Bio::EnsEMBL::DnaAlignFeature
  Bio::EnsEMBL::BaseAlignFeature
  Bio::EnsEMBL::FeaturePair
  Bio::EnsEMBL::SeqFeature
  Bio::EnsEMBL::SeqFeatureI
  Bio::SeqFeatureI
  Bio::RangeI
  Bio::Root::RootI

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

  my $from_slice = $self->contig;

  $self->throw("New contig [$to_slice] is not a Bio::EnsEMBL::Slice")
   unless $to_slice->isa("Bio::EnsEMBL::Slice");

  if ((my $c1 = $from_slice->chr_name) ne (my $c2 = $to_slice->chr_name)) {
    $self->warn("Can't transform between chromosomes: $c1 and $c2");
    return;
  }

  my($start, $end, $strand);

  #first convert to assembly coords
  if($from_slice->strand == 1) {
    $start  = $from_slice->chr_start + $self->start - 1;
    $end    = $from_slice->chr_start + $self->end   - 1;
    $strand = $self->strand;
  } else {
    $start  = $from_slice->chr_end - $self->end   + 1;
    $end    = $from_slice->chr_end - $self->start + 1;
    $strand = $self->strand;
  }

  #now convert to the other slice's coords 
  if($to_slice->strand == 1) {
    $self->start ($start - $to_slice->chr_start + 1); 
    $self->end   ($end   - $to_slice->chr_start + 1); 
    $self->strand($strand);
  } else {
    $self->start ($to_slice->chr_end - $end   + 1);
    $self->end   ($to_slice->chr_end - $start + 1);
    $self->strand($strand * -1);
  }

  $self->contig($to_slice);

  return $self;

  my($self) = @_;

  #print STDERR "transforming ".$self." to raw contig coords\n";
  $self->throw("can't transform coordinates of $self without a contig defined")
   unless $self->contig;

  my $slice = $self->contig;

  unless($slice->adaptor) {
    $self->throw("can't transform coordinates of $self without an adaptor " .
		 "attached to the feature's slice");
  }

  my $dbh = $slice->adaptor->db;

  my $mapper = 
    $dbh->get_AssemblyMapperAdaptor->fetch_by_type($slice->assembly_type);
  my $rca = $dbh->get_RawContigAdaptor;

  #first convert the features coordinates to assembly coordinates
  my($start, $end, $strand);
  if($slice->strand == 1) {
    $start  = $slice->chr_start + $self->start - 1;
    $end    = $slice->chr_start + $self->end   - 1;
    $strand = $self->strand;
  } else {
    $start = $slice->chr_end - $self->end   + 1;
    $end   = $slice->chr_end - $self->start + 1;
    $strand = $self->strand * -1;
  }

  #convert the assembly coordinates to RawContig coordinates
  my @mapped = $mapper->map_coordinates_to_rawcontig(
    $slice->chr_name,
    $start,
    $end,
    $strand
  );

  unless (@mapped) {
    $self->throw("couldn't map $self");
    return $self;
  }

  if (@mapped == 1) {

    if ($mapped[0]->isa("Bio::EnsEMBL::Mapper::Gap")) {
      $self->warn("feature lies on gap\n");
      return;
    }

    my $rc = $rca->fetch_by_dbID($mapped[0]->id);

    $self->start     ($mapped[0]->start);
    $self->end       ($mapped[0]->end);
    $self->strand    ($mapped[0]->strand);
    $self->seqname   ($mapped[0]->id);
    #print STDERR "setting contig to be ".$mapped[0]->id."\n";
    $self->contig($rca->fetch_by_dbID($mapped[0]->id));

    return $self;
  }
  else {

    # more than one object returned from mapper
    # possibly more than one RawContig in region

    my (@gaps, @coords);

    foreach my $m (@mapped) {

	if ($m->isa("Bio::EnsEMBL::Mapper::Gap")) {
	    push @gaps, $m;
	}
	elsif ($m->isa("Bio::EnsEMBL::Mapper::Coordinate")) {
	    push @coords, $m;
	}
    }

