$stream = Bio::SeqIO->new(-file => $filename, -format => 'swiss');

    while ( my $seq = $stream->next_seq() ) {
	# do something with $seq
    }

   print "ID   ", $func($seq), "\n";

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_ac_generation_func'} = $value;
    }
    return $obj->{'_ac_generation_func'};

  my( $self, $str ) = @_;
  
  $self->throw("Argument to crc32() must be ref to scalar")
    unless ref($str) eq 'SCALAR';
  
  $self->_generateCRCTable() unless exists $self->{'_crcTable'};
  
  my $len = length($$str);
  
  my $crc = 0xFFFFFFFF;
  for (my $i = 0; $i < $len; $i++) {
    # Get upper case value of each letter
    my $int = ord uc substr $$str, $i, 1;
    $crc = (($crc >> 8) & 0x00FFFFFF) ^ 
      ${$self->{'_crcTable'}}[ ($crc ^ $int) & 0xFF ];
  }
  return $crc;

    my ($self, $sequence) = @_;
    my $POLY64REVh = 0xd8000000;
    my @CRCTableh = 256;
    my @CRCTablel = 256;
    my $initialized;       
    

    my $seq = $$sequence;
      
    my $crcl = 0;
    my $crch = 0;
    if (!$initialized) {
	$initialized = 1;
	for (my $i=0; $i<256; $i++) {
	    my $partl = $i;
	    my $parth = 0;
	    for (my $j=0; $j<8; $j++) {
		my $rflag = $partl & 1;
		$partl >>= 1;
		$partl |= (1 << 31) if $parth & 1;
		$parth >>= 1;
		$parth ^= $POLY64REVh if $rflag;
	    }
	    $CRCTableh[$i] = $parth;
	    $CRCTablel[$i] = $partl;
	}
    }
    
    foreach (split '', $seq) {
	my $shr = ($crch & 0xFF) << 24;
	my $temp1h = $crch >> 8;
	my $temp1l = ($crcl >> 8) | $shr;
	my $tableindex = ($crcl ^ (unpack "C", $_)) & 0xFF;
	$crch = $temp1h ^ $CRCTableh[$tableindex];
	$crcl = $temp1l ^ $CRCTablel[$tableindex];
    }
    my $crc64 = sprintf("%08X%08X", $crch, $crcl);
        
    return $crc64;
      

  # 10001000001010010010001110000100
  # 32
  my $poly = 0xEDB88320;
  my ($self) = shift;
        
  $self->{'_crcTable'} = [];
  foreach my $i (0..255) {
    my $crc = $i;
    for (my $j=8; $j > 0; $j--) {
      if ($crc & 1) {
	$crc = ($crc >> 1) ^ $poly;
      }
      else {
	$crc >>= 1;
      }
    }
    ${$self->{'_crcTable'}}[$i] = $crc;
  }

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_id_generation_func'} = $value;
    }
    return $obj->{'_id_generation_func'};

  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);
   
  # hash for functions for decoding keys.
  $self->{'_func_ftunit_hash'} = {};
  $self->_show_dna(1); # sets this to one by default. People can change it
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(new Bio::Seq::SeqFactory
			      (-verbose => $self->verbose(), 
			       -type => 'Bio::Seq::RichSeq'));      
  }

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_kw_generation_func'} = $value;
    }
    return $obj->{'_kw_generation_func'};

}

1;

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_post_sort'} = $value;
    }
    return $obj->{'_post_sort'};

   my ($self,$fth,$always_quote) = @_;
   $always_quote ||= 0;
   my ($start,$end) = ('?', '?');
   
   if( ! ref $fth || ! $fth->isa('Bio::SeqIO::FTHelper') ) {
       $fth->warn("$fth is not a FTHelper class. ".
		  "Attempting to print, but there could be tears!");
   }

   if( $fth->loc =~ /(\?|\d+|\>\d+|<\d+)?\.\.(\?|\d+|<\d+|>\d+)?/ ) {
       $start = $1 if defined $1;
       $end = $2 if defined $2;

       # to_FTString only returns one value when start == end, #JB955
       # so if no match is found, assume it is both start and end #JB955
   } else {
       $start = $end = $fth->loc; 
   }
   
   my $desc = "";
   $desc = @{$fth->field->{"description"}}[0]."." 
       if exists $fth->field->{"description"};
   $self->_write_line_swissprot_regex(sprintf("FT   %-8s %6s %6s       ",
					      substr($fth->key,0,8),
					      $start,$end),
				      "FT                                ",
				      $desc.'.','\s+|$',80);
}
#'

