[Bioperl-guts-l] bioperl-live/Bio/Ontology GOterm.pm, 1.23, 1.24 InterProTerm.pm, 1.11, 1.12 OBOEngine.pm, 1.9, 1.10 OBOterm.pm, 1.6, 1.7 Ontology.pm, 1.20, 1.21 OntologyEngineI.pm, 1.17, 1.18 OntologyI.pm, 1.9, 1.10 OntologyStore.pm, 1.13, 1.14 Path.pm, 1.8, 1.9 PathI.pm, 1.7, 1.8 Relationship.pm, 1.15, 1.16 RelationshipFactory.pm, 1.5, 1.6 RelationshipI.pm, 1.10, 1.11 RelationshipType.pm, 1.18, 1.19 SimpleGOEngine.pm, 1.37, 1.38 SimpleOntologyEngine.pm, 1.18, 1.19 Term.pm, 1.32, 1.33 TermFactory.pm, 1.7, 1.8 TermI.pm, 1.18, 1.19

Senduran Balasubramaniam sendu at dev.open-bio.org
Tue Sep 26 18:03:12 EDT 2006


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

Modified Files:
	GOterm.pm InterProTerm.pm OBOEngine.pm OBOterm.pm Ontology.pm 
	OntologyEngineI.pm OntologyI.pm OntologyStore.pm Path.pm 
	PathI.pm Relationship.pm RelationshipFactory.pm 
	RelationshipI.pm RelationshipType.pm SimpleGOEngine.pm 
	SimpleOntologyEngine.pm Term.pm TermFactory.pm TermI.pm 
Log Message:
use base, return true

Index: PathI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/PathI.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** PathI.pm	20 Sep 2006 19:08:59 -0000	1.7
--- PathI.pm	26 Sep 2006 22:03:10 -0000	1.8
***************
*** 79,87 ****
  
  package Bio::Ontology::PathI;
- use vars qw(@ISA);
  use strict;
- use Bio::Ontology::RelationshipI;
  
! @ISA = qw( Bio::Ontology::RelationshipI );
  
  
--- 79,85 ----
  
  package Bio::Ontology::PathI;
  use strict;
  
! use base qw(Bio::Ontology::RelationshipI);
  
  

Index: TermI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/TermI.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** TermI.pm	20 Sep 2006 19:08:59 -0000	1.18
--- TermI.pm	26 Sep 2006 22:03:10 -0000	1.19
***************
*** 89,97 ****
  
  package Bio::Ontology::TermI;
- use vars qw( @ISA );
  use strict;
- use Bio::Root::RootI;
  
! @ISA = qw( Bio::Root::RootI );
  
  
--- 89,95 ----
  
  package Bio::Ontology::TermI;
  use strict;
  
! use base qw(Bio::Root::RootI);
  
  

Index: OBOEngine.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/OBOEngine.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** OBOEngine.pm	20 Sep 2006 19:08:59 -0000	1.9
--- OBOEngine.pm	26 Sep 2006 22:03:10 -0000	1.10
***************
*** 74,83 ****
  use Bio::Ontology::SimpleGOEngine::GraphAdaptor;
  
- use vars qw( @ISA );
  use strict;
- use Bio::Root::Root;
  use Bio::Ontology::RelationshipType;
  use Bio::Ontology::RelationshipFactory;
- use Bio::Ontology::OntologyEngineI;
  use Data::Dumper;
  
--- 74,80 ----
***************
*** 91,96 ****
  use constant ONTOLOGY   => "ONTOLOGY";
  
! @ISA = qw( Bio::Root::Root
!            Bio::Ontology::OntologyEngineI );
  
  
--- 88,92 ----
  use constant ONTOLOGY   => "ONTOLOGY";
  
! use base qw(Bio::Root::Root Bio::Ontology::OntologyEngineI);
  
  

Index: RelationshipFactory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/RelationshipFactory.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** RelationshipFactory.pm	4 Jul 2006 22:23:18 -0000	1.5
--- RelationshipFactory.pm	26 Sep 2006 22:03:10 -0000	1.6
***************
*** 82,92 ****
  
  package Bio::Ontology::RelationshipFactory;
- use vars qw(@ISA);
  use strict;
  
  use Bio::Root::Root;
- use Bio::Factory::ObjectFactory;
  
