[Bioperl-guts-l] bioperl-live/Bio/Tree AlleleNode.pm, 1.13, 1.14 Compatible.pm, 1.6, 1.7 DistanceFactory.pm, 1.8, 1.9 Node.pm, 1.50, 1.51 NodeI.pm, 1.35, 1.36 NodeNHX.pm, 1.10, 1.11 RandomFactory.pm, 1.18, 1.19 Statistics.pm, 1.12, 1.13 Tree.pm, 1.22, 1.23 TreeFunctionsI.pm, 1.29, 1.30 TreeI.pm, 1.17, 1.18

Senduran Balasubramaniam sendu at dev.open-bio.org
Tue Sep 26 18:03:23 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Tree
In directory dev.open-bio.org:/tmp/cvs-serv29288/Bio/Tree

Modified Files:
	AlleleNode.pm Compatible.pm DistanceFactory.pm Node.pm 
	NodeI.pm NodeNHX.pm RandomFactory.pm Statistics.pm Tree.pm 
	TreeFunctionsI.pm TreeI.pm 
Log Message:
use base, return true

Index: Compatible.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/Compatible.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Compatible.pm	29 Aug 2006 07:51:00 -0000	1.6
--- Compatible.pm	26 Sep 2006 22:03:20 -0000	1.7
***************
*** 130,142 ****
  
  package Bio::Tree::Compatible;
- use vars qw(@ISA);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::Root::Root;
  use Set::Scalar;
  
! @ISA = qw(Bio::Root::Root);
  
  =head2 postorder_traversal
--- 130,140 ----
  
  package Bio::Tree::Compatible;
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
  use Set::Scalar;
  
! use base qw(Bio::Root::Root);
  
  =head2 postorder_traversal

Index: Node.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/Node.pm,v
retrieving revision 1.50
retrieving revision 1.51
diff -C2 -d -r1.50 -r1.51
*** Node.pm	2 Sep 2006 16:11:53 -0000	1.50
--- Node.pm	26 Sep 2006 22:03:21 -0000	1.51
***************
*** 71,81 ****
  
  package Bio::Tree::Node;
! use vars qw(@ISA $CREATIONORDER);
  use strict;
  
- use Bio::Root::Root;
- use Bio::Tree::NodeI;
  
! @ISA = qw(Bio::Root::Root Bio::Tree::NodeI);
  
  BEGIN { 
--- 71,79 ----
  
  package Bio::Tree::Node;
! use vars qw($CREATIONORDER);
  use strict;
  
  
! use base qw(Bio::Root::Root Bio::Tree::NodeI);
  
  BEGIN { 

Index: NodeI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/NodeI.pm,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** NodeI.pm	4 Jul 2006 22:23:27 -0000	1.35
--- NodeI.pm	26 Sep 2006 22:03:21 -0000	1.36
***************
*** 109,118 ****
  
  package Bio::Tree::NodeI;
- use vars qw(@ISA);
  use strict;
- use Bio::Root::RootI;
  no warnings 'recursion';
  
! @ISA = qw(Bio::Root::RootI);
  
  =head2 add_Descendent
--- 109,116 ----
  
  package Bio::Tree::NodeI;
  use strict;
  no warnings 'recursion';
  
! use base qw(Bio::Root::RootI);
  
  =head2 add_Descendent

Index: Statistics.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/Statistics.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** Statistics.pm	4 Jul 2006 22:23:27 -0000	1.12
--- Statistics.pm	26 Sep 2006 22:03:21 -0000	1.13
***************
*** 67,76 ****
  
  package Bio::Tree::Statistics;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Root::Root;
  
! @ISA = qw(Bio::Root::Root);
  
  =head2 new
--- 67,74 ----
  
  package Bio::Tree::Statistics;
  use strict;
  
  
! use base qw(Bio::Root::Root);
  
  =head2 new

Index: DistanceFactory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/DistanceFactory.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** DistanceFactory.pm	4 Jul 2006 22:23:27 -0000	1.8
--- DistanceFactory.pm	26 Sep 2006 22:03:20 -0000	1.9
***************
*** 87,91 ****
  
  package Bio::Tree::DistanceFactory;
! use vars qw(@ISA $DefaultMethod $Precision);
  use strict;
  
--- 87,91 ----
  
  package Bio::Tree::DistanceFactory;
! use vars qw($DefaultMethod $Precision);
  use strict;
  
***************
*** 94,102 ****
  $Precision = 5;
  
- use Bio::Root::Root;
  use Bio::Tree::Node;
  use Bio::Tree::Tree;
  
! @ISA = qw(Bio::Root::Root);
  
  =head2 new
--- 94,101 ----
  $Precision = 5;
  
  use Bio::Tree::Node;
  use Bio::Tree::Tree;
  
! use base qw(Bio::Root::Root);
  
  =head2 new

Index: NodeNHX.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/NodeNHX.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** NodeNHX.pm	4 Jul 2006 22:23:27 -0000	1.10
--- NodeNHX.pm	26 Sep 2006 22:03:21 -0000	1.11
***************
*** 74,83 ****
  
  package Bio::Tree::NodeNHX;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Tree::Node;
  
