[Bioperl-guts-l] bioperl-live/Bio/Matrix/PSM IO.pm, 1.16, 1.17 InstanceSite.pm, 1.16, 1.17 ProtMatrix.pm, 1.18, 1.19 ProtPsm.pm, 1.10, 1.11 Psm.pm, 1.15, 1.16 PsmHeader.pm, 1.12, 1.13 PsmHeaderI.pm, 1.11, 1.12 PsmI.pm, 1.9, 1.10 SiteMatrix.pm, 1.39, 1.40

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
In directory dev.open-bio.org:/tmp/cvs-serv22328/Bio/Matrix/PSM

Modified Files:
	IO.pm InstanceSite.pm ProtMatrix.pm ProtPsm.pm Psm.pm 
	PsmHeader.pm PsmHeaderI.pm PsmI.pm SiteMatrix.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: SiteMatrix.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/SiteMatrix.pm,v
retrieving revision 1.39
retrieving revision 1.40
diff -C2 -d -r1.39 -r1.40
*** SiteMatrix.pm	26 Sep 2006 22:03:09 -0000	1.39
--- SiteMatrix.pm	14 Jun 2007 14:16:12 -0000	1.40
***************
*** 23,30 ****
               -lA=>$la, -lC=>$lc,-lG=>$lg,-lT=>$l,
               -IC=>$ic,-e_val=>$score, -id=>$mid);
!   my $site=new Bio::Matrix::PSM::SiteMatrix(%param);
    #Or get it from a file:
    use Bio::Matrix::PSM::IO;
!   my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'transfac');
    while (my $psm=$psmIO->next_psm) {
      #Now we have a Bio::Matrix::PSM::Psm object, 
--- 23,30 ----
               -lA=>$la, -lC=>$lc,-lG=>$lg,-lT=>$l,
               -IC=>$ic,-e_val=>$score, -id=>$mid);
!   my $site=Bio::Matrix::PSM::SiteMatrix->new(%param);
    #Or get it from a file:
    use Bio::Matrix::PSM::IO;
!   my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'transfac');
    while (my $psm=$psmIO->next_psm) {
      #Now we have a Bio::Matrix::PSM::Psm object, 
***************
*** 154,158 ****
  
   Title   : new
!  Usage   : my $site=new Bio::Matrix::PSM::SiteMatrix(-pA=>$a,-pC=>$c,
  						     -pG=>$g,-pT=>$t,
  						     -IC=>$ic,
--- 154,158 ----
  
   Title   : new
!  Usage   : my $site=Bio::Matrix::PSM::SiteMatrix->new(-pA=>$a,-pC=>$c,
  						     -pG=>$g,-pT=>$t,
  						     -IC=>$ic,

Index: ProtPsm.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/ProtPsm.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** ProtPsm.pm	26 Sep 2006 22:03:09 -0000	1.10
--- ProtPsm.pm	14 Jun 2007 14:16:12 -0000	1.11
***************
*** 13,17 ****
  
    #To get a ProtPsm object from a file use the Psm parser:
!   my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'psiblast', -file=>$file);
  
    # Now go through all entities in the file with next_psm, which
--- 13,17 ----
  
    #To get a ProtPsm object from a file use the Psm parser:
!   my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'psiblast', -file=>$file);
  
    # Now go through all entities in the file with next_psm, which

Index: Psm.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/Psm.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Psm.pm	26 Sep 2006 22:03:09 -0000	1.15
--- Psm.pm	14 Jun 2007 14:16:12 -0000	1.16
***************
*** 13,17 ****
  
    #To get a Psm object from a file use the Psm parser:
!   my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'meme', -file=>$file);
  
    # Now go through all entities in the file with next_psm, which
--- 13,17 ----
  
    #To get a Psm object from a file use the Psm parser:
!   my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme', -file=>$file);
  
    # Now go through all entities in the file with next_psm, which
***************
*** 35,39 ****
  
   #or create from memmory:
!   my $psm= new Bio::Matrix::PSM::Psm( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,
         -id=>$id,
         -instances=>$instances, -e_val=>$e_val,
--- 35,39 ----
  
