[Bioperl-guts-l] bioperl-run/Bio/Tools/Run Primer3.pm,1.7,1.8

[Robert Edwards]

Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run
In directory pub.open-bio.org:/tmp/cvs-serv30275/bioperl-run/Bio/Tools/Run

Modified Files:
	Primer3.pm 
Log Message:
minor change to program_dir in Bio::Tools::Run::Primer3 which could never be set and then checked later


Index: Primer3.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Primer3.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Primer3.pm	20 Oct 2004 02:44:39 -0000	1.7
--- Primer3.pm	2 Mar 2005 01:52:44 -0000	1.8
***************
*** 272,278 ****
  
   Title   : program_dir
!  Usage   : $factory->program_dir(@params)
!  Function: returns the program directory, obtiained from ENV variable.
!  Returns:  string
   Args    :
  
--- 272,278 ----
  
   Title   : program_dir
!  Usage   : $primer3->program_dir($dir)
!  Function: returns the program directory, which may also be obtained from ENV variable.
!  Returns :  string
   Args    :
  
***************
*** 280,292 ****
  
  sub program_dir {
! 	my ($self, $dir) = @_;
! 	if ($dir) {
        $self->{'program_dir'}=$dir;
! 	} elsif ($ENV{PRIMER3}) {
        $self->{'program_dir'}=Bio::Root::IO->catfile($ENV{PRIMER3});
! 	} else {
        $self->{'program_dir'}='/usr/local/bin';
! 	}
! 	return $self->{'program_dir'}
  }
  
--- 280,298 ----
  
  sub program_dir {
!    my ($self, $dir) = @_;
!    if ($dir) {
        $self->{'program_dir'}=$dir;
!    } 
!    
!    # we need to stop here if we know what the answer is, otherwise we can never set it and then call it later
!    return $self->{'program_dir'} if $self->{'program_dir'};
!    
!    if ($ENV{PRIMER3}) {
        $self->{'program_dir'}=Bio::Root::IO->catfile($ENV{PRIMER3});
!    } else {
        $self->{'program_dir'}='/usr/local/bin';
!    }
!    
!    return $self->{'program_dir'}
  }