[Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/PAML Codeml.pm, 1.40, 1.41 Yn00.pm, 1.19, 1.20

Jason Stajich jason at pub.open-bio.org
Sun Nov 6 17:20:53 EST 2005


Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/PAML
In directory pub.open-bio.org:/tmp/cvs-serv15481/Bio/Tools/Run/Phylo/PAML

Modified Files:
	Codeml.pm Yn00.pm 
Log Message:
email addr mangle; don't double write outfile, quiet when not defined


Index: Yn00.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/PAML/Yn00.pm,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** Yn00.pm	9 Oct 2005 14:49:27 -0000	1.19
--- Yn00.pm	6 Nov 2005 22:20:51 -0000	1.20
***************
*** 3,7 ****
  # BioPerl module for Bio::Tools::Run::Phylo::PAML::Yn00
  #
! # Cared for by Jason Stajich <jason at bioperl.org>
  #
  # Copyright Jason Stajich
--- 3,7 ----
  # BioPerl module for Bio::Tools::Run::Phylo::PAML::Yn00
  #
! # Cared for by Jason Stajich <jason-AT-bioperl_DOT_org>
  #
  # Copyright Jason Stajich

Index: Codeml.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/PAML/Codeml.pm,v
retrieving revision 1.40
retrieving revision 1.41
diff -C2 -d -r1.40 -r1.41
*** Codeml.pm	6 Nov 2005 21:46:43 -0000	1.40
--- Codeml.pm	6 Nov 2005 22:20:51 -0000	1.41
***************
*** 478,481 ****
--- 478,482 ----
     my %params = $self->get_parameters;
     while( my ($param,$val) = each %params ) {
+        next if $param eq 'outfile';
         print CODEML "$param = $val\n";
     }
***************
*** 718,722 ****
  sub set_parameter{
     my ($self,$param,$value) = @_;
!    unless ($self->{'no_param_checks'} == 1) {
         if ( ! defined $VALIDVALUES{$param} ) { 
             $self->warn("unknown parameter $param will not be set unless you force by setting no_param_checks to true");
--- 719,723 ----
  sub set_parameter{
     my ($self,$param,$value) = @_;
!    unless (defined $self->{'no_param_checks'} && $self->{'no_param_checks'} == 1) {
         if ( ! defined $VALIDVALUES{$param} ) { 
             $self->warn("unknown parameter $param will not be set unless you force by setting no_param_checks to true");



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