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;
  }

      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;
    
        if ( $line=~m/^Alignments of top-scoring domains/ ) {
          while( my $rest = $self->_readline() ) { last if $rest =~ m!^//! }
        }

        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{raw_score} = $score;
            $feature{p_value} = sprintf ("%.3e", $evalue);
            $feature{score} = $feature{p_value};
            $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 $feature1= Bio::SeqFeature::Generic->new( -seq_id  =>$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/wiki/Mailing_lists  - About the mailing lists

  http://bugzilla.open-bio.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 _