my $feat = Bio::EnsEMBL::FeaturePair->new(
      -start      => 132_231,
      -end        => 132_321,
      -strand     => -1,
      -slice      => $slice,
      -hstart     => 10,
      -hend       => 100,
      -hstrand    => 1,
      -score      => 100,
      -percent_id => 92.0,
      -hseqname   => 'ALUSX10.1',
      -analysis   => $analysis
    );

    my $hit_start  = $feat->hstart();
    my $hit_end    = $feat->hend();
    my $hit_strand = $feat->hstrand();
    my $analysis   = $feat->analysis();

  $clone = $slice_adpator->fetch_by_region( 'clone', 'HS120G22' );

  $fp = Bio::EnsEMBL::FeaturePair(
    -start      => 100,
    -end        => 220,
    -strand     => 1,
    -slice      => $clone,
    -hstart     => 1,
    -hend       => 40,
    -hstrand    => 1,
    -percent_id => 92.0,
    -score      => 100,
    -hseqname   => 'SW:HBA_HUMAN',
    -species    => 'Homo sapiens',
    -hspecies   => 'Homo sapiens'
  );

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

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

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

  my $self = shift;
  return $self->{'hseqname'} || '';

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

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

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

  deprecate('Use start(), end(), strand(), slice(), etc. methods instead.');

  if($arg) {
    $self->start($arg->start());
    $self->end($arg->end());
    $self->strand($arg->strand());
    $self->score($arg->score());
    $self->percent_id($arg->percent_id());
    $self->analysis($arg->analysis);
    if($arg->contig){
      $self->slice($arg->contig);
    }
  }

  return $self;

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

  deprecate('Use hstart(),hend(),hstrand(),hseqname() methods instead.');

  if (defined($arg)) {
    $self->hstart($arg->start());
    $self->hend($arg->end());
    $self->hstrand($arg->strand());
    $self->hseqname($arg->seqname());
    return $arg;
  }

  return new Bio::EnsEMBL::Feature(
		    -START      => $self->hstart(),
		    -END        => $self->hend(),
        -STRAND     => $self->hstrand(),
		    -SCORE      => $self->score(),
		    -PERCENT_ID => $self->percent_id(),
		    -ANALYSIS   => $self->analysis,
        -SEQNAME    => $self->hseqname());

    my ($self) = @_;

    deprecate('Do not use');

    my $str .= (defined $self->slice) ?  $self->slice->name()."\t":  "\t";
    $str .=  "\t"; #source tag
    $str .=  "\t"; #primary tag
    $str .= (defined $self->start)    ?  $self->start."\t"        :  "\t";
    $str .= (defined $self->end)      ?  $self->end."\t"          :  "\t";
    $str .= (defined $self->score)    ?  $self->score."\t"        :  "\t";
    $str .= (defined $self->strand)   ?  $self->strand."\t"       :  ".\t";
    $str .=  ".\t"; #phase
    $str .=  ".\t"; #end phase

    my $hstrand = "+";

    if (($self->hstrand)&&($self->hstrand == -1)) {
      $hstrand = "-";
    }

    #Append a few FeaturePair specific things
    $str .= (defined $self->hseqname)   ?   $self->hseqname."\t"    :  "\t";
    $str .= (defined $self->hstart)     ?   $self->hstart."\t"      :  "\t";
    $str .= (defined $self->hend)       ?   $self->hend."\t"        :  "\t";
    $str .= (defined $self->hstrand)    ?   $hstrand."\t"           :  "\t";
    $str .= (defined $self->hphase)     ?   $self->hphase."\t"      :  ".\t";

    return $str;

   my ($self, $arg) = @_;
 
   if ( defined $arg ) {
      $self->{'group_id'} = $arg ;
   }
   return $self->{'group_id'};

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

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

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

  deprecate('This method does nothing useful.');

  if (defined($value)) {
    $self->{_hend_phase} = $value;
  }
  return $self->{_hend_phase};

