File: ChangeLog-before-1.4.2

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commit 510dc41f32a72b86df1aa9021de140a64e6393de
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 26 15:03:14 2011 +0900

    BioRuby 1.4.2 is released.

 ChangeLog |  954 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 954 insertions(+), 0 deletions(-)

commit 3acc1e098839cacbe85b5c23367ab14e0c4fe3ea
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 26 15:01:49 2011 +0900

    Preparation for bioruby-1.4.2 release.

 bioruby.gemspec    |    2 +-
 lib/bio/version.rb |    2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

commit bf69125192fa01ae3495e094e7ef1b5e895954ad
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 26 14:42:02 2011 +0900

    updated bioruby.gemspec

 bioruby.gemspec |    3 +++
 1 files changed, 3 insertions(+), 0 deletions(-)

commit e0a3ead917812199c6a0e495f3afa6a636bbf0c5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 26 14:39:54 2011 +0900

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

 README.rdoc |   20 +++++++++++++++++---
 1 files changed, 17 insertions(+), 3 deletions(-)

commit 1da0a1ce6eddcef8f8fc811b0a2cf8d58f880642
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 26 14:38:13 2011 +0900

    updated doc/Tutorial.rd.html

 doc/Tutorial.rd.html |   41 ++++++++++++++++++++---------------------
 1 files changed, 20 insertions(+), 21 deletions(-)

commit a8b90367b830e58b397536be3dada10cdde97aab
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 26 14:36:24 2011 +0900

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

 doc/Tutorial.rd |   12 ------------
 1 files changed, 0 insertions(+), 12 deletions(-)

commit e17546cb90a012cd1f51674ceb4c8da5dd516bdf
Author: Michael O'Keefe <okeefm@rpi.edu>
Date:   Tue Aug 23 20:15:44 2011 -0400

    Updated tutorial
    
     * Updated tutorial
       (original commit id: 7b9108657961cf2354278e04971c32059b3ed4e2
        and some preceding commits)

 doc/Tutorial.rd |   55 ++++++++++++++++++++++++++++++++-----------------------
 1 files changed, 32 insertions(+), 23 deletions(-)

commit de8a394129c752a0b9a5975a73c5eb582d9681d3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 26 13:24:27 2011 +0900

    fix typo and change order of lines

 RELEASE_NOTES.rdoc |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit 1cf2a11199655e4c9f5fc49c5a588b99c18ab7ca
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 26 13:16:11 2011 +0900

    RELEASE_NOTE.rdoc modified to reflect recent changes

 RELEASE_NOTES.rdoc |   14 ++++++++++++++
 1 files changed, 14 insertions(+), 0 deletions(-)

commit b44871a5866eeb2d379f080b39b09693c9e9e3cc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 26 13:15:14 2011 +0900

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

 lib/bio/shell/plugin/entry.rb |   10 +++++++---
 1 files changed, 7 insertions(+), 3 deletions(-)

commit 179e7506b008a220d5dd42ce1a6c7ce589c3fcda
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 26 12:26:52 2011 +0900

    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.

 lib/bio/io/ncbirest.rb           |  122 +++++++++++++++++++++++++++++++++++++-
 lib/bio/shell/plugin/ncbirest.rb |    6 ++-
 2 files changed, 126 insertions(+), 2 deletions(-)

commit 99b31379bb41c7cad34c1e7dc00f802da37de1cd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Aug 25 19:03:43 2011 +0900

    New method Bio::Fastq#to_s
    
     * New method Bio::Fastq#to_s.
       Thanks to Tomoaki NISHIYAMA who wrote a patch.
       (https://github.com/bioruby/bioruby/pull/37)

 lib/bio/db/fastq.rb            |   14 ++++++++++++++
 test/unit/bio/db/test_fastq.rb |   14 ++++++++++++++
 2 files changed, 28 insertions(+), 0 deletions(-)

commit 8ab772b37850c3874b55cf37d091046394cda5bd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Aug 25 15:23:00 2011 +0900

    RELEASE_NOTES.rdoc changed to reflect recent changes.

 RELEASE_NOTES.rdoc |   16 ++++++++++++++++
 1 files changed, 16 insertions(+), 0 deletions(-)

commit 8db6abdcc81db6a58bdd99e7f8d410b1a74496b1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Aug 25 14:28:42 2011 +0900

    A test connecting to DDBJ BLAST web service is enabled.

 test/functional/bio/appl/test_blast.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 121ad93c0c1f018ee389972ac5e5e8cc395f00d1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Aug 25 14:15:23 2011 +0900

    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)

 lib/bio.rb                              |    1 +
 lib/bio/appl/blast/ddbj.rb              |   33 +---
 lib/bio/db/genbank/ddbj.rb              |    3 +-
 lib/bio/io/ddbjrest.rb                  |  344 +++++++++++++++++++++++++++++++
 test/functional/bio/io/test_ddbjrest.rb |   47 +++++
 5 files changed, 399 insertions(+), 29 deletions(-)
 create mode 100644 lib/bio/io/ddbjrest.rb
 create mode 100644 test/functional/bio/io/test_ddbjrest.rb

commit 7e8ba7c1388204daa5245d2128d01f6f40298185
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Aug 18 00:08:51 2011 +0900

    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)

 RELEASE_NOTES.rdoc               |    8 ++++++--
 lib/bio/db/fastq/format_fastq.rb |    4 ++--
 test/unit/bio/db/test_fastq.rb   |   12 ++++++++++++
 3 files changed, 20 insertions(+), 4 deletions(-)

commit 0fb65211519febff18413c589fe7af753ee2e61d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Aug 17 22:02:03 2011 +0900

    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.
       (https://github.com/bioruby/bioruby/pull/36)

 KNOWN_ISSUES.rdoc                              |    5 +
 RELEASE_NOTES.rdoc                             |   20 ++-
 lib/bio/db/embl/sptr.rb                        |  214 +++++++++++++++++++++---
 test/unit/bio/db/embl/test_sptr.rb             |   12 +-
 test/unit/bio/db/embl/test_uniprot_new_part.rb |  208 +++++++++++++++++++++++
 5 files changed, 430 insertions(+), 29 deletions(-)
 create mode 100644 test/unit/bio/db/embl/test_uniprot_new_part.rb

commit 0d066ab6b8fc19f1cf6e66e07c2065775739cccd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Aug 13 00:58:51 2011 +0900

    preparation for release: alpha test version 1.4.2-alpha1

 bioruby.gemspec    |   23 +++++++++++++++++++++--
 lib/bio/version.rb |    4 ++--
 2 files changed, 23 insertions(+), 4 deletions(-)

commit 55ece17775f5d24cf62f93d54ded5dc6eed53584
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 12 21:57:25 2011 +0900

    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.
       (https://github.com/bioruby/bioruby/pull/13)

 test/functional/bio/test_command.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit 2f464aae016387cd50031f9d9664e78e220e2d01
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 12 20:37:18 2011 +0900

    RELEASE_NOTES.rdoc is updated following recent changes.

 RELEASE_NOTES.rdoc |   21 ++++++++++++++-------
 1 files changed, 14 insertions(+), 7 deletions(-)

commit d1a193684afdfd4c632ef75a978d4f3680d1bdf3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Aug 12 20:30:53 2011 +0900

    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.

 KNOWN_ISSUES.rdoc |   40 ++++++++++++++++++++++++++++++----
 README.rdoc       |   61 ++++++++++++++++++++--------------------------------
 2 files changed, 59 insertions(+), 42 deletions(-)

commit b5cbdc6ab7e81aae4db9aeb708fac57ffbce5636
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Jul 16 00:12:17 2011 +0900

    Added topics for the release notes

 RELEASE_NOTES.rdoc |   39 ++++++++++++++++++++++++++++++++++++++-
 1 files changed, 38 insertions(+), 1 deletions(-)

commit f062b5f37a6d8ad35b5b10c942fd61e1a4d37e08
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Jul 2 01:05:42 2011 +0900

    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.
       (https://github.com/bioruby/bioruby/issues/10)

 lib/bio/util/restriction_enzyme.rb                 |    3 +
 .../restriction_enzyme/range/sequence_range.rb     |   14 ++--
 .../range/sequence_range/calculated_cuts.rb        |   75 +++++++++++++++-----
 .../range/sequence_range/fragment.rb               |    4 +-
 4 files changed, 69 insertions(+), 27 deletions(-)

commit 735379421d9d6b7ceb06b91dcfcca6d5ff841236
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Jul 2 00:59:58 2011 +0900

    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.

 lib/bio/util/restriction_enzyme/dense_int_array.rb |  195 ++++++++++++++
 .../util/restriction_enzyme/sorted_num_array.rb    |  219 +++++++++++++++
 .../restriction_enzyme/test_dense_int_array.rb     |  201 ++++++++++++++
 .../restriction_enzyme/test_sorted_num_array.rb    |  281 ++++++++++++++++++++
 4 files changed, 896 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/util/restriction_enzyme/dense_int_array.rb
 create mode 100644 lib/bio/util/restriction_enzyme/sorted_num_array.rb
 create mode 100644 test/unit/bio/util/restriction_enzyme/test_dense_int_array.rb
 create mode 100644 test/unit/bio/util/restriction_enzyme/test_sorted_num_array.rb

commit 6cbb0c230d1a0bf3125c3b0fdb9ec3333d9564f8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jun 30 20:47:26 2011 +0900

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

 sample/test_restriction_enzyme_long.rb | 4403 ++++++++++++++++++++++++++++++++
 1 files changed, 4403 insertions(+), 0 deletions(-)
 create mode 100644 sample/test_restriction_enzyme_long.rb

commit 413442bd7424f837c73d8170ced8e01a01f87a59
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue May 24 23:26:41 2011 +0900

    Added a test for Bio::FastaFormat#entry_overrun etc.
    
