[BioRuby-cvs] bioruby ChangeLog,1.30,1.31

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby
In directory pub.open-bio.org:/tmp/cvs-serv1559

Modified Files:
	ChangeLog 
Log Message:
* added sirna, fastacmd


Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** ChangeLog	7 Aug 2005 16:45:58 -0000	1.30
--- ChangeLog	9 Aug 2005 09:07:03 -0000	1.31
***************
*** 1,14 ****
  2005-08-08  Naohisa Goto <ng at bioruby.org>
  
  	* lib/bio/appl/bl2seq/report.rb:
  	  Newly added bl2seq (BLAST 2 sequences) output parser.
  	* lib/bio/appl/blast/format0.rb:
  	  Added `self.class::` before F0dbstat.new for bl2seq/report.rb
  
  2005-08-07  Naohisa Goto <ng at bioruby.org>
  
  	* lib/bio/db/genbank/common.rb
! 	Avoid NoMethodError (private method `chomp` called for nil:NilClass)
! 	when parsing features of
  	    ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/
  	    Salmonella_typhimurium_LT2/AE006468.gbk
--- 1,47 ----
+ 2005-08-09  Toshiaki Katayama <k at bioruby.org>
+ 
+ 	* lib/bio/util/sirna.rb:
+ 
+ 	  Newly added method for desing of siRNA, contributed by
+ 	  Itoshi Nikaido.  The lib/bio/util/ directory if reserved
+ 	  for bioinfomatics algorithms implemented by pure Ruby.
+ 
+ 	* lib/bio/io/fastacmd.rb:
+ 
+ 	  Newly added wrapper for NCBI fastacmd program, contributed by
+ 	  Shinji Shigenobu.
+ 
  2005-08-08  Naohisa Goto <ng at bioruby.org>
  
  	* lib/bio/appl/bl2seq/report.rb:
+ 
  	  Newly added bl2seq (BLAST 2 sequences) output parser.
+ 
  	* lib/bio/appl/blast/format0.rb:
+ 
  	  Added `self.class::` before F0dbstat.new for bl2seq/report.rb
  
+ 2005-08-07  Toshiaki Katayama <k at bioruby.org>
+ 
+ 	* lib/bio/sequence.rb, lib/bio/data/na.rb, lib/bio/data/aa.rb:
+ 
+ 	  Bio::NucleicAcid, Bio::AminoAcid classes are refactored to have
+ 	  Data module, and this module is included and extended to make
+ 	  all methods as both of instance methods and extend methods.
+ 
+ 	  Bio::Sequence::NA class is rewrited (molecular_weight, to_re methods)
+ 	  to use Bio::NucleicAcid.
+ 
+ 	  Bio::Sequence::NA#molecular_weight method is fixed to subtract
+ 	  two hydrogens for each base.
+ 
+ 	* lib/bio/db/medline.rb: publication_type (pt) method added.
+ 
  2005-08-07  Naohisa Goto <ng at bioruby.org>
  
  	* lib/bio/db/genbank/common.rb
! 
! 	  Avoid NoMethodError (private method `chomp` called for nil:NilClass)
! 	  when parsing features of
  	    ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/
  	    Salmonella_typhimurium_LT2/AE006468.gbk
***************
*** 49,54 ****
          * lib/bio/db/go.rb
  
!           Newly added Bio::GO::External2go class for parsing 
!           external2go file.
  
  2005-03-10  Naohisa Goto <ng at bioruby.org>
--- 82,86 ----
          * lib/bio/db/go.rb
  
!           Newly added Bio::GO::External2go class for parsing external2go file.
  
  2005-03-10  Naohisa Goto <ng at bioruby.org>
***************
*** 61,70 ****
  
  	* lib/bio/io/flatfile.rb
! 	  * Added file format autodetection for Bio::KEGG::KO,
! 	    Bio::KEGG::GLYCAN, Bio::KEGG::REACTION, Bio::Blat::Report
! 	    and Bio::Sim4::Report.
! 	  * In order to distinguish Bio::KEGG::REACTION and 
! 	    Bio::KEGG::COMPOUND, autodetection regexp. of
! 	    Bio::KEGG::COMPOUND were modified.
  
  2005-02-09  KATAYAMA Toshiaki <k at bioruby.org>
--- 93,104 ----
  
  	* lib/bio/io/flatfile.rb
! 
! 	  Added file format autodetection for Bio::KEGG::KO,
! 	  Bio::KEGG::GLYCAN, Bio::KEGG::REACTION, Bio::Blat::Report
! 	  and Bio::Sim4::Report.
! 
! 	  In order to distinguish Bio::KEGG::REACTION and 
! 	  Bio::KEGG::COMPOUND, autodetection regexp. of
! 	  Bio::KEGG::COMPOUND were modified.
  
  2005-02-09  KATAYAMA Toshiaki <k at bioruby.org>