use Bio::Tools::Hmmpfam;
  my $hmmpfam_parser = new Bio::Tools::Hmmpfam(-fh =>$filehandle );
  while( my $hmmpfam_feat = $hmmpfam_parser->next_result ) {
        push @hmmpfam_feat, $hmmpfam_feat;
  }

 Parser for Hmmpfam  program

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

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

      return $self;

    my ($self) = @_;
    my $filehandle;
    
 my $line;

    my $id;
    while ($_=$self->_readline()) {
         $line = $_;
         chomp $line;
    
        
        last if $line=~m/^Alignments of top-scoring domains/;
        next if ($line=~m/^Model/ || /^\-/ || /^$/);
        
        if ($line=~m/^Query sequence:\s+(\S+)/) {
           $id = $1;
           $self->seqname($id);
        }
       
       if (my ($hid, $start, $end, $hstart, $hend, $score, $evalue) = $line=~m/^(\S+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s+(\S+)/) {
            my %feature;
            
            ($feature{name}) = $self->seqname;
            $feature{score} = $score;
            $feature{p_value} = sprintf ("%.3e", $evalue);
            $feature{start} = $start;
            $feature{end} = $end;
            $feature{hname} = $hid;
            $feature{hstart} = $hstart;
            $feature{hend} = $hend;
            ($feature{source}) = 'pfam';
            $feature{primary} = $hid;
            ($feature{program}) = 'pfam';
            ($feature{db}) = 'db1';
            ($feature{logic_name}) = 'hmmpfam';
            my $new_feat = $self->create_feature (\%feature);
            return $new_feat
        
        }
        next;

    }
    return;

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



    my $feature1= Bio::SeqFeature::Generic->new( -seqname    =>$feat->{name},
                                                -start      =>$feat->{start},
                                                -end        =>$feat->{end},
                                                -score      =>$feat->{score},
                                                -source     =>$feat->{source},
                                                -primary    =>$feat->{primary},
                                                   );
    


    my $feature2= Bio::SeqFeature::Generic->new(
                                                 -start      =>$feat->{hstart},
                                                 -end        =>$feat->{hend},
                                                  );




    my $featurepair = Bio::SeqFeature::FeaturePair->new;
    $featurepair->feature1 ($feature1);
    $featurepair->feature2 ($feature2);
   
   $featurepair->add_tag_value('evalue',$feat->{p_value});
   $featurepair->add_tag_value('percent_id','NULL');
   $featurepair->add_tag_value("hid",$feat->{primary});
    return  $featurepair;

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

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

    return $self->{'seqname'};

 User feedback is an integral part of the evolution of this and other
 Bioperl modules. Send your comments and suggestions preferably to
 the Bioperl mailing list.  Your participation is much appreciated.

 bioperl-l@bioperl.org              - General discussion
 http://bioperl.org/MailList.shtml  - About the mailing lists

 Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via
 email or the web:

 bioperl-bugs@bioperl.org
 http://bugzilla.bioperl.org/

 Email: fugui@worf.fugu-sg.org

 The rest of the documentation details each of the object methods.
 Internal methods are usually preceded with a _