use Bio::Tools::Est2Genome;

  my $featureiter = new Bio::Tools::Est2Genome(-file => 'output.est2genome');

  # This is going to be fixed to use the SeqAnalysisI next_feature
  # Method eventually when we have the objects to put the data in
  # properly
  while( my $f = $featureiter->parse_next_gene ) {
   # process Bio::SeqFeature::Generic objects here
  }

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

    # call the inherited method first
    my $make = $self->SUPER::_initialize_state(@args);

    my ($genome_is_first) = $self->_rearrange([qw(GENOMEFIRST)], @args);

    delete($self->{'_genome_is_first'});
    $self->{'_genome_is_first'} = $genome_is_first if(defined($genome_is_first));
    $self->analysis_method("est2genome");

#-------------
    my ($self, $method) = @_;
    if($method && ($method !~ /est2genome/i)) {
	$self->throw("method $method not supported in " . ref($self));
    }
    return $self->SUPER::analysis_method($method);

   my ($self,$return_gene) = @_;
   return $self->_parse_gene_struct if $return_gene;
   my $seensegment = 0;
   my @features;
   my ($qstrand,$hstrand) = (1,1);
   my $lasthseqname;
   while( defined($_ = $self->_readline) ) {
       if( /Note Best alignment is between (reversed|forward) est and (reversed|forward) genome, (but|and) splice\s+sites imply\s+(forward gene|REVERSED GENE)/) {
	   if( $seensegment ) {
	       $self->_pushback($_);
	       return wantarray ? @features :\@ features;
	   }
	   $hstrand = -1 if $1 eq 'reversed';
	   $qstrand = -1 if $4 eq 'REVERSED GENE';
	   #$self->debug( "1=$1, 2=$2, 4=$4\n");
       }
       elsif( /^Exon/ ) {
	   my ($name,$len,$score,$qstart,$qend,$qseqname,
	       $hstart,$hend, $hseqname) = split;
	   $lasthseqname = $hseqname;
	   my $query = new Bio::SeqFeature::Similarity(-primary => $name,
						       -source  => $self->analysis_method,
						       -seq_id => $qseqname, # FIXME WHEN WE REDO THE GENERIC NAME CHANGE
						       -start   => $qstart,
						       -end     => $qend,
						       -strand  => $qstrand,
						       -score   => $score,
						       -tag => {
#							   'Location' => "$hstart..$hend",
							   'Sequence' => "$hseqname",
							   }
						       );
	   my $hit = new Bio::SeqFeature::Similarity(-primary => 'exon_hit',
						     -source  => $self->analysis_method,
						     -seq_id => $hseqname,
						     -start   => $hstart,
						     -end     => $hend,
						     -strand  => $hstrand,
						     -score   => $score,
						     -tag => {
#							 'Location' => "$qstart..$qend",
							 'Sequence' => "$qseqname",
							
						     }
						     );
	   push @features, new Bio::SeqFeature::SimilarityPair
	       (-query => $query,
		-hit   => $hit,
		-source => $self->analysis_method);
       } elsif( /^([\-\+\?])(Intron)/) {
	   my ($name,$len,$score,$qstart,$qend,$qseqname) = split;
	   push @features, new Bio::SeqFeature::Generic(-primary => $2,
							-source => $self->analysis_method,
							-start => $qstart,
							-end   => $qend,
							-strand => $qstrand,
							-score  => $score,
							-seq_id => $qseqname,
							-tag => {
							    'Sequence' => $lasthseqname});
       } elsif( /^Span/ ) {
       } elsif( /^Segment/ ) {
	   $seensegment = 1;
       } elsif( /^\s+$/ ) { # do nothing
       } else {
	   $self->warn( "unknown line $_\n");
       }
   }
   return unless( @features );
   return wantarray ? @features :\@ features;

