[Bioperl-guts-l] bioperl-live/Bio/Structure Atom.pm, 1.12, 1.12.4.1 Chain.pm, 1.11, 1.11.4.1 Entry.pm, 1.27, 1.27.4.1 IO.pm, 1.12, 1.12.4.1 Model.pm, 1.10, 1.10.4.1 Residue.pm, 1.11, 1.11.4.1 StructureI.pm, 1.7, 1.7.4.1

Mon Oct 2 19:10:33 EDT 2006

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

Modified Files:
      Tag: branch-1-5-2
	Atom.pm Chain.pm Entry.pm IO.pm Model.pm Residue.pm 
	StructureI.pm 
Log Message:
merge from HEAD

Index: Residue.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Structure/Residue.pm,v
retrieving revision 1.11
retrieving revision 1.11.4.1
diff -C2 -d -r1.11 -r1.11.4.1
*** Residue.pm	4 Jul 2006 22:23:23 -0000	1.11
--- Residue.pm	2 Oct 2006 23:10:31 -0000	1.11.4.1
***************
*** 56,66 ****

  package Bio::Structure::Residue;
- use vars qw(@ISA);
  use strict;

- use Bio::Root::Root;
  use Bio::Structure::Chain;
  use Bio::Structure::Atom;
! @ISA = qw(Bio::Root::Root);

--- 56,64 ----

  package Bio::Structure::Residue;
  use strict;

  use Bio::Structure::Chain;
  use Bio::Structure::Atom;
! use base qw(Bio::Root::Root);

Index: Chain.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Structure/Chain.pm,v
retrieving revision 1.11
retrieving revision 1.11.4.1
diff -C2 -d -r1.11 -r1.11.4.1
*** Chain.pm	27 Jul 2006 22:39:37 -0000	1.11
--- Chain.pm	2 Oct 2006 23:10:31 -0000	1.11.4.1
***************
*** 56,66 ****

  package Bio::Structure::Chain;
- use vars qw(@ISA);
  use strict;

- use Bio::Root::Root;
  use Bio::Structure::Entry;
  use Bio::Structure::Model;
! @ISA = qw(Bio::Root::Root);

--- 56,64 ----

  package Bio::Structure::Chain;
  use strict;

  use Bio::Structure::Entry;
  use Bio::Structure::Model;
! use base qw(Bio::Root::Root);

Index: Atom.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Structure/Atom.pm,v
retrieving revision 1.12
retrieving revision 1.12.4.1
diff -C2 -d -r1.12 -r1.12.4.1
*** Atom.pm	4 Jul 2006 22:23:23 -0000	1.12
--- Atom.pm	2 Oct 2006 23:10:31 -0000	1.12.4.1
***************
*** 55,64 ****

  package Bio::Structure::Atom;
- use vars qw(@ISA);
  use strict;

- use Bio::Root::Root;
  use Bio::Structure::Residue;
! @ISA = qw(Bio::Root::Root);

--- 55,62 ----

  package Bio::Structure::Atom;
  use strict;

  use Bio::Structure::Residue;
! use base qw(Bio::Root::Root);

Index: IO.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Structure/IO.pm,v
retrieving revision 1.12
retrieving revision 1.12.4.1
diff -C2 -d -r1.12 -r1.12.4.1
*** IO.pm	27 Jul 2006 16:23:50 -0000	1.12
--- IO.pm	2 Oct 2006 23:10:31 -0000	1.12.4.1
***************
*** 149,153 ****
    @structures = <$fh>;

! Other operations, such as read(), sysread(), write(), close(), and printf() 
  are not supported.

--- 149,153 ----
    @structures = <$fh>;

! Other operations, such as read(), sysread(), write(), close(), and printf()
  are not supported.

***************
*** 172,179 ****
  =head2 Mailing Lists

! User feedback is an integral part of the evolution of this
! and other Bioperl modules. Send your comments and suggestions preferably
!  to one of the Bioperl mailing lists.
! Your participation is much appreciated.

    bioperl-l at bioperl.org                  - General discussion
--- 172,178 ----
  =head2 Mailing Lists

! User feedback is an integral part of the evolution of this and other
! Bioperl modules. Send your comments and suggestions preferably to one
! of the Bioperl mailing lists.  Your participation is much appreciated.

    bioperl-l at bioperl.org                  - General discussion
***************
*** 188,196 ****
    http://bugzilla.open-bio.org/

! =head1 AUTHOR - Ewan Birney, Lincoln Stein, Kris Boulez

! Email birney at ebi.ac.uk, kris.boulez at algonomics.com

- Describe contact details here

  =head1 APPENDIX
--- 187,194 ----
    http://bugzilla.open-bio.org/

! =head1 AUTHORS - Ewan Birney, Lincoln Stein, Kris Boulez

! Email birney at ebi.ac.uk, lstein at cshl.org, kris.boulez at algonomics.com

  =head1 APPENDIX
***************
*** 206,217 ****

  use strict;
- use vars qw(@ISA);

- use Bio::Root::Root;
- use Bio::Root::IO;
  use Bio::PrimarySeq;
  use Symbol();

! @ISA = qw(Bio::Root::Root Bio::Root::IO);

  =head2 new
--- 204,212 ----

  use strict;

  use Bio::PrimarySeq;
  use Symbol();