    # initial version implemented by HL 05/10/2000
    # FIXME this may not be perfect, so please review 
    my ($self,$buffer) = @_;
    my ($key,   # The key of the feature
        $loc,   # The location line from the feature
        $desc,  # The descriptive text
        );
    
    if ($$buffer =~ /^FT   (\w+)\s+([\d\?\<]+)\s+([\d\?\>]+)\s*(.*)$/) {
        $key = $1;
        my $loc1 = $2;
        my $loc2 = $3;
	$loc = "$loc1..$loc2";
	if($4 && (length($4) > 0)) {
	    $desc = $4;
	    chomp($desc);
	} else {
	    $desc = "";
	}
	# Read all the continuation lines up to the next feature
	while (defined($_ = $self->_readline) && /^FT\s{20,}(\S.*)$/) {
	    $desc .= $1;
	    chomp($desc);
	}
	$desc =~ s/\.$//;
    } else {
        # No feature key. What's this?
	$self->warn("No feature key in putative feature table line: $_");
        return;
    } 
    
    # Put the first line of the next feature into the buffer
    $$buffer = $_;

    # Make the new FTHelper object
    my $out = new Bio::SeqIO::FTHelper(-verbose => $self->verbose());
    $out->key($key);
    $out->loc($loc);
    
    # store the description if there is one
    if($desc && (length($desc) > 0)) {
	$out->field->{"description"} ||= [];
	push(@{$out->field->{"description"}}, $desc);
    }
    return $out;

   my ($self,$buffer) = @_;
   my (@refs);
   my ($b1, $b2, $rp, $title, $loc, $au, $med, $com, $pubmed);
   
   if ($$buffer !~ /^RP/) {
       $$buffer = $self->_readline;
   }
   if( !defined $$buffer ) { return undef; }
   if( $$buffer =~ /^RP/ ) {
       if ($$buffer =~ /^RP   (SEQUENCE OF (\d+)-(\d+).*)/) { 
	   $rp=$1;
	   $b1=$2;
	   $b2=$3; 
       }
       elsif ($$buffer =~ /^RP   (.*)/) {
	   $rp=$1;
       }
       
   }
   while( defined ($_ = $self->_readline) ) {
       #/^CC/ && last;
       /^RN/ && last; # separator between references ! LP 07/25/2000
       #/^SQ/ && last; # there may be sequences without CC lines! HL 05/11/2000
       /^[^R]/ && last; # may be the safest exit point HL 05/11/2000
       /^RX   MEDLINE;\s+(\d+)/ && do {$med=$1};
       /^RX   MEDLINE=(\d+);\s+PubMed=(\d+);/ && do {$med=$1;$pubmed=$2};
       /^RA   (.*)/ && do { $au .= $au ? " $1" : $1;   next;};
       /^RT   (.*)/ && do { $title .= $title ? " $1" : $1; next;};
       /^RL   (.*)/ && do { $loc .= $loc ? " $1" : $1; next;};
       /^RC   (.*)/ && do { $com .= $com ? " $1" : $1; next;};
   }
   
   my $ref = new Bio::Annotation::Reference;
   $au =~ s/;\s*$//g;
   if( defined $title ) {
       $title =~ s/;\s*$//g;
   }
   
   $ref->start($b1);
   $ref->end($b2);
   $ref->authors($au);
   $ref->title($title);
   $ref->location($loc);
   $ref->medline($med);
   $ref->pubmed($pubmed) if (defined $pubmed);
   $ref->comment($com);
   $ref->rp($rp);

   push(@refs,$ref);
   $$buffer = $_;
   return\@ refs;

    my( $self, $buffer ) = @_;
    my $org;

