[Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/PAML ModelResult.pm, 1.13, 1.14 Result.pm, 1.26, 1.27

Senduran Balasubramaniam sendu at dev.open-bio.org
Thu Jun 14 10:16:20 EDT 2007


Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML
In directory dev.open-bio.org:/tmp/cvs-serv22328/Bio/Tools/Phylo/PAML

Modified Files:
	ModelResult.pm Result.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: ModelResult.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML/ModelResult.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** ModelResult.pm	8 Mar 2007 16:32:40 -0000	1.13
--- ModelResult.pm	14 Jun 2007 14:16:18 -0000	1.14
***************
*** 19,23 ****
    # get a ModelResult from a PAML::Result object
    use Bio::Tools::Phylo::PAML;
!   my $paml = new Bio::Tools::Phylo::PAML(-file => 'mlc');
    my $result = $paml->next_result;
    foreach my $model ( $result->get_NSSite_results ) {
--- 19,23 ----
    # get a ModelResult from a PAML::Result object
    use Bio::Tools::Phylo::PAML;
!   my $paml = Bio::Tools::Phylo::PAML->new(-file => 'mlc');
    my $result = $paml->next_result;
    foreach my $model ( $result->get_NSSite_results ) {
***************
*** 89,93 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tools::Phylo::PAML::ModelResult();
   Function: Builds  a new Bio::Tools::Phylo::PAML::ModelResult object 
   Returns : an instance of Bio::Tools::Phylo::PAML::ModelResult
--- 89,93 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tools::Phylo::PAML::ModelResult->new();
   Function: Builds  a new Bio::Tools::Phylo::PAML::ModelResult object 
   Returns : an instance of Bio::Tools::Phylo::PAML::ModelResult

Index: Result.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML/Result.pm,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** Result.pm	8 Mar 2007 15:55:37 -0000	1.26
--- Result.pm	14 Jun 2007 14:16:18 -0000	1.27
***************
*** 19,23 ****
    # see Bio::Tools::Phylo::PAML for example usage
    use Bio::Tools::Phylo::PAML;
!   my $parser = new Bio::Tools::Phylo::PAML
      (-file => "./results/mlc", -dir => "./results/");
  
--- 19,23 ----
    # see Bio::Tools::Phylo::PAML for example usage
    use Bio::Tools::Phylo::PAML;
!   my $parser = Bio::Tools::Phylo::PAML->new
      (-file => "./results/mlc", -dir => "./results/");
  



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