[Bioperl-guts-l] bioperl-live/Bio/PopGen Genotype.pm, 1.10, 1.10.4.1 GenotypeI.pm, 1.3, 1.3.4.1 HtSNP.pm, 1.6, 1.6.4.1 IO.pm, 1.6, 1.6.4.1 Individual.pm, 1.15, 1.15.4.1 IndividualI.pm, 1.7, 1.7.4.1 Marker.pm, 1.7, 1.7.4.1 MarkerI.pm, 1.6, 1.6.4.1 PopStats.pm, 1.10, 1.10.4.1 Population.pm, 1.19, 1.19.4.1 PopulationI.pm, 1.9, 1.9.4.1 Statistics.pm, 1.34, 1.34.4.1 TagHaplotype.pm, 1.5, 1.5.4.1 Utilities.pm, 1.7, 1.7.4.1

Senduran Balasubramaniam sendu at dev.open-bio.org
Mon Oct 2 19:10:25 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/PopGen
In directory dev.open-bio.org:/tmp/cvs-serv28352/Bio/PopGen

Modified Files:
      Tag: branch-1-5-2
	Genotype.pm GenotypeI.pm HtSNP.pm IO.pm Individual.pm 
	IndividualI.pm Marker.pm MarkerI.pm PopStats.pm Population.pm 
	PopulationI.pm Statistics.pm TagHaplotype.pm Utilities.pm 
Log Message:
merge from HEAD

Index: Marker.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/Marker.pm,v
retrieving revision 1.7
retrieving revision 1.7.4.1
diff -C2 -d -r1.7 -r1.7.4.1
*** Marker.pm	4 Jul 2006 22:23:19 -0000	1.7
--- Marker.pm	2 Oct 2006 23:10:23 -0000	1.7.4.1
***************
*** 71,81 ****
  
  package Bio::PopGen::Marker;
- use vars qw(@ISA);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::Root::Root;
- use Bio::PopGen::MarkerI;
  
  use vars qw($UniqueCounter);
--- 71,78 ----
***************
*** 83,87 ****
  $UniqueCounter = 0;
  
! @ISA = qw(Bio::Root::Root Bio::PopGen::MarkerI);
  
  =head2 new
--- 80,84 ----
  $UniqueCounter = 0;
  
! use base qw(Bio::Root::Root Bio::PopGen::MarkerI);
  
  =head2 new

Index: Utilities.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/Utilities.pm,v
retrieving revision 1.7
retrieving revision 1.7.4.1
diff -C2 -d -r1.7 -r1.7.4.1
*** Utilities.pm	4 Jul 2006 22:23:19 -0000	1.7
--- Utilities.pm	2 Oct 2006 23:10:23 -0000	1.7.4.1
***************
*** 65,74 ****
  Email jason-at-open-bio-dot-org
  
- Describe contact details here
- 
- =head1 CONTRIBUTORS
- 
- Additional contributors names and emails here
- 
  =head1 APPENDIX
  
--- 65,68 ----
***************
*** 83,95 ****
  
  package Bio::PopGen::Utilities;
- use vars qw(@ISA);
  use strict;
  
  use Bio::Align::DNAStatistics;
- use Bio::Root::Root;
  use Bio::PopGen::Population;
  use Bio::PopGen::Individual;
  
! @ISA = qw(Bio::Root::Root );
  
  
--- 77,87 ----
  
  package Bio::PopGen::Utilities;
  use strict;
  
  use Bio::Align::DNAStatistics;
  use Bio::PopGen::Population;
  use Bio::PopGen::Individual;
  
! use base qw(Bio::Root::Root);
  
  

Index: Genotype.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/Genotype.pm,v
retrieving revision 1.10
retrieving revision 1.10.4.1
diff -C2 -d -r1.10 -r1.10.4.1
*** Genotype.pm	4 Jul 2006 22:23:19 -0000	1.10
--- Genotype.pm	2 Oct 2006 23:10:23 -0000	1.10.4.1
***************
*** 73,77 ****
  
  package Bio::PopGen::Genotype;
! use vars qw(@ISA $BlankAlleles);
  use strict;
  
--- 73,77 ----
  
  package Bio::PopGen::Genotype;
! use vars qw($BlankAlleles);
  use strict;
  
***************
*** 81,89 ****
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::PopGen::GenotypeI;
- use Bio::Root::Root;
  
  
! @ISA = qw(Bio::Root::Root  Bio::PopGen::GenotypeI);
  
  =head2 new
--- 81,87 ----
  # Object preamble - inherits from Bio::Root::Root
  
  
  
! use base qw(Bio::Root::Root Bio::PopGen::GenotypeI);
  
  =head2 new

Index: Population.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/Population.pm,v
retrieving revision 1.19
retrieving revision 1.19.4.1
diff -C2 -d -r1.19 -r1.19.4.1
*** Population.pm	4 Jul 2006 22:23:19 -0000	1.19
--- Population.pm	2 Oct 2006 23:10:23 -0000	1.19.4.1
***************
*** 88,102 ****
  
  package Bio::PopGen::Population;
- use vars qw(@ISA);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::Root::Root;
- use Bio::PopGen::PopulationI;
  use Bio::PopGen::Marker;
  use Bio::PopGen::Genotype;
  