    $_ = $$buffer;
    my( $subspecies, $species, $genus, $common, $variant, $ncbi_taxid );
    my @class;
    my ($binomial, $descr);
    my $osline = "";

    while (defined( $_ ||= $self->_readline )) {
	last unless /^O[SCGX]/;
	# believe it or not, but OS may come multiple times -- at this time
	# we can't capture multiple species
	if(/^OS\s+(\S.+)/ && (! defined($binomial))) {
	    $osline .= " " if $osline;
	    $osline .= $1;
	    if($osline =~ s/(,|, and|\.)$//) {
		($binomial, $descr) = $osline =~ /(\S[^\(]+)(.*)/;
		($genus, $species, $subspecies) = split(/\s+/, $binomial);
		$species = "sp." unless $species;
		while($descr =~ /\(([^\)]+)\)/g) {
		    my $item = $1;
		    # strain etc may not necessarily come first (yes, swissprot
		    # is messy)
		    if((! defined($variant)) &&
		       (($item =~ /(^|[^\(\w])([Ss]train|isolate|serogroup|serotype|subtype|clone)\b/) ||
			($item =~ /^(biovar|pv\.|type\s+)/))) {
			$variant = $item;
		    } elsif($item =~ s/^subsp\.\s+//) {
			if(! $subspecies) {
			    $subspecies = $item;
			} elsif(! $variant) {
			    $variant = $item;
			}
		    } elsif(! defined($common)) {
			# we're only interested in the first common name
			$common = $item;
			if((index($common, '(') >= 0) &&
			   (index($common, ')') < 0)) {
			    $common .= ')';
			}
		    }
		}
	    }
        }
        elsif (s/^OC\s+//) {
            push(@class, split /[\;\.]\s*/);
	    if($class[0] =~ /viruses/i) { 
		# viruses have different OS/OC syntax
		my @virusnames = split(/\s+/, $binomial);
		$species = (@virusnames > 1) ? pop(@virusnames) : '';
		$genus = join(" ", @virusnames);
		$subspecies = undef;
	    }
        }
	elsif (/^OG\s+(.*)/) {
	    $org = $1;
	}
	elsif (/^OX\s+(.*)/ && (! defined($ncbi_taxid))) {
            my $taxstring = $1;
	    # we only keep the first one and ignore all others
            if ($taxstring =~ /NCBI_TaxID=([\w\d]+)/) {
                $ncbi_taxid = $1;
            } else {
                $self->throw("$taxstring doesn't look like NCBI_TaxID");
            }
	}
        
        $_ = undef; # Empty $_ to trigger read of next line
    }
    
    $$buffer = $_;
    
    # Don't make a species object if it is "Unknown" or "None"
    return if $genus =~ /^(Unknown|None)$/i;

    if ($class[$#class] eq $genus) {
        push( @class, $species );
    } else {
        push( @class, $genus, $species );
    }

    @class = reverse @class;
    
    my $taxon = Bio::Species->new();
    $taxon->classification(\@ class, "FORCE" ); # no name validation please
    $taxon->common_name( $common      ) if $common;
    $taxon->sub_species( $subspecies ) if $subspecies;
    $taxon->organelle  ( $org         ) if $org;
    $taxon->ncbi_taxid ( $ncbi_taxid  ) if $ncbi_taxid;
    $taxon->variant($variant)           if $variant;

    # done
    return $taxon;

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_show_dna'} = $value;
    }
    return $obj->{'_show_dna'};

   my $obj = shift;
   if( @_ ) {
      my $value = shift;
      $obj->{'_sv_generation_func'} = $value;
    }
    return $obj->{'_sv_generation_func'};

   my ($self,$pre1,$pre2,$line,$length) = @_;

   $length || die "Miscalled write_line_swissprot without length. Programming error!";
   my $subl = $length - length $pre2;
   my $linel = length $line;
   my $i;

   my $sub = substr($line,0,$length - length $pre1);

   $self->_print( "$pre1$sub\n");
   
   for($i= ($length - length $pre1);$i < $linel;) {
       $sub = substr($line,$i,($subl));
       $self->_print( "$pre2$sub\n");
       $i += $subl;
   }

   my ($self,$pre1,$pre2,$line,$regex,$length) = @_;
   
   #print STDOUT "Going to print with $line!\n";

