[BioRuby-cvs] bioruby ChangeLog,1.32,1.33

Tue Aug 9 07:38:40 EDT 2005

Update of /home/repository/bioruby/bioruby
In directory pub.open-bio.org:/tmp/cvs-serv2232

Modified Files:
	ChangeLog 
Log Message:
* prepared for 0.6.3 release

Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** ChangeLog	9 Aug 2005 11:19:15 -0000	1.32
--- ChangeLog	9 Aug 2005 11:38:37 -0000	1.33
***************
*** 1,4 ****
--- 1,9 ----
  2005-08-09  Toshiaki Katayama <k at bioruby.org>

+ 	* BioRuby 0.6.3 is released.
+ 
+ 	  This version would be the final release to support Ruby 1.6 series
+ 	  (as long as no serious bug is found:).
+ 
  	* lib/bio/util/sirna.rb:

***************
*** 12,15 ****
--- 17,25 ----
  	  Shinji Shigenobu.

+ 	* lib/bio/appl/hmmer/report.rb:
+ 
+ 	  Bug fixed by Masashi Fujita when the position of sequence
+ 	  rarely becomes '-' instead of digits.
+ 
  2005-08-08  Mitsuteru Nakao <n at bioruby.org>

***************
*** 38,66 ****
  	  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

  2005-07-11  Toshiaki Katayama <k at bioruby.org>

! 	* bin/br_pmfetch.rb
! 	  * added sort by page option (--sort page)

! 	* lib/io/higet.rb

  	  Newly added Bio::HGC::HiGet class for HiGet SOAP service.
--- 48,78 ----
  	  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 class methods.

! 	  Bio::Sequence::NA and AA classes are rewrited (molecular_weight,
! 	  to_re methods) to use Bio::NucleicAcid.

  	  Bio::Sequence::NA#molecular_weight method is fixed to subtract
! 	  two hydrogens per each base.

! 	* lib/bio/db/medline.rb: publication_type (pt) method is 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

  2005-07-11  Toshiaki Katayama <k at bioruby.org>

! 	* bin/br_pmfetch.rb:

! 	  Added sort by page option (--sort page)
! 
! 	* lib/io/higet.rb:

  	  Newly added Bio::HGC::HiGet class for HiGet SOAP service.
***************
*** 72,76 ****
  2005-06-21  Naohisa Goto <ng at bioruby.org>

! 	* lib/bio/appl/blast/report.rb

  	  Newly added support for reading BLAST -m 7 result files
--- 84,88 ----
  2005-06-21  Naohisa Goto <ng at bioruby.org>

! 	* lib/bio/appl/blast/report.rb:

  	  Newly added support for reading BLAST -m 7 result files
***************
*** 80,84 ****
  	  supported by Bio::FlatFile)

! 	* lib/bio/io/flatfile.rb

  	  Added file format autodetection of BLAST XML format.
--- 92,96 ----
  	  supported by Bio::FlatFile)

! 	* lib/bio/io/flatfile.rb:

  	  Added file format autodetection of BLAST XML format.
***************
*** 90,94 ****
  2005-04-04  Mitsuteru Nakao <n at bioruby.org>

!         * lib/bio/db/go.rb

            Newly added Bio::GO::External2go class for parsing external2go file.
--- 102,106 ----
  2005-04-04  Mitsuteru Nakao <n at bioruby.org>

!         * lib/bio/db/go.rb:

            Newly added Bio::GO::External2go class for parsing external2go file.
***************
*** 96,100 ****
  2005-03-10  Naohisa Goto <ng at bioruby.org>

! 	* lib/bio/io/flatfile.rb

  	  Added file format autodetection of Spidey (Bio::Spidey::Report).
--- 108,112 ----
  2005-03-10  Naohisa Goto <ng at bioruby.org>

! 	* lib/bio/io/flatfile.rb:

  	  Added file format autodetection of Spidey (Bio::Spidey::Report).
***************
*** 102,106 ****
  2005-03-10  Naohisa Goto <ng at bioruby.org>

! 	* lib/bio/io/flatfile.rb

  	  Added file format autodetection for Bio::KEGG::KO,
--- 114,118 ----
  2005-03-10  Naohisa Goto <ng at bioruby.org>

! 	* lib/bio/io/flatfile.rb:

  	  Added file format autodetection for Bio::KEGG::KO,
***************
*** 114,118 ****
  2005-02-09  KATAYAMA Toshiaki <k at bioruby.org>

! 	* lib/bio/db/kegg/genes.rb

  	  Added cu method which returns codon usage in Hash for the
--- 126,130 ----
  2005-02-09  KATAYAMA Toshiaki <k at bioruby.org>

! 	* lib/bio/db/kegg/genes.rb:

  	  Added cu method which returns codon usage in Hash for the
***************
*** 123,136 ****
  	* BioRuby 0.6.2 released.

! 	* test/all_tests.rb

  	  Unit tests for some classes are newly incorporated by
  	  Moses Hohman.  You can try it by 'ruby install.rb test'

! 	* lib/bio/appl/spidey/report.rb

  	  Newly added Spidey result parser class.

! 	* lib/bio/appl/blat/report.rb

  	  Newly added BLAT result parser class.
--- 135,148 ----
  	* BioRuby 0.6.2 released.

! 	* test/all_tests.rb:

  	  Unit tests for some classes are newly incorporated by
  	  Moses Hohman.  You can try it by 'ruby install.rb test'

! 	* lib/bio/appl/spidey/report.rb:

  	  Newly added Spidey result parser class.

! 	* lib/bio/appl/blat/report.rb:

  	  Newly added BLAT result parser class.