168d167
<    my $genename = "";
210,214c209,211
<        elsif(/^GN\s+(.*)/) {
< 	   $genename .= " " if $genename;
< 	   $genename .= $1;
< 	   # has GN terminated yet?
< 	   if($genename =~ s/[\. ]+$//) {
---
>        elsif(/^GN\s+/) {
> 	   my $genename_rowsref = $self->_read_swissprot_GeneNames($_);
> 	   if (defined $genename_rowsref->[0]) {
216,220c213,215
< 	       foreach my $gene (split(/ AND /, $genename)) {
< 		   $gene =~ s/^\(//;
< 		   $gene =~ s/\)$//;
< 		   $gn->add_value([-1,-1], split(/ OR /, $gene));
<                }
---
> 	       foreach my $row (@$genename_rowsref) {
> 		   $gn->add_value([-1,-1], @$row);
> 	       }
223c218
<            }
---
> 	   }	       
301c296,297
<    
---
> 
> 
1005a1002,1004
> 
> 
> 
1281a1281,1332
> =head2 _read_swissprot_GeneNames
> 
>  Title   : _read_swissprot_GeneNames
>  Usage   :
>  Function: Reads gene names from new swissprot format. Internal function.
>  Example :
>  Returns : 
>  Args    :
> 
> 
> =cut
> 
> sub _read_swissprot_GeneNames {
>    my ($self,$line) = @_;
>    my @genename_rows;
>    my $genename = ""; # for parsing the old format
>    local $_ = $line;
>    while( defined $_ ) {
>        if (/GN\s+Name=([^;]+);\s+Synonyms=(.+);/) {
> 	   push @genename_rows, [$1, split(/;\s+/, $2)];
>        }
>        elsif (/Name=([^;]+)/) {
> 	   push @genename_rows, [$1];
>        }
>        elsif (/GN\s+and/ and @genename_rows) {
> 	   # nothing - skip "GN and" lines in new format
>        }
>        elsif (/GN\s+(.+)/) {
> 	   # old format line
> 	   $genename .= " " if $genename;	       
> 	   $genename .= $1;
>        }
>        else { # not GN line 
> 	   $self->_pushback($_); # want this line to go back on the list
> 	   last; 
>        } 
> 
>        # has the old-style GN terminated yet?
>        if($genename =~ s/[\. ]+$//) {
> 	   foreach my $gene (split(/ AND /, $genename)) {
> 	       $gene =~ s/^\(//;
> 	       $gene =~ s/\)$//;
> 	       push @genename_rows, [split(/ OR /, $gene)];
> 	   }
>        }
>        $_ = $self->_readline;
> 
>    }
> 
>    return \@genename_rows;
> }
>