   $length || die "Miscalled write_line_swissprot without length. Programming error!";

   if( length $pre1 != length $pre2 ) {
       print STDERR "len 1 is ", length $pre1, " len 2 is ", length $pre2, "\n";
       die "Programming error - cannot called write_line_swissprot_regex with different length\n pre1 ($pre1) and\n pre2 ($pre2) tags!";
   }

   my $subl = $length - (length $pre1) -1 ;
   my @lines;

   while($line =~ m/(.{1,$subl})($regex)/g) {
       push(@lines, $1.$2);
   }
   
   my $s = shift @lines;
   $self->_print( "$pre1$s\n");
   foreach my $s ( @lines ) {
       $self->_print( "$pre2$s\n");
   }

   my ($self,@args) = @_;
   my ($pseq,$c,$line,$name,$desc,$acc,$seqc,$mol,$div,
       $date,$comment,@date_arr);
   
   my $genename = "";
   my ($annotation, %params, @features) = ( new Bio::Annotation::Collection);

   $line = $self->_readline;

   if( !defined $line) {
       return undef; # no throws - end of file
   }

   if( $line =~ /^\s+$/ ) {
       while( defined ($line = $self->_readline) ) {
   	   $line =~ /\S/ && last;
       }
   }
   if( !defined $line ) {
       return undef; # end of file
   }
   
   # fixed to allow _DIVISION to be optional for bug #946
   # see bug report for more information
   $line =~ /^ID\s+([^\s_]+)(_([^\s_]+))?\s+([^\s;]+);\s+([^\s;]+);/ 
     || $self->throw("swissprot stream with no ID. Not swissprot in my book");
   
   if( $3 ) {
       $name = "$1$2";
       $params{'-division'} = $3;
   } else {
       $name = $1;
       $params{'-division'} = 'UNK';
       $params{'-primary_id'} = $1;
   }
   $params{'-alphabet'} = 'protein';
    # this is important to have the id for display in e.g. FTHelper, otherwise
    # you won't know which entry caused an error
   $params{'-display_id'} = $name;
   
   my $buffer = $line;

   BEFORE_FEATURE_TABLE :
   until( !defined ($buffer) ) {
       $_ = $buffer;
       
       # Exit at start of Feature table
       last if /^FT/;
       # and at the sequence at the latest HL 05/11/2000
       last if /^SQ/;

       # Description line(s)
       if (/^DE\s+(\S.*\S)/) {
           $desc .= $desc ? " $1" : $1;
       }
       #Gene name
       elsif(/^GN\s+(.*)/) {
	   $genename .= " " if $genename;
	   $genename .= $1;
	   # has GN terminated yet?
	   if($genename =~ s/[\. ]+$//) {
	       my $gn = Bio::Annotation::StructuredValue->new();
	       foreach my $gene (split(/ AND /, $genename)) {
		   $gene =~ s/^\(//;
		   $gene =~ s/\)$//;
		   $gn->add_value([-1,-1], split(/ OR /, $gene));
               }
	       $annotation->add_Annotation('gene_name',$gn,
					   "Bio::Annotation::SimpleValue");
           }
       }
       #accession number(s)
       elsif( /^AC\s+(.+)/) {
	   my @accs = split(/[; ]+/, $1); # allow space in addition
	   $params{'-accession_number'} = shift @accs 
	       unless defined $params{'-accession_number'};
	   push @{$params{'-secondary_accessions'}}, @accs;
       }
       #version number
       elsif( /^SV\s+(\S+);?/ ) {
	   my $sv = $1;
	   $sv =~ s/\;//;
	   $params{'-seq_version'} = $sv;
       }
       #date
       elsif( /^DT\s+(.*)/ ) {
	   my $date = $1;
	   $date =~ s/\;//;
	   $date =~ s/\s+$//;
	   push @{$params{'-dates'}}, $date;
       }
       # Organism name and phylogenetic information
       elsif (/^O[SCG]/) {
           my $species = $self->_read_swissprot_Species(\$buffer);
           $params{'-species'}= $species;
	   # now we are one line ahead -- so continue without reading the next
	   # line   HL 05/11/2000
	   next;
       }
       # References
       elsif (/^R/) {
	   my $refs = $self->_read_swissprot_References(\$buffer);