! use base qw(Bio::Root::Root Bio::Root::IO);

  =head2 new
***************
*** 232,247 ****
      my ($caller, at args) = @_;
      my $class = ref($caller) || $caller;
!     
      # or do we want to call SUPER on an object if $caller is an
      # object?
      if( $class =~ /Bio::Structure::IO::(\S+)/ ) {
! 	my ($self) = $class->SUPER::new(@args);	
  	$self->_initialize(@args);
  	return $self;
!     } else { 

  	my %param = @args;
  	@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
! 	my $format = $param{'-format'} || 
  	    $class->_guess_format( $param{-file} || $ARGV[0] ) ||
  		'pdb';
--- 227,242 ----
      my ($caller, at args) = @_;
      my $class = ref($caller) || $caller;
! 
      # or do we want to call SUPER on an object if $caller is an
      # object?
      if( $class =~ /Bio::Structure::IO::(\S+)/ ) {
! 	my ($self) = $class->SUPER::new(@args);
  	$self->_initialize(@args);
  	return $self;
!     } else {

  	my %param = @args;
  	@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
! 	my $format = $param{'-format'} ||
  	    $class->_guess_format( $param{-file} || $ARGV[0] ) ||
  		'pdb';
***************
*** 300,307 ****
  sub _initialize {
      my($self, @args) = @_;
!     
      # not really necessary unless we put more in RootI
      $self->SUPER::_initialize(@args);
!     
      # initialize the IO part
      $self->_initialize_io(@args);
--- 295,302 ----
  sub _initialize {
      my($self, @args) = @_;
! 
      # not really necessary unless we put more in RootI
      $self->SUPER::_initialize(@args);
! 
      # initialize the IO part
      $self->_initialize_io(@args);
***************
*** 336,340 ****

  # Do we want people to read out the sequence directly from a $structIO stream
! # 
  ##=head2 next_primary_seq
  ##
--- 331,335 ----

  # Do we want people to read out the sequence directly from a $structIO stream
! #
  ##=head2 next_primary_seq
  ##
***************
*** 432,437 ****
  $load: $format cannot be found
  Exception $@
! For more information about the Structure::IO system please see the 
! Bio::Structure::IO docs.  This includes ways of checking for formats at 
  compile time, not run time
  END
--- 427,432 ----
  $load: $format cannot be found
  Exception $@
! For more information about the Structure::IO system please see the
! Bio::Structure::IO docs.  This includes ways of checking for formats at
  compile time, not run time
  END

Index: StructureI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Structure/StructureI.pm,v
retrieving revision 1.7
retrieving revision 1.7.4.1
diff -C2 -d -r1.7 -r1.7.4.1
*** StructureI.pm	27 Jul 2006 13:14:23 -0000	1.7
--- StructureI.pm	2 Oct 2006 23:10:31 -0000	1.7.4.1
***************
*** 46,55 ****
  Email kris.boulez at algonomics.com

- Describe contact details here
- 
- =head1 CONTRIBUTORS
- 
- Additional contributors names and emails here
- 
  =head1 APPENDIX

--- 46,49 ----
***************
*** 64,72 ****

  package Bio::Structure::StructureI;
- use Bio::Root::RootI;
- use vars qw(@ISA);
  use strict;

! @ISA = qw(Bio::Root::RootI);

  1;
--- 58,64 ----

  package Bio::Structure::StructureI;
  use strict;

! use base qw(Bio::Root::RootI);

  1;

Index: Model.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Structure/Model.pm,v
retrieving revision 1.10
retrieving revision 1.10.4.1
diff -C2 -d -r1.10 -r1.10.4.1
*** Model.pm	4 Jul 2006 22:23:23 -0000	1.10
--- Model.pm	2 Oct 2006 23:10:31 -0000	1.10.4.1
***************
*** 55,65 ****

  package Bio::Structure::Model;
- use vars qw(@ISA);
  use strict;

- use Bio::Root::Root;
  use Bio::Structure::Entry;
  use Bio::Structure::Chain;
! @ISA = qw(Bio::Root::Root);

--- 55,63 ----

  package Bio::Structure::Model;
  use strict;

  use Bio::Structure::Entry;
  use Bio::Structure::Chain;
! use base qw(Bio::Root::Root);

Index: Entry.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Structure/Entry.pm,v
retrieving revision 1.27
retrieving revision 1.27.4.1
diff -C2 -d -r1.27 -r1.27.4.1
*** Entry.pm	27 Jul 2006 13:52:29 -0000	1.27
--- Entry.pm	2 Oct 2006 23:10:31 -0000	1.27.4.1
***************
*** 61,69 ****

  package Bio::Structure::Entry;
- use vars qw(@ISA);
  use strict;

- use Bio::Root::Root;
- use Bio::Structure::StructureI;
  use Bio::Structure::Model;
  use Bio::Structure::Chain;
--- 61,66 ----
***************
*** 71,75 ****
  use Tie::RefHash;

! @ISA = qw(Bio::Root::Root Bio::Structure::StructureI);

  =head2 new()
--- 68,72 ----
  use Tie::RefHash;

! use base qw(Bio::Root::Root Bio::Structure::StructureI);

  =head2 new()