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

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=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;