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

Tue Jul 5 08:08:40 EDT 2005

Update of /home/repository/bioperl/bioperl-live/Bio/Tools
In directory pub.open-bio.org:/tmp/cvs-serv9309/Bio/Tools

Modified Files:
	Primer3.pm 
Log Message:
POD fixes

Index: Primer3.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Primer3.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Primer3.pm	15 Jun 2005 15:53:42 -0000	1.8
--- Primer3.pm	5 Jul 2005 12:08:38 -0000	1.9
***************
*** 146,160 ****
  $ID = 'Bio::Tools::Primer3';

! =head2 new()

! Title   : new()
! Usage   : my $primer3 = Bio::Tools::Primer3->new(-file=>$file) 
!           to read a primer3 output file.
! Function: Parse primer3 output
! Returns : Doesn't return anything. If called with a filename will 
!           allow you to retrieve the results
! Args    : -file (optional) file of primer3 results to parse -verbose 
!           (optional) set verbose output
! Notes   : 

  =cut
--- 146,160 ----
  $ID = 'Bio::Tools::Primer3';

! =head2 new

!   Title   : new()
!   Usage   : my $primer3 = Bio::Tools::Primer3->new(-file=>$file) 
!             to read a primer3 output file.
!   Function: Parse primer3 output
!   Returns : Doesn't return anything. If called with a filename will 
!             allow you to retrieve the results
!   Args    : -file (optional) file of primer3 results to parse -verbose 
!             (optional) set verbose output
!   Notes   : 

  =cut
***************
*** 173,187 ****

! =head2 number_of_results()

! Title   : number_of_results()
! Usage   : $primer3->number_of_results()
! Function: Retrieve the number of primers returned from Primer3.
! Returns : A scalar
! Args    : None
! Notes   : This returns the count of the primers returned by Primer3 
!            (aka how many of them there are). 
!            This is one more than the maximum offset into the zero 
!            based list of primers that is accessed by primer_results().

  =cut
--- 173,187 ----

! =head2 number_of_results

!   Title   : number_of_results()
!   Usage   : $primer3->number_of_results()
!   Function: Retrieve the number of primers returned from Primer3.
!   Returns : A scalar
!   Args    : None
!   Notes   : This returns the count of the primers returned by Primer3 
!              (aka how many of them there are). 
!              This is one more than the maximum offset into the zero 
!              based list of primers that is accessed by primer_results().

  =cut
***************
*** 193,205 ****

! =head2 all_results()

! Title   : all_results()
! Usage   : $primer3->all_results() to print all results or 
!           $primer3->all_results('primer3 result name', 
!           'other results') to return a specific result
! Function: Retrieve the results returned from Primer3.
! Returns : A reference to a hash
! Args    : Optional array of results to retrieve

  =cut
--- 193,205 ----

! =head2 all_results

!   Title   : all_results()
!   Usage   : $primer3->all_results() to print all results or 
!             $primer3->all_results('primer3 result name', 
!             'other results') to return a specific result
!   Function: Retrieve the results returned from Primer3.
!   Returns : A reference to a hash
!   Args    : Optional array of results to retrieve

  =cut
***************
*** 223,234 ****

! =head2 primer_results()

! Title   : primer_results()
! Usage   : $primer3->primer_results(2) to print results for the third 
!           choice primer (indexed on 0)
! Function: Retrieve the results returned from Primer3 for specific primer pairs.
! Returns : A reference to a hash
! Args    : A number between 0 and the maximum number of primers to retrieve

  =cut
--- 223,234 ----

! =head2 primer_results

!   Title   : primer_results()
!   Usage   : $primer3->primer_results(2) to print results for the third 
!             choice primer (indexed on 0)
!   Function: Retrieve the results returned from Primer3 for specific primer pairs.
!   Returns : A reference to a hash
!   Args    : A number between 0 and the maximum number of primers to retrieve

  =cut
***************
*** 243,254 ****
  }

! =head2 _readfile()

! Title   : _readfile()
! Usage   : $self->_readfile();
! Function: An internal function that reads a file and sets up the results
! Returns : Nothing.
! Args    : None
! Notes   : 

  =cut
--- 243,254 ----
  }

! =head2 _readfile

!   Title   : _readfile()
!   Usage   : $self->_readfile();
!   Function: An internal function that reads a file and sets up the results
!   Returns : Nothing.
!   Args    : None
!   Notes   : 

  =cut
***************
*** 278,291 ****
  }

! =head2 primer_stream()

! Title   : primer_stream()
! Usage   : while (my $primed_seq  = $primer3->primer_stream()) {
! Function: Retrieve the primer/sequences one at a time
! Returns : Returns a Bio::Seq::PrimedSeq feature, one at a time
! Args    : None
! Notes   : Deprecated. I should just delete this, but my test scripts will 
!           all break. This will be removed before it goes really live, and is 
!           just a link to next_primer

--- 278,291 ----
  }

! =head2 primer_stream

!   Title   : primer_stream()
!   Usage   : while (my $primed_seq  = $primer3->primer_stream()) {
!   Function: Retrieve the primer/sequences one at a time
!   Returns : Returns a Bio::Seq::PrimedSeq feature, one at a time
!   Args    : None
!   Notes   : Deprecated. I should just delete this, but my test scripts will 
!             all break. This will be removed before it goes really live, and is 
!             just a link to next_primer

***************
*** 300,312 ****

! =head2 next_primer()

! Title   : next_primer()
! Usage   : while (my $primed_seq  = $primer3->next_primer()) {
! Function: Retrieve the primer/sequences one at a time
! Returns : Returns a Bio::Seq::PrimedSeq feature, one at a time
! Args    : None
! Notes   : Use $primed_seq->annotated_seq to get an annotated sequence 
!           object you can write out.

  =cut
--- 300,312 ----

! =head2 next_primer

!   Title   : next_primer()
!   Usage   : while (my $primed_seq  = $primer3->next_primer()) {
!   Function: Retrieve the primer/sequences one at a time
!   Returns : Returns a Bio::Seq::PrimedSeq feature, one at a time
!   Args    : None
!   Notes   : Use $primed_seq->annotated_seq to get an annotated sequence 
!             object you can write out.

  =cut
***************
*** 359,371 ****
  }

! =head2 _set_variable()

! Title   : _set_variable()
! Usage   : $self->_set_variable('variable name', 'value');
! Function: An internal function that sets a variable
! Returns : Nothing.
! Args    : None
! Notes   : Mainly used by Bio::Tools::Run::Primer3 to set 
!           $self->{results} and $self->seqobject

  =cut
--- 359,371 ----
  }

! =head2 _set_variable

!   Title   : _set_variable()
!   Usage   : $self->_set_variable('variable name', 'value');
!   Function: An internal function that sets a variable
!   Returns : Nothing.
!   Args    : None
!   Notes   : Mainly used by Bio::Tools::Run::Primer3 to set 
!             $self->{results} and $self->seqobject

  =cut
***************
*** 377,389 ****
   }

! =head2 _separate()

! Title   : _separate()
! Usage   : $self->_separate();
! Function: An internal function that groups the results by number 
!           (e.g. primer pair 1, etc)
! Returns : Nothing.
! Args    : None
! Notes   : 

  =cut
--- 377,389 ----
   }

! =head2 _separate

!   Title   : _separate()
!   Usage   : $self->_separate();
!   Function: An internal function that groups the results by number 
!             (e.g. primer pair 1, etc)
!   Returns : Nothing.
!   Args    : None
!   Notes   : 

  =cut