	   foreach my $r (@$refs) {
	       $annotation->add_Annotation('reference',$r);
	   }
	   # now we are one line ahead -- so continue without reading the next
	   # line   HL 05/11/2000
	   next;
       }
       #Comments
       elsif (/^CC\s{3}(.*)/) {
	   $comment .= $1;
	   $comment .= "\n";
	   while (defined ($buffer = $self->_readline)) {
	       if ($buffer =~ /^CC\s{3}(.*)/) {
		   $comment .= $1;
		   $comment .= "\n";
	       }
	       else {
		   last;
	       }
	   }
	   my $commobj = Bio::Annotation::Comment->new();
	   # note: don't try to process comments here -- they may contain
           # structure. LP 07/30/2000
	   $commobj->text($comment);
	   $annotation->add_Annotation('comment',$commobj);
	   $comment = "";
	   # now we are one line ahead -- so continue without reading the next
	   # line   HL 05/11/2000
	   next;
       }
       #DBLinks
       elsif (/^DR\s+(\S+)\;\s+(\S+)\;\s+(\S+)[\;\.](.*)$/) {
	   my $dblinkobj =  Bio::Annotation::DBLink->new();
	   $dblinkobj->database($1);
	   $dblinkobj->primary_id($2);
	   $dblinkobj->optional_id($3);
	   my $comment = $4;
	   if(length($comment) > 0) {
	       # edit comment to get rid of leading space and trailing dot
	       if( $comment =~ /^\s*(\S+)\./ ) {
		   $dblinkobj->comment($1);
	       } else {
		   $dblinkobj->comment($comment);
	       }
	   }
	   $annotation->add_Annotation('dblink',$dblinkobj);
       }
       #keywords
       elsif( /^KW\s+(.*)$/ ) {
	   my @kw = split(/\s*\;\s*/,$1);
	   defined $kw[-1] && $kw[-1] =~ s/\.$//;
	   push @{$params{'-keywords'}}, @kw;   
       }


       # Get next line. Getting here assumes that we indeed need to read the
       # line.
       $buffer = $self->_readline;
   }
   
   $buffer = $_;
      
   FEATURE_TABLE :
   # if there is no feature table, or if we've got beyond, exit loop or don't
   # even enter    HL 05/11/2000
   while (defined ($buffer) && ($buffer =~ /^FT/)) {
       my $ftunit = $self->_read_FTHelper_swissprot(\$buffer);
       
       # process ftunit
       # when parsing of the line fails we get undef returned
       if($ftunit) {
	   push(@features,
		$ftunit->_generic_seqfeature($self->location_factory(),
					     $params{'-seqid'}, "SwissProt"));
       } else {
	   $self->warn("failed to parse feature table line for seq " .
		       $params{'-display_id'});
       }
   }
   if( $buffer !~ /^SQ/  ) {
       while( defined($_ = $self->_readline) ) {
	   /^SQ/ && last;
       }
   }
   $seqc = "";	
   while( defined ($_ = $self->_readline) ) {
       /^\/\// && last;
       $_ = uc($_);
       s/[^A-Za-z]//g;
       $seqc .= $_;
   }

   my $seq=  $self->sequence_factory->create
       (-verbose  => $self->verbose,
	%params,
	-seq      => $seqc,
	-desc     => $desc,
	-features =>\@ features,
	-annotation => $annotation,
	);

   # The annotation doesn't get added by the contructor
   $seq->annotation($annotation);

   return $seq;

    my ($self,@seqs) = @_;
    foreach my $seq ( @seqs ) {
	$self->throw("Attempting to write with no seq!") unless defined $seq;

	if( ! ref $seq || ! $seq->isa('Bio::SeqI') ) {
	    $self->warn(" $seq is not a SeqI compliant module. Attempting to dump, but may fail!");
	}

	my $i;
	my $str = $seq->seq;

	my $mol;
	my $div;
	my $len = $seq->length();

	if ( !$seq->can('division') || ! defined ($div = $seq->division()) ) {
	    $div = 'UNK';
	}

	if( ! $seq->can('alphabet') || ! defined ($mol = $seq->alphabet) ) {
	    $mol = 'XXX';
	}

	my $temp_line;
	if( $self->_id_generation_func ) {
	    $temp_line = &{$self->_id_generation_func}($seq);
	} else {
	    #$temp_line = sprintf ("%10s     STANDARD;      %3s;   %d AA.",
	    #		     $seq->primary_id()."_".$div,$mol,$len);
	    # Reconstructing the ID relies heavily upon the input source having
	    # been in a format that is parsed as this routine expects it -- that is,
	    # by this module itself. This is bad, I think, and immediately breaks
	    # if e.g. the Bio::DB::GenPept module is used as input.
	    # Hence, switch to display_id(); _every_ sequence is supposed to have
	    # this. HL 2000/09/03
	    $mol =~ s/protein/PRT/;
	    $temp_line = sprintf ("%10s     STANDARD;      %3s;   %d AA.",
				  $seq->display_id(), $mol, $len);
	}

