# do not use this class directly it is available through Bio::SearchIO
    use Bio::SearchIO;
    my $in = new Bio::SearchIO(-format => 'hmmer',
			       -file   => 't/data/L77119.hmmer');
    while( my $result = $in->next_result ) {
	# this is a Bio::Search::Result::HMMERResult object
	print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
	while( my $hit = $result->next_hit ) {
	    print $hit->name(), "\n";
	    while( my $hsp = $hit->next_hsp ) {
		print "length is ", $hsp->length(), "\n";
	    }
	}
    }

     # mapping of HMMER items to Bioperl hash keys
    %MODEMAP = ('HMMER_Output'    => 'result',
		'Hit'             => 'hit',
		'Hsp'             => 'hsp'
		);

    %MAPPING = ( 
		 'Hsp_bit-score'  => 'HSP-bits',
		 'Hsp_score'      => 'HSP-score',
		 'Hsp_evalue'     => 'HSP-evalue',
		 'Hsp_query-from' => 'HSP-query_start',
		 'Hsp_query-to'   => 'HSP-query_end',
		 'Hsp_hit-from'   => 'HSP-hit_start',
		 'Hsp_hit-to'     => 'HSP-hit_end',
		 'Hsp_positive'   => 'HSP-conserved',
		 'Hsp_identity'   => 'HSP-identical',
		 'Hsp_gaps'       => 'HSP-hsp_gaps',
		 'Hsp_hitgaps'    => 'HSP-hit_gaps',
		 'Hsp_querygaps'  => 'HSP-query_gaps',
		 'Hsp_qseq'       => 'HSP-query_seq',
		 'Hsp_hseq'       => 'HSP-hit_seq',
		 'Hsp_midline'    => 'HSP-homology_seq',
		 'Hsp_align-len'  => 'HSP-hsp_length',
		 'Hsp_query-frame'=> 'HSP-query_frame',
		 'Hsp_hit-frame'  => 'HSP-hit_frame',

		 'Hit_id'        => 'HIT-name',
		 'Hit_len'       => 'HIT-length',
		 'Hit_accession' => 'HIT-accession',
		 'Hit_desc'      => 'HIT-description',
		 'Hit_signif'    => 'HIT-significance',
		 'Hit_score'     => 'HIT-score',
		 
		 'HMMER_program'   => 'RESULT-algorithm_name',
		 'HMMER_version'   => 'RESULT-algorithm_version',
		 'HMMER_query-def' => 'RESULT-query_name',
		 'HMMER_query-len' => 'RESULT-query_length',
		 'HMMER_query-acc' => 'RESULT-query_accession',
		 'HMMER_querydesc' => 'RESULT-query_description',
		 'HMMER_hmm'       => 'RESULT-hmm_name',		 
		 'HMMER_seqfile'   => 'RESULT-sequence_file',
		 );
    $DEFAULT_HIT_FACTORY_CLASS     = 'Bio::Factory::HMMERHitFactory';
    $DEFAULT_HSP_FACTORY_CLASS     = 'Bio::Factory::HMMERHSPFactory';
    $DEFAULT_RESULT_FACTORY_CLASS  = 'Bio::Factory::HMMERResultFactory';

    my ($self,@args) = @_;
    $self->SUPER::_initialize(@args);
    my $handler = $self->_eventHandler;
    # new object initialization code
    $handler->register_factory('result',
                               Bio::Factory::ObjectFactory->new(
                                      -type      => 'Bio::Search::Result::HMMERResult',
                                      -interface => 'Bio::Search::Result::ResultI'));

    $handler->register_factory('hit', 
                               Bio::Factory::ObjectFactory->new(
                                       -type      => 'Bio::Search::Hit::HMMERHit',
                                       -interface => 'Bio::Search::Hit::HitI'));