     * Added a test for Bio::FastaFormat#entry_overrun.
     * Removed a void test class.

 test/unit/bio/db/test_fasta.rb |   24 ++++++++++++------------
 1 files changed, 12 insertions(+), 12 deletions(-)

commit b74020ff9b5c9fc8531c584898a329987008870e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue May 24 22:21:17 2011 +0900

    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.
       (https://github.com/bioruby/bioruby/issues/35)
     * Test method for Bio::FastaFormat#query is added.

 lib/bio/db/fasta.rb            |    2 +-
 test/unit/bio/db/test_fasta.rb |   22 ++++++++++++++++++++++
 2 files changed, 23 insertions(+), 1 deletions(-)

commit 80e49373e0e9013442680ba33499be80c58471db
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue May 17 22:33:56 2011 +0900

    Changed database name in the example.
    
     * Changed database name in the example.
       Thanks to Philipp Comans who reports the issue.

 lib/bio/appl/blast.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 7427d1f1355a6c190c6bf8522978e462dea64134
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu May 12 22:15:37 2011 +0900

    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.
       ( https://github.com/bioruby/bioruby/issues/34 )

 lib/bio/appl/blast/genomenet.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit c1c231b0a17c06ec042534245ed903e0256a59ed
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue May 10 20:57:17 2011 +0900

    updated doc/Tutorial.rd.html

 doc/Tutorial.rd.html |   34 ++++++++++++++++++----------------
 1 files changed, 18 insertions(+), 16 deletions(-)

commit 5261c926cae8dac890d7d0380e84f2eb88912417
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Thu May 5 12:07:54 2011 +0200

    Tutorial: Fixed URL and the intro

 doc/Tutorial.rd |   34 ++++++++++++++++++++--------------
 1 files changed, 20 insertions(+), 14 deletions(-)

commit 71de394053376f4759d705c52e6f16eca3da9d62
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Wed Mar 9 10:26:53 2011 +0100

    Tutorial: Added a commnet for rubydoctest, changed Ruby version
    
     * Added a comment for rubydoctest
     * Changed example Ruby version representation
     * This is part of commit ba5b9c2d29223860252451110a99d4ff0250395d
       and modified to merge with the current HEAD.

 doc/Tutorial.rd |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 1d27153065b8e8595a470b2201961b0a39bf8ca1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Apr 28 23:58:57 2011 +0900

    updated doc/Tutorial.rd.html

 doc/Tutorial.rd.html |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit ae9beff3bc43db3724a292b10a214583d9fbc111
Author: Michael O'Keefe <okeemf@rpi.edu>
Date:   Wed Apr 6 11:46:54 2011 -0400

    Updated through the section on Homology searching with BLAST

 doc/Tutorial.rd      |   64 ++++++++++++++++++++--------------------------
 doc/Tutorial.rd.html |   68 ++++++++++++++++++++++----------------------------
 2 files changed, 58 insertions(+), 74 deletions(-)

commit 971da799b16628a927abd7dd6c218994506f8fd8
Author: Michael O'Keefe <okeemf@rpi.edu>
Date:   Thu Mar 24 18:29:20 2011 -0400

    Updated the html file generated from the RDoc

 doc/Tutorial.rd.html |  224 ++++++++++++++++++++++++++------------------------
 1 files changed, 117 insertions(+), 107 deletions(-)

commit c6afd7eeed121926b56d300cb4170b5024f29eb0
Author: Michael O'Keefe <okeemf@rpi.edu>
Date:   Thu Mar 24 18:08:17 2011 -0400

    Finished updating the tutorial

 doc/Tutorial.rd |   16 ++++++++--------
 1 files changed, 8 insertions(+), 8 deletions(-)

commit 7349ac550ec03e2c5266496297becbdb3f4e0edd
Author: Michael O'Keefe <okeemf@rpi.edu>
Date:   Thu Mar 24 15:56:37 2011 -0400

    Edited tutorial up through the extra stuff section

 doc/Tutorial.rd |   28 ++++++++++++++--------------
 1 files changed, 14 insertions(+), 14 deletions(-)

commit 32ba3b15ad00d02b12ef2b44636505e23caaf620
Author: Michael O'Keefe <okeemf@rpi.edu>
Date:   Thu Mar 24 15:26:48 2011 -0400

    Updated tutorial up through BioSQL

 doc/Tutorial.rd |  172 ++++++++++++++++++-------------------------------------
 1 files changed, 57 insertions(+), 115 deletions(-)

commit 249580edb49a13545708fdcb559104217e37f162
Author: Michael O'Keefe <okeemf@rpi.edu>
Date:   Thu Mar 24 12:09:03 2011 -0400

    Updated tutorial through the section on alignments

 doc/Tutorial.rd |   40 +++++++++++++++++++++++++++++++++-------
 1 files changed, 33 insertions(+), 7 deletions(-)

commit 54f7b54044bb245ec5953dc7426f1c434b41f24f
Author: Michael O'Keefe <okeemf@rpi.edu>
Date:   Thu Mar 24 11:51:23 2011 -0400

    Updated the tutorial (mostly grammar fixes) up until GenBank

 doc/Tutorial.rd |   31 +++++++++++++++----------------
 1 files changed, 15 insertions(+), 16 deletions(-)

commit f046a52081a8af0e9afbf65fd2673c29689be769
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Feb 8 12:58:50 2011 +0900

    Added a test protein sequence data for BLAST test.

 test/data/fasta/EFTU_BACSU.fasta |    8 ++++++++
 1 files changed, 8 insertions(+), 0 deletions(-)
 create mode 100644 test/data/fasta/EFTU_BACSU.fasta

commit f61a5f4bdde16fa051f43cbe3efef4570b415a6a
Author: Anthony Underwood <email2ants@gmail.com>
Date:   Mon Jan 31 12:44:55 2011 +0000

    Bug fix: GenBank sequence output should format date as 27-JAN-2011
    
     * Bug fix: GenBank sequence output should format date as 27-JAN-2011
       rather than 2011-01-27 as specified by offical GenBank specs.

 lib/bio/db/genbank/format_genbank.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit be144e75a059058ab000a55d7bf535597e7e2617
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Feb 3 20:28:03 2011 +0900

    Added tests for remote BLAST execution via GenomeNet and DDBJ.
    
     * Added tests for remote BLAST execution via GenomeNet and DDBJ.
       Currently, a test for DDBJ BLAST web API is disabled because
       it takes relatively long time.
     * Tests to retrieve remote BLAST database information for GenomeNet
       and DDBJ servers are also added.

 test/functional/bio/appl/blast/test_remote.rb |   93 +++++++++++++++++++++++++
 test/functional/bio/appl/test_blast.rb        |   61 ++++++++++++++++
 2 files changed, 154 insertions(+), 0 deletions(-)
 create mode 100644 test/functional/bio/appl/blast/test_remote.rb
 create mode 100644 test/functional/bio/appl/test_blast.rb

commit 67314f1f1a248954c030f7ffe048faf862bf07d2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Feb 3 20:19:11 2011 +0900

    Updated _parse_databases following the changes in the DDBJ server
    
     * Updated _parse_databases following the changes in the DDBJ server.
       Changed to use (NT) or (AA) in the tail of each description.
       Thanks to DDBJ to improve their web service API.

 lib/bio/appl/blast/ddbj.rb |   29 ++++++++++++++++++++---------
 1 files changed, 20 insertions(+), 9 deletions(-)

commit d6aad2f4cc53c1227c86b6b573644cca15c9ed82
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Feb 2 00:02:32 2011 +0900

    Release notes for the next release is added.

 RELEASE_NOTES.rdoc |   38 ++++++++++++++++++++++++++++++++++++++
 1 files changed, 38 insertions(+), 0 deletions(-)
 create mode 100644 RELEASE_NOTES.rdoc

commit b4a30cc8ac9472b9e1c2a298afc624d0229c64c9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Feb 1 23:33:18 2011 +0900

    Bug fix: Execution failure due to the changes of DDBJ BLAST server

 lib/bio/appl/blast/ddbj.rb |    4 +++-
 1 files changed, 3 insertions(+), 1 deletions(-)

commit d30cb5975febd8b526088612c4fb9689a6cc46ba
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Feb 1 23:01:34 2011 +0900

    Support for database "mine-aa" and "mine-nt" with KEGG organism codes
    
     * Added support for database "mine-aa" and "mine-nt" combined with
       KEGG organism codes. When database name starts with mine-aa or
       mine-nt, space-separated list of KEGG organism codes can be given.
       For example, "mine-aa eco bsu hsa".

 lib/bio/appl/blast/genomenet.rb |   11 +++++++++++
 1 files changed, 11 insertions(+), 0 deletions(-)

commit abcba798ccf57894dcd570a6578ef78db30a3e25
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Feb 1 22:20:02 2011 +0900

    RELEASE_NOTES.rdoc is renamed to doc/RELEASE_NOTES-1.4.1.rdoc

 RELEASE_NOTES.rdoc           |  104 ------------------------------------------
 doc/RELEASE_NOTES-1.4.1.rdoc |  104 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 104 insertions(+), 104 deletions(-)
 delete mode 100644 RELEASE_NOTES.rdoc
 create mode 100644 doc/RELEASE_NOTES-1.4.1.rdoc

commit 8719cf4e06fc8a8cd0564aeb0b95372a7a0bcefb
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Feb 1 22:07:32 2011 +0900

    Bug: Options "-v" and "-b" should be used for the limit of hits.
    
     * Bug: Options "-v" and "-b" should be used for the limit of hits,
       and "-V" and "-B" should not be used for the purpose.

 lib/bio/appl/blast/genomenet.rb |    8 ++++----
 1 files changed, 4 insertions(+), 4 deletions(-)

commit 974b640badae9837fe9fc173d690b27c9b045454
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Feb 1 20:34:50 2011 +0900

    Bug fix: Workaround for a change in the GenomeNet BLAST site.
    
