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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 INTO
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19 =cut
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20
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21 package Bio::EnsEMBL::DBSQL::SeqRegionSynonymAdaptor;
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22 use vars qw(@ISA);
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23 use strict;
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24
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25
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26 use Bio::EnsEMBL::DBSQL::BaseAdaptor;
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27 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
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28 use Bio::EnsEMBL::SeqRegionSynonym;
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29
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30 @ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
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31
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32
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33 sub get_synonyms{
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34 my $self = shift;
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35 my $seq_id = shift;
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36
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37 my @results;
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38
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39 my $sth = $self->prepare("select seq_region_synonym_id, synonym, external_db_id from seq_region_synonym where seq_region_id = ?");
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40 $sth->bind_param(1, $seq_id, SQL_INTEGER);
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41 $sth->execute();
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42 my $dbid;
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43 my $alt_name;
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44 my $ex_db;
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45 $sth->bind_columns(\$dbid, \$alt_name, \$ex_db);
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46 while($sth->fetch()){
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47 push @results, Bio::EnsEMBL::SeqRegionSynonym->new(-adaptor => $self,
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48 -synonym => $alt_name,
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49 -dbID => $dbid,
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50 -external_db_id => $ex_db,
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51 -seq_region_id => $seq_id);
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52 }
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53 $sth->finish;
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54
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55 return \@results;
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56 }
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57
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58 sub store {
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59 my $self = shift;
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60 my $syn = shift;
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61
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62 return if($syn->is_stored($self->db));
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63
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64 if(!defined($syn->seq_region_id)){
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65 throw("seq_region_id is needed to store a seq_region_synoym");
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66 }
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67
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68 my $sth = $self->prepare("INSERT IGNORE INTO seq_region_synonym (seq_region_id, synonym, external_db_id) VALUES (?, ?, ?)");
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69 $sth->bind_param(1, $syn->seq_region_id, SQL_INTEGER);
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70 $sth->bind_param(2, $syn->name , SQL_VARCHAR);
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71 $sth->bind_param(3, $syn->external_db_id, SQL_INTEGER);
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72 $sth->execute;
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73 $syn->{'dbID'} = $sth->{'mysql_insertid'};
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74 $sth->finish;
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75 }
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76
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77
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78
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79 1;
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