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revision 1.10, Fri Aug 26 17:00:42 2011 UTC revision 1.11, Tue Mar 26 23:16:17 2013 UTC
# Line 1240  Line 1240 
1240      return gb_loc_position( $loc, $acc )   if $loc =~ /^$position$/;      return gb_loc_position( $loc, $acc )   if $loc =~ /^$position$/;
1241    
1242      my $paranthetical;      my $paranthetical;
1243        {
1244           no warnings;
1245         $paranthetical = qr/\([^()]*(?:(??{$paranthetical})[^()]*)*\)/;         $paranthetical = qr/\([^()]*(?:(??{$paranthetical})[^()]*)*\)/;
1246        }
1247      my $complement = qr/(?:$contigid:)?complement$paranthetical/;      my $complement = qr/(?:$contigid:)?complement$paranthetical/;
1248      return gb_loc_complement( $loc, $acc ) if $loc =~ /^$complement$/;      return gb_loc_complement( $loc, $acc ) if $loc =~ /^$complement$/;
1249    
# Line 1333  Line 1336 
1336      my ( $loc, $acc ) = @_;      my ( $loc, $acc ) = @_;
1337    
1338      my $paranthetical;      my $paranthetical;
1339        {
1340           no warnings;
1341         $paranthetical    = qr/\([^()]*(?:(??{$paranthetical})[^()]*)*\)/;         $paranthetical    = qr/\([^()]*(?:(??{$paranthetical})[^()]*)*\)/;
1342        }
1343      my $contigid         = qr/[^\s:(),]+/;      my $contigid         = qr/[^\s:(),]+/;
1344      my $complement_parts = qr/(?:($contigid):)?complement($paranthetical)/;      my $complement_parts = qr/(?:($contigid):)?complement($paranthetical)/;
1345    
# Line 1357  Line 1363 
1363      my ( $loc, $acc ) = @_;      my ( $loc, $acc ) = @_;
1364    
1365      my $paranthetical;      my $paranthetical;
1366        {
1367           no warnings;
1368         $paranthetical    = qr/\([^()]*(?:(??{$paranthetical})[^()]*)*\)/;         $paranthetical    = qr/\([^()]*(?:(??{$paranthetical})[^()]*)*\)/;
1369        }
1370      my $contigid         = qr/[^\s:(),]+/;      my $contigid         = qr/[^\s:(),]+/;
1371      my $complement       = qr/(?:$contigid:)?complement$paranthetical/;      my $complement       = qr/(?:$contigid:)?complement$paranthetical/;
1372      my $join             = qr/(?:$contigid:)?join$paranthetical/;      my $join             = qr/(?:$contigid:)?join$paranthetical/;
# Line 1392  Line 1401 
1401      my ( $loc, $acc ) = @_;      my ( $loc, $acc ) = @_;
1402    
1403      my $paranthetical;      my $paranthetical;
1404        {
1405           no warnings;
1406         $paranthetical    = qr/\([^()]*(?:(??{$paranthetical})[^()]*)*\)/;         $paranthetical    = qr/\([^()]*(?:(??{$paranthetical})[^()]*)*\)/;
1407        }
1408      my $contigid         = qr/[^\s:(),]+/;      my $contigid         = qr/[^\s:(),]+/;
1409      my $complement       = qr/(?:$contigid:)?complement$paranthetical/;      my $complement       = qr/(?:$contigid:)?complement$paranthetical/;
1410      my $join             = qr/(?:$contigid:)?join$paranthetical/;      my $join             = qr/(?:$contigid:)?join$paranthetical/;

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