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Aug 26, 2011

  1. Naohisa Goto

    BioRuby 1.4.2 is released.

    authored August 26, 2011
  2. Naohisa Goto

    Preparation for bioruby-1.4.2 release.

    authored August 26, 2011
  3. Naohisa Goto

    updated bioruby.gemspec

    authored August 26, 2011
  4. Naohisa Goto

    Added PLUGIN section to README.rdoc, and some changes made.

    authored August 26, 2011
  5. Naohisa Goto

    updated doc/Tutorial.rd.html

    authored August 26, 2011
  6. Naohisa Goto

    Removed sections contain obsolete (404 Not Found) URL in Tutorial.rd.

    authored August 26, 2011
  7. Michael O'Keefe

    Updated tutorial

     * Updated tutorial
       (original commit id: 7b91086
        and some preceding commits)
    authored August 23, 2011 ngoto committed August 26, 2011
  8. Naohisa Goto

    fix typo and change order of lines

    authored August 26, 2011
  9. Naohisa Goto

    RELEASE_NOTE.rdoc modified to reflect recent changes

    authored August 26, 2011
  10. Naohisa Goto

    In BioRuby Shell, getent() fails when EMBOSS seqret does not found.

    authored August 26, 2011
  11. Naohisa Goto

    New methods Bio::NCBI::REST::EFetch.nucleotide and protein

     * New methods Bio::NCBI::REST::EFetch.nucleotide and protein,
       to get data from "nucleotide" and "protein" database respectively.
       Because NCBI changed not to accept "gb" format for the database
       "sequence", the two new methods are added for convenience.
     * In BioRuby Shell, efetch method uses the above new methods.
    authored August 26, 2011

Aug 25, 2011

  1. Naohisa Goto

    New method Bio::Fastq#to_s

     * New method Bio::Fastq#to_s.
       Thanks to Tomoaki NISHIYAMA who wrote a patch.
       (#37)
    authored August 25, 2011
  2. Naohisa Goto

    RELEASE_NOTES.rdoc changed to reflect recent changes.

    authored August 25, 2011
  3. Naohisa Goto

    A test connecting to DDBJ BLAST web service is enabled.

    authored August 25, 2011
  4. Naohisa Goto

    Bio::DDBJ::REST::*. new classes for DDBJ REST web services.

     * Bio::DDBJ::REST::*: new classes for DDBJ REST web services (WABI).
       Currently not all services are covered. (lib/bio/io/ddbjrest.rb)
     * autoload of the above (lib/bio/db/genbank/ddbj.rb, lib/bio.rb)
     * Tests for the above (but still incomplete)
       (test/functional/bio/io/test_ddbjrest.rb)
     * Remote BLAST using DDBJ server now uses REST interface instead
       of SOAP, for Ruby 1.9.x support.
       (lib/bio/appl/blast/ddbj.rb)
    authored August 25, 2011

Aug 17, 2011

  1. Naohisa Goto

    In Fastq formatter, default width value changed to nil

     * In Bio::Sequence#output(:fastq) (Fastq output formatter),
       default width value is changed from 70 to nil, which means
       "without wrapping".  close [Feature #3191]
       (https://redmine.open-bio.org/issues/3191)
    authored August 18, 2011
  2. Naohisa Goto

    Bug fix: Bio::SPTR follow-up of UniProtKB format changes

     * Bug fix: Bio::SPTR follow-up of UniProtKB format changes.
     * Tests are added about the fix.
     * Bug fix: Bio::SPTR#cc_web_resource should be private.
     * Incompatible changes in Bio::SPTR#cc("WEB RESOURCE") is
       documented in RELEASE_NOTES.rdoc.
     * KNOWN_ISSUES.rdoc: description about incompleteness of the fix.
     * Thanks to Nicholas Letourneau who reports the issue.
       (#36)
    authored August 17, 2011

Aug 12, 2011

  1. Naohisa Goto

    preparation for release: alpha test version 1.4.2-alpha1

    authored August 13, 2011
  2. Naohisa Goto

    Test bug fix: use sort command in PATH

     * Test bug fix: FuncTestCommandQuery: use sort command in PATH.
       Thanks to Tomoaki Nishiyama who reports the issue.
       (#13)
    authored August 12, 2011
  3. Naohisa Goto

    RELEASE_NOTES.rdoc is updated following recent changes.

    authored August 12, 2011
  4. Naohisa Goto

    README.rdoc: changed required Ruby version etc.