	$self->_print( "ID   $temp_line\n");

	# if there, write the accession line
	local($^W) = 0;	# supressing warnings about uninitialized fields

	if( $self->_ac_generation_func ) {
	    $temp_line = &{$self->_ac_generation_func}($seq);
	    $self->_print( "AC   $temp_line\n");
	} else {
	    if ($seq->can('accession_number') ) {
		$self->_print("AC   ",$seq->accession_number,";");
		if ($seq->can('get_secondary_accessions') ) {
		    foreach my $sacc ($seq->get_secondary_accessions) {
			$self->_print(" ",$sacc,";");
		    }
		    $self->_print("\n");
		}
		else {
		    $self->_print("\n");
		}
	    }
	    # otherwise - cannot print <sigh>
	}

	# Date lines

	if( $seq->can('get_dates') ) {
	    foreach my $dt ( $seq->get_dates() ) {
		$self->_write_line_swissprot_regex("DT   ","DT   ",
						   $dt,"\\s\+\|\$",80);
	    }
	}

	#Definition lines
	$self->_write_line_swissprot_regex("DE   ","DE   ",$seq->desc(),"\\s\+\|\$",80);

	#Gene name
	if ((my @genes = $seq->annotation->get_Annotations('gene_name') ) ) {
	    $self->_print("GN   ",
			  join(' OR ',
			       map {
				   $_->isa("Bio::Annotation::StructuredValue") ?
				       $_->value(-joins => [" AND ", " OR "]) :
				       $_->value();
			       } @genes),
			  ".\n");
	}

	# Organism lines
	if ($seq->can('species') && (my $spec = $seq->species)) {
	    my($species, @class) = $spec->classification();
	    my $genus = $class[0];
	    my $OS = "$genus $species";
	    if ($class[$#class] =~ /viruses/i) {
		# different OS / OC syntax for viruses LP 09/16/2000
		shift @class;
	    }
	    if (my $ssp = $spec->sub_species) {
		$OS .= " $ssp";
	    }
	    foreach (($spec->variant, $spec->common_name)) {
		$OS .= " ($_)" if $_;
	    }
	    $self->_print( "OS   $OS.\n");
	    my $OC = join('; ', reverse(@class)) .'.';
	    $self->_write_line_swissprot_regex("OC   ","OC   ",$OC,"\;\|\$ ",80);
	    if ($spec->organelle) {
		$self->_write_line_swissprot_regex("OG   ","OG   ",$spec->organelle,"\;\|\$ ",80);
	    }
	    if ($spec->ncbi_taxid) {
		$self->_print("OX   NCBI_TaxID=".$spec->ncbi_taxid.";\n");
	    }
	}

	# Reference lines
	my $t = 1;
	foreach my $ref ( $seq->annotation->get_Annotations('reference') ) {
	    $self->_print( "RN   [$t]\n");
	    # changed by lorenz 08/03/00
	    # j.gilbert and h.lapp agreed that the rp line in swissprot seems 
	    # more like a comment than a parseable value, so print it as is
	    if ($ref->rp) {
		$self->_write_line_swissprot_regex("RP   ","RP   ",$ref->rp,
						   "\\s\+\|\$",80);
	    }
	    if ($ref->comment) {
		$self->_write_line_swissprot_regex("RC   ","RC   ",$ref->comment,
						   "\\s\+\|\$",80);
	    }
	    if ($ref->medline) {
		# new RX format in swissprot LP 09/17/00
		if ($ref->pubmed) {
		    $self->_write_line_swissprot_regex("RX   ","RX   ",
						       "MEDLINE=".$ref->medline.
						       "; PubMed=".$ref->pubmed.";",
						       "\\s\+\|\$",80);
		} else {
		    $self->_write_line_swissprot_regex("RX   MEDLINE; ","RX   MEDLINE; ",
						       $ref->medline.".","\\s\+\|\$",80);
		}
	    }
	    my $author = $ref->authors .';' if($ref->authors);
	    my $title = $ref->title .';' if( $ref->title);