   #or create from memmory:
!   my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,
         -id=>$id,
         -instances=>$instances, -e_val=>$e_val,
***************
*** 125,129 ****
  
   Title   : new
!  Usage   : my $psm= new Bio::Matrix::PSM::Psm( -pA=>\@pA,-pC=>\@pC,
  					       -pG=>\@pG,-pT=>\@pT,-id=>$id,
  					       -instances=>$instances, 
--- 125,129 ----
  
   Title   : new
!  Usage   : my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,
  					       -pG=>\@pG,-pT=>\@pT,-id=>$id,
  					       -instances=>$instances, 
***************
*** 218,222 ****
  sub matrix {
      my $self = shift;
!     my $prev = new Bio::Matrix::PSM::SiteMatrix(-pA=>$self->{probA}, 
  						-pC=>$self->{probC},
  						-pG=>$self->{probG},
--- 218,222 ----
  sub matrix {
      my $self = shift;
!     my $prev = Bio::Matrix::PSM::SiteMatrix->new(-pA=>$self->{probA}, 
  						-pC=>$self->{probC},
  						-pG=>$self->{probG},

Index: InstanceSite.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/InstanceSite.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** InstanceSite.pm	26 Sep 2006 22:03:09 -0000	1.16
--- InstanceSite.pm	14 Jun 2007 14:16:12 -0000	1.17
***************
*** 83,87 ****
  
   Title   : new
!  Usage   : my $isntance=new Bio::Matrix::PSM::InstanceSite 
                           (-seq=>'TATAAT', -id=>"TATAbox1",
                            -accession_number='ENSG00000122304', -mid=>'TB1',
--- 83,87 ----
  
   Title   : new
!  Usage   : my $isntance=Bio::Matrix::PSM::InstanceSite->new 
                           (-seq=>'TATAAT', -id=>"TATAbox1",
                            -accession_number='ENSG00000122304', -mid=>'TB1',
***************
*** 263,267 ****
  	$obj->{'_annotation'} = $value;
      } elsif( ! defined $obj->{'_annotation'}) {
! 	$obj->{'_annotation'} = new Bio::Annotation::Collection();
      }
      return $obj->{'_annotation'};
--- 263,267 ----
  	$obj->{'_annotation'} = $value;
      } elsif( ! defined $obj->{'_annotation'}) {
! 	$obj->{'_annotation'} = Bio::Annotation::Collection->new();
      }
      return $obj->{'_annotation'};

Index: PsmHeader.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/PsmHeader.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** PsmHeader.pm	26 Sep 2006 22:03:09 -0000	1.12
--- PsmHeader.pm	14 Jun 2007 14:16:12 -0000	1.13
***************
*** 64,68 ****
  
   Title   : new
!  Usage   : my $header= new Bio::Matrix::PSM::PsmHeader(-seq=>\%seq, 
  						       -mid=>\%mid, 
  						       -width=>\%width,
--- 64,68 ----
  
   Title   : new
!  Usage   : my $header= Bio::Matrix::PSM::PsmHeader->new(-seq=>\%seq, 
  						       -mid=>\%mid, 
  						       -width=>\%width,

Index: PsmI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/PsmI.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** PsmI.pm	26 Sep 2006 22:03:09 -0000	1.9
--- PsmI.pm	14 Jun 2007 14:16:12 -0000	1.10
***************
*** 12,16 ****
  
    # To get a Psm object from a file use the Psm parser:
!   my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'meme', -file=>$file);
  
    # Now go through all entities in the file with next_psm, which
--- 12,16 ----
  
    # To get a Psm object from a file use the Psm parser:
!   my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme', -file=>$file);
  
    # Now go through all entities in the file with next_psm, which
***************
*** 34,38 ****
  
    # or create from memmory:
!   my $psm= new Bio::Matrix::PSM::Psm( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,
                                        -id=>$id,
                                        -instances=>$instances, -e_val=>$e_val,
--- 34,38 ----
  
    # or create from memmory:
!   my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,
                                        -id=>$id,
                                        -instances=>$instances, -e_val=>$e_val,
***************
*** 124,128 ****
  
   Title   : new
!  Usage   : my $psm= new Bio::Matrix::PSM::Psm( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,
  					       -pT=>\@pT,-id=>$id,
  					       -instances=>$instances, 
--- 124,128 ----
  
