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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/DBSQL/SplicingTranscriptPairAdaptor.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,143 @@
+=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]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::DBSQL::SlicingTranscriptPairAdaptor - Database adaptor for the retrieval and
+storage of SplicingTranscriptPair objects
+
+=head1 SYNOPSIS
+
+  use Bio::EnsEMBL::Registry;
+
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+    -host => 'ensembldb.ensembl.org',
+    -user => 'anonymous',
+  );
+
+  $se_adaptor =
+    Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "SplicingTranscriptPair" );
+
+
+=head1 DESCRIPTION
+
+This is a database aware adaptor for the retrieval and storage of SplicingTranscriptPairs
+objects.
+
+=head1 METHODS
+
+=cut
+package Bio::EnsEMBL::DBSQL::SplicingTranscriptPairAdaptor;
+
+use strict;
+
+use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::SplicingTranscriptPair;
+
+use vars '@ISA';
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
+
+
+
+sub fetch_all_by_SplicingEvent{
+  my ($self, $splicing_event) = @_;
+  
+
+  my ($splicing_transcript_pair_id, $transcript_id_1, $transcript_id_2);
+
+  my $splicing_event_id = $splicing_event->dbID;
+  
+  my $sql = "select splicing_transcript_pair_id, transcript_id_1, transcript_id_2 from splicing_transcript_pair where splicing_event_id = $splicing_event_id";
+
+  my $sth = $self->prepare($sql);
+
+  $sth->execute();
+  $sth->bind_columns(\$splicing_transcript_pair_id, \$transcript_id_1, \$transcript_id_2);
+
+  my @pairs;
+
+  while($sth->fetch()){
+    push( @pairs,
+          $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingTranscriptPair', {
+                                    'adaptor'   => $self,
+                                    'dbID'      => $splicing_transcript_pair_id,
+                                    'transcript_id_1'   => $transcript_id_1,
+                                    'transcript_id_2'   => $transcript_id_2,
+				    'start'             => $splicing_event->start,
+                                    'end'               => $splicing_event->end
+                                  } ) );
+    
+  }
+  $sth->finish;
+  return \@pairs;
+
+}
+
+
+
+
+# _tables
+#  Arg [1]    : none
+#  Description: PROTECTED implementation of superclass abstract method.
+#               Returns the names, aliases of the tables to use for queries.
+#  Returntype : list of listrefs of strings
+#  Exceptions : none
+#  Caller     : internal
+#  Status     : At Risk
+
+sub _tables {
+  my $self = shift;
+
+  return ([ 'splicing_transcript_pair', 'stp' ]);
+}
+
+# _columns
+#  Arg [1]    : none
+#  Example    : none
+#  Description: PROTECTED implementation of superclass abstract method.
+#               Returns a list of columns to use for queries.
+#  Returntype : list of strings
+#  Exceptions : none
+#  Caller     : internal
+#  Status     : At Risk
+
+sub _columns {
+  my $self = shift;
+
+#  my $created_date = $self->db->dbc->from_date_to_seconds("gsi.created_date");
+#  my $modified_date = $self->db->dbc->from_date_to_seconds("gsi.modified_date");
+
+  return ( 'stp.splicing_transcript_pair_id','stp.transcript_id_1', 'stp.transcript_id_2');
+
+}
+
+sub list_dbIDs {
+  my ($self,$ordered) = @_;
+
+  return $self->_list_dbIDs("splicing_transcript_pair", undef, $ordered);
+}
+
+
+1;
+
+