    $handler->register_factory('hsp', 
                               Bio::Factory::ObjectFactory->new(
                                       -type      => 'Bio::Search::HSP::HMMERHSP',
                                       -interface => 'Bio::Search::HSP::HSPI'));
    $self->{'_hmmidline'} = 'HMMER 2.2g (August 2001)';

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

   if( $self->in_element('hsp') && 
       $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/o &&
       defined $data->{'Data'} ) {
       $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
   }  
   return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/o );
   
   $self->{'_last_data'} = $data->{'Data'};

   my ($self,$data) = @_;
   $self->start_element($data);
   $self->characters($data);
   $self->end_element($data);

   my ($self) = @_;
   return $self->{'_result'};

    my ($self,$data) = @_;
    my $nm = $data->{'Name'};
    my $type = $MODEMAP{$nm};
    my $rc;

    if($nm eq 'HMMER_program' ) {
	if( $self->{'_last_data'} =~ /(HMM\S+)/i ) {
	    $self->{'_reporttype'} = uc $1;
	}   
    }
    # Hsp are sort of weird, in that they end when another
    # object begins so have to detect this in end_element for now
    if( $nm eq 'Hsp' ) {
	foreach ( qw(Hsp_qseq Hsp_midline Hsp_hseq) ) {
	    $self->element({'Name' => $_,
			    'Data' => $self->{'_last_hspdata'}->{$_}});
	}
	$self->{'_last_hspdata'} = {};
    }
    if( $type ) {
	if( $self->_eventHandler->will_handle($type) ) {
	    my $func = sprintf("end_%s",lc $type);
	    $rc = $self->_eventHandler->$func($self->{'_reporttype'},
					      $self->{'_values'});	    
	}
	my $lastelem = shift @{$self->{'_elements'}};
    } elsif( $MAPPING{$nm} ) { 	
	if ( ref($MAPPING{$nm}) =~ /hash/i ) {
	    my $key = (keys %{$MAPPING{$nm}})[0];	    
	    $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'};
	} else {
	    $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};
	}
    } else { 
	$self->debug( "unknown nm $nm, ignoring\n");
    }
    $self->{'_last_data'} = ''; # remove read data if we are at 
				# end of an element
    $self->{'_result'} = $rc if( defined $type && $type eq 'result' );
    return $rc;

   my ($self,$name) = @_; 
   return 0 if ! defined $self->{'_elements'}->[0];
   return ( $self->{'_elements'}->[0] eq $name)

   my ($self) = @_;
   my $seentop = 0;
   my $reporttype;
   my ($last,@hitinfo,@hspinfo,%hspinfo,%hitinfo);
   
   my @alignemnt_lines;

