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

                             perc_ident, external_db_id, hcoverage, align_type)
     VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)"    # 16 arguments, external_data removed and align_type added
  );

FEATURE:
  foreach my $feat (@feats) {
    if ( !ref $feat || !$feat->isa("Bio::EnsEMBL::DnaDnaAlignFeature") )
    {
      throw("feature must be a Bio::EnsEMBL::DnaDnaAlignFeature, not a [". ref($feat). "]." );
    }

    if ( $feat->is_stored($db) ) {
      warning( "DnaDnaAlignFeature [".$feat->dbID()."] is already stored in this database." );
      next FEATURE;
    }

    my $hstart  = $feat->hstart();
    my $hend    = $feat->hend();
    my $hstrand = $feat->hstrand();
    $self->_check_start_end_strand( $hstart, $hend, $hstrand, $feat->hslice );

    my $cigar_string = $feat->cigar_string();
    if ( !$cigar_string ) {
      $cigar_string = $feat->length() . 'M';
      warning( "DnaDnaAlignFeature does not define a cigar_string.\n"
          . "Assuming ungapped block with cigar_line=$cigar_string ." );
    }
    my $align_type = $feat->align_type();

    my $hseqname = $feat->hseqname();
    if ( !$hseqname ) {
      throw("DnaDnaAlignFeature must define an hseqname.");
    }

    if ( !defined( $feat->analysis ) ) {
      throw(
        "An analysis must be attached to the features to be stored.");
    }

    #store the analysis if it has not been stored yet
    if ( !$feat->analysis->is_stored($db) ) {
      $analysis_adaptor->store( $feat->analysis() );
    }

    my $original = $feat;
    my $seq_region_id;
    ( $feat, $seq_region_id ) = $self->_pre_store($feat);
    
    $sth->bind_param( 1,  $seq_region_id,        SQL_INTEGER );
    $sth->bind_param( 2,  $feat->start,          SQL_INTEGER );
    $sth->bind_param( 3,  $feat->end,            SQL_INTEGER );
    $sth->bind_param( 4,  $feat->strand,         SQL_TINYINT );
    $sth->bind_param( 5,  $hstart,               SQL_INTEGER );
    $sth->bind_param( 6,  $hend,                 SQL_INTEGER );
    $sth->bind_param( 7,  $hstrand,              SQL_TINYINT );
    $sth->bind_param( 8,  $hseqname,             SQL_VARCHAR );
    $sth->bind_param( 9,  $cigar_string,         SQL_LONGVARCHAR );
    $sth->bind_param( 10, $feat->analysis->dbID, SQL_INTEGER );
    $sth->bind_param( 11, $feat->score,          SQL_DOUBLE );
    $sth->bind_param( 12, $feat->p_value,        SQL_DOUBLE );
    $sth->bind_param( 13, $feat->percent_id,     SQL_FLOAT );
    $sth->bind_param( 14, $feat->external_db_id, SQL_INTEGER );
    $sth->bind_param( 15, $feat->hcoverage,      SQL_DOUBLE );
    $sth->bind_param( 16, $feat->align_type,     SQL_VARCHAR);
    $sth->execute();

    my $dbId = $self->last_insert_id("${tablename}_id", undef, $tablename);

    # store attributes if there are any
    my $attr_adaptor = $db->get_AttributeAdaptor();
    $attr_adaptor->store_on_DnaDnaAlignFeature($dbId, $feat->get_all_Attributes);

    $original->dbID( $dbId );
    $original->adaptor($self);
  } ## end foreach my $feat (@feats)

  $sth->finish();
} ## end sub store


=head2 remove

  Arg [1]    : A feature $feature 
  Example    : $feature_adaptor->remove($feature);
  Description: This removes a feature from the database.  The table the
               feature is removed from is defined by the abstract method
               _tablename, and the primary key of the table is assumed
               to be _tablename() . '_id'.  The feature argument must 
               be an object implementing the dbID method, and for the
               feature to be removed from the database a dbID value must
               be returned.
  Returntype : none
  Exceptions : thrown if $feature arg does not implement dbID(), or if
               $feature->dbID is not a true value
  Caller     : general
  Status     : Stable

=cut


sub remove {
  my ($self, $feature) = @_;

  if(!$feature || !ref($feature) || !$feature->isa('Bio::EnsEMBL::Feature')) {
    throw('Feature argument is required');
  }

  if(!$feature->is_stored($self->db)) {
    throw("This feature is not stored in this database");
  }

  my @tabs = $self->_tables;
  my ($table) = @{$tabs[0]};

  my $sth = $self->prepare("DELETE FROM $table WHERE ${table}_id = ?");
  $sth->bind_param(1,$feature->dbID,SQL_INTEGER);
  $sth->execute();

  # remove the attributes associated with this feature
  my $attrib_adaptor = $self->db->get_AttributeAdaptor;
  $attrib_adaptor->remove_from_DnaDnaAlignFeature($feature);

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

              $end += $seq_region_len;
              $start += $seq_region_len if $seq_region_end > $dest_slice_start;

            } elsif ($seq_region_start <= $dest_slice_end) {
              # do nothing
            } elsif ($seq_region_end >= $dest_slice_start) {
              $start += $seq_region_len;
              $end += $seq_region_len;

            } elsif ($seq_region_end <= $dest_slice_end) {
              $end += $seq_region_len if $end < 0;

            } elsif ($seq_region_start > $seq_region_end) {
              $end += $seq_region_len;
            }

          } else {

            if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
              # do nothing
            } elsif ($seq_region_start > $seq_region_end) {
              if ($seq_region_start <= $dest_slice_end) {
                $start -= $seq_region_len;
              } elsif ($seq_region_end >= $dest_slice_start) {
                $end += $seq_region_len;
              }
            }
          }
        }

        $seq_region_start = $start;
        $seq_region_end = $end;
        $seq_region_strand *= -1;

      } ## end else [ if ( $dest_slice_strand...)]

      # Throw away features off the end of the requested slice or on
      # different seq_region.
      if ($seq_region_end < 1
          || $seq_region_start > $dest_slice_length
          || ($dest_slice_sr_id != $seq_region_id)) {
        next FEATURE;
      }
      $slice = $dest_slice;
    }

    # Finally, create the new DnaAlignFeature.
    push( @features,
          $self->_create_feature_fast(
             'Bio::EnsEMBL::DnaDnaAlignFeature', {
               'slice'           => $slice,
               'start'           => $seq_region_start,
               'end'             => $seq_region_end,
               'strand'          => $seq_region_strand,
               'hseqname'        => $hit_name,
               'hstart'          => $hit_start,
               'hend'            => $hit_end,
               'hstrand'         => $hit_strand,
               'score'           => $score,
               'p_value'         => $evalue,
               'percent_id'      => $perc_ident,
               'cigar_string'    => $cigar_line,
               'analysis'        => $analysis,
               'adaptor'         => $self,
               'dbID'            => $dna_align_feature_id,
               'external_db_id'  => $external_db_id,
               'hcoverage'       => $hcoverage,
               'align_type'      => $align_type,
               'dbname'          => $external_db_name,
               'db_display_name' => $external_display_db_name
             } ) );

  } ## end while ( $sth->fetch() )

  return \@features;
} ## end sub _objs_from_sth

=head2 list_dbIDs

  Arg [1]    : none
  Example    : @feature_ids = @{$dna_align_feature_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all dna align features in 
               the current db
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable

=cut

sub list_dbIDs {
   my ($self, $ordered) = @_;

   return $self->_list_dbIDs("dna_align_feature",undef, $ordered);
}

1;