    # case where only one RawContig maps
    if (@coords == 1) {

        $self->start  ($coords[0]->start);
        $self->end    ($coords[0]->end);
        $self->strand ($coords[0]->strand);
        $self->seqname($coords[0]->id);
	#print STDERR "2 setting contig to be ".$coords[0]->id."\n";
        $self->contig ($rca->fetch_by_dbID($coords[0]->id));

	$self->warn("Feature [$self] truncated as lies partially on a gap");
        return $self;
    }

    unless ($self->is_splittable) {
        $self->warn("Feature spans >1 raw contig - can't split\n");
        return;
    }

    my @out;
    my $obj = ref $self;

    SPLIT: foreach my $map (@mapped) {

      if ($map->isa("Bio::EnsEMBL::Mapper::Gap")) {
	$self->warn("piece of evidence lies on gap\n");
	next SPLIT;
      }

      my $feat = $obj->new;

      $feat->start  ($map->start);
      $feat->end    ($map->end);
      $feat->strand ($map->strand);
      #print STDERR "3 setting contig to be ".$mapped[0]->id."\n";
      $feat->contig ($rca->fetch_by_dbID($map->id));
      $feat->adaptor($self->adaptor) if $self->adaptor();
      $feat->display_label($self->display_label) if($self->can('display_label'));
      $feat->analysis($self->analysis);
      push @out, $feat;
    }
    
    return @out;
  }
}


1;

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

  $self->throw("can't transform coordinates of $self without a contig defined")
    unless $self->contig;

  unless($self->contig->adaptor) {
    $self->throw("cannot transform coordinates of $self without adaptor " .
		 "attached to contig");
  }

  my $dbh = $self->contig->adaptor->db;

  my $mapper = 
    $dbh->get_AssemblyMapperAdaptor->fetch_by_type($slice->assembly_type);
  my $rca = $dbh->get_RawContigAdaptor;

  my @mapped = $mapper->map_coordinates_to_assembly(
    $self->contig->dbID,
    $self->start,
    $self->end,
    $self->strand
  );

  unless (@mapped) {
    $self->throw("couldn't map $self to Slice");
  }

  unless (@mapped == 1) {
    $self->throw("$self should only map to one chromosome - " .
		 "something bad has happened ...");
  }

  if ($mapped[0]->isa("Bio::EnsEMBL::Mapper::Gap")) {
    $self->warn("feature lies on gap\n");
    return;
  }

  if( ! defined $slice->chr_name() ) {
    my $slice_adaptor = $slice->adaptor();
    %$slice = %{$slice_adaptor->fetch_by_chr_name( $mapped[0]->id() )};
  }
   
  # mapped coords are on chromosome - need to convert to slice
  if($slice->strand == 1) {
    $self->start  ($mapped[0]->start - $slice->chr_start + 1);
    $self->end    ($mapped[0]->end   - $slice->chr_start + 1);
    $self->strand ($mapped[0]->strand);
  } else {
    $self->start  ($slice->chr_end - $mapped[0]->end   + 1);
    $self->end    ($slice->chr_end - $mapped[0]->start + 1);
    $self->strand ($mapped[0]->strand * -1);
  }

  $self->seqname($mapped[0]->id);

  #set the contig to the slice
  $self->contig($slice);

  return $self;

   my ($self,$feat,$expand) = @_;

   if( !$feat->isa('Bio::SeqFeatureI') ) {
       $self->warn("$feat does not implement Bio::SeqFeatureI. Will add it anyway, but beware...");
   }

   if( $expand eq 'EXPAND' ) {
       # if this doesn't have start/end set - forget it!
       if( !defined $self->start && !defined $self->end ) {
           $self->start($feat->start());
           $self->end($feat->end());
           $self->strand($feat->strand);
       } else {
           my ($start,$end);
           if( $feat->start < $self->start ) {
               $start = $feat->start;
           }

           if( $feat->end > $self->end ) {
               $end = $feat->end;
           }

           $self->start($start);
           $self->end($end);

