Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Browse files

* updated for BioRuby 0.6.0 release

  • Loading branch information...
commit d568d6ce1999a4b2ccdaba307cde19438588dacf 1 parent 5183726
@ktym ktym authored
Showing with 64 additions and 1 deletion.
  1. +64 −1 ChangeLog
View
65 ChangeLog
@@ -1,3 +1,66 @@
+2004-08-24 KATAYAMA Toshiaki <k@bioruby.org>
+
+ * BioRuby 0.6.0 released.
+ * many fixes for Ruby 1.8
+ * updated for genome.ad.jp -> genome.jp transition
+
+ * lib/bio/db/pdb.rb
+
+ Newly added parser for PDB contributed by Alex Gutteridge (EBI).
+
+ * lib/bio/data/codontable.rb
+
+ Bio::CodonTable is rewrited to be a class instead of static variable.
+ Now it can hold table definition, start codons, stop codons and
+ added methods to detect start/stop codons and reverse translation.
+
+ Also includes sample code to show codon table in ANSI colored
+ ascii art, have fun.
+
+ * lib/bio/sequence.rb
+
+ Bio::Sequence::NA#translate is rewrited to accept an user defined
+ codon table as a Bio::CodonTable object and any character can be
+ specified for the unknown codon. This method runs about 30% faster
+ than ever before.
+
+ Bio::Sequence::AA#to_re method is added for the symmetry.
+
+ Bio::Seq will be changed to hold generic rich sequence features.
+ This means Bio::Seq is no longer an alias of Bio::Sequence but
+ is a sequence object model, something like contents of a GenBank
+ entry, common in BioPerl, BioJava etc.
+
+ * lib/bio/io/soapwsdl.rb
+
+ Newly added common interface for SOAP/WSDL in BioRuby
+ used by keggapi.rb, ddbjxml.rb.
+
+ * lib/bio/io/keggapi.rb
+
+ Completely rewrited to support KEGG API v3.0
+
+ * lib/bio/io/esoap.rb
+
+ Newly added client library for Entrez Utilities SOAP interface.
+
+ * lib/bio/db/genbank, lib/bio/db/embl
+
+ Refactored to use common.rb as a common module.
+
+ * bin/pmfetch.rb
+
+ Newly added command to search PubMed.
+
+ * bin/biofetch.rb, flatfile.rb, biogetseq.rb
+
+ Renamed to have .rb suffix.
+
+ * sample/biofetch.rb
+
+ Rewrited to use KEGG API instead of DBGET
+
+
2003-10-13 KATAYAMA Toshiaki <k@bioruby.org>
* BioRuby 0.5.3 released.
@@ -26,7 +89,7 @@
Fixed to be loaded in Ruby 1.8.0 without warnings.
- * doc/KEGG_API.rd.ja:
+ * doc/KEGG_API.rd.ja
Newly added a Japanese document on the KEGG API.
Please sign in to comment.
Something went wrong with that request. Please try again.