[Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo/PAML Result.pm, 1.18, 1.19

Albert Vilella avilella at pub.open-bio.org
Thu Jan 26 11:55:24 EST 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML
In directory pub.open-bio.org:/tmp/cvs-serv31180

Modified Files:
	Result.pm 
Log Message:
adding seqfile method -- it may not make sense for this to set, but it makes to get


Index: Result.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML/Result.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** Result.pm	22 Sep 2005 09:25:24 -0000	1.18
--- Result.pm	26 Jan 2006 16:55:22 -0000	1.19
***************
*** 158,161 ****
--- 158,162 ----
             -aamldistmat => Bio::Matrix::PhylipDist   (only for pairwise AAML)
             -ntfreq    => array ref of NT frequencies (only for BASEML)
+            -seqfile    => seqfile used
             -kappa_mat => Bio::Matrix::PhylipDist of kappa values (only for BASEML)
             -alpha_mat => Bio::Matrix::PhylipDist of alpha values (only for BASEML)
***************
*** 181,185 ****
        $aafreq, $aadistmat, 
        $aamldistmat,
!       $ntfreqs, $kappa_mat,$alpha_mat,
        $NSSitesresults,$input_params,$rst,$rst_persite,$rst_trees ) = 
  	  $self->_rearrange([qw
--- 182,186 ----
        $aafreq, $aadistmat, 
        $aamldistmat,
!       $ntfreqs, $seqfile, $kappa_mat, $alpha_mat,
        $NSSitesresults,$input_params,$rst,$rst_persite,$rst_trees ) = 
  	  $self->_rearrange([qw
***************
*** 190,194 ****
  			      STATS AAFREQ AADISTMAT
  			      AAMLDISTMAT 
! 			      NTFREQ
  			      KAPPA_DISTMAT
  			      ALPHA_DISTMAT
--- 191,195 ----
  			      STATS AAFREQ AADISTMAT
  			      AAMLDISTMAT 
! 			      NTFREQ SEQFILE
  			      KAPPA_DISTMAT
  			      ALPHA_DISTMAT
***************
*** 249,252 ****
--- 250,254 ----
  
    $self->version($version)   if defined $version;
+   $self->seqfile($seqfile)   if defined $seqfile;
    $self->model($model)       if defined $model;
    if( defined $patterns ) {
***************
*** 599,602 ****
--- 601,621 ----
     $self->{'_version'} = shift if @_;
     return $self->{'_version'};
+ }
+ 
+ =head2 seqfile
+ 
+  Title   : seqfile
+  Usage   : $obj->seqfile($newval)
+  Function: Get/Set seqfile
+  Returns : value of seqfile
+  Args    : newvalue (optional)
+ 
+ 
+ =cut
+ 
+ sub seqfile{
+    my $self = shift;
+    $self->{'_seqfile'} = shift if @_;
+    return $self->{'_seqfile'};
  }
  



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