   $self->start_document();
   while( defined ($_ = $self->_readline )) {
       my $lineorig = $_;
       chomp;
       if( /^HMMER\s+(\S+)\s+\((.+)\)/o ) {	   
	   my ($prog,$version) = split;
	   if( $seentop ) {
	       $self->_pushback($_);
	       $self->end_element({'Name' => 'HMMER_Output'});
	       return $self->end_document();
	   }
	   $self->{'_hmmidline'} = $_;
	   $self->start_element({'Name' => 'HMMER_Output'});
	   $self->{'_result_count'}++;
	   $seentop = 1;
	   if( defined $last ) { 
	       ($reporttype) = split(/\s+/,$last);
	       $self->element({'Name' => 'HMMER_program',
			       'Data' => uc ($reporttype)});
	   }
	   $self->element({'Name' => 'HMMER_version',
			   'Data' => $version});
       } elsif( s/^HMM file:\s+//o ) {
	   $self->{'_hmmfileline'} = $lineorig;
	   $self->element({'Name' => 'HMMER_hmm',
			   'Data' => $_});
       } elsif( s/^Sequence\s+(file|database):\s+//o ) {
	   $self->{'_hmmseqline'} = $lineorig;
	   $self->element({'Name' => 'HMMER_seqfile',
			   'Data' => $_});
       } elsif( s/^Query(\s+(sequence|HMM))?:\s+//o) {
	   if( ! $seentop ) {	       
               # we're in a multi-query report
	       $self->_pushback($self->{'_hmmidline'});
	       $self->_pushback($self->{'_hmmfileline'});	       
	       $self->_pushback($self->{'_hmmseqline'});
	       $self->_pushback($lineorig);
	       next;
	   }
	   s/\s+$//;
	   $self->element({'Name' => 'HMMER_query-def',
			   'Data' => $_});
       } elsif( s/^Accession:\s+//o ) {
	   s/\s+$//;
	   $self->element({'Name' => 'HMMER_query-acc',
			   'Data' => $_});
       } elsif( s/^Description:\s+//o ) {
	   s/\s+$//;
	   $self->element({'Name' => 'HMMER_querydesc',
			   'Data' => $_});	   
       } elsif(  defined $self->{'_reporttype'} &&
		 $self->{'_reporttype'} eq 'HMMSEARCH' ) {
	   # PROCESS HMMSEARCH RESULTS HERE
	   if( /^Scores for complete sequences/o ) {
	       while( defined($_ = $self->_readline) ) {
		   last if( /^\s+$/);
		   next if( /^Sequence\s+Description/o || /^\-\-\-/o );
		   my @line = split;
		   my ($name, $n,$evalue,$score)= (shift @line,
						   pop   @line,
						   pop   @line,
						   pop   @line);
		   my $desc = join(' ', @line);
		   push @hitinfo, [ $name, $desc,$evalue,$score];
		   $hitinfo{$name} = $#hitinfo;
	       }
	   } elsif( /^Parsed for domains:/o ) {
	       @hspinfo = ();
	       
	       while( defined($_ = $self->_readline) ) {
		   last if( /^\s+$/);
		   next if( /^(Model|Sequence)\s+Domain/o || /^\-\-\-/o );
		   if( my ($n,$domainnum,$domainct, @vals) = 
		       (m!^(\S+)\s+      # host name
			(\d+)/(\d+)\s+   # num/num (ie 1 of 2) 
			(\d+)\s+(\d+).+? # sequence start and end
			(\d+)\s+(\d+)\s+ # hmm start and end
			\S+\s+           # []
			(\S+)\s+         # score
			(\S+)            # evalue
			\s*$!ox ) ) {
                       # array lookup so that we can get rid of things 
                       # when they've been processed
                       my $info = $hitinfo[$hitinfo{$n}];
                       if( !defined $info ) { 
                           $self->warn("Incomplete Sequence information, can't find $n hitinfo says $hitinfo{$n}"); 
                           next;
                       }
                       push @hspinfo, [ $n, @vals];
		   }
	       }
	   } elsif( /^Alignments of top/o  ) {
	       my ($prelength,$lastdomain,$count,$width);
	       $count = 0;
	       my %domaincounter;
	       my $second_tier=0;
	       while( defined($_ = $self->_readline) ) {
		   next if( /^Align/o ||
			    /^\s+RF\s+[x\s]+$/o);
		   if( /^Histogram/o || m!^//!o ) {
		       if( $self->in_element('hsp')) {
			   $self->end_element({'Name' => 'Hsp'});
		       }
		       if( $self->within_element('hit')) {
			   $self->end_element({'Name' => 'Hit'});
		       }
		       last;
		   }
		   chomp;
		   