! @ISA = qw(Bio::Tree::Node);
  
  =head2 new
--- 74,81 ----
  
  package Bio::Tree::NodeNHX;
  use strict;
  
  
! use base qw(Bio::Tree::Node);
  
  =head2 new

Index: TreeI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/TreeI.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** TreeI.pm	12 Aug 2006 11:00:03 -0000	1.17
--- TreeI.pm	26 Sep 2006 22:03:21 -0000	1.18
***************
*** 72,80 ****
  
  package Bio::Tree::TreeI;
- use Bio::Tree::NodeI;
- use vars qw(@ISA);
  use strict;
  
! @ISA = qw(Bio::Tree::NodeI);
  
  =head2 get_nodes
--- 72,78 ----
  
  package Bio::Tree::TreeI;
  use strict;
  
! use base qw(Bio::Tree::NodeI);
  
  =head2 get_nodes

Index: TreeFunctionsI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/TreeFunctionsI.pm,v
retrieving revision 1.29
retrieving revision 1.30
diff -C2 -d -r1.29 -r1.30
*** TreeFunctionsI.pm	20 Sep 2006 10:20:02 -0000	1.29
--- TreeFunctionsI.pm	26 Sep 2006 22:03:21 -0000	1.30
***************
*** 77,85 ****
  
  package Bio::Tree::TreeFunctionsI;
- use vars qw(@ISA);
  use strict;
- use  Bio::Tree::TreeI;
  
! @ISA = qw(Bio::Tree::TreeI);
  
  =head2 find_node
--- 77,83 ----
  
  package Bio::Tree::TreeFunctionsI;
  use strict;
  
! use base qw(Bio::Tree::TreeI);
  
  =head2 find_node

Index: AlleleNode.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/AlleleNode.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** AlleleNode.pm	4 Jul 2006 22:23:27 -0000	1.13
--- AlleleNode.pm	26 Sep 2006 22:03:20 -0000	1.14
***************
*** 76,89 ****
  
  package Bio::Tree::AlleleNode;
! use vars qw(@ISA $UIDCOUNTER);
  use strict;
  BEGIN { $UIDCOUNTER = 1 }
  
- use Bio::Tree::Node;
- use Bio::PopGen::IndividualI;
  use Bio::PopGen::Individual;
  use Bio::PopGen::Genotype;
  
! @ISA = qw(Bio::Tree::Node Bio::PopGen::IndividualI );
  
  =head2 new
--- 76,87 ----
  
  package Bio::Tree::AlleleNode;
! use vars qw($UIDCOUNTER);
  use strict;
  BEGIN { $UIDCOUNTER = 1 }
  
  use Bio::PopGen::Individual;
  use Bio::PopGen::Genotype;
  
! use base qw(Bio::Tree::Node Bio::PopGen::IndividualI);
  
  =head2 new

Index: RandomFactory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/RandomFactory.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** RandomFactory.pm	4 Jul 2006 22:23:27 -0000	1.18
--- RandomFactory.pm	26 Sep 2006 22:03:21 -0000	1.19
***************
*** 92,96 ****
  
  package Bio::Tree::RandomFactory;
! use vars qw(@ISA $PRECISION_DIGITS $DefaultNodeType %Defaults);
  use strict;
  
--- 92,96 ----
  
  package Bio::Tree::RandomFactory;
! use vars qw($PRECISION_DIGITS $DefaultNodeType %Defaults);
  use strict;
  
***************
*** 102,111 ****
  	     );
  
- use Bio::Factory::TreeFactoryI;
- use Bio::Root::Root;
  use Bio::Tools::RandomDistFunctions;
  use Bio::Tree::Tree;
  
! @ISA = qw(Bio::Root::Root Bio::Factory::TreeFactoryI );
  
  =head2 new
--- 102,109 ----
  	     );
  
  use Bio::Tools::RandomDistFunctions;
  use Bio::Tree::Tree;
  
! use base qw(Bio::Root::Root Bio::Factory::TreeFactoryI);
  
  =head2 new

Index: Tree.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/Tree.pm,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** Tree.pm	20 Sep 2006 10:20:02 -0000	1.22
--- Tree.pm	26 Sep 2006 22:03:21 -0000	1.23
***************
*** 68,81 ****
  
  package Bio::Tree::Tree;
- use vars qw(@ISA);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::Root::Root;
- use Bio::Tree::TreeFunctionsI;
- use Bio::Tree::TreeI;
  
! @ISA = qw(Bio::Root::Root Bio::Tree::TreeI Bio::Tree::TreeFunctionsI   );
  
  =head2 new
--- 68,77 ----
  
  package Bio::Tree::Tree;
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
  
! use base qw(Bio::Root::Root Bio::Tree::TreeI Bio::Tree::TreeFunctionsI);
  
  =head2 new



More information about the Bioperl-guts-l mailing list