    * Bug fix: Workaround for a change in the GenomeNet BLAST site.
      Thanks to the anonymous reporter. The patch was originally made
      by Toshiaki Katyama.

 lib/bio/appl/blast/genomenet.rb |    7 +++----
 1 files changed, 3 insertions(+), 4 deletions(-)

commit 001d3e3570c77185cece4aed1be5be2ed6f94f7e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jan 6 23:39:19 2011 +0900

    Added tests to check the previous Bio::Reference#endnote fix.

 test/unit/bio/test_reference.rb |   30 ++++++++++++++++++++++++++++++
 1 files changed, 30 insertions(+), 0 deletions(-)

commit e1cd766abe24dbcc08a42103127c75ad0ab929aa
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jan 6 23:07:35 2011 +0900

    Bio::Reference#pubmed_url is updated to follow recent NCBI changes.

 lib/bio/reference.rb            |    5 ++---
 test/unit/bio/test_reference.rb |    5 +++++
 2 files changed, 7 insertions(+), 3 deletions(-)

commit 48024313a7568a38f4291618708541ae1dac312c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jan 6 22:56:37 2011 +0900

    Bug fix: Bio::Reference#endnote fails when url is not set
    
     * Bug fix: Bio::Reference#endnote fails when url is not set.
       Thanks to Warren Kibbe who reports the bug.
       (https://github.com/bioruby/bioruby/issues#issue/15)

 lib/bio/reference.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 577278a95340abfa32d3e67415d3a10bc74b82c0
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Fri Dec 17 12:16:31 2010 +0100

    Bug fix: In Bio::MEDLINE#reference, doi field should be filled.
    
     * Bug fix: In Bio::MEDLINE#reference, doi field should be filled.
       (https://github.com/bioruby/bioruby/issues#issue/29)

 lib/bio/db/medline.rb            |    1 +
 test/unit/bio/db/test_medline.rb |    1 +
 2 files changed, 2 insertions(+), 0 deletions(-)

commit daa20c85681576d3bfbdc8f87580a4b6227b122c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jan 6 20:25:03 2011 +0900

    Bug fix: Bio::Newick#reparse failure
    
     * Bug fix: Bio::Newick#reparse failure.
       Thanks to jdudley who reports the bug.
       (https://github.com/bioruby/bioruby/issues#issue/28)
     * Tests are added to confirm the bug fix.

 lib/bio/db/newick.rb            |    4 +++-
 test/unit/bio/db/test_newick.rb |   12 ++++++++++++
 2 files changed, 15 insertions(+), 1 deletions(-)

commit 16117aefdf57ac3ae16b5568f462f7b919ef005f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Jan 6 20:14:18 2011 +0900

    Use setup for the preparation of adding more test methods.

 test/unit/bio/db/test_newick.rb |   14 ++++++++++----
 1 files changed, 10 insertions(+), 4 deletions(-)

commit e5dc5896a5c6249e2a6cb03d63a3c2ade36b67e7
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 19 21:07:13 2010 +0900

    Ruby 1.9 support: suppressed warning "mismatched indentations"

 test/unit/bio/db/pdb/test_pdb.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 1bce41c7ebed46ac6cf433b047fe6a4c3a538089
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 19 21:05:06 2010 +0900

    Ruby 1.9 support: Suppressed warning "shadowing outer local variable"

 lib/bio/db/pdb/residue.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 0f31727769833ccf9d6891ae192da1bc180223e0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 19 21:04:07 2010 +0900

    Ruby 1.9 support: Suppressed warning "shadowing outer local variable"

 lib/bio/location.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 70c1135b171fcf47dd9dc1bc396d15d1c3acfa62
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 19 21:02:57 2010 +0900

    Ruby 1.9 support: Suppressed warning "shadowing outer local variable"

 lib/bio/db/pdb/pdb.rb |   14 +++++++-------
 1 files changed, 7 insertions(+), 7 deletions(-)

commit a77e4ab78211a85aa052ca6645a2051a4f3b76d8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 19 20:42:22 2010 +0900

    Ruby 1.9 support: use Array#join instead of Array#to_s

 lib/bio/db/pdb/pdb.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 734c2e54613e3ed5efd95e1212feab8f014d5f19
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 19 20:38:11 2010 +0900

    Changed to use assert_instance_of
    
     * Changed to use assert_instance_of(klass, obj) instead of
       assert_equal(klass, obj.class).

 test/unit/bio/db/pdb/test_pdb.rb |   16 ++++++++--------
 1 files changed, 8 insertions(+), 8 deletions(-)

commit 490286018c8ce314da441c646ea9c5fb3f765c95
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 19 20:24:36 2010 +0900

    Float::EPSILON was too small for the delta tolerance.

 test/unit/bio/db/pdb/test_pdb.rb |   20 ++++++++++----------
 1 files changed, 10 insertions(+), 10 deletions(-)

commit e92d225cadabe63fe23c7c32a4d1d50a371366cc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 19 20:16:30 2010 +0900

    Ruby 1.9 support: use assert_in_delta

 test/unit/bio/db/pdb/test_pdb.rb |   24 +++++++++++++++---------
 1 files changed, 15 insertions(+), 9 deletions(-)

commit 41452971a132ef55de3486022962fa2c333b4c85
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 19 13:19:39 2010 +0900

    Fixed Object#id problem and suppressed warning messages.
    
     * Changed not to call nil.id (==4) invoked from chain.id.
     * Suppressed warning message about useless use of a variable.
     * Suppressed waring about conflict of IDs when testing
       addResidue, addLigand and addChain methods.

 test/unit/bio/db/pdb/test_pdb.rb |  119 +++++++++++++++++++-------------------
 1 files changed, 59 insertions(+), 60 deletions(-)

commit b4af5826f77002933de9d3c2ddfcc5a7cb5629db
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 17 22:26:26 2010 +0900

    Adjusted copyright line

 test/unit/bio/db/pdb/test_pdb.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 06fd989072b2287a3accbb60684b8a029bfc0ac3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 17 21:54:05 2010 +0900

    A module name is changed to avoid potential name conflict.
    
     * A module name is changed to avoid potential name conflict.
     * Removed a Shift_JIS character (Zenkaku space) in a comment line.

 test/unit/bio/db/pdb/test_pdb.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 09007f93abe8c9c5e7561f082b55ca307a7d4a1e
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Thu Jul 15 21:06:28 2010 +0900

    Added more unit tests for Bio::PDB
    
     * Added more unit tests for Bio::PDB.
     * This is part of combinations of the 13 commits:
       * 555f7b49a43e7c35c82cd48b199af96ca93d4179
       * 2b5c87a9ada248597e0517e22191bb4c88be2a42
       * a16e24fa35debdcacd11cf36fdf0e60fe82b3684
       * e3607c0f7154a4156fd53ed17470aa3628cd2586
       * 4e74c9107f09c5eb3fc7fc9ec38d9d773fe89367
       * 605fb0a222f70eeaa1e576d31af484a9a6a2ac27
       * 2c8b2b5496fee04b886bfcbd11fb99948816cc28
       * 202cf2b1b57fbcac215aa135cf6343af6a49d2ef
       * f13c070c763c9035451c3639e6e29c9a156947cd
       * 843378e608bd1ef27a713d9be2d50f0f56915b0b
       * a9078b8a586b66d8026af612d9a5999c6c77de33
       * f0174a8ca3ee136271c51047fce12597d3fbb58c
       * 6675fd930718e41ad009f469b8167f81c9b2ad52

 test/unit/bio/db/pdb/test_pdb.rb | 3281 +++++++++++++++++++++++++++++++++++++-
 1 files changed, 3276 insertions(+), 5 deletions(-)

commit 2f6a1d29b14d89ac39b408582c9865ad06560ae1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Nov 6 00:41:21 2010 +0900

    Adjusted test data file path, required files and header descriptions.

 test/unit/bio/db/test_litdb.rb |    8 ++++----
 1 files changed, 4 insertions(+), 4 deletions(-)

commit d3394e69c98b3be63c8287af84dc530830fb977a
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Fri Jun 18 17:11:25 2010 +0900

    added unit test for Bio::LITDB with a sample file

 test/data/litdb/1717226.litdb  |   13 +++++
 test/unit/bio/db/test_litdb.rb |   95 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 108 insertions(+), 0 deletions(-)
 create mode 100644 test/data/litdb/1717226.litdb
 create mode 100644 test/unit/bio/db/test_litdb.rb

commit cef1d2c824f138fe268d20eaa9ffd85223c85ef9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 23:54:31 2010 +0900

    Adjusted test data file path, required files and header descriptions.

 test/unit/bio/db/test_nbrf.rb |    8 ++++----
 1 files changed, 4 insertions(+), 4 deletions(-)

commit e892e7f9b9b4daadeff44c9e479e6f51f02e383e
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Fri Jun 25 13:20:46 2010 +0900

    Added unit tests for Bio::NBRF with test data.
    
     * Added unit tests for Bio::NBRF with test data.
     * This is part of combinations of the two commits:
       * 53873a82182e072e738da20381dcb2bfd8bc9e96
         (Modified the unit test for Bio::NBRF)
       * 4675cf85aa9c0b4de9f527f9c6bb80804fdaaaa9
         (Modified Bio::TestNBRF and Bio::TestTRANSFAC.)

 test/data/pir/CRAB_ANAPL.pir  |    6 +++
 test/unit/bio/db/test_nbrf.rb |   82 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 88 insertions(+), 0 deletions(-)
 create mode 100644 test/data/pir/CRAB_ANAPL.pir
 create mode 100644 test/unit/bio/db/test_nbrf.rb

commit 4922d5151138312d5a09ac60a06419c23978ba3c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 23:07:13 2010 +0900

    Mock class for testing is moved under the test class
    
     * Mock class for testing is moved under the test class, to avoid
       potential name conflicts.

 test/unit/bio/db/genbank/test_common.rb |   25 ++++++++++++-------------
 1 files changed, 12 insertions(+), 13 deletions(-)

commit 8f630700bc6dd8c183d08291c66c665394873586
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 23:01:32 2010 +0900

    Adjusted header descriptions.

 test/unit/bio/db/genbank/test_common.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit ab3d6384ca721fb6004efb5988461eecefad4d6b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 22:58:21 2010 +0900

    Adjusted test data file path and header descriptions.

 test/unit/bio/db/genbank/test_genpept.rb |    8 ++++----
 1 files changed, 4 insertions(+), 4 deletions(-)

commit 1d24aecfac9dbc190cdc3eef0956451cc88cfe4f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 5 22:54:19 2010 +0900

    Adjusted test data file path, required files and header descriptions.

 test/unit/bio/db/genbank/test_genbank.rb |   12 ++++++++----
 1 files changed, 8 insertions(+), 4 deletions(-)

commit 09275d8661f3d49a7e40be59a086ba33659b2448
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Thu Jun 17 22:08:15 2010 +0900

    Added unit tests for Bio::GenPept newly.
    
