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lib/Bio/EnsEMBL/DBSQL/IntronSupportingEvidenceAdaptor.pm  view on Meta::CPAN

  return $sf->dbID();
}

=head2 store_transcript_linkage

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence Evidence to link
  Arg[2]      : Bio::EnsEMBL::Transcript Transcript to link
  Arg[3]      : Integer an optional ID to give if the Transcript's own ID is possibly incorrect
  Example     : $isea->store_transcript_linkage($ise, $transcript);
                $isea->store_transcript_linkage($ise, $transcript, $tid);
  Description : Links a Transcript to a portion of Intron evidence
  Returntype  : None
  Exceptions  : Thrown if the given object is not a Transcript, if the 
                transcript is not stored, if the supporting evidence is not
                stored and for any DB exception. 

=cut

sub store_transcript_linkage {
  my ($self, $sf, $transcript, $transcript_id) = @_;
  assert_ref($sf, 'Bio::EnsEMBL::IntronSupportingEvidence', 'intron_supporting_evidence');
  assert_ref($transcript, 'Bio::EnsEMBL::Transcript', 'transcript');
  
  throw "Cannot perform the link. The IntronSupportingEvidence must be persisted first" unless $sf->is_stored($self->db());
  
  my $insert_ignore = $self->insert_ignore_clause();
  my $sql = qq{
${insert_ignore} into transcript_intron_supporting_evidence
(transcript_id, intron_supporting_evidence_id, previous_exon_id, next_exon_id)
values (?,?,?,?)
  };

  my $intron = $sf->get_Intron($transcript);
  my ($previous_exon, $next_exon) = ($intron->prev_Exon(), $intron->next_Exon());
  $transcript_id ||= $transcript->dbID();
  
  my $params = [
    [$transcript_id, SQL_INTEGER],
    [$sf->dbID(), SQL_INTEGER],
    [$previous_exon->dbID(), SQL_INTEGER],
    [$next_exon->dbID(), SQL_INTEGER],
  ];
  $self->dbc()->sql_helper()->execute_update(-SQL => $sql, -PARAMS => $params);
  
  return;
}

####### UPDATE

=head2 update

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence Evidence to update
  Example     : $isea->update($ise);
  Description : Updates all attributes of an evidence object
  Returntype  : None
  Exceptions  : Thrown if the given object is not a IntronSupportingEvidence,
                if the object is not stored and for normal DB errors

=cut

sub update {
  my ($self, $sf) = @_;
  assert_ref($sf, 'Bio::EnsEMBL::IntronSupportingEvidence', 'intron_supporting_evidence');
  if (! $sf->is_stored($self->db())) {
    throw "Cannot update the supporting evidence if it has not already been stored in this database";
  }
  
  my $params = [
    [$sf->analysis()->dbID(), SQL_INTEGER],
    [$sf->slice()->get_seq_region_id(), SQL_INTEGER],
    [$sf->start(), SQL_INTEGER],
    [$sf->end(), SQL_INTEGER],
    [$sf->strand(), SQL_INTEGER],
    [$sf->hit_name(), SQL_VARCHAR],
    [$sf->score(), SQL_FLOAT],
    [$sf->score_type(), SQL_VARCHAR],
    [$sf->is_splice_canonical() || 0, SQL_INTEGER],
    [$sf->dbID(), SQL_INTEGER],
  ];
  
  my $sql = <<'SQL';
UPDATE intron_supporting_evidence
SET analysis_id =?, seq_region_id =?, seq_region_start =?, 
seq_region_end =?, seq_region_strand =?, hit_name =?, score =?, score_type =?,
is_splice_canonical =?
WHERE intron_supporting_evidence_id =?
SQL
  
  $self->dbc()->sql_helper()->execute_update(-SQL => $sql, -PARAMS => $params);
  return;
}

####### DELETION

=head2 remove

  Arg[1]      : Bio::EnsEMBL::IntronSupportingEvidence
  Example			: $isea->remove($ise);
  Description	: Deletes the given IntronSupportingEvidence from the database. 
                This can only occur if the object has no linked transcripts
  Returntype 	: None
  Exceptions 	: Thrown if the IntronSupportingEvidence is not stored, if
                the object has linked transcripts and in the event of any
                database error

=cut

sub remove {
  my ($self, $sf) = @_;
  assert_ref($sf, 'Bio::EnsEMBL::IntronSupportingEvidence', 'intron_supporting_evidence');
  if (! $sf->is_stored($self->db())) {
    throw "Cannot delete the supporting evidence if it has not already been stored in this database";
  }
  if($sf->has_linked_transcripts()) {
    throw sprintf('Cannot delete supporting evidence %d. It still has transcripts attached', $sf->dbID());
  }
  $self->dbc()->sql_helper()->execute_update(
    -SQL => 'DELETE from intron_supporting_evidence where intron_supporting_evidence_id =?', 
    -PARAMS => [[$sf->dbID(), SQL_INTEGER]],
  );
  return;