       }
   } else {
     if( !defined($feat->start()) || !defined($feat->end()) ||
         !defined($self->start())  || !defined($self->end())) {
       $self->throw( "This SeqFeature and the sub_SeqFeature must define".
                     " start and end.");
     }
     if($feat->start() > $feat->end() || $self->start() > $self->end()) {
       $self->throw("This SeqFeature and the sub_SeqFeature must have " .
                    "start that is less than or equal to end.");
     }
     if($feat->start() < $self->start() || $feat->end() > $self->end() ) {
       $self->throw("$feat is not contained within parent feature, " .
                    "and expansion is not valid");
     }
   }

   push(@{$self->{'_gsf_sub_array'}},$feat);

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

   if( !defined $self->{'_gsf_tag_hash'}->{$tag} ) {
       $self->{'_gsf_tag_hash'}->{$tag} = [];
   }

   push(@{$self->{'_gsf_tag_hash'}->{$tag}},$value);

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

   return keys %{$self->{'_gsf_tag_hash'}};

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

   if (defined($value)) {
     unless(ref($value) && $value->isa('Bio::EnsEMBL::Analysis')) {
       $self->throw("Analysis is not a Bio::EnsEMBL::Analysis object "
		    . "but a $value object");
     }

     $self->{_analysis} = $value;
   } else {
     #if _analysis is not defined, create a new analysis object
     unless(defined $self->{_analysis}) {
       $self->{_analysis} = new Bio::EnsEMBL::Analysis();
     }
   }

   return $self->{_analysis};

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

   $self->contig($seq);

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

  if ($arg) {
    unless (defined $arg && ref $arg && $arg->isa("Bio::PrimarySeqI")) {
      $self->throw("Must attach Bio::PrimarySeqI objects to SeqFeatures");
    }
    
    $self->{'_gsf_seq'} = $arg;
    
    # attach to sub features if they want it
    
    foreach my $sf ($self->sub_SeqFeature) {
      if ($sf->can("attach_seq")) {
	$sf->attach_seq($arg);
      }
    }
  }
  #print STDERR "contig is ".$self->{'_gsf_seq'}." with name ".$self->{'_gsf_seq'}->name."\n" unless(!$self->{'_gsf_seq'});
#  my ($p, $f, $l) = caller;
#  print STDERR "Caller = ".$f." ".$l."\n";
  return $self->{'_gsf_seq'};

   my ($self,$tag) = @_;
   if( ! exists $self->{'_gsf_tag_hash'}->{$tag} ) {
       $self->throw("asking for tag value that does not exist $tag");
   }

   return @{$self->{'_gsf_tag_hash'}->{$tag}};

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

    if (defined($value)) {
        if( $value !~ /^\-?\d+/ ) {
            $self->throw("[$value] is not a valid end");
        }
	
        $self->{'_gsf_end'} = $value;
    }

   return $self->{'_gsf_end'};

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

    if (defined($value))
    {
            $self->throw("Valid values for Phase are [0,1,2]") if ($value < 0 || $value > 2);
            $self->{_end_phase} = $value;
    }

    return $self->{_end_phase};

   my ($self) = @_;

   return $self->contig;

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

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

    return $self->{'_external_db'};

   my ($self) = @_;

   $self->{'_gsf_sub_array'} = []; # zap the array implicitly.

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

    if (defined($value)) {
        if( $value != 1 && $value != 2 && $value != 3 ) {
            $self->throw("'$value' is not a valid frame");
       }
        $self->{'_gsf_frame'} = $value;
    }

    return $self->{'_gsf_frame'};

   my ($self) = @_;

   my $str;

   my $strand = "+";
   
   if ((defined $self->strand)&&($self->strand == -1)) {
     $strand = "-";
   }
   
   $str .= (defined $self->seqname)     ?   $self->seqname."\t"      :  "\t";
   $str .= (defined $self->source_tag)  ?   $self->source_tag."\t"   :  "\t";
   $str .= (defined $self->primary_tag) ?   $self->primary_tag."\t"  :  "\t";
   $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)      ?   $strand."\t"             :  ".\t";
   $str .= (defined $self->phase)       ?   $self->phase."\t"        :  ".\t";
   eval{
     $str .= (defined $self->end_phase)   ?   $self->end_phase."\t"        :  ".\t";
   };

   return $str;

   my ($self,$tag) = (shift, shift);

   return exists $self->{'_gsf_tag_hash'}->{$tag};