     * Added unit tests for Bio::GenPept newly.
     * This is part of the commit 8e46ff42b627791f259033d5a20c1610e32cfa62
       (Added unit tests for NBRF and GenPept newly.)

 test/data/genbank/CAA35997.gp            |   48 ++++++++++++++++++
 test/unit/bio/db/genbank/test_genpept.rb |   81 ++++++++++++++++++++++++++++++
 2 files changed, 129 insertions(+), 0 deletions(-)
 create mode 100644 test/data/genbank/CAA35997.gp
 create mode 100644 test/unit/bio/db/genbank/test_genpept.rb

commit 2cde22cb358a2b7ec8197866fe35a0b46ebf9b00
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Thu Jun 24 18:52:37 2010 +0900

    Added unit tests for Bio::NCBIDB::Common
    
     * Added unit tests for Bio::NCBIDB::Common.
     * This is part of combination of the 4 commits:
       * 7da8d557e8ee53da9d93c6fadfd0d8f493977c81
         (added test/unit/bio/db/genbank/test_common.rb newly)
       * 2b5c87a9ada248597e0517e22191bb4c88be2a42
         (Modified a few lines of Bio::NCBIDB::TestCommon,
          Bio::TestPDBRecord and Bio::TestPDB)
       * 10c043535dd7bf5b9682b4060183f494742c53df
         (Modified unit test for Bio::GenBank::Common)
       * 0af08fb988e08948a54e33273861b5460b7f6b2d
         (Modified the unit test for Bio::GenBank)

 test/unit/bio/db/genbank/test_common.rb |  275 +++++++++++++++++++++++++++++++
 1 files changed, 275 insertions(+), 0 deletions(-)
 create mode 100644 test/unit/bio/db/genbank/test_common.rb

commit f775d9b7f7deda2e30d4196d4cf507b59936a654
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Sat Jun 26 17:54:32 2010 +0900

    Added unit tests for Bio::GenBank with test data.
    
     * Added unit tests for Bio::GenBank with test data.
     * This is part of combination of the two commits:
       * 555f7b49a43e7c35c82cd48b199af96ca93d4179
         (added test_genbank.rb and test_go.rb with the test files.
         modified test_pdb.rb)
       * a46f895bf378ce08143ff031ddda302f970c270a
         (Modified Bio::GenBank and Bio::Nexus)

 test/data/genbank/SCU49845.gb            |  167 +++++++++++++
 test/unit/bio/db/genbank/test_genbank.rb |  397 ++++++++++++++++++++++++++++++
 2 files changed, 564 insertions(+), 0 deletions(-)
 create mode 100644 test/data/genbank/SCU49845.gb
 create mode 100644 test/unit/bio/db/genbank/test_genbank.rb

commit 33621c1f4c16173efd05861759f577b2c4733a53
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 29 16:45:22 2010 +0900

    Bio::BIORUBY_EXTRA_VERSION is changed to ".5000".

 bioruby.gemspec    |    2 +-
 lib/bio/version.rb |    2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

commit cfb2c744f3762689077f5bf2092f715d25e066ed
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 22 13:02:03 2010 +0900

    BioRuby 1.4.1 is released.

 ChangeLog |   55 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 55 insertions(+), 0 deletions(-)

commit 92cfda14c08b270ed1beca33153125141f88510e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 22 13:00:09 2010 +0900

    Preparation for bioruby-1.4.1 release.

 bioruby.gemspec    |    2 +-
 lib/bio/version.rb |    2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

commit d7999539392bba617b041e3120b5b2d785301f24
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 22 10:27:02 2010 +0900

    Newly added issue is copied from KNOWN_ISSUES.rdoc to the release note.

 RELEASE_NOTES.rdoc |   15 +++++++++++++++
 1 files changed, 15 insertions(+), 0 deletions(-)

commit a9f287658441038a4e9bb220502523de039417f9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 22 10:26:44 2010 +0900

    updated description of an issue

 KNOWN_ISSUES.rdoc |   12 +++++++-----
 1 files changed, 7 insertions(+), 5 deletions(-)

commit bb946d1c97d1eb0de62c8b509bbfb02d67efffeb
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 23:17:25 2010 +0900

    Added an issue about command-line string escaping on Windows with Ruby 1.9.

 KNOWN_ISSUES.rdoc |    8 ++++++++
 1 files changed, 8 insertions(+), 0 deletions(-)

commit fe7d26516cc6b9a3cf8c16e6f8204a4d5eb5e5ae
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 20:34:32 2010 +0900

    Added descriptions.

 RELEASE_NOTES.rdoc |   52 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 52 insertions(+), 0 deletions(-)

commit fd5da3b47ebce1df46922f20d013439faef483e9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 18:27:44 2010 +0900

    ChangeLog is updated.

 ChangeLog | 1657 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 1657 insertions(+), 0 deletions(-)

commit fab16977d23bb3a5fdfc976eece14dfdabdcac4d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 18:07:43 2010 +0900

    preparation for release candidate 1.4.1-rc1

 bioruby.gemspec    |   40 ++++++++++++++++++++++++++++++++++++++--
 lib/bio/version.rb |    4 ++--
 2 files changed, 40 insertions(+), 4 deletions(-)

commit 119cc3bf5582735a5df574450ec685fd2f989b5d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 18:05:13 2010 +0900

    Temporarily removed for packaging new version. It will be reverted later.

 doc/howtos/sequence_codon.txt |   38 --------------------------------------
 1 files changed, 0 insertions(+), 38 deletions(-)
 delete mode 100644 doc/howtos/sequence_codon.txt

commit 1b1b3752e3c98a29caf837bfc12c1ed79a04dba2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 16:48:43 2010 +0900

    Fixed typo, reported by Tomoaki NISHIYAMA.

 KNOWN_ISSUES.rdoc |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 47ed7e5eaca4a261ef0fd4f76909c930e52aadd5
Merge: c002142 548cb58
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 16:17:59 2010 +0900

    Merge branch 'test-defline-by-jtprince'

commit 548cb58aaad06bb9161e09f7b4ae45729898ca5e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 16:16:28 2010 +0900

    adjusted filename in header

 test/unit/bio/db/fasta/test_defline_misc.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 95be260708ef21be7848a5d4b7c494cc6bb3d81f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 16:14:58 2010 +0900

    Renamed to test_defline_misc.rb to resolve the file name conflict.

 test/unit/bio/db/fasta/test_defline.rb      |  490 ---------------------------
 test/unit/bio/db/fasta/test_defline_misc.rb |  490 +++++++++++++++++++++++++++
 2 files changed, 490 insertions(+), 490 deletions(-)
 delete mode 100644 test/unit/bio/db/fasta/test_defline.rb
 create mode 100644 test/unit/bio/db/fasta/test_defline_misc.rb

commit 1e7628e2c396330743d4904b100d62d2c2773bf0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 16:11:14 2010 +0900

    Test bug fix: mistake in test_get method in two classes.

 test/unit/bio/db/fasta/test_defline.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit c479f56f14fb531e31c7e5fdd02f6c934ac468fa
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 16:06:46 2010 +0900

    Test bug fix: test classes should inherit Test::Unit::TestCase.

 test/unit/bio/db/fasta/test_defline.rb |   10 +++++-----
 1 files changed, 5 insertions(+), 5 deletions(-)

commit 0e8ea46e5a239df5c1da3c63e602376c04191ef4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 15:55:02 2010 +0900

    Bug fix: syntax error in Ruby 1.8.7 due to a comma.

 test/unit/bio/db/fasta/test_defline.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 62a2c1d7c47fbef7a7e7c4f1c079f98fa74e5099
Author: John Prince <jtprince@gmail.com>
Date:   Tue Oct 19 11:20:16 2010 -0600

    added individual unit tests for Bio::FastaDefline

 test/unit/bio/db/fasta/test_defline.rb |  490 ++++++++++++++++++++++++++++++++
 1 files changed, 490 insertions(+), 0 deletions(-)
 create mode 100644 test/unit/bio/db/fasta/test_defline.rb

commit c002142cdb478b0ad08b7bd5e3331c7b643222f1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 15:36:58 2010 +0900

    Adjusted file paths and the copyright line.

 test/unit/bio/db/fasta/test_defline.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit a5818c5f8ae07e4ec4bdcc2229df9a59bded63f0
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Thu Jun 17 11:54:15 2010 +0900

    Newly added unit tests for Bio::FastaDefline
    
     * Newly added unit tests for Bio::FastaDefline.
     * This is part of combination of the two commits:
       bd2452caf0768e7000d19d462465b1772e3c030b
       (modified test file for Bio::FastaDefline)
       cae1b6c00cdb9044cb0dfb4db58e6acfe9b7d246
       (Added test/unit/bio/db/fasta/test_defline.rb and
        test/unit/bio/db/kegg/test_kgml.rb with the sample file newly.)

 test/unit/bio/db/fasta/test_defline.rb |  160 ++++++++++++++++++++++++++++++++
 1 files changed, 160 insertions(+), 0 deletions(-)
 create mode 100644 test/unit/bio/db/fasta/test_defline.rb

commit 4addb906df442adf4ed20275428070b651abbf07
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 15:08:46 2010 +0900

    Added note for a dead link, updated a URL, and added a new reference.

 lib/bio/db/fasta/defline.rb |    8 ++++++--
 1 files changed, 6 insertions(+), 2 deletions(-)

commit e636f123adf28688748cc5bbbc6e0c817358d475
Author: John Prince <jtprince@gmail.com>
Date:   Thu Oct 14 15:38:07 2010 -0600

    included TREMBL prefix to list of NSIDs (tr|)
    
     * Included TREMBL prefix to list of NSIDs (tr|).
       This is a standard prefix found in UniprotKB FASTA files.

 lib/bio/db/fasta/defline.rb |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit 5277eb0b5376a0dc217dc051c49993c505956400
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 14:16:03 2010 +0900

    Bug fix: Bio::ClustalW::Report#get_sequence may fail
    
     * Bug fix: Bio::ClustalW::Report#get_sequence may fail when the second
       argument of Bio::ClustalW::Report.new is specified.

 lib/bio/appl/clustalw/report.rb |    5 +++--
 1 files changed, 3 insertions(+), 2 deletions(-)

commit 81b9238abb643573a4051dc0f10c4f9a2cff40fa
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 14:21:52 2010 +0900

    Added a test class to test the second argument of Bio::ClustalW::Report.new.

 test/unit/bio/appl/clustalw/test_report.rb |   19 +++++++++++++++++++
 1 files changed, 19 insertions(+), 0 deletions(-)

commit 3e9b149aec91585732a34efaa960c96bcec2eef8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 13:22:38 2010 +0900

    Ruby 1.9.2 support: defined Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands#initialize
    
     * Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands#initialize
       is explicitly defined, due to the behavior change of argument number
       check in the default initialize method in Ruby 1.9.2.

