[BioRuby-cvs] bioruby ChangeLog,1.83,1.83.2.1

[Jan Aerts]

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv15755

Modified Files:
      Tag: BRANCH-biohackathon2008
	ChangeLog 
Log Message:
* Rewrote some of the code for converting EMBL files into Bio::Sequence.
* Added functionality to export Bio::Sequence to EMBL format.

Changes:
* renamed Sequence::Format#wrap and #fold to String#wrap and #fold (stored in bio.rb)
* lib/bio/db/common.rb:
    - rewrote def ref and def references
    - added to_biosequence
    - def references now returns an Array instead of a Bio::References object (tests changed accordingly)
* lib/bio/db/embl/embl.rb
    - def ft now returns Array instead of Bio::Features object (tests changed accordingly)
* lib/bio/db/embl/format.erb
* lib/bio/sequence/common.rb
    - added def format_embl


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.83
retrieving revision 1.83.2.1
diff -C2 -d -r1.83 -r1.83.2.1
*** ChangeLog	12 Feb 2008 05:32:23 -0000	1.83
--- ChangeLog	20 Feb 2008 09:56:21 -0000	1.83.2.1
***************
*** 1,2 ****
--- 1,27 ----
+ 2008-02-20  Jan Aerts <jandot at bioruby.org>
+         * lib/bio/db/fasta.rb
+         * lib/bio/db/fasta/format.erb
+         * test/unit/bio/db/test_fasta.rb
+ 
+           Renamed #to_seq to #to_biosequence to reflect that same method in
+           embl.rb, genbank.rb and others.
+ 
+ 2008-02-20  Jan Aerts <jandot at bioruby.org>
+         * lib/bio.rb
+         * lib/bio/db/embl/common.rb
+         * lib/bio/db/embl/embl.rb
+         * lib/bio/db/embl/format.erb
+         * lib/bio/sequence/common.rb
+         * lib/bio/sequence/format.rb
+         * test/unit/bio/db/embl/test_embl_to_bioseq.rb
+ 
+         Fixed some bugs in importing EMBL files and added functionality to
+         export a Bio::Sequence to EMBL format.
+ 
+ 2008-02-18  Jan Aerts <jandot at bioruby.org>
+         * lib/bio/reference.rb
+ 
+           Added export method to EMBL format.
+ 
  2008-02-12  Naohisa Goto <ng at bioruby.org>