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

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

    return $self->{'seqname'};

}

1;

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