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

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

    return $self->{_id};

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

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

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

   return $self->end - $self->start +1;

  my ($self, $start, $end, $strand)  = @_;

  $self->{'_gsf_start'} = $start;
  $self->{'_gsf_end'} = $end;
  if(defined $strand) {
    $self->{'_gsf_strand'} = $strand;
  }

  my($caller,@args) = @_;

  my $self = {};

  if(ref $caller) {
    bless $self, ref $caller;
  } else {
    bless $self, $caller;
  }

  $self->{'_gsf_tag_hash'} = {};
  $self->{'_gsf_sub_array'} = [];
  $self->{'_parse_h'} = {};
  $self->{'_is_splittable'} = 0;

  my ($start,$end,$strand,$frame,$score,$analysis,$seqname, $source_tag,
      $primary_tag, $percent_id, $p_value, $phase, $end_phase) =

      &rearrange([qw(START
                            END
                            STRAND
                            FRAME
                            SCORE
                            ANALYSIS
                            SEQNAME
                            SOURCE_TAG
                            PRIMARY_TAG
                            PERCENT_ID
                            P_VALUE
                            PHASE
                            END_PHASE
                            )],@args);

  #  $gff_string && $self->_from_gff_string($gff_string);

  if ( defined $analysis  && $analysis ne "")   { $self->analysis($analysis)};
  if ( defined ($start) && $start ne "" )       { $self->start($start)};
  if ( defined ($end )  && $end   ne "" )       { $self->end($end)}
  if ( defined $strand  && $strand ne "")       { $self->strand($strand)}
  if ( defined $frame  && $frame ne "")         { $self->frame($frame)}
  if ( defined $score  && $score ne "")         { $self->score($score)}
  if ( defined $seqname && $seqname ne "")      { $self->seqname($seqname)};
  if ( defined $percent_id && $percent_id ne ""){ $self->percent_id($percent_id)};
  if ( defined $p_value && $p_value ne "")      { $self->p_value($p_value)};
  if ( defined $phase && $phase ne "")          { $self->phase($phase)};
  if ( defined $end_phase && $end_phase ne "")  { $self->end_phase($end_phase)};

  return $self; # success - we hope!

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

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

    return $self->{_p_value};

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

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

    return $self->{_percent_id};

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

    if (defined($value) )
    {
        $self->throw("Valid values for Phase are [0,1,2]") if ($value < 0 || $value > 2);
            $self->{_phase} = $value;
    }

    return $self->{_phase};

  my ($self,$arg) = @_;
  
  if (defined($arg)) {
    # throw warnings about setting primary tag
    my ($p,$f,$l) = caller;
    $self->warn("$f:$l setting primary_tag now deprecated." .
		"Primary tag is delegated to analysis object");
  }

  unless($self->analysis) {
    return '';
  }
  
  return $self->analysis->gff_feature();

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

    if(defined ($value) ) {
      if( $value !~ /^[+-]?\d+\.?\d*(e-\d+)?/ ) {
          $self->throw("'$value' is not a valid score");
      }
      $self->{'_gsf_score'} = $value;
  }

  return $self->{'_gsf_score'};

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

   if( defined $arg ) {
       $self->throw("Calling SeqFeature::Generic->seq with an argument. " .
		    "You probably want attach_seq");
   }

   if( ! exists $self->{'_gsf_seq'} ) {
       return undef;
   }

   # assumming our seq object is sensible, it should not have to yank
   # the entire sequence out here.

   my $seq = $self->{'_gsf_seq'}->trunc($self->start(),$self->end());


   if( $self->strand == -1 ) {

       # ok. this does not work well (?)
       #print STDERR "Before revcom", $seq->str, "\n";
       $seq = $seq->revcom;
       #print STDERR "After  revcom", $seq->str, "\n";
   }

   return $seq;

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

   my $seq = $self->contig();

   if(defined $seqname) {
     $self->{_seqname} = $seqname;
   } else {
     if($seq && ref $seq && $seq->can('name')) {
       $self->{_seqname} = $seq->name();
     } 
   }

   return $self->{_seqname};

