();
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75 $sth->bind_columns(\$splicing_event_feature_id, \$exon_id, \$transcript_id, \$feature_order, \$transcript_association, \$type, \$start, \$end);
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76
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77 my @features;
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78
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79 while($sth->fetch()){
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80 push( @features,
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81 $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEventFeature', {
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82 'start' => $start,
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83 'end' => $end,
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84 'adaptor' => $self,
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85 'dbID' => $splicing_event_feature_id,
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86 'exon_id' => $exon_id,
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87 'transcript_id' => $transcript_id,
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88 'slice' => $splicing_event->slice,
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89 'type' => $type,
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90 'feature_order' => $feature_order,
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91 'transcript_association' => $transcript_association
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92 } ) );
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93
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94 }
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95 $sth->finish;
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96 return \@features;
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97
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98 }
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99
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100
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101
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102
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103 # _tables
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104 # Arg [1] : none
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105 # Description: PROTECTED implementation of superclass abstract method.
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106 # Returns the names, aliases of the tables to use for queries.
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107 # Returntype : list of listrefs of strings
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108 # Exceptions : none
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109 # Caller : internal
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110 # Status : At Risk
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111
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112 sub _tables {
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113 my $self = shift;
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114
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115 return ([ 'splicing_event_feature', 'sef' ]);
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116 }
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117
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118 # _columns
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119 # Arg [1] : none
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120 # Example : none
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121 # Description: PROTECTED implementation of superclass abstract method.
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122 # Returns a list of columns to use for queries.
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123 # Returntype : list of strings
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124 # Exceptions : none
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125 # Caller : internal
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126 # Status : At Risk
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127
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128 sub _columns {
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129 my $self = shift;
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130
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131 # my $created_date = $self->db->dbc->from_date_to_seconds("gsi.created_date");
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132 # my $modified_date = $self->db->dbc->from_date_to_seconds("gsi.modified_date");
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133
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134 return ( 'sef.splicing_event_id','sef.exon_id', 'sef.feature_order', 'sef.transcript_association', 'sef.type', 'sef.start', 'sef.end' );
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135
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136 }
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137
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138 sub list_dbIDs {
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139 my ($self,$ordered) = @_;
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140
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141 return $self->_list_dbIDs("splicing_event_feature", undef, $ordered);
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142 }
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143
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144
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145 1;
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146
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147
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