[BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.10,1.11

[Naohisa Goto]

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

Modified Files:
	Changes-0.7.rd 
Log Message:
* added changelogs for Bio::Alignment
* added "to be written..." to changelogs of Bio::PDB


Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Changes-0.7.rd	18 Dec 2005 18:20:34 -0000	1.10
--- Changes-0.7.rd	18 Dec 2005 18:44:26 -0000	1.11
***************
*** 165,168 ****
--- 165,186 ----
  * Bio::GFF3 is renamed to Bio::GFF::GFF3
  
+ --- Bio::Alignment
+ 
+ * 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...
+ 
  --- Bio::PDB
  
***************
*** 182,185 ****
--- 200,204 ----
    Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
    Bio::PDB::DataType.
+ * There are more and more changes to be written...
  
  === Deleted files