 .../double_stranded/aligned_strands.rb             |    5 +++++
 1 files changed, 5 insertions(+), 0 deletions(-)

commit cfe31c02d4bd0d97e588d25dc30188da6be81e85
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 11:49:08 2010 +0900

    Ruby 1.9.2 support: assert_in_delta for a float value.

 test/unit/bio/db/test_aaindex.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 3f5d2ccb9ac8bc44febc88d441f47aeddf7f12ff
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 11:41:38 2010 +0900

    Ruby 1.9.2 support: using assert_in_delta for float values.
    
     * Ruby 1.9.2 support: using assert_in_delta for float values.
       The patch is written by Tomoaki NISHIYAMA during BH2010.10.

 test/unit/bio/util/test_contingency_table.rb |   14 +++++++-------
 1 files changed, 7 insertions(+), 7 deletions(-)

commit f357929bc5dcf8295b0a11a09b4025e3592d9eda
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 11:16:37 2010 +0900

    Small changes for README.rdoc.

 README.rdoc |    5 +++--
 1 files changed, 3 insertions(+), 2 deletions(-)

commit c6c567fe9602ae8d7d343a5773f51d8aa22c8876
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 21 11:12:17 2010 +0900

    Shows message when running "ruby setup.rb test" with Ruby1.9.

 setup.rb |    5 +++++
 1 files changed, 5 insertions(+), 0 deletions(-)

commit 9b66463c4150a679e63289e0cee3c4d1200c7d0f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 20 17:53:36 2010 +0900

    Added description about incompatible the change in Bio::AAindex2.

 RELEASE_NOTES.rdoc |    6 ++++++
 1 files changed, 6 insertions(+), 0 deletions(-)

commit 327ea878d4e15b99711d8121a54698da29d4b0aa
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 20 17:35:53 2010 +0900

    Changed the expected return values in the unit tests, following the last change to Bio::AAindex2.
    
     * Changed the expected return values in the unit tests,
     following the last change to Bio::AAindex2.
     * The patch is written by Tomoaki NISHIYAMA during BH2010.10.

 test/unit/bio/db/test_aaindex.rb |   15 ++++++++-------
 1 files changed, 8 insertions(+), 7 deletions(-)

commit 31963b43daab2801087f5f6d23b04e357bb7b1e2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 20 17:32:26 2010 +0900

    Ruby 1.9.2 support: Incompatible change: the symmetric elements for triangular matrix should be copied
    
     * Ruby 1.9.2 support: Incompatible change: the symmetric elements
       for triangular matrix should be copied. The patch is written by
       Tomoaki NISHIYAMA during BH2010.10.

 lib/bio/db/aaindex.rb |   12 +++++++++++-
 1 files changed, 11 insertions(+), 1 deletions(-)

commit e8a1d65984781466eff9d5a262f18cb1c3e01056
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 20 16:10:51 2010 +0900

    Test bug fix: confusion between assert and assert_equal
    
     * Test bug fix: the assert should be assert_equal. The bug was
       found with Ruby 1.9.2-p0.

 test/unit/bio/db/embl/test_sptr.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit feb2cda47beab91e2fc3dddf99d5cc1cacf3fbae
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 20 14:59:40 2010 +0900

    Test bug fix: confusion between assert and assert_equal, and apparently wrong expected values.
    
     * Test bug fix: the assert should be assert_equal. The bug was found
       with Ruby 1.9.2-p0.
     * In the test_rates_hundred_and_fiftieth_position method, the index
       for @example_rates and the expected value of the third assertion
       were apparently wrong.
     * Reported by Tomoaki NISHIYAMA during BH2010.10.

 test/unit/bio/appl/paml/codeml/test_rates.rb |   12 ++++++------
 1 files changed, 6 insertions(+), 6 deletions(-)

commit ffc03a11a4ef7b36ea78de58d4c8d4e9259093c4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 16 01:06:36 2010 +0900

    Tests for Bio::KEGG::PATHWAY are improved with new test data.

 test/data/KEGG/ec00072.pathway        |   23 +
 test/data/KEGG/hsa00790.pathway       |   59 ++
 test/data/KEGG/ko00312.pathway        |   16 +
 test/data/KEGG/rn00250.pathway        |  114 ++++
 test/unit/bio/db/kegg/test_pathway.rb | 1055 +++++++++++++++++++++++++++++++++
 5 files changed, 1267 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/ec00072.pathway
 create mode 100644 test/data/KEGG/hsa00790.pathway
 create mode 100644 test/data/KEGG/ko00312.pathway
 create mode 100644 test/data/KEGG/rn00250.pathway

commit 1e1d974c2c72ddf5a45e41c6f2510729fb65a4ad
Author: Toshiaki Katayama <k@bioruby.org>
Date:   Tue Jul 20 11:46:52 2010 +0900

    Added methods for parsing KEGG PATHWAY fields.
    
     * Added methods for parsing KEGG PATHWAY fields.
     * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb
       and modified to merge with the current HEAD (original commit
       message: Changes for TogoWS).

 lib/bio/db/kegg/pathway.rb |  146 +++++++++++++++++++++++++++++++++++++++++++-
 1 files changed, 145 insertions(+), 1 deletions(-)

commit 957c8ee630538a8c49c52339cb3c0364e5328378
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 16 00:50:42 2010 +0900

    Private method strings_as_hash is moved to Bio::KEGG::Common::StringsAsHash.

 lib/bio/db/kegg/common.rb |   18 ++++++++++++++++++
 lib/bio/db/kegg/module.rb |   19 +++++--------------
 2 files changed, 23 insertions(+), 14 deletions(-)

commit b7fd85382bccceaa29958d5daf98ca0a513e5a9a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 15 22:01:05 2010 +0900

    Renamed Bio::KEGG::*#pathway_modules to modules, etc.
    
     * Renamed following methods in Bio::KEGG::ORTHOLOGY and
       Bio::KEGG:PATHWAY classes: pathway_modules to modules,
       pathway_modules_as_strings to modules_as_strings, and
       pathway_modules_as_hash to modules_as_hash.
     * Unit tests are also modified.

 lib/bio/db/kegg/common.rb               |   18 +++++++++---------
 lib/bio/db/kegg/orthology.rb            |   10 +++++-----
 lib/bio/db/kegg/pathway.rb              |   10 +++++-----
 test/unit/bio/db/kegg/test_orthology.rb |   12 ++++++------
 test/unit/bio/db/kegg/test_pathway.rb   |   20 ++++++++++----------
 5 files changed, 35 insertions(+), 35 deletions(-)

commit 02aea9f18ff6e3079309a76d04d02ea1f2902e7b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 15 00:20:48 2010 +0900

    Modified tests for Bio::KEGG::GENES following the changes of the class.

 test/unit/bio/db/kegg/test_genes.rb |   30 +++++++++++++++++++++++++++++-
 1 files changed, 29 insertions(+), 1 deletions(-)

commit f4b45ea629734ecff820483475d83fef6cbe068e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Oct 14 23:57:18 2010 +0900

    Reverted Bio::KEGG::GENES#genes, gene and motif methods and modified.
    
     * Reverted Bio::KEGG::GENES#genes, gene and motif methods which are
       removed in the last commit. To avoid code duplication, they are
       also modified to use other methods, and RDoc is added about the
       deprecation or change of the methods.
     * Modified RDoc.

 lib/bio/db/kegg/genes.rb |   32 +++++++++++++++++++++++++++++++-
 1 files changed, 31 insertions(+), 1 deletions(-)

commit dd987911cb4a84e23565bb37707611d054c22101
Author: Toshiaki Katayama <k@bioruby.org>
Date:   Tue Jul 20 11:46:52 2010 +0900

    New methods Bio::KEGG::GENES#keggclass etc.
    
     * New methods and aliases are added: Bio::KEGG::GENES#keggclass,
       keggclasses, names_as_array, names, motifs_as_strings,
       motifs_as_hash, motifs.
     * Removed Bio::KEGG::GENES#genes, gene and motif methods.
     * Added a comment about deprecation of CODON_USAGE lines.
     * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb
       (original commit message: Changes for TogoWS).

 lib/bio/db/kegg/genes.rb |   41 ++++++++++++++++++++++++++---------------
 1 files changed, 26 insertions(+), 15 deletions(-)

commit b2575f5acfeca269c93a35baa3809fdac17a7271
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 13 23:12:33 2010 +0900

    Release notes for the upcoming release version.

 RELEASE_NOTES.rdoc |   31 +++++++++++++++++++++++++++++++
 1 files changed, 31 insertions(+), 0 deletions(-)
 create mode 100644 RELEASE_NOTES.rdoc

commit 83992875c45a1fdd54d042c923dee51119026e49
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 13 23:11:21 2010 +0900

    Renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.0.rdoc.