   my ($self) = @_;
   my $seensegment = 0;
   my @features;
   my ($qstrand,$hstrand) = (1,1);
   my $lasthseqname;
   my $gene = new Bio::SeqFeature::Gene::GeneStructure(-source => $self->analysis_method);
   my $transcript = new Bio::SeqFeature::Gene::Transcript(-source => $self->analysis_method);
   my @suppf;
   my @exon;
   while( defined($_ = $self->_readline) ) {
       if( /Note Best alignment is between (reversed|forward) est and (reversed|forward) genome, (but|and) splice\s+sites imply\s+(forward gene|REVERSED GENE)/) {
	      if( $seensegment ) {
	       $self->_pushback($_);
	       return $gene;
	      }
    	   $hstrand = -1 if $1 eq 'reversed';
    	   $qstrand = -1 if $4 eq 'REVERSED GENE';
       }
       elsif( /^Exon/ ) {
    	   my ($name,$len,$score,$qstart,$qend,$qseqname,$hstart,$hend, $hseqname) = split;
    	   $lasthseqname = $hseqname;
    	   my $exon = new Bio::SeqFeature::Gene::Exon(-primary => $name,
						       -source  => $self->analysis_method,
						       -seq_id => $qseqname, # FIXME WHEN WE REDO THE GENERIC NAME CHANGE
						       -start   => $qstart,
						       -end     => $qend,
						       -strand  => $qstrand,
						       -score   => $score,
						       -tag => {
                            #'Location' => "$hstart..$hend",
           							   'Sequence' => "$hseqname",
							              }
						       );
          $transcript->seq_id($qseqname) unless $transcript->seq_id;
          $exon->add_tag_value('phase',0);
          push @exon, $exon;
              
       } elsif( /^([\-\+\?])(Intron)/) {
         next; #intron auto matically built from exons..hope thats ok..
       } elsif( /^Span/ ) {
       } elsif( /^Segment/ ) {
    	    my ($name,$len,$score,$qstart,$qend,$qseqname,$hstart,$hend, $hseqname) = split;
	         my $query = new Bio::SeqFeature::Similarity(-primary => $name,
						       -source  => $self->analysis_method,
						       -seq_id => $qseqname, # FIXME WHEN WE REDO THE GENERIC NAME CHANGE
						       -start   => $qstart,
						       -end     => $qend,
						       -strand  => $qstrand,
						       -score   => $score,
						       -tag => {
#							   'Location' => "$hstart..$hend",
							   'Sequence' => "$hseqname",
							   }
						     );
      	   my $hit = new Bio::SeqFeature::Similarity(-primary => 'exon_hit',
                                           						     -source  => $self->analysis_method,
                                          						     -seq_id => $hseqname,
                                          						     -start   => $hstart,
                                          						     -end     => $hend,
                                          						     -strand  => $hstrand,
                                          						     -score   => $score,
                                          						     -tag => {
                                                            #	'Location' => "$qstart..$qend",
                                               							 'Sequence' => "$qseqname",
						                                                }
						     );
        	   my $support =  new Bio::SeqFeature::SimilarityPair (-query => $query,
                                                              		-hit   => $hit,
                                                              		-source => $self->analysis_method);
             push @suppf, $support;
       } elsif( /^\s+$/ ) { # do nothing
       } else {
      	   $self->warn( "unknown line $_\n");
       }
   }
   return unless $#exon >=0;
   foreach my $e(@exon){
    my @add;
    foreach my $sf(@suppf){
      if($sf->overlaps($e)){
          push @add,$sf;
      }
    }
    $e->add_tag_value('supporting_feature',@add);
    $transcript->add_exon($e);
  }
  
   $gene->add_transcript($transcript);
   $gene->seq_id($transcript->seq_id);
   return $gene;

    my ($self) = shift;
    $self->throw("We haven't really done this right, yet, use parse_next_gene");

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  http://bugzilla.open-bio.org/

 Title   : new
 Usage   : my $obj = new Bio::Tools::Est2Genome();
 Function: Builds a new Bio::Tools::Est2Genome object
 Returns : an instance of Bio::Tools::Est2Genome
 Args    : -file => 'output.est2genome' or
           -fh   => \*EST2GENOMEOUTPUT
           -genomefirst => 1  # genome was the first input (not standard)