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

  deprecate('This method does nothing useful.');

  if (defined($value)) {
    $self->{_hphase} = $value;
  }

  return $self->{_hphase};

  my $self = shift;
  my $slice = $self->{'hslice'};

  return undef if(!$slice);

  if($slice->strand == 1) {
    return undef if(!defined($self->{'hend'}));
    return $slice->start() + $self->{'hend'} - 1;
  } else {
    return undef if(!defined($self->{'hstart'}));
    return $slice->end() - $self->{'hstart'} + 1;
  }

  my $self = shift;
  my $slice = $self->{'hslice'};

  return ($slice) ? $slice->seq_region_name() : undef;

  my $self = shift;
  my $slice = $self->{'hslice'};

  return undef if(!$slice);

  if($slice->strand == 1) {
    return undef if(!defined($self->{'hstart'}));
    return $slice->start() + $self->{'hstart'} - 1;
  } else {
    return undef if(!defined($self->{'hend'}));
    return $slice->end() - $self->{'hend'} + 1;
  }

  my $self = shift;
  my $slice = $self->{'hslice'};

  return ($slice) ? $slice->strand() * $self->{'hstrand'} : undef;

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

  my $self = shift;

  if(@_) {
    my $sl = shift;
    if(defined($sl) && (!ref($sl) || !$sl->isa('Bio::EnsEMBL::Slice'))) {
      throw('slice argument must be a Bio::EnsEMBL::Slice');
    }

    $self->{'hslice'} = $sl;
  }

  return $self->{'hslice'};

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

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

  my $self = shift;

  if(@_) {
    my $hstrand = shift;
    if(defined($hstrand) && $hstrand != 1 && $hstrand != 0 && $hstrand != -1) {
      throw('hstrand must be one of (-1,0,1)');
    }
    $self->{'hstrand'} = $hstrand;
  }

  return $self->{'hstrand'};

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

    if (defined($arg)) {
        return $self->{'_identical_matches'} = $arg;
    } 
    return $self->{'_identical_matches'};

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

    if (! defined $slice && defined $self->hslice) {
      $slice = $self->hslice;
    }

    my $hstart   = $self->{'hstart'};
    my $hend     = $self->{'hend'};
    my $hstrand  = $self->{'hstrand'};
    my $hspecies = $self->{'hspecies'};
    my $hseqname = $self->{'hseqname'};

    my $start   = $self->{'start'};
    my $end     = $self->{'end'};
    my $strand  = $self->{'strand'};
    my $species = $self->{'species'};
    my $seqname = $self->seqname();

    $self->{'start'} = $hstart;
    $self->{'end'}   = $hend;
    $self->{'strand'} = $hstrand;
    $self->{'species'} = $hspecies;
    $self->{'seqname'} = $hseqname if(defined($hseqname));

    $self->{'hstart'}   = $start;
    $self->{'hend'}     = $end;
    $self->{'hstrand'}  = $strand;
    $self->{'hseqname'} = $seqname;
    $self->{'hspecies'} = $species;

    $self->{'hslice'} = $self->slice;
    $self->{'slice'} = $slice;

   my ($self, $arg) = @_;
 
   if ( defined $arg ) {
      $self->{'level_id'} = $arg ;
   }
   return $self->{'level_id'};

  my $caller = shift;

  my $class = ref($caller) || $caller;

  my $self = $class->SUPER::new(@_);

  my ($hstart,$hend,$hstrand,$percent_id,$score, $species, $hspecies,
      $p_value, $hseqname, $f1,$f2, $coverage, $hcoverage, $group_id,$level_id, $external_db_id, $extra_data, $external_db_name, $external_display_db_name) =
    rearrange(['HSTART','HEND','HSTRAND','PERCENT_ID','SCORE','SPECIES',
               'HSPECIES', 'P_VALUE', 'HSEQNAME', 'FEATURE1','FEATURE2',
               'COVERAGE', 'HCOVERAGE', 'GROUP_ID','LEVEL_ID', 'EXTERNAL_DB_ID', 'EXTRA_DATA', 'DBNAME', 'DB_DISPLAY_NAME'], @_);

  if(defined($hstart) && defined($hend) && ($hend < $hstart)) {
    throw('HSTART must be less than or equal to HEND');
  }

  if(defined($hstrand) && $hstrand != 1 && $hstrand != -1 && $hstrand != 0) {
    throw('HSTRAND must be one of (0,1,-1)');
  }

