[BioRuby-cvs] bioruby ChangeLog,1.44,1.45

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby
In directory pub.open-bio.org:/tmp/cvs-serv30685

Modified Files:
	ChangeLog 
Log Message:
* added changelogs for Bio::Alignment
* added "to be written..." to changelogs of Bio::PDB


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.44
retrieving revision 1.45
diff -C2 -d -r1.44 -r1.45
*** ChangeLog	18 Dec 2005 18:20:34 -0000	1.44
--- ChangeLog	18 Dec 2005 18:44:25 -0000	1.45
***************
*** 15,18 ****
--- 15,19 ----
  	    Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
  	    Bio::PDB::DataType.
+ 	  * There are more and more changes to be written...
  
  	* lib/bio/db/pdb/atom.rb
***************
*** 20,23 ****
--- 21,46 ----
  	    Instead, please use Bio::PDB::Record::ATOM and
              Bio::PDB::Record::HETATM.
+ 
+ 2005-12-02  Naohisa Goto <ng:bioruby.org>
+ 
+ 	* lib/bio/alignment.rb
+ 	  * Old Bio::Alignment class is renamed to
+ 	    Bio::Alignment::OriginalAlignment.
+ 	    Now, new Bio::Alignment is a module. However,
+ 	    you don't mind so much because most of the class methods
+ 	    previously existed are defined to delegate to the new
+ 	    Bio::Alignment::OriginalAlignment class,
+             for keeping backward compatibility.
+ 	  * New classes and modules are introduced. Please refer RDoc.
+ 	  * each_site and some methods changed to return Bio::Alignment::Site,
+ 	    which inherits Array (previously returned Array).
+ 	  * consensus_iupac now returns only standard bases
+ 	    'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v',
+ 	    'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or
+ 	    '?' (or missing_char, in EnumerableExtension#consensus_iupac).
+ 	    Note that consensus_iupac now does not return u and invalid
+ 	    letters not defined in IUPAC standard even if all bases
+ 	    are equal.
+ 	  * There are more and more changes to be written...
  
  2005-11-05  Toshiaki Katayama <k at bioruby.org>