 RELEASE_NOTES.rdoc           |  167 ------------------------------------------
 doc/RELEASE_NOTES-1.4.0.rdoc |  167 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 167 insertions(+), 167 deletions(-)
 delete mode 100644 RELEASE_NOTES.rdoc
 create mode 100644 doc/RELEASE_NOTES-1.4.0.rdoc

commit f649629eb6216aeabbd2020bcac9b7f870b12395
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 13 21:58:58 2010 +0900

    Added acknowledgement to Kozo Nishida for KEGG parsers.

 RELEASE_NOTES.rdoc |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit 379f177edc0f95dee1ec0c2d2cf679c27918e41b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 8 16:31:58 2010 +0900

    Fixed a variable name mistake in Bio::Command, and English grammer fix.
    
     * Fixed a variable name mistake in Bio::Command#no_fork?.
     * English grammer fix for comments. Thanks to Andrew Grimm who
       reports the fix.

 lib/bio/command.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit 1344c27c90438d8c8840ee507d0ab43224f89054
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 6 23:47:26 2010 +0900

    Bug fix: fork(2) is called on platforms that do not support it.
    
     * Bug fix: fork(2) is called on platforms that do not support it.
       Thanks to Andrew Grimm who reports the bug
       (fork() is called on platforms that do not support it;
       http://github.com/bioruby/bioruby/issues#issue/6).
     * Bio::Command#call_command and query_command can now fall back
       into using popen when fork(2) is not implemented.
     * Detection of Windows platform is improved. The idea of the code
       is taken from Redmine's platform.rb.

 lib/bio/command.rb                  |   98 +++++++++++++++++++++++++++++------
 test/functional/bio/test_command.rb |    9 +--
 2 files changed, 84 insertions(+), 23 deletions(-)

commit 0bfa1c3a8d7b8d03919d54a2a241ca96a79bad83
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 6 15:49:51 2010 +0900

    Bug fix: Bio::MEDLINE#reference is changed not to put empty values
    
     * Bug fix: Bio::MEDLINE#reference is changed not to put empty values
       in the returned Bio::Reference object. I think the original bahavior
       is a bug. This is an incompatible change but the effect is very small.

 lib/bio/db/medline.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 8e0bc03d79a1f20743c29f0a44e273d362eaa2cd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 6 15:39:34 2010 +0900

    Bug fix: Bio::MEDLINE#initialize should handle continuation of lines.
    
     * Bug fix: Bio::MEDLINE#initialize should handle continuation of lines.
       Thanks to Steven Bedrick who reports the bug
       (Bio::MEDLINE#initialize handles multi-line MeSH terms incorrectly;
       http://github.com/bioruby/bioruby/issues#issue/7).

 lib/bio/db/medline.rb |    6 +++++-
 1 files changed, 5 insertions(+), 1 deletions(-)

commit 728de78b438108e44066a7ce7490632c81108fb6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Oct 6 15:29:10 2010 +0900

    Added unit tests for Bio::MEDLINE with test data.
    
     * Added unit tests for Bio::MEDLINE with test data. The data is
       taken from NCBI and the abstract was removed to avoid possible
       copyright problem. The choice of the data (PMID: 20146148) is
       suggested by Steven Bedrick in a bug report (Bio::MEDLINE#initialize
       handles multi-line MeSH terms incorrectly).

 test/data/medline/20146148_modified.medline |   54 ++++++++++
 test/unit/bio/db/test_medline.rb            |  148 +++++++++++++++++++++++++++
 2 files changed, 202 insertions(+), 0 deletions(-)
 create mode 100644 test/data/medline/20146148_modified.medline

commit 930095817ce60793ac909a4d01731d1f97bc4fa5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 29 20:51:12 2010 +0900

    Bug fix: NoMethodError in Bio::Tree#collect_edge!
    
     * Bug fix: NoMethodError in Bio::Tree#collect_edge!.
       Thanks to Kazuhiro Hayashi who reports the bug.

 lib/bio/tree.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit c7927ec4743ddc4ec4501790bbed097b69f616e7
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 29 20:49:44 2010 +0900

    Modified and improved tests for Bio::Tree.

 test/unit/bio/test_tree.rb |  393 +++++++++++++++++++++++++++-----------------
 1 files changed, 240 insertions(+), 153 deletions(-)

commit 0161148c9b4d9ea404af92b4baf8241239a283de
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Fri Jul 16 00:09:39 2010 +0900

    Modified unit tests for Bio::Tree
    
     * Modified unit tests for Bio::Tree.
     * This is part of combination of the two commits:
       * 6675fd930718e41ad009f469b8167f81c9b2ad52
         (Modified unit tests and classes)
       * a6dc63ffe3460ea8d8980b3d6c641356881e0862
         (Modified unit test for Bio::Tree)

 test/unit/bio/test_tree.rb |  174 +++++++++++++++++++++++++++++++++++++++++++-
 1 files changed, 173 insertions(+), 1 deletions(-)

commit 31ded691a9329e45fe563e5f70138648d3b30bbf
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Thu Jul 15 21:06:28 2010 +0900

    Bug fix: Bio::Tree#remove_edge_if did not work.
    
     * Bug fix: Bio::Tree#remove_edge_if did not work.
     * This is part of commit 6675fd930718e41ad009f469b8167f81c9b2ad52
       (original commit message: Modified unit tests and classes)
       and removed a comment line.

 lib/bio/tree.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit d0a3af23c74004688a8fc0b5be3d09f7144e33a1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 22 19:23:50 2010 +0900

    Renamed test/data/go/part_of_* to avoid possible confusion
    
     * Renamed test/data/go/part_of_* to selected_* to avoid possible
       confusion: The word "part_of" is a keyword in Gene Ontology.

 test/data/go/part_of_component.ontology    |   12 ----------
 test/data/go/part_of_gene_association.sgd  |   31 ----------------------------
 test/data/go/part_of_wikipedia2go          |   13 -----------
 test/data/go/selected_component.ontology   |   12 ++++++++++
 test/data/go/selected_gene_association.sgd |   31 ++++++++++++++++++++++++++++
 test/data/go/selected_wikipedia2go         |   13 +++++++++++
 test/unit/bio/db/test_go.rb                |    6 ++--
 7 files changed, 59 insertions(+), 59 deletions(-)
 delete mode 100644 test/data/go/part_of_component.ontology
 delete mode 100644 test/data/go/part_of_gene_association.sgd
 delete mode 100644 test/data/go/part_of_wikipedia2go
 create mode 100644 test/data/go/selected_component.ontology
 create mode 100644 test/data/go/selected_gene_association.sgd
 create mode 100644 test/data/go/selected_wikipedia2go

commit e4f82da52402f8175bd92b50209b09bc83bfddd6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 22 19:21:36 2010 +0900

    Removed unused test/data/go/wikipedia2go.txt.

 test/data/go/wikipedia2go.txt |  728 -----------------------------------------
 1 files changed, 0 insertions(+), 728 deletions(-)
 delete mode 100644 test/data/go/wikipedia2go.txt

commit 5003fd53b0a3852fa23b76ad6ec8e9e76d5850fc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 16 22:37:31 2010 +0900

    Adjusted test data file paths and header lines in test_go.rb.
    
     * Adjusted test data file paths.
     * Adjusted copyright and description in the header.

 test/unit/bio/db/test_go.rb |   26 +++++++++++++++++---------
 1 files changed, 17 insertions(+), 9 deletions(-)

commit 540cb7ab27e79634f5436476cce51cc20ca0f70f
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Thu Jul 15 21:06:28 2010 +0900

    Added tests for Bio::GO classes.
    
     * Added tests for Bio::GO classes.
     * This is part of combination of the three commits:
       * 555f7b49a43e7c35c82cd48b199af96ca93d4179
         (added test_genbank.rb and test_go.rb with the test files.
          modified test_pdb.rb)
       * e966f17546427b8ad39cb9942807ceb8a068d746
         (modified test/unit/bio/db/test_go.rb and added the test files
          for each GO class)
       * 6675fd930718e41ad009f469b8167f81c9b2ad52
         (Modified unit tests and classes)

 test/unit/bio/db/test_go.rb |  163 +++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 163 insertions(+), 0 deletions(-)
 create mode 100644 test/unit/bio/db/test_go.rb

commit 5ff01f7dfbc3661d8c66b44874a2ba4ff2f96b56
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Fri Jun 11 21:02:29 2010 +0900

    Added test data for Bio::GO classes.
    
     * Added test data for Bio::GO classes.
     * This is part of combination of the three commits:
       * 555f7b49a43e7c35c82cd48b199af96ca93d4179
         (added test_genbank.rb and test_go.rb with the test files.
          modified test_pdb.rb)
       * e966f17546427b8ad39cb9942807ceb8a068d746
         (modified test/unit/bio/db/test_go.rb and added the test files
          for each GO class)
       * 6675fd930718e41ad009f469b8167f81c9b2ad52
         (Modified unit tests and classes)
     * License for the test data is the public domain.
       ( http://wiki.geneontology.org/index.php/Legal_FAQ )

 test/data/go/part_of_component.ontology   |   12 +
 test/data/go/part_of_gene_association.sgd |   31 ++
 test/data/go/part_of_wikipedia2go         |   13 +
 test/data/go/wikipedia2go.txt             |  728 +++++++++++++++++++++++++++++
 4 files changed, 784 insertions(+), 0 deletions(-)
 create mode 100644 test/data/go/part_of_component.ontology
 create mode 100644 test/data/go/part_of_gene_association.sgd
 create mode 100644 test/data/go/part_of_wikipedia2go
 create mode 100644 test/data/go/wikipedia2go.txt

commit d4210673a1a696bfb02c93b7743e60dea1a5fcc8
Author: Kazuhiro Hayashi <k.hayashi.info@gmail.com>
Date:   Thu Jul 15 21:06:28 2010 +0900

    Bug fix: Typo and missing field in Bio::GO::GeneAssociation#to_str.
    
