my $xref = Bio::EnsEMBL::IdentityXref->new(
    -XREF_IDENTITY    => 80.4,
    -ENSEMBL_IDENTITY => 90.1,
    -SCORE            => 90,
    -EVALUE           => 12,
    -CIGAR_LINE       => '23MD3M2I40M',
    -XREF_START       => 1,
    -XREF_END         => 68,
    -ENSEMBL_START    => 10,
    -ENSEMBL_END      => 77,
    -ADAPTOR          => $adaptor,
    -PRIMARY_ID       => $primary_id,
    -DBNAME           => 'SwissProt'
  );

  my $self = shift;
  $self->{'cigar_line'} = shift if( @_ );
  return $self->{'cigar_line'};

   my $self = shift;
  $self->{'ensembl_end'} = shift if( @_ );
  return $self->{'ensembl_end'};

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'ensembl_identity'} = $value;
    }
    return $obj->{'ensembl_identity'};

   my $self = shift;
  $self->{'ensembl_start'} = shift if( @_ );
  return $self->{'ensembl_start'};

   my $self = shift;
  $self->{'evalue'} = shift if( @_ );
  return $self->{'evalue'};

  my ( $self ) = @_;
  # parse the cigar_line and create a mapper ...
  if( exists $self->{'_cached_mapper'} ) {
    return $self->{'_cached_mapper'};
  }

  my ( @lens, @chars );

  # if there is no cigar line, nothing is going to be loaded
  if( $self->cigar_line() ) {
    my @pre_lens = split( '[DMI]', $self->cigar_line() );
    @lens = map { if( ! $_ ) { 1 } else { $_ }} @pre_lens;
    @chars = grep { /[DMI]/ } split( //, $self->cigar_line() );
  }
  my $translation_start = $self->ensembl_start();
  my $translation_end = $self->ensembl_end();
  my $query_start = $self->xref_start();
  my $query_end = $self->xref_end();

  #  my $hit_id = $self->display_id();
  my $ensembl_id = "ensembl_id";
  my $external_id = "external_id";
  # now build the mapper
  my $mapper = Bio::EnsEMBL::Mapper->new( "external", "ensembl" );


  for( my $i=0; $i<=$#lens; $i++ ) {
    my $length = $lens[$i];
    my $char = $chars[$i];
    if( $char eq "M" ) {
      $mapper->add_map_coordinates( $external_id, $query_start,
                                    $query_start + $length - 1, 1,
                                    $ensembl_id, $translation_start,
                                    $translation_start + $length - 1);
      $query_start += $length;
      $translation_start += $length;

    } elsif( $char eq "D" ) {
      $translation_start += $length;
    } elsif( $char eq "I" ) {
      $query_start += $length;
    }
  }

  $self->{'_cached_mapper'} = $mapper;

  return $mapper;

  my $self = shift;
  my $feature = shift;


  my $fstart = $feature->start();
  my $fend = $feature->end();

  my $mapper = $self->get_mapper();
  my @coords = $mapper->map_coordinates( "external_id", $fstart, $fend, 1,
                                         "external" );

  return @coords;
}


###########################
# DEPRECATED METHODS FOLLOW
###########################

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($query_identity, $target_identity, $score, $evalue, 
        $cigar_line, $query_start, $query_end, $translation_start,
        $translation_end, $analysis, $xref_identity, $ensembl_identity, 
        $xref_start, $xref_end, $ensembl_start, $ensembl_end) = rearrange(
        [qw(QUERY_IDENTITY TARGET_IDENTITY SCORE EVALUE CIGAR_LINE 
            QUERY_START QUERY_END TRANSLATION_START TRANSLATION_END
            ANALYSIS XREF_IDENTITY ENSEMBL_IDENTITY XREF_START XREF_END ENSEMBL_START ENSEMBL_END)], @args);

    if((defined($query_identity) or defined($target_identity) or defined($query_start) or defined ($query_end) or
       defined($translation_start) or defined($translation_end)) and !$error_shown){
      print STDERR "Arguments have now been changed to stop confusion so please replace the following\n";
      print STDERR "\tQUERY_IDENTITY\t->\tXREF_IDENTITY\n";
      print STDERR "\tTARGET_IDENTITY\t->\tENSEMBL_IDENTITY\n";
      print STDERR "\tQUERY_START\t->\tXREF_START\n";
      print STDERR "\tQUERY_END\t->\tXREF_END\n";
      print STDERR "\tTRANSLATION_START\t->\tENSEMBL_START\n";
      print STDERR "\tTRANSLATION_END\t->\tENSEMBL_END\n";
      print STDERR "The old arguments will be removed in a futute release so please change your code to the new names\n";
      $error_shown = 1;
    }
    $self->{'xref_identity'} = $query_identity || $xref_identity;
    $self->{'ensembl_identity'} = $target_identity || $ensembl_identity;
    $self->{'score'} = $score;
    $self->{'evalue'} = $evalue;
    $self->{'cigar_line'} = $cigar_line;
    $self->{'xref_start'} = $query_start || $xref_start;
    $self->{'xref_end'} = $query_end || $xref_start;
    $self->{'ensembl_start'} = $translation_start || $ensembl_start;
    $self->{'ensembl_end'} = $translation_end || $ensembl_end;
    $self->{'analysis'} = $analysis;

    return $self;

  deprecate("Use xref_end instead");
  xref_end(@_);

}


1;

  deprecate("Use xref_identity instead");
  xref_identity(@_);

  deprecate("Use xref_start instead");
  xref_start(@_);

   my $self = shift;
  $self->{'score'} = shift if( @_ );
  return $self->{'score'};

  deprecate("Use ensembl_identity instead");
  ensembl_identity(@_);

  my $self= shift;
  my $feature = shift;

  my $fstart = $feature->start();
  my $fend = $feature->end();

  my $mapper = $self->get_mapper();
  my @result;

  my @coords = $mapper->map_coordinates( "external_id", $fstart, $fend, 
                                           1, "external" );

  for my $coord ( @coords ) {
    if( $coord->isa( "Bio::EnsEMBL::Mapper::Coordinate" )) {
      my $new_feature;
      %{$new_feature} = %$feature;
      bless $new_feature, ref( $feature );
      $new_feature->start( $coord->start() );
      $new_feature->end( $coord->end() );

      push( @result, $new_feature );
    }
  }

  return\@ result;

  deprecate("Use ensembl_end instead");
  ensembl_end(@_);

  deprecate("Use ensembl_start instead");
  ensembl_start(@_);

   my $self = shift;
  $self->{'xref_end'} = shift if( @_ );
  return $self->{'xref_end'};

   my $obj = shift;
   if( @_ ) {
       my $value = shift;
       $obj->{'xref_identity'} = $value;
   }
   return $obj->{'xref_identity'};

   my $self = shift;
  $self->{'xref_start'} = shift if( @_ );
  return $self->{'xref_start'};

  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>.