[BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.2,1.3

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv26493/doc

Modified Files:
	Changes-0.7.rd 
Log Message:
* kegg/microarray to kegg/expression, pathway, genbank.rb, embl.rb


Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** Changes-0.7.rd	26 Sep 2005 07:27:19 -0000	1.2
--- Changes-0.7.rd	4 Nov 2005 17:33:29 -0000	1.3
***************
*** 62,63 ****
--- 62,105 ----
  is ambiguous.
  
+ --- Bio::KEGG::Microarrays, Bio::KEGG::Microarray
+ 
+ * lib/bio/db/kegg/microarray.rb is renamed to lib/bio/db/kegg/expression.rb
+ * Bio::KEGG::Microarray is renamed to Bio::KEGG::EXPRESSION
+ * Bio::KEGG::Microarrays is removed
+ 
+ Bio::KEGG::Microarrays was intended to store a series of microarray
+ expressions as a Hash of Array -like data structure,
+ 
+   gene1 => [exp1, exp2, exp3, ... ]
+   gene2 => [exp1, exp2, exp3, ... ]
+ 
+ however, it is not utilized well and more suitable container class
+ can be proposed.  Until then, this class is removed.
+ 
+ --- Bio::Pathway
+ 
+ * Bio::Pathway#nodes returns an Array of the node objects instead of
+   the number of the node objects.
+ * Bio::Pathway#edges returns an Array of the edge objects instead of
+   the number of the edge objects.
+ 
+ === Deleted files
+ 
+ : lib/bio/db/genbank.rb
+ : lib/bio/db/embl.rb
+ 
+ These files are removed as we changed to use autoload.  You can safely
+ replace
+ 
+   require 'bio/db/genbank'
+ 
+ or
+ 
+   require 'bio/db/embl'
+ 
+ in your code to
+ 
+   require 'bio'
+ 
+ and this change will also speeds up loading time if you only need
+ one of the sub classes under the genbank/ or embl/ directory.