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

    if (defined($arg)) {
        # throw warnings about setting primary tag
        my ($p,$f,$l) = caller;
        $self->warn("$f:$l setting source_tag now deprecated. " .
		    "Source tag is delegated to analysis object");
    }

    unless($self->analysis) {
      return "";
    }

   return $self->analysis->gff_source();

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

    if (defined($value)) {
        if ($value !~ /^\-?\d+/ ) {
        $self->throw("$value is not a valid start");
    }
	
    $self->{'_gsf_start'} = $value
   }

    return $self->{'_gsf_start'};

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

    if (defined($value)) {
        if( $value eq '+' ) { $value = 1; }
        if( $value eq '-' ) { $value = -1; }
        if( $value eq '.' ) { $value = 0; }

        if( $value != -1 && $value != 1 && $value != 0 ) {
            $self->throw("$value is not a valid strand info");
        }
        $self->{'_gsf_strand'} = $value;
    }

    return $self->{'_gsf_strand'};

   my ($self) = @_;

   if($self->{'_gsf_sub_array'}){
     return @{$self->{'_gsf_sub_array'}};
   }else{
     return;
   }

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

  unless (defined $slice) {

    if ((defined $self->contig) &&
      ($self->contig->isa("Bio::EnsEMBL::RawContig"))) {

      # we are already in rawcontig coords, nothing needs to be done
      return $self;

    }
    else {
      # transform to raw_contig coords from Slice coords
      return $self->_transform_to_RawContig();
    }
  }

  if (defined $self->contig) {

    if ($self->contig->isa("Bio::EnsEMBL::RawContig"))  {

      # transform to slice coords from raw contig coords
      return $self->_transform_to_Slice($slice);
    }
    elsif ($self->contig->isa( "Bio::EnsEMBL::Slice" )) {

      # transform to slice coords from other slice coords
      return $self->_transform_between_Slices($slice);
    }
    else {

      # Unknown contig type
      $self->throw("Cannot transform unknown contig type @{[$self->contig]}");
    }
  }
  else {

    #Can't convert to slice coords without a contig to work with
    return $self->throw("Object's contig is not defined - cannot transform");
  }

    my ($self) = @_;

    $self->vthrow("Seqname not defined in feature")     unless defined($self->seqname);
    $self->vthrow("start not defined in feature")       unless defined($self->start);
    $self->vthrow("end not defined in feature")         unless defined($self->end);
    $self->vthrow("strand not defined in feature")      unless defined($self->strand);
    $self->vthrow("score not defined in feature")       unless defined($self->score);
    $self->vthrow("analysis not defined in feature")    unless defined($self->analysis);

    if ($self->end < $self->start) {
      $self->vthrow("End coordinate < start coordinate");
    }

    my ($self,$num) = @_;
    $self->throw("Seqname not defined in feature")     unless defined($self->seqname);
    $self->throw("start not defined in feature")       unless defined($self->start);
    $self->throw("end not defined in feature")         unless defined($self->end);
    if ($num == 1) {
        $self->throw("score not defined in feature")       unless defined($self->score);
        $self->throw("percent_id not defined in feature") unless defined($self->percent_id);
        $self->throw("evalue not defined in feature") unless defined($self->p_value);
    }
    $self->throw("analysis not defined in feature")    unless defined($self->analysis);
}



# These methods are specified in the SeqFeatureI interface but we don't want
# people to store data in them.  These are just here in order to keep
# existing code working

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

    print(STDERR "Error validating feature [$message]\n");
    print(STDERR "   Seqname     : [" . $self->{_seqname} . "]\n");
    print(STDERR "   Start       : [" . $self->{_gsf_start} . "]\n");
    print(STDERR "   End         : [" . $self->{_gsf_end} . "]\n");
    print(STDERR "   Strand      : [" .
        ((defined ($self->{_gsf_strand})) ? $self->{_gsf_strand} : "undefined") . "]\n");

    print(STDERR "   Score       : [" . $self->{_gsf_score} . "]\n");

    print(STDERR "   Analysis    : [" . $self->{_analysis}->dbID . "]\n");

    $self->throw("Invalid feature - see dump on STDERR");

  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>.