[Bioperl-guts-l] bioperl-run/Bio/Tools/Run Primer3.pm,1.14,1.15

[Jason Stajich]

Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run
In directory pub.open-bio.org:/tmp/cvs-serv20786

Modified Files:
	Primer3.pm 
Log Message:
small code/doc cleanup


Index: Primer3.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Primer3.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Primer3.pm	14 Dec 2005 21:08:45 -0000	1.14
--- Primer3.pm	24 Jan 2006 01:14:23 -0000	1.15
***************
*** 77,80 ****
--- 77,88 ----
    print "There were ", $results->number_of_results, " primers\n";
  
+ Bio::Tools::Run::Primer3 creates the input files needed to design primers
+ using primer3 and provides mechanisms to access data in the primer3
+ output files.
+ 
+ This module provides a bioperl interface to the program primer3. See
+ http://www-genome.wi.mit.edu/genome_software/other/primer3.html for
+ details and to download the software.
+ 
  This module is based on one written by Chad Matsalla
  (bioinformatics1 at dieselwurks.com). I have ripped some of his code, and 
***************
*** 217,223 ****
  
   Title   : new()
!  Usage   : my $primer3 = Bio::Tools::Primer3->new(-file=>$file) to read 
             a primer3 output file.
!            my $primer3 = Bio::Tools::Primer3->new(-seq=>sequence object) 
             design primers against sequence
   Function: Start primer3 working and adds a sequence. At the moment it 
--- 225,231 ----
  
   Title   : new()
!  Usage   : my $primer3 = Bio::Tools::Run::Primer3->new(-file=>$file) to read 
             a primer3 output file.
!            my $primer3 = Bio::Tools::Run::Primer3->new(-seq=>sequence object) 
             design primers against sequence
   Function: Start primer3 working and adds a sequence. At the moment it 
***************
*** 401,405 ****
   Usage   : $primer3->run();
   Function: Run the primer3 program with the arguments that you have supplied.
!  Returns : A Bio::Tools::Run::Primer3 object containing the results.
   Args    : None.
   Note    : See the Bio::Tools::Primer3 documentation for those functions.
--- 409,413 ----
   Usage   : $primer3->run();
   Function: Run the primer3 program with the arguments that you have supplied.
!  Returns : A Bio::Tools::Primer3 object containing the results.
   Args    : None.
   Note    : See the Bio::Tools::Primer3 documentation for those functions.
***************
*** 408,412 ****
  
  sub run {
! 	my($self,%args) = @_;
  	my $executable = $self->executable;
  	my $input = $self->{'primer3_input'};
--- 416,420 ----
  
  sub run {
! 	my($self) = @_;
  	my $executable = $self->executable;
  	my $input = $self->{'primer3_input'};
***************
*** 461,465 ****
  	$self->cleanup;
  	# convert the results to individual results
! 	$self->{results_obj} = new Bio::Tools::Primer3;
  	$self->{results_obj}->_set_variable('results', $self->{results});
  	$self->{results_obj}->_set_variable('seqobject', $self->{seqobject});
--- 469,473 ----
  	$self->cleanup;
  	# convert the results to individual results
! 	$self->{results_obj} = Bio::Tools::Primer3->new;
  	$self->{results_obj}->_set_variable('results', $self->{results});
  	$self->{results_obj}->_set_variable('seqobject', $self->{seqobject});
***************
*** 477,481 ****
   Title   : arguments()
   Usage   : $hashref = $primer3->arguments();
!  Function: Describes the options that you can set through Bio::Tools::Primer3, 
             with a brief (one line) description of what they are and their 
             default values
--- 485,489 ----
   Title   : arguments()
   Usage   : $hashref = $primer3->arguments();
!  Function: Describes the options that you can set through Bio::Tools::Run::Primer3, 
             with a brief (one line) description of what they are and their 
             default values