	    $self->_write_line_swissprot_regex("RA   ","RA   ",$author,"\\s\+\|\$",80);
	    $self->_write_line_swissprot_regex("RT   ","RT   ",$title,"\\s\+\|\$",80);
	    $self->_write_line_swissprot_regex("RL   ","RL   ",$ref->location,"\\s\+\|\$",80);
	    $t++;
	}

	# Comment lines

	foreach my $comment ( $seq->annotation->get_Annotations('comment') ) {
	    foreach my $cline (split ("\n", $comment->text)) {
		while (length $cline > 74) {
		    $self->_print("CC   ",(substr $cline,0,74),"\n");
		    $cline = substr $cline,74;
		}
		$self->_print("CC   ",$cline,"\n");
	    }
	}

	foreach my $dblink ( $seq->annotation->get_Annotations('dblink') ) 
	{
	    if (defined($dblink->comment)&&($dblink->comment)) {
		$self->_print("DR   ",$dblink->database,"; ",$dblink->primary_id,"; ",
			      $dblink->optional_id,"; ",$dblink->comment,".\n");
	    } elsif($dblink->optional_id) {
		$self->_print("DR   ",$dblink->database,"; ",
			      $dblink->primary_id,"; ",
			      $dblink->optional_id,".\n");
	    }
	    else {
		$self->_print("DR   ",$dblink->database,
			      "; ",$dblink->primary_id,"; ","-.\n");
	    }
	}   

	# if there, write the kw line
	{
	    my( $kw );
	    if( my $func = $self->_kw_generation_func ) {
		$kw = &{$func}($seq);
	    } elsif( $seq->can('keywords') ) {		
		$kw = $seq->keywords;
		if( ref($kw) =~ /ARRAY/i ) {
		    $kw = join("; ", @$kw);
		}
		$kw .= '.' if( $kw !~ /\.$/ );
	    }	    
	    $self->_write_line_swissprot_regex("KW   ","KW   ",
					       $kw, "\\s\+\|\$",80);           
	}

        #Check if there are seqfeatures before printing the FT line
        my @feats = $seq->can('top_SeqFeatures') ? $seq->top_SeqFeatures : ();
	if ($feats[0]) {
	    if( defined $self->_post_sort ) {

		# we need to read things into an array. Process. Sort them. Print 'em

		my $post_sort_func = $self->_post_sort();
		my @fth;

		foreach my $sf ( @feats ) {
		    push(@fth,Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq));
		}
		@fth = sort { &$post_sort_func($a,$b) } @fth;

		foreach my $fth ( @fth ) {
		    $self->_print_swissprot_FTHelper($fth);
		}
	    } else {
		# not post sorted. And so we can print as we get them.
		# lower memory load...

		foreach my $sf ( @feats ) {
		    my @fth = Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq);
		    foreach my $fth ( @fth ) {
			if( ! $fth->isa('Bio::SeqIO::FTHelper') ) {
			    $sf->throw("Cannot process FTHelper... $fth");
			}

			$self->_print_swissprot_FTHelper($fth);
		    }
		}
	    }

	    if( $self->_show_dna() == 0 ) {
		return;
	    }
	}
	# finished printing features.

	# molecular weight
	my $mw = ${Bio::Tools::SeqStats->get_mol_wt($seq->primary_seq)}[0];
	# checksum
	# was crc32 checksum, changed it to crc64 
	my $crc64 = $self->_crc64(\$str); 
	$self->_print( sprintf("SQ   SEQUENCE  %4d AA;  %d MW;  %16s CRC64;\n",
			       $len,$mw,$crc64));
	$self->_print( "     ");
	my $linepos;
	for ($i = 0; $i < length($str); $i += 10) {
	    $self->_print( substr($str,$i,10), " ");
	    $linepos += 11;
	    if( ($i+10)%60 == 0 && (($i+10) < length($str))) {
		$self->_print( "\n     ");
	    }
	}
	$self->_print( "\n//\n");

	$self->flush if $self->_flush_on_write && defined $self->_fh;
	return 1;
    }
}

# Thanks to James Gilbert for the following two. LP 08/01/2000

  bioperl-l@bioperl.org          - General discussion
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  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

 Title   : _filehandle
 Usage   : $obj->_filehandle($newval)
 Function: 
 Example : 
 Returns : value of _filehandle
 Args    : newvalue (optional)