my $obj = Bio::EnsEMBL::Analysis::Runnable::MiniGenewise->new(
      -genomic  => $genseq,
      -features => $features)

    $obj->run

    my @newfeatures = $obj->output;

  #my ($self, $gene) = @_;
  my ($self, $transcript) = @_;

  my $strand = 1;
  $strand = -1 if($self->is_reversed);
  my @converted_exons;
  my @all_supp_features;
  
  # need to convert all the exons and all the supporting features
  my @exons = @{$transcript->get_all_Exons};
  my $nexon = scalar(@exons);
  
 TEXON:for(my $i=0; $i < $nexon; $i++) {
    my $exon = $exons[$i];
    $exon->strand($strand);
    
    # need to convert whole exon back to genomic coordinates
   
    my @genomics = @{$self->miniseq->convert_SeqFeature($exon)};
 
    if(!@genomics){
      warning(id($exon)." ".coord_string($exon)." didn't produce any features ".
              "when converted to genomic coordinates, skipping");
      return undef;
    }
    if (@genomics > 1) {
      # all hell will break loose as the sub alignments will probably 
      # not map cheerfully and we may start introducing in frame stops ...
      # for now, ignore this feature.
      warning("Warning : feature converts into " . scalar(@genomics).
              " features; ");
      if ($i == $nexon - 1) {
        warning("Skipping last exon $i");
        next TEXON;
      } elsif ($exon->phase == $exons[$i+1]->phase) {
        warning("Skipping compatible exon $i");
        next TEXON;
      } else {
        warning("Cannot skip exon without adjusting phase; skipping gene");
        return undef;
      }
    }  else {
      my $genomic_exon = create_Exon($genomics[0]->start, $genomics[0]->end,
                                     $exon->phase, $exon->end_phase, $strand,
                                     $self->analysis, undef, undef, $self->query);
      # also need to convert each of the sub alignments back to genomic coordinates
      foreach my $sf (@{$exon->get_all_supporting_features}) {
        my @features;
        my @ungapped = $sf->ungapped_features;
        foreach my $aln (@ungapped) {
          my @alns = @{$self->miniseq->convert_PepFeaturePair($aln)};
          if ($#alns > 0) {
            warning("Warning : sub_align feature converts into > 1 features " . 
                    scalar(@alns));
          }
          my $align = create_feature_from_gapped_pieces
            ("Bio::EnsEMBL::DnaPepAlignFeature",\@ alns, 100, undef, 
             undef, $self->query, $self->protein_sequence->id, $self->analysis);
          push @features,$align;
        }
        push @all_supp_features,@features;
        
        my $gapped = create_feature_from_gapped_pieces
          ("Bio::EnsEMBL::DnaPepAlignFeature",\@ features, 100, undef, 
           undef, $self->query, $self->protein_sequence->id, $self->analysis);
        $genomic_exon->add_supporting_features($gapped);
      }
      push(@converted_exons,$genomic_exon);
    }
  }
  
  # make a new transcript from @converted_exons
  my $converted_transcript  = new Bio::EnsEMBL::Transcript;
  my $converted_translation = new Bio::EnsEMBL::Translation;
  $converted_transcript->translation($converted_translation);
  
  if (scalar(@all_supp_features)) {
    my $daf = create_feature_from_gapped_pieces
      ("Bio::EnsEMBL::DnaPepAlignFeature",\@ all_supp_features, 100, undef, 
       undef, $self->query, $self->protein_sequence->id, $self->analysis);
    $converted_transcript->add_supporting_features($daf);
  }
  
  if ($#converted_exons < 0) {
    warning("Odd.  No exons found in MiniGenewise running on ".
            $self->query->seq_region_name." ".$self->protein_sequence->id);
    return undef;
  } else {
    if ($converted_exons[0]->strand == -1) {
      @converted_exons = sort {$b->start <=> $a->start} @converted_exons;
    } else {
      @converted_exons = sort {$a->start <=> $b->start} @converted_exons;
    }
    
    $converted_translation->start_Exon($converted_exons[0]);
    $converted_translation->end_Exon  ($converted_exons[$#converted_exons]);
    
    # phase is relative to the 5' end of the transcript (start translation)
    if ($converted_exons[0]->phase == 0) {
      $converted_translation->start(1);
    } elsif ($converted_exons[0]->phase == 1) {
      $converted_translation->start(3);
    } elsif ($converted_exons[0]->phase == 2) {
      $converted_translation->start(2);
    }
    
    $converted_translation->end  ($converted_exons[$#converted_exons]->end -
                                  $converted_exons[$#converted_exons]->start + 1);
    foreach my $exon(@converted_exons){
      $converted_transcript->add_Exon($exon);
    }
  }
  