     * README.rdoc: now Ruby 1.8.6 or later is required.
     * README.rdoc: removed old obsolete descriptions.
     * README.rdoc: modified about RubyGems.
     * KNOWN_ISSUES.rdoc: moved descriptions about older RubyGems and CVS
       from README.rdoc.
     * KNOWN_ISSUES.rdoc: modified about end-of-life Ruby versions.
    authored August 12, 2011

Jul 15, 2011

  1. Naohisa Goto

    Added topics for the release notes

    authored July 16, 2011

Jul 01, 2011

  1. Naohisa Goto

    Speedup of Bio::RestrictionEnzyme::Analysis.cut.

     * Speedup of Bio::RestrictionEnzyme::Analysis.cut. The new code
       is 50 to 80 fold faster than the previous code when cutting
       1Mbp sequence running on Ruby 1.9.2p180.
     * Thanks to Tomoaki NISHIYAMA who wrote the first version of the
       patch. Thanks to ray1729 (on GitHub) who reports the issue.
       (#10)
    authored July 02, 2011
  2. Naohisa Goto

    New classes (for internal use only) for restriction enzyme classes

     * New classes Bio::RestrictionEnzyme::SortedNumArray and
       Bio::RestrictionEnzyme::DenseIntArray. Both of them are for
       Bio::RestrictionEnzyme internal use only. They will be used
       for the speedup of restriction enzyme analysis.
    authored July 02, 2011
  3. Naohisa Goto

    A sample benchmark script for Bio::RestrictionEnzyme::Analysis.cut

    authored June 30, 2011

May 24, 2011

  1. Naohisa Goto

    Added a test for Bio::FastaFormat#entry_overrun etc.

     * Added a test for Bio::FastaFormat#entry_overrun.
     * Removed a void test class.
    authored May 24, 2011
  2. Naohisa Goto

    Bug fix: Bio::FastaFormat#query passes nil to the given factory

     * Bug fix: Bio::FastaFormat#query passes nil to the given factory
       object. Thanks to Philipp Comans who reports the bug.
       (#35)
     * Test method for Bio::FastaFormat#query is added.
    authored May 24, 2011

May 17, 2011

  1. Naohisa Goto

    Changed database name in the example.

     * Changed database name in the example.
       Thanks to Philipp Comans who reports the issue.
    authored May 17, 2011

May 12, 2011

  1. Naohisa Goto

    Bug fix: changed GenomeNet remote BLAST URL.

     * Bug fix: changed GenomeNet remote BLAST host name and path.
       Thanks to Philipp Comans who reports the bug.
       ( #34 )
    authored May 12, 2011

May 10, 2011

  1. Naohisa Goto

    updated doc/Tutorial.rd.html

    authored May 10, 2011
  2. Pjotr Prins

    Tutorial: Fixed URL and the intro

    authored May 05, 2011 ngoto committed May 10, 2011
  3. Pjotr Prins

    Tutorial: Added a commnet for rubydoctest, changed Ruby version

     * Added a comment for rubydoctest
     * Changed example Ruby version representation
     * This is part of commit ba5b9c2
       and modified to merge with the current HEAD.
    authored March 09, 2011 ngoto committed May 10, 2011

Apr 28, 2011

  1. Naohisa Goto

    updated doc/Tutorial.rd.html

    authored April 28, 2011

Apr 06, 2011

  1. Updated through the section on Homology searching with BLAST

    authored April 06, 2011

Mar 24, 2011

  1. Updated the html file generated from the RDoc

    authored March 24, 2011
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