		   if( /^\s*(.+):\s+domain\s+(\d+)\s+of\s+(\d+)\,\s+from\s+(\d+)\s+to\s+(\d+)/o ) {
		       my ($name,$domainct,$domaintotal,
			   $from,$to) = ($1,$2,$3,$4,$5);
		       $domaincounter{$name}++;		       
		       if( ! defined $lastdomain || $lastdomain ne $name ) {
			   if( $self->within_element('hit') ) {
			       if( $self->within_element('hsp') ) {
				   $self->end_element({'Name' => 'Hsp'});
			       }
			       $self->end_element({'Name' => 'Hit'});
			   }
			   $self->start_element({'Name' => 'Hit'});
			   my $info = [@{$hitinfo[$hitinfo{$name}] || $self->throw("Could not find hit info for $name: Insure that your database contains only unique sequence names")}];
			   if( $info->[0] ne $name ) { 
			       $self->throw("Somehow the Model table order does not match the order in the domains (got ".$info->[0].", expected $name)"); 
			   }
			   $self->element({'Name' => 'Hit_id',
					   'Data' => shift @{$info}});
			   $self->element({'Name' => 'Hit_desc',
					   'Data' => shift @{$info}});
			   $self->element({'Name' => 'Hit_signif',
					   'Data' => shift @{$info}});
			   $self->element({'Name' => 'Hit_score',
					   'Data' => shift @{$info}});
		       }
		       $self->end_element({'Name' => 'Hsp'})
			   if $self->in_element('hsp');
		       
		       $self->start_element({'Name' => 'Hsp'});
		       $self->element({'Name' => 'Hsp_identity',
				       'Data' => 0});
		       $self->element({'Name' => 'Hsp_positive',
				       'Data' => 0});
		       my $HSPinfo = shift @hspinfo;
		       my $id = shift @$HSPinfo;
		       if( $id ne $name ) { 
			   $self->throw("Somehow the domain list details do not match the table (got $id, expected $name)");
		       }
		       if( $domaincounter{$name} == $domaintotal) {
			   $hitinfo[$hitinfo{$name}] = undef;
		       }

		       $self->element({'Name' => 'Hsp_hit-from',
				       'Data' => shift @$HSPinfo});
		       $self->element({'Name' => 'Hsp_hit-to',
				       'Data' => shift @$HSPinfo});
		       $self->element({'Name' => 'Hsp_query-from',
				       'Data' => shift @$HSPinfo});
		       $self->element({'Name' => 'Hsp_query-to',
				       'Data' => shift @$HSPinfo});
		       $self->element({'Name' => 'Hsp_score',
				       'Data' => shift @$HSPinfo});
		       $self->element({'Name' => 'Hsp_evalue',
				       'Data' => shift @$HSPinfo});
		       $lastdomain = $name;
		   } else { 
		       # Might want to change this so that it
		       # accumulates all the of the alignment lines into 
		       # three array slots and then tests for the 
		       # end of the line		       
		       if( /^(\s+\*\-\>)(\S+)/o  ) { # start of domain
			   $prelength = CORE::length($1);
			   $width = 0;
			   # $width = CORE::length($2);
			   $self->element({'Name' =>'Hsp_qseq',
					   'Data' => $2});
			   $count = 0;
			   $second_tier = 0;
		       } elsif ( /^(\s+)(\S+)\<\-\*\s*$/o ) { #end of domain
			   $self->element({'Name' =>'Hsp_qseq',
					   'Data' => $2});
			   $width = CORE::length($2);
			   $count = 0;
		       } elsif( ($count != 1 && /^\s+$/o) ||
				 CORE::length($_) == 0 ||
				/^\s+\-?\*\s*$/ ) {
			   next;
		       } elsif( $count == 0 ) {
			   $prelength -= 3 unless ($second_tier++);
			   unless( defined $prelength) { 
			       # $self->warn("prelength not set"); 
			       next;
			   }
			   $self->element({'Name' => 'Hsp_qseq',
					   'Data' => substr($_,$prelength)});
		       } elsif( $count == 1) { 
			   if( ! defined $prelength ) { 
			       $self->warn("prelength not set"); 
			   }
			   if( $width ) {
			       $self->element({'Name' => 'Hsp_midline',
					       'Data' => substr($_,
								$prelength,
								$width)});
			   } else { 
			       $self->debug( "midline is $_\n") if( CORE::length($_) <= $prelength && $self->verbose > 0);
			       $self->element({'Name' => 'Hsp_midline',
					       'Data' => substr($_,
								$prelength)});
			   }
		       } elsif( $count == 2) {
			   if( /^\s+(\S+)\s+(\d+|\-)\s+(\S*)\s+(\d+|\-)/o ) {
			       $self->element({'Name' => 'Hsp_hseq',
					       'Data'  => $3});
			   } else {
			       $self->warn("unrecognized line: $_\n");
			   }
		       }
		       $count = 0 if $count++ >= 2;
		   }
	       }
	   } elsif(  /^Histogram/o || m!^//!o ) { 

