[BioRuby-cvs] bioruby ChangeLog,1.53,1.54
Naohisa Goto
ngoto at dev.open-bio.org
Fri Oct 6 09:53:40 UTC 2006
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>
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