     * Bug fix: Typo and missing field in Bio::GO::GeneAssociation#to_str.
     * This is part of commit 6675fd930718e41ad009f469b8167f81c9b2ad52
       (original commit message: Modified unit tests and classes)
       and modified. The bug is also reported by Ralf Stephan
       ([BioRuby] [PATCH] GO annotations fixes and improvements).

 lib/bio/db/go.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit acab0bb4a4e0f970f8f6be3aea2c371f63a49fa7
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Aug 25 22:58:42 2010 +0900

    Database names used in tests are changed, following the change of TogoWS.
    
     * Database names used in tests are changed, following the change of
       TogoWS: "gene" to "kegg-genes" and "enzyme" to "kegg-enzyme".

 test/functional/bio/io/test_togows.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit 1fb1f1cc5ca3edb42de03874b3527ce0cf0de294
Author: Toshiaki Katayama <k@bioruby.org>
Date:   Tue Jul 20 11:46:52 2010 +0900

    Database name used in tests is changed, following the change of TogoWS.
    
     * The database name "genbank" is changed to "nucleotide", following
       the change in TogoWS.
     * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb.
       (Original commit message: Changes for TogoWS)

 test/functional/bio/io/test_togows.rb |   10 +++++-----
 1 files changed, 5 insertions(+), 5 deletions(-)

commit 1db4b8011f4fee158aeb78ec2d76c76688714788
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Aug 11 23:33:49 2010 +0900

    New method Bio::Fastq#mask for masking low score regions.
    
     * New method Bio::Fastq#mask for masking low score regions is added
       with unit tests. This method is implemented as a shortcut of
       Bio::Sequence#mask_with_quality_score method.

 lib/bio/db/fastq.rb            |   15 +++++++++++++++
 test/unit/bio/db/test_fastq.rb |   36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+), 0 deletions(-)

commit 72b47b2391a01c5f4214fd188abe0857cd3ed166
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Aug 11 23:04:57 2010 +0900

    New module Bio::Sequence::SequenceMasker to help masking a sequence.
    
     * New module Bio::Sequence::SequenceMasker to help masking a sequence.
       The module is only expected to be included in Bio::Sequence.
       In the future, methods in this module might be moved to
       Bio::Sequence or other module and this module might be removed.
     * Unit tests for Bio::Sequence::SequenceMasker are also added.

 lib/bio/sequence.rb                            |    2 +
 lib/bio/sequence/sequence_masker.rb            |   95 +++++++++++++
 test/unit/bio/sequence/test_sequence_masker.rb |  169 ++++++++++++++++++++++++
 3 files changed, 266 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/sequence/sequence_masker.rb
 create mode 100644 test/unit/bio/sequence/test_sequence_masker.rb

commit a2b21fa31c87fc47ae375380fb34958460414107
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Aug 11 22:59:46 2010 +0900

    New method Bio::Sequence#output_fasta, a replacement for to_fasta.
    
     * New method Bio::Sequence#output_fasta, a replacement for
       Bio::Sequence#to_fasta. This is also implemented as a shortcut of
       Bio::Sequence#output(:fasta).

 lib/bio/sequence/format.rb |   14 ++++++++++++++
 1 files changed, 14 insertions(+), 0 deletions(-)

commit d139a1e3e7f77317102eaa24649515541761a212
Author: Toshiaki Katayama <k@bioruby.org>
Date:   Tue Jul 20 11:46:52 2010 +0900

    File format autodetection for Bio::KEGG::PATHWAY and Bio::KEGG::MODULE.
    
     * Added file format autodetection for Bio::KEGG::PATHWAY and
       Bio::KEGG::MODULE.
     * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb.
       (Original commit message: Changes for TogoWS)

 lib/bio/io/flatfile/autodetection.rb |    6 ++++++
 1 files changed, 6 insertions(+), 0 deletions(-)

commit 920d92c13b44921a3f58ddbd8566e7a90dd59996
Author: Toshiaki Katayama <k@bioruby.org>
Date:   Tue Jul 20 11:46:52 2010 +0900

    Added autoload for Bio::KEGG::PATHWAY and Bio::KEGG::MODULE.
    
     * Added autoload for Bio::KEGG::PATHWAY and Bio::KEGG::MODULE.
     * This is part of commit e2abe5764f3ded91c82689245f19a0412d3a7afb.
       (Original commit message: Changes for TogoWS)

 lib/bio.rb |    2 ++
 1 files changed, 2 insertions(+), 0 deletions(-)

commit bf342c28e0c75c9b48770144f421dd12babd9d0e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Aug 17 23:19:47 2010 +0900

    Unit tests for Bio::KEGG::MODULE is modified and improved.

 test/unit/bio/db/kegg/test_module.rb |  194 ++++++++++++++++++++++++++++++----
 1 files changed, 173 insertions(+), 21 deletions(-)

commit 1742568a4f27e75a19441e4a4437ca3f1c0251f8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Aug 17 23:15:44 2010 +0900

    In Bio::KEGG::MODULE, an internal-only method is changed to private.

 lib/bio/db/kegg/module.rb |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

commit 8f5ff66cca678ac6be75a7dda1ff840ac3111f42
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Aug 17 23:10:39 2010 +0900

    Removed unused comments.

 lib/bio/db/kegg/module.rb |   32 --------------------------------
 1 files changed, 0 insertions(+), 32 deletions(-)

commit f9d23fb32eeb15dc57580e25653d3f2fff5fa1dc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Aug 17 22:59:18 2010 +0900

    Reverted Bio::KEGG::MODULE#keggclass.
    
     * Reverted Bio::KEGG::MODULE#keggclass.
     * Removed keggclasses and keggclasses_as_array methods, because
       they are inconsistent with Bio::KEGG::ORTHOLOGY#keggclasses.

 lib/bio/db/kegg/module.rb |    6 +-----
 1 files changed, 1 insertions(+), 5 deletions(-)

commit 94188d23ad843c7cb998c99f46371e540ce457dc
Author: Toshiaki Katayama <k@bioruby.org>
Date:   Tue Jul 20 11:41:50 2010 +0900

    For Bio::KEGG::MODULE, methods are added and modified.
    
     * For Bio::KEGG::MODULE, methods are added and modified.
       * New methods: definition, etc.
       * Removed methods: pathway, orthologies, keggclass, etc.
       * Changed methods: reactions, compounds, etc.
     * (Original commit message: Changes for TogoWS)

 lib/bio/db/kegg/module.rb |  136 +++++++++++++++++++++++++++++++++++++++++---
 1 files changed, 126 insertions(+), 10 deletions(-)

commit 92efc03707a49fa0b2c02e7b2f8b53749a75ad59
Author: Kozo Nishida <kozo-ni@cg04.naist.jp>
Date:   Thu Feb 4 22:59:20 2010 +0900

    New class Bio::KEGG::MODULE, parser for KEGG MODULE (Pathway Module).

 lib/bio/db/kegg/module.rb            |   83 ++++++++++++++++++++++++++++++
 test/data/KEGG/M00118.module         |   44 ++++++++++++++++
 test/unit/bio/db/kegg/test_module.rb |   94 ++++++++++++++++++++++++++++++++++
 3 files changed, 221 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/kegg/module.rb
 create mode 100644 test/data/KEGG/M00118.module
 create mode 100644 test/unit/bio/db/kegg/test_module.rb

commit b7c75cc6023d5dc9096111fde99a6e89db2e4bdc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed May 12 01:13:52 2010 +0900

    Improvement of tests for Bio::KEGG::ORTHOLOGY using updated test data.

 test/unit/bio/db/kegg/test_orthology.rb |   95 +++++++++++++++++++++++++++++++
 1 files changed, 95 insertions(+), 0 deletions(-)

commit f61c232371f6f673044960b0626486b2e8e160b8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed May 12 01:11:16 2010 +0900

    Updated test data K02338.orthology to follow KEGG format changes.

 test/data/KEGG/K02338.orthology |  232 ++++++++++++++++++++++++++++++---------
 1 files changed, 180 insertions(+), 52 deletions(-)

commit 2aa060f42263392877683a47ef9bd744ef4de7f8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed May 12 01:03:18 2010 +0900

    Incompatible change of Bio::KEGG::ORTHOLOGY#pathways, and added new methods
    
     * Incompatible change of Bio::KEGG::ORTHOLOGY#pathways due to the
       changes of KEGG ORTHOLOGY format changes: Because PATHWAY field
       is added, the method is changed to return a hash. The pathway
       method of old behavior is renamed to pathways_in_keggclass
       for compatibility.
     * New methods are added to Bio::KEGG::ORTHOLOGY: references,
       pathways_as_strings, pathways_as_hash, pathway_modules,
       pathway_modules_as_hash, pathway_modules_as_strings.

 lib/bio/db/kegg/orthology.rb |   41 ++++++++++++++++++++++++++++++++++++++++-
 1 files changed, 40 insertions(+), 1 deletions(-)

commit 2e6754f2598f66f29afb573c3dc83592089b411c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed May 12 00:59:26 2010 +0900

    Changed to use Bio::KEGG::Common::PathwayModulesAsHash.

 lib/bio/db/kegg/pathway.rb |   25 ++++++++-----------------
 1 files changed, 8 insertions(+), 17 deletions(-)

commit 527920da990f4374e20333d6852b810ea73ead02
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed May 12 00:55:10 2010 +0900

    New module Bio::KEGG::Common::PathwayModulesAsHash (internal use only)
    
     * New module Bio::KEGG::Common::PathwayModulesAsHash is added,
       based on Bio::KEGG::PATHWAY#pathway_modules_as_hash method.
       Note that the method is Bio::KEGG::* internal use only.

 lib/bio/db/kegg/common.rb |   22 ++++++++++++++++++++++
 1 files changed, 22 insertions(+), 0 deletions(-)

commit 36041377dbafce642180eb1c664ee36ef21d3bfb
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Mar 19 23:25:56 2010 +0900

    New method Bio::KEGG::PATHWAY#references.
    