! @ISA = qw(Bio::Root::Root Bio::PopGen::PopulationI );
  
  =head2 new
--- 88,99 ----
  
  package Bio::PopGen::Population;
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
  use Bio::PopGen::Marker;
  use Bio::PopGen::Genotype;
  
! use base qw(Bio::Root::Root Bio::PopGen::PopulationI);
  
  =head2 new

Index: Statistics.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/Statistics.pm,v
retrieving revision 1.34
retrieving revision 1.34.4.1
diff -C2 -d -r1.34 -r1.34.4.1
*** Statistics.pm	4 Jul 2006 22:23:19 -0000	1.34
--- Statistics.pm	2 Oct 2006 23:10:23 -0000	1.34.4.1
***************
*** 133,141 ****
  
  Email jason-at-bioperl-dot-org
! Matt Hahn E<lt>matthew.hahn-at-duke.dukeE<gt>
! 
! =head1 CONTRIBUTORS
! 
! Additional contributors names and emails here
  
  =head1 APPENDIX
--- 133,137 ----
  
  Email jason-at-bioperl-dot-org
! Email matthew-dot-hahn-at-duke-dot-edu
  
  =head1 APPENDIX
***************
*** 151,160 ****
  
  package Bio::PopGen::Statistics;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  
! @ISA = qw(Bio::Root::Root );
  
  =head2 new
--- 147,154 ----
  
  package Bio::PopGen::Statistics;
  use strict;
  
  
! use base qw(Bio::Root::Root);
  
  =head2 new

Index: HtSNP.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/HtSNP.pm,v
retrieving revision 1.6
retrieving revision 1.6.4.1
diff -C2 -d -r1.6 -r1.6.4.1
*** HtSNP.pm	4 Jul 2006 22:23:19 -0000	1.6
--- HtSNP.pm	2 Oct 2006 23:10:23 -0000	1.6.4.1
***************
*** 300,309 ****
  use Storable qw(dclone);
  
! use vars qw (@ISA);
  use strict;
  
- use Bio::Root::Root;
  
! @ISA = qw(Bio::Root::Root);
  
  my $USAGE = 'Usage:
--- 300,308 ----
  use Storable qw(dclone);
  
! use vars qw ();
  use strict;
  
  
! use base qw(Bio::Root::Root);
  
  my $USAGE = 'Usage:

Index: PopStats.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/PopStats.pm,v
retrieving revision 1.10
retrieving revision 1.10.4.1
diff -C2 -d -r1.10 -r1.10.4.1
*** PopStats.pm	4 Jul 2006 22:23:19 -0000	1.10
--- PopStats.pm	2 Oct 2006 23:10:23 -0000	1.10.4.1
***************
*** 65,77 ****
  
  package Bio::PopGen::PopStats;
- use vars qw(@ISA);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::Root::Root;
  
  
! @ISA = qw(Bio::Root::Root );
  
  =head2 new
--- 65,75 ----
  
  package Bio::PopGen::PopStats;
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
  
  
! use base qw(Bio::Root::Root);
  
  =head2 new

Index: GenotypeI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/GenotypeI.pm,v
retrieving revision 1.3
retrieving revision 1.3.4.1
diff -C2 -d -r1.3 -r1.3.4.1
*** GenotypeI.pm	4 Jul 2006 22:23:19 -0000	1.3
--- GenotypeI.pm	2 Oct 2006 23:10:23 -0000	1.3.4.1
***************
*** 46,55 ****
  Email jason-at-bioperl.org
  
- Describe contact details here
- 
- =head1 CONTRIBUTORS
- 
- Additional contributors names and emails here
- 
  =head1 APPENDIX
  
--- 46,49 ----
***************
*** 64,73 ****
  
  package Bio::PopGen::GenotypeI;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::RootI;
  
! @ISA = qw( Bio::Root::RootI );
  
  =head2 marker_name
--- 58,65 ----
  
  package Bio::PopGen::GenotypeI;
  use strict;
  
  
! use base qw(Bio::Root::RootI);
  
  =head2 marker_name

Index: MarkerI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/MarkerI.pm,v
retrieving revision 1.6
retrieving revision 1.6.4.1
diff -C2 -d -r1.6 -r1.6.4.1
*** MarkerI.pm	4 Jul 2006 22:23:19 -0000	1.6
--- MarkerI.pm	2 Oct 2006 23:10:23 -0000	1.6.4.1
***************
*** 74,84 ****
  
  package Bio::PopGen::MarkerI;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::RootI;
- use Bio::AnnotatableI;
  
! @ISA = qw( Bio::Root::RootI Bio::AnnotatableI);
  
  
--- 74,81 ----
  
  package Bio::PopGen::MarkerI;
  use strict;
  
