$pafa =
    $registry->get_adaptor( 'Human', 'Core', 'ProteinAlignFeature' );

  my @features = @{ $pafa->fetch_all_by_Slice($slice) };

  $pafa->store(@features);

  my $self = shift;

  #warning _objs_from_hashref method depends on ordering of this list 
  return qw( paf.protein_align_feature_id
             paf.seq_region_id
             paf.seq_region_start
             paf.seq_region_end
             paf.analysis_id
             paf.seq_region_strand
             paf.hit_start
             paf.hit_end
             paf.hit_name
             paf.cigar_line
             paf.evalue
             paf.perc_ident
             paf.score
             paf.external_db_id
             paf.hcoverage
	     exdb.db_name
	     exdb.db_display_name);

    return (['external_db',"exdb.external_db_id = paf.external_db_id"]);

  my ($self, $sth, $mapper, $dest_slice) = @_;

  #
  # This code is ugly because an attempt has been made to remove as many
  # function calls as possible for speed purposes.  Thus many caches and
  # a fair bit of gymnastics is used.
  #

  my $sa = $self->db()->get_SliceAdaptor();
  my $aa = $self->db->get_AnalysisAdaptor();

  my @features;
  my %analysis_hash;
  my %slice_hash;
  my %sr_name_hash;
  my %sr_cs_hash;

  my ($protein_align_feature_id, $seq_region_id, $seq_region_start,
      $seq_region_end, $analysis_id, $seq_region_strand, $hit_start,
      $hit_end, $hit_name, $cigar_line, $evalue, $perc_ident, $score,
      $external_db_id, $hcoverage, $external_db_name, $external_display_db_name );

  $sth->bind_columns(\$protein_align_feature_id,\$ seq_region_id,\$
           seq_region_start,\$seq_region_end,\$ analysis_id,\$
           seq_region_strand,\$ hit_start,\$hit_end,\$ hit_name,\$
           cigar_line,\$ evalue,\$ perc_ident,\$ score,\$
           external_db_id,\$ hcoverage,\$ external_db_name,\$ external_display_db_name );

  my $asm_cs;
  my $cmp_cs;
  my $asm_cs_vers;
  my $asm_cs_name;
  my $cmp_cs_vers;
  my $cmp_cs_name;
  if($mapper) {
    $asm_cs = $mapper->assembled_CoordSystem();
    $cmp_cs = $mapper->component_CoordSystem();
    $asm_cs_name = $asm_cs->name();
    $asm_cs_vers = $asm_cs->version();
    $cmp_cs_name = $cmp_cs->name();
    $cmp_cs_vers = $cmp_cs->version();
  }

  my $dest_slice_start;
  my $dest_slice_end;
  my $dest_slice_strand;
  my $dest_slice_length;
  my $dest_slice_sr_name;
  my $dest_slice_sr_id;
  if($dest_slice) {
    $dest_slice_start  = $dest_slice->start();
    $dest_slice_end    = $dest_slice->end();
    $dest_slice_strand = $dest_slice->strand();
    $dest_slice_length = $dest_slice->length();
    $dest_slice_sr_name = $dest_slice->seq_region_name();
    $dest_slice_sr_id  = $dest_slice->get_seq_region_id();
  }

  FEATURE: while($sth->fetch()) {
    #get the analysis object
    my $analysis = $analysis_hash{$analysis_id} ||=
      $aa->fetch_by_dbID($analysis_id);

    #get the slice object
    my $slice = $slice_hash{"ID:".$seq_region_id};

    if(!$slice) {
      $slice = $sa->fetch_by_seq_region_id($seq_region_id);
      $slice_hash{"ID:".$seq_region_id} = $slice;
      $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
      $sr_cs_hash{$seq_region_id} = $slice->coord_system();
    }

    my $sr_name = $sr_name_hash{$seq_region_id};
    my $sr_cs   = $sr_cs_hash{$seq_region_id};
    #
    # remap the feature coordinates to another coord system
    # if a mapper was provided
    #
    if($mapper) {

      ($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
        $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end,
                          $seq_region_strand, $sr_cs);

      #skip features that map to gaps or coord system boundaries
      next FEATURE if(!defined($seq_region_id));

 #     #get a slice in the coord system we just mapped to
 #     if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
        $slice = $slice_hash{"ID:".$seq_region_id} ||=
          $sa->fetch_by_seq_region_id($seq_region_id);
#      } else {
#        $slice = $slice_hash{"ID:".$seq_region_id} ||=
#          $sa->fetch_by_seq_region_id($asm_cs_name, $sr_name, undef, undef, undef,
#                               $asm_cs_vers);
#      }
    }

