[Bioperl-guts-l] bioperl-run/Bio/Tools/Run Primer3.pm,1.8,1.9

[Robert Edwards]

Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run
In directory pub.open-bio.org:/tmp/cvs-serv30482/bioperl-run/Bio/Tools/Run

Modified Files:
	Primer3.pm 
Log Message:
minor change to included_region in Bio::Tools::Run::Primer3 to make default set correctly


Index: Primer3.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Primer3.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Primer3.pm	2 Mar 2005 01:52:44 -0000	1.8
--- Primer3.pm	2 Mar 2005 02:26:31 -0000	1.9
***************
*** 335,345 ****
  		if (uc($key) eq "INCLUDED_REGION") {
  			# this must be a comma separated start, length.
! 			unless ($args{$key} =~ /\,/) {
! 				my $sequencelength;
! 				# we don't have a length, hence we need to add the length of the 
! 				# sequence less the start.
! 				foreach my $input (@$inputarray) {
! 					if ($input =~ /SEQUENCE=(.*)/) {$sequencelength=length($1)}
! 				}
  				my $length_of_included = $sequencelength-$args{$key};
  				$args{$key} .= ",".$length_of_included;
--- 335,347 ----
  		if (uc($key) eq "INCLUDED_REGION") {
  			# this must be a comma separated start, length.
! 			my $sequencelength;
! 			# we don't have a length, hence we need to add the length of the 
! 			# sequence less the start.
! 			foreach my $input (@$inputarray) {
! 				if ($input =~ /SEQUENCE=(.*)/) {$sequencelength=length($1)}
! 			}
! 		
! 		        if (!$args{$key}) {$args{$key}="0," . $sequencelength}
! 			elsif ($args{$key} !~ /\,/) {
  				my $length_of_included = $sequencelength-$args{$key};
  				$args{$key} .= ",".$length_of_included;