! @ISA = qw(Bio::Factory::ObjectFactory);
  
  =head2 new
--- 82,90 ----
  
  package Bio::Ontology::RelationshipFactory;
  use strict;
  
  use Bio::Root::Root;
  
! use base qw(Bio::Factory::ObjectFactory);
  
  =head2 new

Index: Term.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/Term.pm,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** Term.pm	20 Sep 2006 19:08:59 -0000	1.32
--- Term.pm	26 Sep 2006 22:03:10 -0000	1.33
***************
*** 91,111 ****
  
  package Bio::Ontology::Term;
- use vars qw( @ISA );
  use strict;
  use Bio::Root::Object;
- use Bio::Ontology::TermI;
  use Bio::Ontology::Ontology;
  use Bio::Ontology::OntologyStore;
- use Bio::IdentifiableI;
- use Bio::DescribableI;
  
  use constant TRUE    => 1;
  use constant FALSE   => 0;
  
! @ISA = qw( Bio::Root::Root
!            Bio::Ontology::TermI
!            Bio::IdentifiableI
!            Bio::DescribableI
!          );
  
  
--- 91,103 ----
  
  package Bio::Ontology::Term;
  use strict;
  use Bio::Root::Object;
  use Bio::Ontology::Ontology;
  use Bio::Ontology::OntologyStore;
  
  use constant TRUE    => 1;
  use constant FALSE   => 0;
  
! use base qw(Bio::Root::Root Bio::Ontology::TermI Bio::IdentifiableI Bio::DescribableI);
  
  

Index: OntologyEngineI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/OntologyEngineI.pm,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** OntologyEngineI.pm	20 Sep 2006 19:08:59 -0000	1.17
--- OntologyEngineI.pm	26 Sep 2006 22:03:10 -0000	1.18
***************
*** 83,92 ****
  
  package Bio::Ontology::OntologyEngineI;
- use vars qw(@ISA);
  use strict;
  use Carp;
- use Bio::Root::RootI;
  
! @ISA = qw( Bio::Root::RootI );
  
  =head2 add_term
--- 83,90 ----
  
  package Bio::Ontology::OntologyEngineI;
  use strict;
  use Carp;
  
! use base qw(Bio::Root::RootI);
  
  =head2 add_term

Index: Relationship.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/Relationship.pm,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** Relationship.pm	20 Sep 2006 19:08:59 -0000	1.15
--- Relationship.pm	26 Sep 2006 22:03:10 -0000	1.16
***************
*** 101,112 ****
  
  package Bio::Ontology::Relationship;
- use vars qw( @ISA );
  use strict;
- use Bio::Root::Root;
  use Bio::Ontology::TermI;
- use Bio::Ontology::RelationshipI;
  
! @ISA = qw( Bio::Root::Root
!            Bio::Ontology::RelationshipI );
  
  
--- 101,108 ----
  
  package Bio::Ontology::Relationship;
  use strict;
  use Bio::Ontology::TermI;
  
! use base qw(Bio::Root::Root Bio::Ontology::RelationshipI);
  
  

Index: RelationshipI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/RelationshipI.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** RelationshipI.pm	20 Sep 2006 19:08:59 -0000	1.10
--- RelationshipI.pm	26 Sep 2006 22:03:10 -0000	1.11
***************
*** 90,98 ****
  
  package Bio::Ontology::RelationshipI;
- use vars qw(@ISA);
  use strict;
- use Bio::Root::RootI;
  
! @ISA = qw( Bio::Root::RootI );
  
  =head2 identifier
--- 90,96 ----
  
  package Bio::Ontology::RelationshipI;
  use strict;
  
! use base qw(Bio::Root::RootI);
  
  =head2 identifier

Index: OBOterm.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/OBOterm.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** OBOterm.pm	20 Sep 2006 19:08:59 -0000	1.6
--- OBOterm.pm	26 Sep 2006 22:03:10 -0000	1.7
***************
*** 67,78 ****
  
  package Bio::Ontology::OBOterm;
- use vars qw( @ISA );
  use strict;
- use Bio::Ontology::Term;
  
  use constant TRUE  => 1;
  use constant FALSE => 0;
  