  
! use base qw(Bio::Root::RootI Bio::AnnotatableI);
  
  

Index: IO.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/IO.pm,v
retrieving revision 1.6
retrieving revision 1.6.4.1
diff -C2 -d -r1.6 -r1.6.4.1
*** IO.pm	4 Jul 2006 22:23:19 -0000	1.6
--- IO.pm	2 Oct 2006 23:10:23 -0000	1.6.4.1
***************
*** 61,70 ****
  Email jason-at-bioperl.org
  
- Describe contact details here
- 
- =head1 CONTRIBUTORS
- 
- Additional contributors names and emails here
- 
  =head1 APPENDIX
  
--- 61,64 ----
***************
*** 81,85 ****
  
  package Bio::PopGen::IO;
- use vars qw(@ISA);
  use strict;
  
--- 75,78 ----
***************
*** 87,93 ****
  
  use Bio::Root::Root;
- use Bio::Root::IO;
  
! @ISA = qw(Bio::Root::IO);
  
  =head2 new
--- 80,85 ----
  
  use Bio::Root::Root;
  
! use base qw(Bio::Root::IO);
  
  =head2 new

Index: IndividualI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/IndividualI.pm,v
retrieving revision 1.7
retrieving revision 1.7.4.1
diff -C2 -d -r1.7 -r1.7.4.1
*** IndividualI.pm	4 Jul 2006 22:23:19 -0000	1.7
--- IndividualI.pm	2 Oct 2006 23:10:23 -0000	1.7.4.1
***************
*** 54,63 ****
  Email jason-at-bioperl.org
  
- Describe contact details here
- 
- =head1 CONTRIBUTORS
- 
- Additional contributors names and emails here
- 
  =head1 APPENDIX
  
--- 54,57 ----
***************
*** 72,81 ****
  
  package Bio::PopGen::IndividualI;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::RootI;
  
! @ISA = qw( Bio::Root::RootI );
  
  
--- 66,73 ----
  
  package Bio::PopGen::IndividualI;
  use strict;
  
  
! use base qw(Bio::Root::RootI);
  
  

Index: TagHaplotype.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/TagHaplotype.pm,v
retrieving revision 1.5
retrieving revision 1.5.4.1
diff -C2 -d -r1.5 -r1.5.4.1
*** TagHaplotype.pm	4 Jul 2006 22:23:19 -0000	1.5
--- TagHaplotype.pm	2 Oct 2006 23:10:23 -0000	1.5.4.1
***************
*** 69,80 ****
  
  package Bio::PopGen::TagHaplotype;
- use vars qw(@ISA);
  use strict;
  
  use Data::Dumper;
  use Storable qw(dclone);
- use Bio::Root::Root;
  
! @ISA =qw(Bio::Root::Root);
  
  my $USAGE = <<EOF
--- 69,78 ----
  
  package Bio::PopGen::TagHaplotype;
  use strict;
  
  use Data::Dumper;
  use Storable qw(dclone);
  
! use base qw(Bio::Root::Root);
  
  my $USAGE = <<EOF

Index: Individual.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/Individual.pm,v
retrieving revision 1.15
retrieving revision 1.15.4.1
diff -C2 -d -r1.15 -r1.15.4.1
*** Individual.pm	4 Jul 2006 22:23:19 -0000	1.15
--- Individual.pm	2 Oct 2006 23:10:23 -0000	1.15.4.1
***************
*** 66,70 ****
  
  package Bio::PopGen::Individual;
! use vars qw(@ISA $UIDCOUNTER);
  use strict;
  BEGIN { $UIDCOUNTER = 1 }
--- 66,70 ----
  
  package Bio::PopGen::Individual;
! use vars qw($UIDCOUNTER);
  use strict;
  BEGIN { $UIDCOUNTER = 1 }
***************
*** 72,79 ****
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::Root::Root;
- use Bio::PopGen::IndividualI;
  
! @ISA = qw(Bio::Root::Root Bio::PopGen::IndividualI);
  
  =head2 new
--- 72,77 ----
  # Object preamble - inherits from Bio::Root::Root
  
  
! use base qw(Bio::Root::Root Bio::PopGen::IndividualI);
  
  =head2 new

Index: PopulationI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/PopulationI.pm,v
retrieving revision 1.9
retrieving revision 1.9.4.1
diff -C2 -d -r1.9 -r1.9.4.1
*** PopulationI.pm	4 Jul 2006 22:23:19 -0000	1.9
--- PopulationI.pm	2 Oct 2006 23:10:23 -0000	1.9.4.1
***************
*** 82,91 ****
  
  package Bio::PopGen::PopulationI;
- use vars qw(@ISA);
  use strict;
  use Carp;
- use Bio::Root::RootI;
  
! @ISA = qw( Bio::Root::RootI );
  
  =head2 name
--- 82,89 ----
  
  package Bio::PopGen::PopulationI;
  use strict;
  use Carp;
  
! use base qw(Bio::Root::RootI);
  
  =head2 name



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