   Title   : new
!  Usage   : my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,
  					       -pT=>\@pT,-id=>$id,
  					       -instances=>$instances, 

Index: PsmHeaderI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/PsmHeaderI.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** PsmHeaderI.pm	26 Sep 2006 22:03:09 -0000	1.11
--- PsmHeaderI.pm	14 Jun 2007 14:16:12 -0000	1.12
***************
*** 10,14 ****
   use Bio::Matrix::PSM::IO;
   #Obtain an Bio::Matrix::PSM::IO object:
!  my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'mast');
  
   #Get some general data about the file you are parsing:
--- 10,14 ----
   use Bio::Matrix::PSM::IO;
   #Obtain an Bio::Matrix::PSM::IO object:
!  my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'mast');
  
   #Get some general data about the file you are parsing:
***************
*** 93,97 ****
  
   Title   : new
!  Usage   : my $header= new Bio::Matrix::PSM::PsmHeader
              ( -seq=>\%seq, -mid=>\%mid, -width=>\%width,
                -instances=>\%instances, -header=>\@header, -type=>'mast');
--- 93,97 ----
  
   Title   : new
!  Usage   : my $header= Bio::Matrix::PSM::PsmHeader->new
              ( -seq=>\%seq, -mid=>\%mid, -width=>\%width,
                -instances=>\%instances, -header=>\@header, -type=>'mast');

Index: ProtMatrix.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/ProtMatrix.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** ProtMatrix.pm	8 Mar 2007 16:41:44 -0000	1.18
--- ProtMatrix.pm	14 Jun 2007 14:16:12 -0000	1.19
***************
*** 64,71 ****
  
  
!    my $site = new Bio::Matrix::PSM::ProtMatrix(%param);
     # Or get it from a file:
     use Bio::Matrix::PSM::IO;
!    my $psmIO = new Bio::Matrix::PSM::IO(-file => $file, -format => 'psi-blast');
     while (my $psm = $psmIO->next_psm) {
        #Now we have a Bio::Matrix::PSM::Psm object, 
--- 64,71 ----
  
  
!    my $site = Bio::Matrix::PSM::ProtMatrix->new(%param);
     # Or get it from a file:
     use Bio::Matrix::PSM::IO;
!    my $psmIO = Bio::Matrix::PSM::IO->new(-file => $file, -format => 'psi-blast');
     while (my $psm = $psmIO->next_psm) {
        #Now we have a Bio::Matrix::PSM::Psm object, 
***************
*** 185,189 ****
  
   Title    : new
!  Usage    : my $site = new Bio::Matrix::PSM::ProtMatrix( 
                 %probs,
                 %logs,
--- 185,189 ----
  
   Title    : new
!  Usage    : my $site = Bio::Matrix::PSM::ProtMatrix->new( 
                 %probs,
                 %logs,

Index: IO.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/PSM/IO.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** IO.pm	26 Sep 2006 22:03:09 -0000	1.16
--- IO.pm	14 Jun 2007 14:16:12 -0000	1.17
***************
*** 10,14 ****
    use Bio::Matrix::PSM::IO;
  
!   my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'transfac');
  
    my $release=$psmIO->release; #Using Bio::Matrix::PSM::PsmHeader methods
--- 10,14 ----
    use Bio::Matrix::PSM::IO;
  
!   my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'transfac');
  
    my $release=$psmIO->release; #Using Bio::Matrix::PSM::PsmHeader methods
***************
*** 52,56 ****
  example:
  
!   my $psmIO= new Bio::Matrix::PSM::IO(file=>$file, format=>'transfac');
    my %seq=$psmIO->seq;
  
--- 52,56 ----
  example:
  
!   my $psmIO= Bio::Matrix::PSM::IO->new(file=>$file, format=>'transfac');
    my %seq=$psmIO->seq;
  
***************
*** 109,113 ****
  
   Title   : new
!  Usage   : my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'meme', 
  						 -file=>$file);
   Function: Associates a file with the appropriate parser
--- 109,113 ----
  
   Title   : new
!  Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme', 
  						 -file=>$file);
   Function: Associates a file with the appropriate parser



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