  $self->{'hstart'}     = $hstart;
  $self->{'hend'}       = $hend;
  $self->{'hstrand'}    = $hstrand;
  $self->{'score'}      = $score;
  $self->{'percent_id'} = $percent_id;
  $self->{'species'}    = $species;
  $self->{'hspecies'}   = $hspecies;
  $self->{'hseqname'}   = $hseqname;
  $self->{'coverage'}   = $coverage;
  $self->{'hcoverage'}  = $hcoverage;
  $self->{'p_value'}    = $p_value;
  $self->{'group_id'}   = $group_id;
  $self->{'level_id'}   = $level_id;
  $self->{'external_db_id'} = $external_db_id;
  $self->{'extra_data'} = $extra_data;
  $self->{'dbname'} = $external_db_name;
  $self->{'db_display_name'} = $external_display_db_name;

  #
  # Feature1 and Feature2 arg handling for backwards compatibility
  #
  if($f1) {
    deprecate("Using FEATURE1 arg to construct FeaturePairs" .
              " is deprecated.\nUse the args START,END,STRAND,SLICE instead");

    #eval because we are not exactly sure what f1 arg will look like
    eval {
      $self->{'start'} = $f1->start();
      $self->{'end'}   = $f1->end();
      $self->{'strand'} = $f1->strand();
      $self->{'slice'}  = $f1->contig();
      $self->{'analysis'} = $f1->analysis() if($f1->analysis());
    };
  }

  if($f2) {
    deprecate("Using FEATURE2 arg to construct FeaturePairs is deprecated" .
              "\nUse the args HSTART,HEND,HSTRAND,HSEQNAME instead");

    #eval because we are not exactly sure what f2 arg will look like
    eval {
      $self->{'hseqname'} = $f2->seqname();
      $self->{'hstart'}   = $f2->start();
      $self->{'hend'}     = $f2->end();
      $self->{'hstrand'}  = $f2->strand();
      $self->{'analysis'} = $f2->analysis() if($f2->analysis());
    };
  }

  return $self;

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

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

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

    if (defined($arg)) {
        return $self->{'_positive_matches'} = $arg;
    } 
    return $self->{'_positive_matches'};

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

   my ($self, $start, $end, $strand, $score, $seqname, $hstart, $hend,
        $hstrand, $hseqname, $analysis, $e_value, $perc_id, 
        $phase, $end_phase) = @_;

   deprecate("Use individual Getter/Setters or Constructor arguments " .
             " instead.\nThere is no advantage to using this method.");

   throw('interface fault') if (@_ < 12 or @_ > 15);

   $self->start($start);
   $self->end($end);
   $self->strand($strand);
   $self->score($score);
   $self->seqname($seqname);
   $self->hstart($hstart);
   $self->hend($hend);
   $self->hstrand($hstrand);
   $self->hseqname($hseqname);
   $self->analysis($analysis);
   $self->p_value    ($e_value)   if (defined $e_value);
   $self->percent_id ($perc_id)   if (defined $perc_id);
   $self->phase      ($phase)     if (defined $phase);
   $self->end_phase  ($end_phase) if (defined $end_phase);

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

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

1;

  my ($self) = @_;

  deprecate('This method does nothing and should not be used.');

  my ($self) = @_;

  deprecate('This method does nothing and should not be used.');

  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>.

  Arg [1]    : string  $external_db_name (optional)
  Example    : $ex_db_name = $fp->dbname();
  Description: Getter/Setter for the external_db_name attribute, name of external database
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : At Risk