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

  }

  if($cs->is_sequence_level() && !$not_dna) {
    if(!$seqref) {
      throw("Must provide sequence for sequence level coord system.");
    }
    if(ref($seqref) ne 'SCALAR') {
      throw("Sequence must be a scalar reference.");
    }
    my $seq_len = length($$seqref);

    if($seq_len != $sr_len) {
      throw("Sequence length ($seq_len) must match slice length ($sr_len).");
    }
  } else {
    if($seqref) {
      throw("Cannot provide sequence for non-sequence level seq regions.");
    }
  }

  #store the seq_region

  my $sth = $db->dbc->prepare("INSERT INTO seq_region " .
                              "            ( name, length, coord_system_id ) " .
                              "     VALUES ( ?, ?, ? )"
      );

  $sth->bind_param(1,$sr_name,SQL_VARCHAR);
  $sth->bind_param(2,$sr_len,SQL_INTEGER);
  $sth->bind_param(3,$cs->dbID,SQL_INTEGER);

  $sth->execute();

  my $seq_region_id = $self->last_insert_id('seq_region_id', undef, 'seq_region');

  if(!$seq_region_id) {
    throw("Database seq_region insertion failed.");
  }

  if($cs->is_sequence_level() && !$not_dna) {
    #store sequence if it was provided
    my $seq_adaptor = $db->get_SequenceAdaptor();
    $seq_adaptor->store($seq_region_id, $$seqref);
  }

  #synonyms
  if(defined($slice->{'synonym'})){
    foreach my $syn (@{$slice->{'synonym'}} ){
      $syn->seq_region_id($seq_region_id); # set the seq_region_id
      $syn->adaptor->store($syn);
    }
  }
  
  
  $slice->adaptor($self);

  return $seq_region_id;
}


sub update {
  my $self = shift;
  my $slice = shift;

  #
  # Get all of the sanity checks out of the way before storing anything
  #

  if(!ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
    throw('Slice argument is required');
  }

  my $cs = $slice->coord_system();
  throw("Slice must have attached CoordSystem.") if(!$cs);

  my $db = $self->db();

  if($slice->start != 1 || $slice->strand != 1) {
    throw("Slice must have start==1 and strand==1.");
  }

  if($slice->end() != $slice->seq_region_length()) {
    throw("Slice must have end==seq_region_length");
  }

  my $sr_len = $slice->length();
  my $sr_name  = $slice->seq_region_name();

  if(!$sr_name) {
    throw("Slice must have valid seq region name.");
  }

  #update the seq_region

  my $seq_region_id = $slice->get_seq_region_id();
  my $update_sql = qq(
     UPDATE seq_region
        SET name = ?,
            length = ?,
            coord_system_id = ?
      WHERE seq_region_id = ?
  );

  my $sth = $db->dbc->prepare($update_sql);

  $sth->bind_param(1,$sr_name,SQL_VARCHAR);
  $sth->bind_param(2,$sr_len,SQL_INTEGER);
  $sth->bind_param(3,$cs->dbID,SQL_INTEGER);

  $sth->bind_param(4, $seq_region_id, SQL_INTEGER);

  $sth->execute();

  #synonyms
  if(defined($slice->{'synonym'})){
    foreach my $syn (@{$slice->{'synonym'}} ){
      $syn->seq_region_id($seq_region_id); # set the seq_region_id
      my $syn_adaptor = $db->get_SeqRegionSynonymAdaptor();
      $syn_adaptor->store($syn);
    }
  }