    #
    # If a destination slice was provided convert the coords
    # If the dest_slice starts at 1 and is foward strand, nothing needs doing
    #
    if($dest_slice) {
      if($dest_slice_start != 1 || $dest_slice_strand != 1) {
        if($dest_slice_strand == 1) {
          $seq_region_start = $seq_region_start - $dest_slice_start + 1;
          $seq_region_end   = $seq_region_end   - $dest_slice_start + 1;
        } else {
          my $tmp_seq_region_start = $seq_region_start;
          $seq_region_start = $dest_slice_end - $seq_region_end + 1;
          $seq_region_end   = $dest_slice_end - $tmp_seq_region_start + 1;
          $seq_region_strand *= -1;
        }
      }
       
      #throw away features off the end of the requested slice
      if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
	( $dest_slice_sr_id ne $seq_region_id )) {
	next FEATURE;
      }
      $slice = $dest_slice;
    }

    # Finally, create the new ProteinAlignFeature.
    push(
      @features,
      $self->_create_feature_fast(
        'Bio::EnsEMBL::DnaPepAlignFeature', {
          'slice'        => $slice,
          'start'        => $seq_region_start,
          'end'          => $seq_region_end,
          'strand'       => $seq_region_strand,
          'hseqname'     => $hit_name,
          'hstart'       => $hit_start,
          'hend'         => $hit_end,
          'hstrand'      => 1,                  # dna_pep_align features
                                                # are always hstrand 1
          'score'        => $score,
          'p_value'      => $evalue,
          'percent_id'   => $perc_ident,
          'cigar_string' => $cigar_line,
          'analysis'     => $analysis,
          'adaptor'      => $self,
          'dbID'           => $protein_align_feature_id,
          'external_db_id' => $external_db_id,
          'hcoverage'      => $hcoverage,
	  'dbname'         => $external_db_name,
	  'db_display_name' => $external_display_db_name
        } ) );

  }

  return\@ features;

  my $self = shift;

  return (['protein_align_feature', 'paf'], ['external_db','exdb']);

   my ($self,$ordered) = @_;

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






1;

 my ($self, @feats) = @_;

  throw("Must call store with features") if( scalar(@feats) == 0 );

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

  my $db = $self->db();
  my $slice_adaptor = $db->get_SliceAdaptor();
  my $analysis_adaptor = $db->get_AnalysisAdaptor();

  my $sth = $self->prepare(
     "INSERT INTO $tablename (seq_region_id, seq_region_start, seq_region_end,
                             seq_region_strand, hit_start, hit_end,
                             hit_name, cigar_line,
                             analysis_id, score, evalue, perc_ident, external_db_id, hcoverage)
     VALUES (?,?,?,?,?,?,?,?,?,?, ?, ?, ?, ?)");

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

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

   #sanity check the hstart and hend
   my $hstart  = $feat->hstart();
   my $hend    = $feat->hend();
   $self->_check_start_end_strand($hstart,$hend,1);

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

   my $hseqname = $feat->hseqname();
   if(!$hseqname) {
     throw("DnaPepAlignFeature 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 $slice = $feat->slice();
   if(!defined($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
     throw("A slice must be attached to the features to be stored.");
   }

   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);
   $sth->bind_param(5,$feat->hstart,SQL_INTEGER);
   $sth->bind_param(6,$feat->hend,SQL_INTEGER);
   $sth->bind_param(7,$feat->hseqname,SQL_VARCHAR);
   $sth->bind_param(8,$feat->cigar_string,SQL_LONGVARCHAR);
   $sth->bind_param(9,$feat->analysis->dbID,SQL_INTEGER);
   $sth->bind_param(10,$feat->score,SQL_DOUBLE);
   $sth->bind_param(11,$feat->p_value,SQL_DOUBLE);
   $sth->bind_param(12,$feat->percent_id,SQL_REAL);
   $sth->bind_param(13,$feat->external_db_id,SQL_INTEGER);
   $sth->bind_param(14,$feat->hcoverage,SQL_DOUBLE);

   $sth->execute();
   $original->dbID($sth->{'mysql_insertid'});
   $original->adaptor($self);
 }

 $sth->finish();

  Copyright (c) 1999-2009 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

    /info/about/code_licence.html

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.