! @ISA = qw( Bio::Ontology::Term );
  
  =head2 new
--- 67,76 ----
  
  package Bio::Ontology::OBOterm;
  use strict;
  
  use constant TRUE  => 1;
  use constant FALSE => 0;
  
! use base qw(Bio::Ontology::Term);
  
  =head2 new

Index: GOterm.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/GOterm.pm,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** GOterm.pm	20 Sep 2006 19:08:59 -0000	1.23
--- GOterm.pm	26 Sep 2006 22:03:09 -0000	1.24
***************
*** 93,99 ****
  
  package Bio::Ontology::GOterm;
- use vars qw( @ISA );
  use strict;
- use Bio::Ontology::Term;
  
  use constant GOID_DEFAULT => "GO:0000000";
--- 93,97 ----
***************
*** 101,105 ****
  use constant FALSE        => 0;
  
! @ISA = qw( Bio::Ontology::Term );
  
  
--- 99,103 ----
  use constant FALSE        => 0;
  
! use base qw(Bio::Ontology::Term);
  
  

Index: OntologyStore.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/OntologyStore.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** OntologyStore.pm	4 Jul 2006 22:23:18 -0000	1.13
--- OntologyStore.pm	26 Sep 2006 22:03:10 -0000	1.14
***************
*** 91,100 ****
  
  package Bio::Ontology::OntologyStore;
- use vars qw(@ISA);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::Root::Root;
  use Bio::Ontology::DocumentRegistry;
  use Bio::OntologyIO;
--- 91,98 ----
***************
*** 103,107 ****
  
  
! @ISA = qw(Bio::Root::Root);
  
  # these are the static ontology stores by name and by identifier - there is
--- 101,105 ----
  
  
! use base qw(Bio::Root::Root);
  
  # these are the static ontology stores by name and by identifier - there is

Index: SimpleOntologyEngine.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/SimpleOntologyEngine.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** SimpleOntologyEngine.pm	21 Aug 2006 11:21:14 -0000	1.18
--- SimpleOntologyEngine.pm	26 Sep 2006 22:03:10 -0000	1.19
***************
*** 71,83 ****
  
  package Bio::Ontology::SimpleOntologyEngine;
- use vars qw(@ISA);
  use strict;
  use Carp;
- use Bio::Root::Root;
  use Bio::Ontology::RelationshipFactory;
- use Bio::Ontology::OntologyEngineI;
  use Data::Dumper;
  
! @ISA = qw( Bio::Root::Root Bio::Ontology::OntologyEngineI );
  
  =head2 new
--- 71,80 ----
  
  package Bio::Ontology::SimpleOntologyEngine;
  use strict;
  use Carp;
  use Bio::Ontology::RelationshipFactory;
  use Data::Dumper;
  
! use base qw(Bio::Root::Root Bio::Ontology::OntologyEngineI);
  
  =head2 new

Index: InterProTerm.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/InterProTerm.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** InterProTerm.pm	20 Sep 2006 19:08:59 -0000	1.11
--- InterProTerm.pm	26 Sep 2006 22:03:10 -0000	1.12
***************
*** 81,93 ****
  
  package Bio::Ontology::InterProTerm;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Ontology::Term;
  use Bio::Annotation::Reference;
  
  use constant INTERPRO_ID_DEFAULT => "IPR000000";
  
! @ISA = qw( Bio::Ontology::Term );
  
  =head2 new
--- 81,91 ----
  
  package Bio::Ontology::InterProTerm;
  use strict;
  
  use Bio::Annotation::Reference;
  
  use constant INTERPRO_ID_DEFAULT => "IPR000000";
  
! use base qw(Bio::Ontology::Term);
  
  =head2 new

Index: Ontology.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/Ontology.pm,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** Ontology.pm	21 Aug 2006 11:21:14 -0000	1.20
--- Ontology.pm	26 Sep 2006 22:03:10 -0000	1.21
***************
*** 102,116 ****
  
  package Bio::Ontology::Ontology;
- use vars qw(@ISA);
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
- use Bio::Root::Root;
- use Bio::Ontology::OntologyI;
- use Bio::AnnotatableI;
  #use Bio::Ontology::SimpleOntologyEngine; # loaded dynamically now!
  
