[Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM SiteMatrix.pm, 1.33, 1.34

[Senduran Balasubramaniam]

Update of /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM
In directory dev.open-bio.org:/tmp/cvs-serv12141/Bio/Matrix/PSM

Modified Files:
	SiteMatrix.pm 
Log Message:
Option to do pseudocount correction, threshold for IUPAC, test expectations updated with new behaviour in mind

Index: SiteMatrix.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/SiteMatrix.pm,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** SiteMatrix.pm	30 Aug 2006 18:51:07 -0000	1.33
--- SiteMatrix.pm	1 Sep 2006 12:17:41 -0000	1.34
***************
*** 43,74 ****
    my $count=($seq=~ s/$regexp/$1/eg);
    print "Motif $mid is present $count times in this sequence\n";
-   
- 
-   
  
  =head1 DESCRIPTION
  
! SiteMatrix is designed to provide some basic methods when working with
! position scoring (weight) matrices, such as transcription factor
[...1182 lines suppressed...]
!         push @{$perm[$i]},'G' if ($self->{probG}->[$i]>$thresh);
!         push @{$perm[$i]},'T' if ($self->{probT}->[$i]>$thresh);
!         push @{$perm[$i]},'N' if  ($seq[$i] eq 'N');
!     }
!     my $fpos=shift @perm;
!     my @strings=@$fpos;
!     foreach my $pos (@perm) {
!         my @newstr;
!         foreach my $let (@$pos) {
!             foreach my $string (@strings) {
!                 my $newstring = $string . $let;
!                 push @newstr,$newstring;
!             }
!         }
!         @strings=@newstr;
      }
  	return @strings;
  }
  
  1;