	       while( my $HSPinfo = shift @hspinfo ) {		  
		   my $id = shift @$HSPinfo;
		   my $info = [@{$hitinfo[$hitinfo{$id}]}];
		   next unless defined $info;
		   $self->start_element({'Name' => 'Hit'});
		   $self->element({'Name' => 'Hit_id',
				   'Data' => shift @{$info}});
		   $self->element({'Name' => 'Hit_desc',
				   'Data' => shift @{$info}});
		   $self->element({'Name' => 'Hit_signif',
				   'Data' => shift @{$info}});
		   $self->element({'Name' => 'Hit_score',
				   'Data' => shift @{$info}});
		   $self->start_element({'Name' => 'Hsp'});
		   $self->element({'Name' => 'Hsp_query-from',
				   'Data' => shift @$HSPinfo});
		   $self->element({'Name' => 'Hsp_query-to',
				   'Data' => shift @$HSPinfo});
		   $self->element({'Name' => 'Hsp_hit-from',
				   'Data' => shift @$HSPinfo});
		   $self->element({'Name' => 'Hsp_hit-to',
				   'Data' => shift @$HSPinfo});
		   $self->element({'Name' => 'Hsp_score',
				   'Data' => shift @$HSPinfo});
		   $self->element({'Name' => 'Hsp_evalue',
				   'Data' => shift @$HSPinfo});
		   $self->element({'Name' => 'Hsp_identity',
				   'Data' => 0});
		   $self->element({'Name' => 'Hsp_positive',
				   'Data' => 0});
		   $self->element({'Name' => 'Hsp_positive',
				   'Data' => 0});
		   $self->end_element({'Name' => 'Hsp'});
		   $self->end_element({'Name' => 'Hit'});		   
	       }
	       @hitinfo = ();
	       %hitinfo = ();
	       last;	   
	   }
       } elsif( defined $self->{'_reporttype'} &&
		$self->{'_reporttype'} eq 'HMMPFAM' ) {
	   if( /^Scores for sequence family/o ) {
	       while( defined($_ = $self->_readline) ) {
		   last if( /^\s+$/);
		   next if( /^Model\s+Description/o || /^\-\-\-/o );
		   chomp;
		   my @line = split;
		   my ($model,$n,$evalue,$score) = (shift @line,
						    pop @line,
						    pop @line,
						    pop @line);
		   my $desc = join(' ', @line);
		   push @hitinfo, [ $model, $desc,$score,$evalue,$n];
		   $hitinfo{$model} = $#hitinfo;
	       }
	   } elsif( /^Parsed for domains:/o ) {
	       @hspinfo = ();
	       while( defined($_ = $self->_readline) ) {
		   last if( /^\s+$/);
		   next if( /^Model\s+Domain/o || /^\-\-\-/o );
		   chomp;
		   if( my ($n,$domainnum,$domainct,@vals) = 
			   (m!^(\S+)\s+         # domain name
			    \s+(\d+)/(\d+)\s+   # domain num out of num
			    (\d+)\s+(\d+).+?    # seq start, end
			    (\d+)\s+(\d+)\s+    # hmm start, end
			    \S+\s+              # []
			    (\S+)\s+            # score       
			    (\S+)               # evalue
			    \s*$!ox ) ) {
		       my $hindex = $hitinfo{$n};
		       if( ! defined $hindex ) {
			   push @hitinfo, [ $n, '',$vals[5],$vals[6],
					    $domainct];
			   $hitinfo{$n} = $#hitinfo;
			   $hindex = $#hitinfo;
		       }
		       my $info = $hitinfo[$hindex];
                       if( ! defined $info ) { 
                           $self->warn("incomplete Domain information, can't find $n hitinfo says $hitinfo{$n}"); 
                           next;
                       }
                       push @hspinfo, [ $n, @vals];
		   }
	       }
	   } elsif( /^Alignments of top/o  ) {
	       my ($prelength,$lastdomain,$count,$width);
	       $count = 0;
	       my $second_tier=0;
	       while( defined($_ = $self->_readline) ) {		   
		   next if( /^Align/o || /^\s+RF\s+[x\s]+$/o);
		   
