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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/DBSQL/SplicingEventFeatureAdaptor.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,147 @@
+=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::SlicingEventFeatureAdaptor - Database adaptor for the retrieval and
+storage of SplicingEventFeature objects
+
+=head1 SYNOPSIS
+
+  use Bio::EnsEMBL::Registry;
+
+  Bio::EnsEMBL::Registry->load_registry_from_db(
+    -host => 'ensembldb.ensembl.org',
+    -user => 'anonymous',
+  );
+
+  $se_adaptor =
+    Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "SplicingEventFeature" );
+
+
+=head1 DESCRIPTION
+
+This is a database aware adaptor for the retrieval and storage of SlicingEventFeatures
+objects.
+
+=head1 METHODS
+
+=cut
+package Bio::EnsEMBL::DBSQL::SplicingEventFeatureAdaptor;
+
+use strict;
+
+use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::SplicingEventFeature;
+
+use vars '@ISA';
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
+
+
+
+sub fetch_all_by_SplicingEvent{
+  my ($self, $splicing_event) = @_;
+  
+
+  my ($splicing_event_feature_id, $splicing_event_id, $exon_id, $transcript_id, $feature_order, $transcript_association, $type, $start, $end);
+
+  $splicing_event_id = $splicing_event->dbID;
+  
+  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";
+
+  my $sth = $self->prepare($sql);
+
+  $sth->execute();
+  $sth->bind_columns(\$splicing_event_feature_id, \$exon_id, \$transcript_id, \$feature_order, \$transcript_association, \$type, \$start, \$end);
+
+  my @features;
+
+  while($sth->fetch()){
+    push( @features,
+          $self->_create_feature_fast( 'Bio::EnsEMBL::SplicingEventFeature', {
+                                    'start'     => $start,
+                                    'end'       => $end,
+                                    'adaptor'   => $self,
+                                    'dbID'      => $splicing_event_feature_id,
+                                    'exon_id'   => $exon_id,
+                                    'transcript_id' => $transcript_id,
+                                    'slice'     => $splicing_event->slice,
+                                    'type'      => $type,
+				    'feature_order'            => $feature_order,
+                                    'transcript_association'   => $transcript_association 
+                                  } ) );
+    
+  }
+  $sth->finish;
+  return \@features;
+
+}
+
+
+
+
+# _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_event_feature', 'sef' ]);
+}
+
+# _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 = $self->db->dbc->from_date_to_seconds("gsi.modified_date");
+
+  return ( 'sef.splicing_event_id','sef.exon_id', 'sef.feature_order', 'sef.transcript_association', 'sef.type', 'sef.start', 'sef.end' );
+
+}
+
+sub list_dbIDs {
+  my ($self,$ordered) = @_;
+
+  return $self->_list_dbIDs("splicing_event_feature", undef, $ordered);
+}
+
+
+1;
+
+