[Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM/IO mast.pm, 1.23, 1.24 meme.pm, 1.22, 1.23 psiblast.pm, 1.13, 1.14 transfac.pm, 1.18, 1.19

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


Update of /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/IO
In directory dev.open-bio.org:/tmp/cvs-serv22328/Bio/Matrix/PSM/IO

Modified Files:
	mast.pm meme.pm psiblast.pm transfac.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: meme.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/IO/meme.pm,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** meme.pm	26 Sep 2006 22:03:09 -0000	1.22
--- meme.pm	14 Jun 2007 14:16:12 -0000	1.23
***************
*** 58,62 ****
  
   Title   : new
!  Usage   : my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'meme', 
  						 -file=>$file);
   Function: Associates a file with the appropriate parser
--- 58,62 ----
  
   Title   : new
!  Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme', 
  						 -file=>$file);
   Function: Associates a file with the appropriate parser
***************
*** 207,211 ****
  	if ($line=~/^letter-probability\smatrix/) {
  	    my %matrix_dat=$self->_parseMatrix($motif_id);
! 	    my $psm= new Bio::Matrix::PSM::Psm(%matrix_dat, 
  					       -instances=>$instances, 
  					       -e_val=>$e_val,
--- 207,211 ----
  	if ($line=~/^letter-probability\smatrix/) {
  	    my %matrix_dat=$self->_parseMatrix($motif_id);
! 	    my $psm= Bio::Matrix::PSM::Psm->new(%matrix_dat, 
  					       -instances=>$instances, 
  					       -e_val=>$e_val,
***************
*** 330,334 ****
  	}
  	my $sid = $self->{id} . '@' . $id;
! 	$instance[$i] = new Bio::Matrix::PSM::InstanceSite
  	    (-mid      => $self->{id}, 
  	     -start    => $start, 
--- 330,334 ----
  	}
  	my $sid = $self->{id} . '@' . $id;
! 	$instance[$i] = Bio::Matrix::PSM::InstanceSite->new
  	    (-mid      => $self->{id}, 
  	     -start    => $start, 

Index: mast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/IO/mast.pm,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** mast.pm	26 Sep 2006 22:03:09 -0000	1.23
--- mast.pm	14 Jun 2007 14:16:12 -0000	1.24
***************
*** 62,66 ****
  
   Title   : new
!  Usage   : my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'mast', 
  						                               -file=>$file);
   Function: Associates a file with the appropriate parser
--- 62,66 ----
  
   Title   : new
!  Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'mast', 
  						                               -file=>$file);
   Function: Associates a file with the appropriate parser
***************
*** 175,179 ****
  			next;
  		}
! 		$instances{$id}=new Bio::Matrix::PSM::InstanceSite (-id=>$id,
  																			  -desc=>$key,
  																			  -score=>$eval, 
--- 175,179 ----
  			next;
  		}
! 		$instances{$id}=Bio::Matrix::PSM::InstanceSite->new(-id=>$id,
  																			  -desc=>$key,
  																			  -score=>$eval, 
***************
*** 246,250 ****
      #We don't know the sequence, but we know the length
  	my $seq='N' x ($width*$self->{_factor}); #Future version will have to parse Section tree nad get the real seq
! 	my $instance=new Bio::Matrix::PSM::InstanceSite 
  	    ( -id=>"$id\@$sid", 
  	      -mid=>$id, 
--- 246,250 ----
      #We don't know the sequence, but we know the length
  	my $seq='N' x ($width*$self->{_factor}); #Future version will have to parse Section tree nad get the real seq
! 	my $instance=Bio::Matrix::PSM::InstanceSite->new 
  	    ( -id=>"$id\@$sid", 
  	      -mid=>$id, 
***************
*** 260,264 ****
  	$pos+=$index{$id}*$self->{_factor};
      }
!     my $psm= new Bio::Matrix::PSM::Psm (-instances=> \@instances, 
  					-e_val    => $eval, 
  					-id       => $sid);
--- 260,264 ----
  	$pos+=$index{$id}*$self->{_factor};
      }
!     my $psm= Bio::Matrix::PSM::Psm->new(-instances=> \@instances, 
  					-e_val    => $eval, 
  					-id       => $sid);

Index: psiblast.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/IO/psiblast.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** psiblast.pm	26 Sep 2006 22:03:09 -0000	1.13
--- psiblast.pm	14 Jun 2007 14:16:12 -0000	1.14
***************
*** 57,61 ****
  
   Title   : new
!  Usage   : my $psmIO  =  new Bio::Matrix::PSM::IO(-format=>'psiblast', 
                                                    -file=>$file);
   Function: Associates a file with the appropriate parser
--- 57,61 ----
  
   Title   : new
!  Usage   : my $psmIO  =  Bio::Matrix::PSM::IO->new(-format=>'psiblast', 
                                                    -file=>$file);
   Function: Associates a file with the appropriate parser

Index: transfac.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/IO/transfac.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** transfac.pm	27 Sep 2006 01:11:08 -0000	1.18
--- transfac.pm	14 Jun 2007 14:16:12 -0000	1.19
***************
*** 56,60 ****
  
   Title   : new
!  Usage   : my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'transfac', 
  						 -file=>$file);
   Function: Associates a file with the appropriate parser
--- 56,60 ----
  
   Title   : new
!  Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'transfac', 
  						 -file=>$file);
   Function: Associates a file with the appropriate parser
***************
*** 132,136 ****
      $matrix{-sites}=$sites if ($sites);
      $matrix{-width}=@a;
!     my $psm=new Bio::Matrix::PSM::Psm(%matrix);
      foreach my $ref (@refs) { $psm->add_Annotation('reference',$ref); }
      return $psm;
--- 132,136 ----
      $matrix{-sites}=$sites if ($sites);
      $matrix{-width}=@a;
!     my $psm=Bio::Matrix::PSM::Psm->new(%matrix);
      foreach my $ref (@refs) { $psm->add_Annotation('reference',$ref); }
      return $psm;
***************
*** 236,240 ****
          }
       }
!      my $reference=new Bio::Annotation::Reference (-authors=>$authors, -title=>$title,
                                                      -location=>$loc);
       if ($db eq 'MEDLINE') {
--- 236,240 ----
          }
       }
!      my $reference=Bio::Annotation::Reference->new(-authors=>$authors, -title=>$title,
                                                      -location=>$loc);
       if ($db eq 'MEDLINE') {



More information about the Bioperl-guts-l mailing list