		   if( /^Histogram/o || m!^//!o || /^Query sequence/o ) {
		       if( $self->in_element('hsp')) {
			   $self->end_element({'Name' => 'Hsp'});
		       }
		       if( $self->in_element('hit') ) {
			   $self->end_element({'Name' => 'Hit'});
		       }		       
		       $self->end_element({'Name' => 'HMMER_Output'});
		       if( /^Query sequence/o ) { $self->_pushback($_); }
		       return $self->end_document();		       
		       last;
		   }
		   chomp;
		   if( m/(\S+):.*from\s+(\d+)\s+to\s+(\d+)/o ) {
		       my ($name,$from,$to) = ($1,$2,$3);
		       if( ! defined $lastdomain || $lastdomain ne $name ) {
			   
			   if( $self->within_element('hit') ) {
			       if( $self->in_element('hsp') ) {
				   $self->end_element({'Name' => 'Hsp'});
			       }
			       $self->end_element({'Name' => 'Hit'});
			   }
			   $self->start_element({'Name' => 'Hit'});
			   my $info = [@{$hitinfo[$hitinfo{$name}]}];
			   if( ! defined $info ||
			       $info->[0] ne $name ) {
			       $self->warn("Somehow the Model table order does not match the order in the domains (got ".$info->[0].", expected $name). We're
back loading this from the alignment information instead");
				$info = [$name, '',
					 /score\s+([^,\s]+),\s+E\s+=\s+(\S+)/ox];
			       push @hitinfo, $info;
			       $hitinfo{$name} = $#hitinfo;
			   }

			   $self->element({'Name' => 'Hit_id',
					   'Data' => shift @{$info}});
			   $self->element({'Name' => 'Hit_desc',
					   'Data' => shift @{$info}});
			   $self->element({'Name' => 'Hit_score',
					   'Data' => shift @{$info}});
			   $self->element({'Name' => 'Hit_signif',
					   'Data' => shift @{$info}});
		       }
		       if( $self->within_element('hsp') ) {
			   #if( defined $lastdomain ) {
			   $self->end_element({'Name' => 'Hsp'});
		       } 
		       $self->start_element({'Name' => 'Hsp'});
		       $self->element({'Name' => 'Hsp_identity',
				       'Data' => 0});
		       $self->element({'Name' => 'Hsp_positive',
				       'Data' => 0});
		       my $HSPinfo = shift @hspinfo;
		       my $id = shift @$HSPinfo;

		       if( $id ne $name ) { 
			   $self->throw("Somehow the domain list details do not match the table (got $id, expected $name)");
		       }
		       $self->element({'Name' => 'Hsp_query-from',
				       'Data' => shift @$HSPinfo});
		       $self->element({'Name' => 'Hsp_query-to',
				       'Data' => shift @$HSPinfo});
		       $self->element({'Name' => 'Hsp_hit-from',
				       'Data' => shift @$HSPinfo});
		       $self->element({'Name' => 'Hsp_hit-to',
				       'Data' => shift @$HSPinfo});
		       $self->element({'Name' => 'Hsp_score',
				       'Data' => shift @$HSPinfo});
		       $self->element({'Name' => 'Hsp_evalue',
				       'Data' => shift @$HSPinfo});

