[Bioperl-guts-l] bioperl-live/Bio/SeqIO swiss.pm,1.94,1.95

[Brian Osborne]

Update of /home/repository/bioperl/bioperl-live/Bio/SeqIO
In directory dev.open-bio.org:/tmp/cvs-serv7369/Bio/SeqIO

Modified Files:
	swiss.pm 
Log Message:
Clean up POD a bit

Index: swiss.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/swiss.pm,v
retrieving revision 1.94
retrieving revision 1.95
diff -C2 -d -r1.94 -r1.95
*** swiss.pm	5 Sep 2006 14:42:42 -0000	1.94
--- swiss.pm	5 Sep 2006 15:04:19 -0000	1.95
***************
*** 3,8 ****
  # BioPerl module for Bio::SeqIO::swiss
  #
- # Cared for by Elia Stupka <elia at tll.org.sg>
- #
  # Copyright Elia Stupka
  #
--- 3,6 ----
***************
*** 18,24 ****
  
  It is probably best not to use this object directly, but
! rather go through the SeqIO handler system. Go:
  
!     $stream = Bio::SeqIO->new(-file => $filename, -format => 'swiss');
  
      while ( my $seq = $stream->next_seq() ) {
--- 16,25 ----
  
  It is probably best not to use this object directly, but
! rather go through the SeqIO handler system:
  
!     use Bio::SeqIO;
! 
!     $stream = Bio::SeqIO->new(-file => $filename, 
!                               -format => 'swiss');
  
      while ( my $seq = $stream->next_seq() ) {
***************
*** 28,36 ****
  =head1 DESCRIPTION
  
! This object can transform Bio::Seq objects to and from swissprot flat
  file databases.
  
! There is a lot of flexibility here about how to dump things which I need
! to document fully.
  
  
--- 29,37 ----
  =head1 DESCRIPTION
  
! This object can transform Bio::Seq objects to and from Swissprot flat
  file databases.
  
! There is a lot of flexibility here about how to dump things which needs
! to be documented.
  
  
***************
*** 57,61 ****
  line using a number of tools.
  
! If you want to output annotations in swissprot format they need to be
  stored in a Bio::Annotation::Collection object which is accessible
  through the Bio::SeqI interface method L<annotation()|annotation>.  
--- 58,62 ----
  line using a number of tools.
  
! If you want to output annotations in Swissprot format they need to be
  stored in a Bio::Annotation::Collection object which is accessible
  through the Bio::SeqI interface method L<annotation()|annotation>.  
***************
*** 64,71 ****
  L<Bio::Annotation::Collection> object.
  
!  reference       - Should contain Bio::Annotation::Reference objects
!  comment         - Should contain Bio::Annotation::Comment objects
!  dblink          - Should contain Bio::Annotation::DBLink objects
!  gene_name       - Should contain Bio::Annotation::SimpleValue object
  
  =back
--- 65,72 ----
  L<Bio::Annotation::Collection> object.
  
!  reference   - Should contain Bio::Annotation::Reference objects
!  comment     - Should contain Bio::Annotation::Comment objects
!  dblink      - Should contain Bio::Annotation::DBLink objects
!  gene_name   - Should contain Bio::Annotation::SimpleValue object
  
  =back
***************
*** 76,81 ****
  
  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.
  
--- 77,82 ----
  
  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.
  
***************
*** 86,91 ****
  
  Report bugs to the Bioperl bug tracking system to help us keep track
!  the bugs and their resolution.
!  Bug reports can be submitted via the web:
  
    http://bugzilla.open-bio.org/
--- 87,92 ----
  
  Report bugs to the Bioperl bug tracking system to help us keep track
! the bugs and their resolution.
! Bug reports can be submitted via the web:
  
    http://bugzilla.open-bio.org/
***************
*** 99,110 ****
  =head1 APPENDIX
  
! The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
  
  =cut
  
- 
  # Let the code begin...
  
- 
  package Bio::SeqIO::swiss;
  use vars qw(@ISA @Unknown_names @Unknown_genus);
--- 100,110 ----
  =head1 APPENDIX
  
! The rest of the documentation details each of the object methods. 
! Internal methods are usually preceded with a _
  
  =cut
  
  # Let the code begin...
  
  package Bio::SeqIO::swiss;
  use vars qw(@ISA @Unknown_names @Unknown_genus);
***************
*** 127,135 ****
  # this is for doing species name parsing
  @Unknown_names=('other', 'unidentified',
! 		'unknown organism', 'not specified', 
! 		'not shown', 'Unspecified', 'Unknown', 
! 		'None', 'unclassified', 'unidentified organism', 
! 		'not supplied'
! 	       );
  # dictionary of synonyms for taxid 32644
  # all above can be part of valid species name
--- 127,135 ----
  # this is for doing species name parsing
  @Unknown_names=('other', 'unidentified',
! 					 'unknown organism', 'not specified', 
! 					 'not shown', 'Unspecified', 'Unknown', 
! 					 'None', 'unclassified', 'unidentified organism', 
! 					 'not supplied'
! 					);
  # dictionary of synonyms for taxid 32644
  # all above can be part of valid species name
***************
*** 158,162 ****
   Args    :
  
- 
  =cut
  
--- 158,161 ----
***************
*** 929,935 ****
   Function: Reads the swissprot Organism species and classification
             lines.
! 		   Able to deal with unconventional species names.
   Example : OS Unknown prokaryotic organism
!  		   $genus = undef ; $species = Unknown prokaryotic organism
   Returns : A Bio::Species object
   Args    :
--- 928,934 ----
   Function: Reads the swissprot Organism species and classification
             lines.
! 		     Able to deal with unconventional species names.
   Example : OS Unknown prokaryotic organism
!  		     $genus = undef ; $species = Unknown prokaryotic organism
   Returns : A Bio::Species object
   Args    :