diff variant_effect_predictor/Bio/EnsEMBL/DBSQL/SeqRegionSynonymAdaptor.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/DBSQL/SeqRegionSynonymAdaptor.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,79 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+INTO 
+=cut
+
+package Bio::EnsEMBL::DBSQL::SeqRegionSynonymAdaptor;
+use vars qw(@ISA);
+use strict;
+
+
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
+use Bio::EnsEMBL::SeqRegionSynonym;
+
+@ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
+
+
+sub get_synonyms{
+  my $self = shift;
+  my $seq_id = shift;
+  
+  my @results;
+
+  my $sth = $self->prepare("select seq_region_synonym_id, synonym, external_db_id from seq_region_synonym where seq_region_id = ?");
+  $sth->bind_param(1, $seq_id, SQL_INTEGER);
+  $sth->execute();
+  my $dbid;
+  my $alt_name;
+  my $ex_db;
+  $sth->bind_columns(\$dbid, \$alt_name, \$ex_db);
+  while($sth->fetch()){
+    push @results, Bio::EnsEMBL::SeqRegionSynonym->new(-adaptor => $self,
+                                                       -synonym => $alt_name,
+						       -dbID => $dbid,
+                                                       -external_db_id => $ex_db,
+                                                       -seq_region_id => $seq_id);
+  }
+  $sth->finish;
+
+  return \@results;
+}
+
+sub store {
+  my $self = shift;
+  my $syn = shift;
+
+  return if($syn->is_stored($self->db));
+
+  if(!defined($syn->seq_region_id)){
+    throw("seq_region_id is needed to store a seq_region_synoym");
+  }
+
+  my $sth = $self->prepare("INSERT IGNORE INTO seq_region_synonym (seq_region_id, synonym, external_db_id) VALUES (?, ?, ?)");
+  $sth->bind_param(1, $syn->seq_region_id,  SQL_INTEGER);
+  $sth->bind_param(2, $syn->name         ,  SQL_VARCHAR);
+  $sth->bind_param(3, $syn->external_db_id, SQL_INTEGER);
+  $sth->execute;
+  $syn->{'dbID'} = $sth->{'mysql_insertid'};
+  $sth->finish;
+}
+
+
+
+1;