		       $lastdomain = $name;	       
		   } else { 
		       if( /^(\s+\*\-\>)(\S+)/o  ) { # start of domain
			   $prelength = CORE::length($1);
			   $width = 0;
			   # $width = CORE::length($2);
			   $self->element({'Name' =>'Hsp_hseq',
					   'Data' => $2});
			   $count = 0;
			   $second_tier = 0;
		       } elsif ( /^(\s+)(\S+)\<\-?\*?\s*$/o ) { #end of domain
			   $prelength -= 3 unless ($second_tier++);
			   $self->element({'Name' =>'Hsp_hseq',
					   'Data' => $2});
			   $width = CORE::length($2);
			   $count = 0;
		       } elsif( CORE::length($_) == 0 || 
				($count != 1 && /^\s+$/o) ||
				/^\s+\-?\*\s*$/ ) { 
			   next;
		       } elsif( $count == 0 ) {
			   $prelength -= 3 unless ($second_tier++);
			   unless( defined $prelength) { 
			       # $self->warn("prelength not set"); 
			       next;
			   }
			   $self->element({'Name' => 'Hsp_hseq',
					   'Data' => substr($_,$prelength)});
		       } elsif( $count == 1 ) { 
			   if( ! defined $prelength ) { 
			       $self->warn("prelength not set"); 
			   }			       
			   if( $width ) {
			       $self->element({'Name' => 'Hsp_midline',
					       'Data' => substr($_,$prelength,$width)});
			   } else { 
			       $self->element({'Name' => 'Hsp_midline',
					       'Data' => substr($_,$prelength)});
			   }
		       } elsif( $count == 2 ) {
			   if( /^\s+(\S+)\s+(\d+)\s+(\S+)\s+(\d+)/o ||
			       /^\s+(\S+)\s+(\-)\s+(\S*)\s+(\-)/o 
			       ) {
			       $self->element({'Name' => 'Hsp_qseq',
					       'Data'  => $3});
			   } else {
			       $self->warn("unrecognized line ($count): $_\n");
			   }
		       }
		       $count = 0 if $count++ >= 2;
		   }	       
	       }	   
	   } else { 
	       $self->debug($_);
	   }	   
       }
       $last = $_;
   }

   $self->end_element({'Name' => 'HMMER_Output'}) unless ! $seentop;
   return $self->end_document();

    my $self = shift;
    return $self->{'_result_count'};
}

1;

    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= undef;
    $self->{'_elements'} = [];

   my ($self,$data) = @_;
    # we currently don't care about attributes
   my $nm = $data->{'Name'};    
   my $type = $MODEMAP{$nm};
   if( $type ) {
       if( $self->_eventHandler->will_handle($type) ) {
	   my $func = sprintf("start_%s",lc $type);
	   $self->_eventHandler->$func($data->{'Attributes'});
       }						 
       unshift @{$self->{'_elements'}}, $type;
   }
   if(defined $type && 
      $type eq 'result') {
       $self->{'_values'} = {};
       $self->{'_result'}= undef;
    }

   my ($self,$name) = @_;  
   return 0 if ( ! defined $name ||
		 ! defined  $self->{'_elements'} ||
		 scalar @{$self->{'_elements'}} == 0) ;
   foreach (  @{$self->{'_elements'}} ) {
       return 1 if( $_ eq $name  );
   }
   return 0;

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

 Title   : new
 Usage   : my $obj = new Bio::SearchIO::hmmer();
 Function: Builds a new Bio::SearchIO::hmmer object 
 Returns : Bio::SearchIO::hmmer
 Args    : -fh/-file => HMMER filename
           -format   => 'hmmer'