[Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM InstanceSite.pm, 1.14, 1.15

Stefan Kirov skirov at dev.open-bio.org
Sun Sep 10 17:58:46 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM
In directory dev.open-bio.org:/tmp/cvs-serv12517

Modified Files:
	InstanceSite.pm 
Log Message:
Added frame, which may be necessary if the motif was protein, but the DB is nucleic acid


Index: InstanceSite.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/InstanceSite.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** InstanceSite.pm	4 Jul 2006 22:23:18 -0000	1.14
--- InstanceSite.pm	10 Sep 2006 21:58:44 -0000	1.15
***************
*** 125,128 ****
--- 125,129 ----
      $self->{score}=$args{score};
      $self->{relpos}=$args{relpos};
+     $self->{frame}=$args{frame};
      $self->{anchor}=$args{anchor};
      return $self;
***************
*** 292,294 ****
--- 293,315 ----
  
  
+ =head2 frame
+ 
+  Title   : frame
+  Usage   : my $frane=$instance->frame;
+  Function: Get/Set the frame of a DNA instance with respect to a protein motif used.
+             Returns undef if the motif was not protein or the DB is protein.
+  Throws  :
+  Example :
+  Returns : integer
+  Args    : integer (0, 1, 2)
+ 
+ =cut
+ 
+ sub frame {
+     my $self = shift;
+     my $prev = $self->{frame};
+     if (@_) { $self->{frame} = shift; $self->throw("This is not a legitimate frame") unless (grep(/$self->{frame}/,qw[0 1 2])); }
+     return $prev;
+ }
+ 
  1;



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