[BioRuby-cvs] bioruby ChangeLog,1.53,1.54

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby
In directory dev.open-bio.org:/tmp/cvs-serv15611

Modified Files:
	ChangeLog 
Log Message:
Added Changelog (made by N.Goto)


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.53
retrieving revision 1.54
diff -C2 -d -r1.53 -r1.54
*** ChangeLog	27 Jun 2006 05:44:57 -0000	1.53
--- ChangeLog	6 Oct 2006 09:53:38 -0000	1.54
***************
*** 1,2 ****
--- 1,38 ----
+ 2006-10-05  Naohisa Goto <ng at bioruby.org>
+ 
+ 	* lib/bio/db/newick.rb
+ 
+ 	  Bio::Newick for Newick standard phylogenetic tree parser is
+ 	  newly added (contributed by Daniel Amelang).
+ 
+         * lib/bio/phylogenetictree.rb
+ 
+ 	  Bio::PhylogeneticTree for phylogenetic tree data structure
+ 	  is newly added.
+ 
+ 2006-07-14  Naohisa Goto <ng at bioruby.org>
+ 
+         * lib/bio/command.rb
+ 
+           Bio::Command::Tools and Bio::Command::NetTools are combined
+ 	  and re-constructed into a new Bio::Command module.
+ 
+ 	  lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
+ 	  lib/bio/appl/emboss.rb, lib/bio/appl/psort.rb,
+ 	  lib/bio/appl/hmmer.rb, lib/bio/db/fantom.rb, 
+ 	  lib/bio/io/fastacmd.rb, lib/bio/io/fetch.rb,
+ 	  lib/bio/io/keggapi.rb, lib/bio/io/pubmed.rb, and
+ 	  lib/bio/io/registry.rb are changed to use the new Bio::Command
+ 	  instead of old Bio::Command or Net::HTTP.
+ 
+ 2006-06-29  Naohisa Goto <ng at bioruby.org>
+ 
+         * lib/bio/appl/blat/report.rb
+ 
+ 	  Bio::BLAT::Report::Hit#milli_bad, #percent_identity, #protein?,
+ 	  #score, and #psl_version methods/attributes are newly added,
+ 	  and psl files without headers are supported (discussed in
+ 	  bioruby-ja ML).
+ 
  2006-06-27  Naohisa Goto <ng at bioruby.org>
  
***************
*** 8,11 ****
--- 44,60 ----
  	  is empty.
  
+ 	* lib/bio/db/pdb/pdb.rb
+ 
+ 	  Bio::PDB::ATOM#name, #resName, #iCode, #chaarge, #segID, and
+ 	  #element are changed to strip whitespaces when initializing.
+ 	  Bio::PDB::HETATM is also subject to the above changes.
+ 	  (suggested by Mikael Borg)
+ 
+ 2006-06-12  Naohisa Goto <ng at bioruby.org>
+ 
+         * lib/bio/io/flatfile.rb
+ 
+ 	  Bug fix: Bio::FlatFile.open(klass, filename) didn't work.
+ 
  2006-05-02  Mitsuteru Nakao <n at bioruby.org>
  
***************
*** 14,17 ****
--- 63,74 ----
            Bio::PTS1 first commit.
  
+ 2006-04-30  Naohisa Goto <ng at bioruby.org>
+ 
+         * lib/bio/appl/blast/format0.rb
+ 
+ 	  Bug fix: parse error for hits whose database sequence names
+ 	  contain 'Score', and subsequent hits after them would lost
+ 	  (reported by Tomoaki NISHIYAMA).
+ 
  2006-04-14  Mitsuteru Nakao <n at bioruby.org>
  
***************
*** 21,24 ****
--- 78,92 ----
            Browser.
  
+ 2006-03-22  Naohisa Goto <ng at bioruby.org>
+ 
+         * lib/bio/io/flatfile.rb
+ 
+ 	  Bug fix: Bio::FlatFile raises error for pipes, ARGF, etc.
+ 	  The bug also affects bio/appl/mafft.rb, bio/appl/clustalw.rb,
+ 	  bio/appl/blast.rb, bio/io/fastacmd.rb, and so on.
+ 
+ 	  Bio::FlatFile#entry_start_pos and #entry_ended_pos are
+ 	  changed to be enabled only when Bio::FlatFile#entry_pos_flag
+ 	  is true.
  
  2006-02-27  Toshiaki Katayama <k at bioruby.org>