  $converted_transcript->slice($self->query);

  return $converted_transcript;

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

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

  return $self->{'_padding'};

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

  $self->{features} = [] if(!$self->{features});
  if($arg){
    throw($arg." must be an arrayref of Bio::EnsEMBL::FeaturePair objects")
      unless(ref($arg) eq "ARRAY" && $arg->[0]->isa("Bio::EnsEMBL::FeaturePair"));
    $self->{features} = $arg;
  }
  return $self->{features};

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

  $self->{'_genewise_options'} = {} if(!$self->{'_genewise_options'});

  if ($arg) {
    throw("Must pass genewise options a hash ref not a $arg") 
      unless(ref($arg) eq "HASH");
    $self->{'_genewise_options'} = $arg;
  }

  return $self->{'_genewise_options'};

  my ($self) = @_;

  if (!($self->{_reverse})) {
    my $strand = 0;
    my $fcount = 0;
    my $rcount = 0;

    foreach my $f (@{$self->features}) {
      if ($f->strand == 1){
	$fcount++;
      } elsif ($f->strand == -1) {
	$rcount++;
      }
    }

    if ($fcount > $rcount) {
      $self->{_reverse} = 0;
    } else {
      $self->{_reverse} = 1;
    }
    if($fcount && $rcount){
      warning("Forward and reverse strand features see to have been ".
              "passed to MiniGenewise together");
    }
  }
  return $self->{_reverse};
}

1;

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

  my $pairaln  = new Bio::EnsEMBL::Analysis::Tools::PairAlign;
  my $ff = $self->feature_factory;
  my @genomic_features;
		
  my $prevend     = 0;
  my $count       = 0;
  my $mingap      = $self->minimum_intron;
  my $seqname     = $features->[0]->seqname;

  my @features = sort {$a->start <=> $b->start} @$features;

 FEAT:foreach my $f (@features) {
    my $start = $f->start - $self->exon_padding;
    my $end   = $f->end   + $self->exon_padding;

    if ($start < 1) { 
      $start = 1;
    }

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

    my $gap     =    ($start - $prevend);

    # Extend the region is the gap between features is
    # below a certain size - otherwise start a new region

    if ($count > 0 && ($gap < $mingap)) {

      if ($end < $prevend) { 
        $end = $prevend;
      }
      
      $genomic_features[$#genomic_features]->end($end);
      $prevend     = $end;
	
    } else {
	
      my $newfeature = new Bio::EnsEMBL::Feature;
	
      $newfeature->seqname   ($f->seqname);
      $newfeature->start     ($start);
      $newfeature->end       ($end);
      $newfeature->strand    (1);
      $newfeature->slice($self->query);
      push(@genomic_features,$newfeature);
	
      $prevend     = $end;
    }
    $count++;
  }

  # make a forward strand sequence, but tell genewise to run reversed if the 
  # features are on the reverse strand - handled by _is_reversed

  @genomic_features = sort {$a->start <=> $b->start } @genomic_features;

  # pad the termini of the sequence with 20K (configurable?) of genomic 
  # sequence - to catch small terminal exons that are missed by blast
  my $adjusted_start = $genomic_features[0]->start;
  $adjusted_start -= $self->terminal_padding;
  if($adjusted_start < 1 ) {
    $adjusted_start = 1;
  }
  $genomic_features[0]->start($adjusted_start);

  my $adjusted_end = $genomic_features[$#genomic_features]->end;
  $adjusted_end += $self->terminal_padding;
  if($adjusted_end > $self->query->length) {
    $adjusted_end = $self->query->length;
  }
  $genomic_features[$#genomic_features]->end($adjusted_end);

  my $current_coord = 1;
  foreach my $f (@genomic_features) {
    my $cdna_start = $current_coord;
    my $cdna_end   = $current_coord + ($f->end - $f->start);
    
    my $fp  = $ff->create_feature_pair($f->start, $f->end, $f->strand, undef,
                                       $cdna_start, $cdna_end, 1, 
                                       $f->seqname.".cdna", undef, undef, 
                                       $self->query->seq_region_name, $self->query, 
                                       $self->analysis);
    $pairaln->addFeaturePair($fp);
    $current_coord = $cdna_end+1;
  }

  my $miniseq = new Bio::EnsEMBL::Analysis::Tools::MiniSeq(-id        => 'test',
                                                           -pairalign => $pairaln);

  $self->miniseq($miniseq);
  return $miniseq;

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

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

  return $self->{'_iterate'};