! @ISA = qw(Bio::Root::Root Bio::Ontology::OntologyI Bio::AnnotatableI);
  
  =head2 new
--- 102,112 ----
  
  package Bio::Ontology::Ontology;
  use strict;
  
  # Object preamble - inherits from Bio::Root::Root
  
  #use Bio::Ontology::SimpleOntologyEngine; # loaded dynamically now!
  
! use base qw(Bio::Root::Root Bio::Ontology::OntologyI Bio::AnnotatableI);
  
  =head2 new

Index: SimpleGOEngine.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/SimpleGOEngine.pm,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** SimpleGOEngine.pm	20 Sep 2006 19:08:59 -0000	1.37
--- SimpleGOEngine.pm	26 Sep 2006 22:03:10 -0000	1.38
***************
*** 92,99 ****
  
  use strict;
- use vars qw( @ISA );
- use Bio::Ontology::OBOEngine;
  
! @ISA = qw( Bio::Ontology::OBOEngine );
  
  
--- 92,97 ----
  
  use strict;
  
! use base qw(Bio::Ontology::OBOEngine);
  
  

Index: TermFactory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/TermFactory.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** TermFactory.pm	4 Jul 2006 22:23:18 -0000	1.7
--- TermFactory.pm	26 Sep 2006 22:03:10 -0000	1.8
***************
*** 82,92 ****
  
  package Bio::Ontology::TermFactory;
- use vars qw(@ISA);
  use strict;
  
  use Bio::Root::Root;
- use Bio::Factory::ObjectFactory;
  
! @ISA = qw(Bio::Factory::ObjectFactory);
  
  =head2 new
--- 82,90 ----
  
  package Bio::Ontology::TermFactory;
  use strict;
  
  use Bio::Root::Root;
  
! use base qw(Bio::Factory::ObjectFactory);
  
  =head2 new

Index: Path.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/Path.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** Path.pm	20 Sep 2006 19:08:59 -0000	1.8
--- Path.pm	26 Sep 2006 22:03:10 -0000	1.9
***************
*** 75,85 ****
  
  package Bio::Ontology::Path;
- use vars qw( @ISA );
  use strict;
- use Bio::Ontology::PathI;
- use Bio::Ontology::Relationship;
  
! @ISA = qw( Bio::Ontology::Relationship
!            Bio::Ontology::PathI );
  
  
--- 75,81 ----
  
  package Bio::Ontology::Path;
  use strict;
  
! use base qw(Bio::Ontology::Relationship Bio::Ontology::PathI);
  
  

Index: RelationshipType.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/RelationshipType.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** RelationshipType.pm	20 Sep 2006 19:08:59 -0000	1.18
--- RelationshipType.pm	26 Sep 2006 22:03:10 -0000	1.19
***************
*** 82,88 ****
  
  package Bio::Ontology::RelationshipType;
- use vars qw( @ISA );
  use strict;
- use Bio::Ontology::Term;
  
  
--- 82,86 ----
***************
*** 94,98 ****
  
  
! @ISA = qw( Bio::Ontology::Term );
  
  
--- 92,96 ----
  
  
! use base qw(Bio::Ontology::Term);
  
  

Index: OntologyI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Ontology/OntologyI.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** OntologyI.pm	4 Jul 2006 22:23:18 -0000	1.9
--- OntologyI.pm	26 Sep 2006 22:03:10 -0000	1.10
***************
*** 80,89 ****
  
  package Bio::Ontology::OntologyI;
- use vars qw(@ISA);
  use strict;
  
- use Bio::Ontology::OntologyEngineI;
  
! @ISA = qw( Bio::Ontology::OntologyEngineI );
  
  =head1  Methods defined in this interface.
--- 80,87 ----
  
  package Bio::Ontology::OntologyI;
  use strict;
  
  
! use base qw(Bio::Ontology::OntologyEngineI);
  
  =head1  Methods defined in this interface.



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