[Bioperl-guts-l] bioperl-live/Bio IdentifiableI.pm,1.7,1.8

Brian Osborne bosborne at pub.open-bio.org
Thu Jan 5 22:08:55 EST 2006


Update of /home/repository/bioperl/bioperl-live/Bio
In directory pub.open-bio.org:/tmp/cvs-serv20318/Bio

Modified Files:
	IdentifiableI.pm 
Log Message:
Minor edits


Index: IdentifiableI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/IdentifiableI.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** IdentifiableI.pm	9 Oct 2005 14:53:06 -0000	1.7
--- IdentifiableI.pm	6 Jan 2006 03:08:53 -0000	1.8
***************
*** 1,4 ****
  # $Id$
- 
  #
  # This module is licensed under the same terms as Perl itself. You use,
--- 1,3 ----
***************
*** 12,16 ****
  =head1 SYNOPSIS
  
- 
      # to test this is an identifiable object
  
--- 11,14 ----
***************
*** 18,22 ****
        $obj->throw("$obj does not implement the Bio::IdentifiableI interface");
  
!     # accessors
  
      $object_id = $obj->object_id();
--- 16,20 ----
        $obj->throw("$obj does not implement the Bio::IdentifiableI interface");
  
!     # Accessors
  
      $object_id = $obj->object_id();
***************
*** 24,37 ****
      $authority = $obj->authority();
      $version   = $obj->version();
! 
!     # utility function
! 
!     $lsid        = $obj->lsid_string();      # gives authority:namespace:object_id
!     $ns_string   = $obj->namespace_string(); # gives namespace:object_id.version
! 
  
  =head1 DESCRIPTION
  
! This interface describes methods expected on identifiable objects, ie
  ones which have identifiers expected to make sense across a number of
  instances and/or domains. This interface is modeled after pretty much
--- 22,33 ----
      $authority = $obj->authority();
      $version   = $obj->version();
!     # Gets authority:namespace:object_id
!     $lsid = $obj->lsid_string();      
!     # Gets namespace:object_id.version
!     $ns_string = $obj->namespace_string(); 
  
  =head1 DESCRIPTION
  
! This interface describes methods expected on identifiable objects, i.e.
  ones which have identifiers expected to make sense across a number of
  instances and/or domains. This interface is modeled after pretty much
***************
*** 40,59 ****
   databasename:object_id.version
  
! examples being
  
   swissprot:P012334.2
  
! or
  
   GO:0007048
  
! We also work well with LSID proposals which adds in the concept of an
  authority, being the DNS name of the organisation assigning the namespace.
! Helper functions are provided to make useful strings being
  
  
    lsid_string - string complying to the LSID standard
    namespace_string - string complying to the usual convention of 
!      namespace:object_id.version
  
  =head1 FEEDBACK
--- 36,57 ----
   databasename:object_id.version
  
! Example:
  
   swissprot:P012334.2
  
! or:
  
   GO:0007048
  
! The object will also work with LSID proposals which adds the concept of an
  authority, being the DNS name of the organisation assigning the namespace.
! See L<http://lsid.sourceforge.net/>.
  
+ Helper functions are provided to make useful strings:
  
    lsid_string - string complying to the LSID standard
+ 
    namespace_string - string complying to the usual convention of 
!                      namespace:object_id.version
  
  =head1 FEEDBACK
***************
*** 102,106 ****
             in this namespace of this object. For DNA sequences this
             is its accession_number, similarly for protein sequences
- 
   Returns : A scalar
   Status  : Virtual
--- 100,103 ----
***************
*** 121,125 ****
             later and more relevant, but a single object described
             the same identifier should represent the same concept
- 
   Returns : A number
   Status  : Virtual
--- 118,121 ----
***************
*** 140,144 ****
             granted the namespace, written as the DNS name for  
             organisation (eg, wormbase.org)
- 
   Returns : A scalar
   Status  : Virtual
--- 136,139 ----
***************
*** 159,163 ****
             is valid in, often the database name or the name
             describing the collection 
- 
   Returns : A scalar
   Status  : Virtual
--- 154,157 ----
***************
*** 171,175 ****
  
  
- 
  =head1 Implementation optional functions
  
--- 165,168 ----
***************
*** 203,207 ****
   Function: a string which gives the common notation of
             namespace:object_id.version
- 
   Returns : A scalar
  
--- 196,199 ----



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