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

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

  return $self->{'_minimum_intron'};

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

#FUNCTIONALITY

  my ($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  my( $protein, $features, $minimum_intron, $terminal_padding, $exon_padding, 
      $max_iterate_dist, $genewise_options)
    = rearrange([qw(PROTEIN FEATURES MINIMUM_INTRON TERMINAL_PADDING EXON_PADDING
                    MAX_SPLIT_ITERATE_DIST GENEWISE_OPTIONS)], @args);
  
  ####SETTING_DEFAULTS###
  $self->minimum_intron(1000);
  $self->exon_padding(200);
  $self->terminal_padding(20000);
  $self->max_split_iterate_distance(0);
  #######################
  $self->protein_sequence($protein);
  $self->features($features);
  $self->minimum_intron($minimum_intron);
  $self->exon_padding($exon_padding);
  $self->terminal_padding($terminal_padding);
  $self->max_split_iterate_distance($max_iterate_dist);
  $self->genewise_options($genewise_options);
  
  throw("MiniGenewise needs a query sequence") unless($self->query);
  throw("MiniGenewise needs a peptide sequence") unless($self->protein_sequence);
  throw("MiniGenewise needs an array of features") 
    unless($self->features && scalar(@{$self->features}));
  return $self;
}

#ACCESSOR METHODS

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

  if ($value) {
    throw("Input isn't a Bio::PrimarySeq but ".$value) 
      unless($value->isa("Bio::PrimarySeqI"));
    $self->{'_protein_sequence'} = $value;
  }
  return $self->{'_protein_sequence'};

  my ($self) = @_;

  my $must_try_again = 1;
  my $features = $self->features;
  my $gw_output;
  while($must_try_again){
    $must_try_again = 0;

    $gw_output = $self->run_Genewise($features);
    if($gw_output eq "FAILED"){
      return;
    }
  
    logger_info("Have ".@$gw_output." output from the genewise run");
    
    if($self->max_split_iterate_distance){
    
      my @bridge_features;
      
      foreach my $g(@$gw_output){

        foreach my $e($g->get_all_Exons){

          my @pieces = @{$self->miniseq->convert_SeqFeature($e)};
        
          if (@pieces > 1) {

            @pieces = sort {$a->start <=> $b->start} @pieces;

            my $can_merge = 1;
            for(my $i=1; $i < @pieces; $i++) {
              my $dist = $pieces[$i]->start - $pieces[$i-1]->end - 1;
              if ($dist > $self->max_split_iterate_distance) {
                $can_merge = 0;
                last;
              }
            }

            if ($can_merge) {
              push @bridge_features, Bio::EnsEMBL::Feature
                ->new(-start => $pieces[0]->start,
                      -end   => $pieces[-1]->end);
            }
          }
        }
      }
      if(@bridge_features){
        push(@$features, @bridge_features);
        $must_try_again = 1;
        warning($self->protein_sequence->id." has a predicted feature which splits ".
                " when mapped back to the genomic, trying again");
      }
    }
  }

  my $output = [];
  foreach my $gene(@$gw_output){
    my $new_gene = $self->convert_to_genomic($gene);
    warning("Failed to convert ".$gene." to genomic coordinates, skipping") 
      unless($new_gene);
    push(@$output, $new_gene) if($new_gene);
  }
  $self->output($output);

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

  if(!$features){
    $features = $self->features;
  }
  # foreach my $f(@$features){
  #  print "MINIGENEWISE ".$f->start." ".$f->end." ".$f->strand." ".$f->hseqname."\n";
  #}
  my $miniseq_object = $self->make_MiniSeq($features);
  my $miniseq = $miniseq_object->get_cDNA_sequence;
  my %params = %{$self->genewise_options} if($self->genewise_options);
  my $gw = new Bio::EnsEMBL::Analysis::Runnable::Genewise
      (
       -query   => $miniseq,
       -protein  => $self->protein_sequence,
       -reverse  => $self->is_reversed,
       -analysis => $self->analysis,
       %params
      );
  #throw("Minigenewise Can't run without context in sequence") 
  #  if(!$miniseq =~ /[CATG]{3}/);
  eval{
    $gw->run;
  };
  if($@){
    throw("Failed ".$gw." run $@"); # warning changed to throw() to prevent silent failing
  }
  my @output = @{$gw->output};

  return\@ output;

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

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

  Arg [1]   : Bio::EnsEMBL::Analysis::Runnable::MiniGenewise
  Arg [2]   : various things depending on the accessor
  Function  : to store the passed in variable
  Returntype: various
  Exceptions: methods will throw if the wrong type of variable is passed in
  Example   :