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

  my $overlap ;  
  if ($new_tr) {  
    for my $key  ( keys %{ $self->{different_est_support} } ) {  
      my $stored_tr = $self->{different_est_support}{$key} ;  
  
       if ($stored_tr->seq_region_start <= $new_tr->seq_region_end  && 
           $new_tr->seq_region_start <= $stored_tr->seq_region_end  ) { 
           # new_tr overlaps stored_tr 
  
         # check which transcript has more exons 
         my $new_tr_exons = scalar ( @{  $new_tr->get_all_Exons } )  ; 
         my $stored_tr_exons = scalar(@{$self->{different_est_support}{$stored_tr}->get_all_Exons }); 
         if ($new_tr_exons > $stored_tr_exons ) {  
            delete $self->{different_est_support}{$stored_tr} ;
            if (exists $self->{different_est_support}{$stored_tr}) { 
              throw(" key wasn't delted\n" ) ;  
            }else { 
              warn(" key is deleted\n" ) ;
            } 
            $self->{different_est_support}{$new_tr} = $new_tr ;
         }  
       }else {
         ${$self->{different_est_support}}{$new_tr}=$new_tr ; 
       }
    }
  } 
  return $self->{different_est_support} ;

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

  my ($self, $old_exon, $new_exon  ) = @_ ; 

  my $biotype = $self->biotype ;  
  my @exons = @{ $self->get_all_Exons } ;  
  my $new_tr = Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptExtended->new(); 

  for my $e  (@exons) {
    if ($e eq $old_exon) {
     $e = $new_exon ;
    }
    $new_tr->add_Exon($e) ; 
  }
  $new_tr->biotype($biotype) ; 
  return $new_tr ;

  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'extend_3prim_end'} = $value;
  }
  return $self->{'extend_3prim_end'};

  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'extend_5prim_end'} = $value;
  }
  return $self->{'extend_5prim_end'};

  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'has_3prim_sup'} = $value;
  }
  return $self->{'has_3prim_sup'};

  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'has_5prim_sup'} = $value;
  }
  return $self->{'has_5prim_sup'};

  my($class) = shift;
  if( ref $class ) { 
      $class = ref $class;
  }
  my $self = $class->SUPER::new(@_);
  return $self ;
   
  $self->{different_est_support} = {} ;

  my ($self,$value) = @_;
  if (defined($value)) {
    $self->{'nr_exons_overlapped_est'}+= $value;
  }
  return $self->{'nr_exons_overlapped_est'};

   my ($self,$ex_to_remove ) = @_;
  unless ($ex_to_remove){ 
    throw ("you have to supply an Bio::EnsEMBL::Exon object ".
           "which will be removed from the transcript\n");
  }
  my $clone=[] ; 
  my $ea = $self->{'_trans_exon_array'}; 
  my $nr_before = scalar(@$ea); 
  for my $e (@$ea) {
    if  ($e ne $ex_to_remove ) { 
       push @$clone, $e; 
    }
   } 
  $self->{'_trans_exon_array'} = $clone;
  if ($nr_before == scalar(@$clone) ) { 
    warning( "No matching exon found, exon could not be removed\n" );
   }
  return ;

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

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



1;

  Creation by re-blessing:

  for my $t ( @transcripts ) { 
    bless $t,"Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptExtended";

    $t->ev_set('est') ; 
  }  

  Creation without re-blessing : 

  my $tran = new Bio::EnsEMBL::Transcript(-EXONS => \@exons);