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revision 1.3, Tue Mar 17 13:46:32 2009 UTC revision 1.4, Fri Mar 20 14:37:17 2009 UTC
# Line 1148  Line 1148 
1148  sub get_flanking {  sub get_flanking {
1149    my ( $self, $fid, $before, $after ) = @_;    my ( $self, $fid, $before, $after ) = @_;
1150    
1151      if ( $before < $after ) {
1152        my $this = $before;
1153        $before = $after;
1154        $after = $this;
1155      }
1156    
1157    return if ( !defined( $fid ) || $fid !~ /^fig/ );    return if ( !defined( $fid ) || $fid !~ /^fig/ );
1158    
1159    my $feat_seq = $self->{ 'fig' }->get_dna_seq( $fid );    my $feat_seq = $self->{ 'fig' }->get_dna_seq( $fid );
# Line 1196  Line 1202 
1202        if ( $npost > 0 ) {        if ( $npost > 0 ) {
1203          $seq = lc( substr( $seq, 0 ) );          $seq = lc( substr( $seq, 0 ) );
1204        }        }
1205          elsif ( $npre < 0 ) {
1206            $seq = uc( substr( $seq, 0 ) );
1207          }
1208        elsif ( $length_feat < abs( $npost ) ) {        elsif ( $length_feat < abs( $npost ) ) {
1209          $seq = lc( substr( $seq, 0, $npre ) ) . uc( substr( $seq, $npre, $length_feat ) ) . lc( substr( $seq, ( $npre + $length_feat ) ) );          $seq = lc( substr( $seq, 0, $npre ) ) . uc( substr( $seq, $npre, $length_feat ) ) . lc( substr( $seq, ( $npre + $length_feat ) ) );
1210        }        }

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