     * New method Bio::KEGG::PATHWAY#references.
     * Additional unit tests for Bio::KEGG::PATHWAY with test data.

 lib/bio/db/kegg/pathway.rb            |    8 ++
 test/data/KEGG/map00030.pathway       |   37 ++++++++++
 test/unit/bio/db/kegg/test_pathway.rb |  120 ++++++++++++++++++++++++++++++++-
 3 files changed, 162 insertions(+), 3 deletions(-)
 create mode 100644 test/data/KEGG/map00030.pathway

commit d743892d298786eb9e88e2a51ac9f7774785848f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Mar 19 00:06:20 2010 +0900

    Improvement of Bio::KEGG::Common::References#references.
    
     * Improvement of Bio::KEGG::Common::References#references:
       added support for parsing "journal (year)" style.

 lib/bio/db/kegg/common.rb |    4 ++++
 1 files changed, 4 insertions(+), 0 deletions(-)

commit 35807ae22c9ad9a3ce37ed5c655d1c080f8d2334
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Mar 19 00:02:10 2010 +0900

    Implementation of Bio::KEGG::GENOME#references is moved.
    
     * Implementation of Bio::KEGG::GENOME#references is moved to
       Bio::KEGG::Common::References#references, which will be
       shared with Bio::KEGG::Pathway and other classes.

 lib/bio/db/kegg/common.rb |   61 +++++++++++++++++++++++++++++++++++++++++++-
 lib/bio/db/kegg/genome.rb |   62 +++++---------------------------------------
 2 files changed, 67 insertions(+), 56 deletions(-)

commit 263c37a07203b87e3b33d35adef3aa3ddcf89601
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Mar 17 00:26:56 2010 +0900

    Bug fix: Bio::KEGG::GENES#pathway may fail, and other parse issues due to the format changes of KEGG GENES.
    
     * Bug fix: Bio::KEGG::GENES#pathway may return unexpected value
       after calling pathways, pathways_as_hash or pathways_as_string
       methods.
     * Bio::KEGG::GENES#eclinks, Bio::KEGG::Common::PathwaysAsHash,
       and Bio::KEGG::Common::OrthologsAsHash are modified due to
       the file format changes of KEGG::GENES.

 lib/bio/db/kegg/common.rb |    9 +++++----
 lib/bio/db/kegg/genes.rb  |   17 +++++++++++------
 2 files changed, 16 insertions(+), 10 deletions(-)

commit 364cd405a10d0742091281c5a16b77cb54a8087e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Mar 17 00:25:51 2010 +0900

    New methods Bio::Location#== and Bio::Locations#==.

 lib/bio/location.rb |   39 +++++++++++++++++++++++++++++++++++++++
 1 files changed, 39 insertions(+), 0 deletions(-)

commit 2c7ffd6808e572cf35b82d6e74790447d44d08cc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Mar 17 00:23:00 2010 +0900

    Improved unit tests for Bio::KEGG::GENES with new test data.

 test/data/KEGG/b0529.gene           |   47 +++++++
 test/unit/bio/db/kegg/test_genes.rb |  254 ++++++++++++++++++++++++++++++++++-
 2 files changed, 300 insertions(+), 1 deletions(-)
 create mode 100644 test/data/KEGG/b0529.gene

commit 764869fd42d1e3f96885b3499844bf4fadde80f1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Mar 17 00:10:51 2010 +0900

    Bug fix: Bio::KEGG::GENOME parser issues for PLASMID, REFERENCE, and ORIGINAL_DB fields.
    
     * Bug fix: Fixed parse error for PLASMID fields due to the changes
       of the KEGG GENOME file format. For the bug fix, tag_get and
       tag_cut methods are redefined.
     * Bug fix: Fixed parse error for REFERENCE fields due to the changes
       of the file format.
     * New method Bio::KEGG::GENOME#original_databases is added to get
       ORIGINAL_DB record as an Array of String objects.

 lib/bio/db/kegg/genome.rb |   69 +++++++++++++++++++++++++++++++++++++++-----
 1 files changed, 61 insertions(+), 8 deletions(-)

commit 75db7c6c7132f19e212be36d06643a0f48a7df44
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Mar 17 00:09:09 2010 +0900

    New method Bio::Reference#==.

 lib/bio/reference.rb |   24 ++++++++++++++++++++++++
 1 files changed, 24 insertions(+), 0 deletions(-)

commit 64a6bfb52ca1bb27bd38c86c060e2925f38924fb
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Mar 17 00:07:43 2010 +0900

    Newly added unit tests for Bio::KEGG::GENOME with test data.

 test/data/KEGG/T00005.genome         |  140 ++++++++++++
 test/data/KEGG/T00070.genome         |   34 +++
 test/unit/bio/db/kegg/test_genome.rb |  408 ++++++++++++++++++++++++++++++++++
 3 files changed, 582 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/T00005.genome
 create mode 100644 test/data/KEGG/T00070.genome
 create mode 100644 test/unit/bio/db/kegg/test_genome.rb

commit 21c92bb991c83dce27a4411382c456cdd6029a82
Author: Naohisa Goto <ngoto@gen-info.osaka-u.ac.jp>
Date:   Tue Mar 9 23:24:15 2010 +0900

    Renamed Bio::KEGG::PATHWAY#keggmodules to pathway_modules_as_strings, etc.
    
     * Bio::KEGG::PATHWAY#keggmodules is renamed to
       pathway_modules_as_strings.
     * New method pathway_modules_as_hash and its alias method
       pathway_modules is added.
     * Bio::KEGG::PATHWAY#rel_pathways is renamed to
       rel_pathways_as_strings.
     * New method rel_pathways_as_hash is added, and rel_pathways
       is changed to be the alias of the rel_pathways_as_hash method.
     * Unit tests are also changed.

 lib/bio/db/kegg/pathway.rb            |   42 +++++++++++++++++++++++++++++++-
 test/unit/bio/db/kegg/test_pathway.rb |   29 ++++++++++++++++++++--
 2 files changed, 66 insertions(+), 5 deletions(-)

commit fa10f38716ec2eecd6fa8e8b027085377e9ee421
Author: Naohisa Goto <ngoto@gen-info.osaka-u.ac.jp>
Date:   Tue Mar 9 21:13:18 2010 +0900

    Fixed text indentations.

 lib/bio/db/kegg/pathway.rb            |    4 ++--
 test/unit/bio/db/kegg/test_pathway.rb |   25 +++++++++++++------------
 2 files changed, 15 insertions(+), 14 deletions(-)

commit 0916b0cac5d17ce47ef5cc3382e3167293bcf4c2
Author: Kozo Nishida <kozo-ni@cg04.naist.jp>
Date:   Tue Feb 2 17:34:17 2010 +0900

    Newly added Bio::KEGG::PATHWAY with test code and test data.

 lib/bio/db/kegg/pathway.rb            |   73 +++++++++++++++++++++++++++++++++
 test/data/KEGG/map00052.pathway       |   13 ++++++
 test/unit/bio/db/kegg/test_pathway.rb |   57 +++++++++++++++++++++++++
 3 files changed, 143 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/kegg/pathway.rb
 create mode 100644 test/data/KEGG/map00052.pathway
 create mode 100644 test/unit/bio/db/kegg/test_pathway.rb

commit c3ceea339164754071f03ce13da4f65e08230f40
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Feb 19 00:43:38 2010 +0900

    Tutorial.rd.html is regenerated.

 doc/Tutorial.rd.html |   55 +++++++++++++++++++++++++++++++++++++++++++++++++-
 1 files changed, 54 insertions(+), 1 deletions(-)

commit 315da0213edfece696d22cc4648cb7a74f18ad34
Author: Ra <ilpuccio.febo@gmail.com>
Date:   Sun Feb 7 10:38:36 2010 +0100

    Added BioSQL docs links

 doc/Tutorial.rd |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 22374415873906f4bcd3e84950c14b5f0b6c7e61
Author: Ra <ilpuccio.febo@gmail.com>
Date:   Sun Feb 7 02:39:16 2010 +0100

    Added link to BioSQL install doc.

 doc/Tutorial.rd |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 4d18dd2f5a3f18348e5f4aa07b14c104d3a65f5b
Author: Ra <ilpuccio.febo@gmail.com>
Date:   Fri Feb 5 21:30:36 2010 +0100

    Added other examples about BioSQL

 doc/Tutorial.rd |   36 ++++++++++++++++++++++++++++--------
 1 files changed, 28 insertions(+), 8 deletions(-)

commit b704f01cd0799ab1a7e3975119e9d6139ddfbd51
Author: Ra <ilpuccio.febo@gmail.com>
Date:   Wed Jan 27 21:08:25 2010 +0100

    BioSQL tutorial continue...

 doc/Tutorial.rd |   18 ++++++++++++++++--
 1 files changed, 16 insertions(+), 2 deletions(-)

commit 1993a1566b5ade937703d0291c4eaf2de673d170
Author: Ra <ilpuccio.febo@gmail.com>
Date:   Wed Jan 27 20:32:23 2010 +0100

    BioSQL tutorial inital draft.

 doc/Tutorial.rd |   25 ++++++++++++++++++++++++-
 1 files changed, 24 insertions(+), 1 deletions(-)

commit 09047b664a03492d7546d92b619faacee72d0cd5
Author: Jan Aerts <jan.aerts@gmail.com>
Date:   Sun Feb 7 17:58:59 2010 +0900

    Added code example that will serve as basis for sequence/codon howto

 doc/howtos/sequence_codon.txt |   38 ++++++++++++++++++++++++++++++++++++++
 1 files changed, 38 insertions(+), 0 deletions(-)
 create mode 100644 doc/howtos/sequence_codon.txt

commit c1e2165ba801cccd52135b13ed36713517e1fa8a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Feb 5 12:50:38 2010 +0900

    Suppressed "warning: parenthesize argument(s) for future version" in Ruby 1.8.5.

 lib/bio/appl/paml/codeml/report.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit f7ce9ba6a2f4e680ee40017a21aa95d05baf34f4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Feb 4 20:26:00 2010 +0900

    Added :startdoc: and removed an empty line for RDoc.

 lib/bio/appl/paml/codeml/report.rb |    4 +++-
 1 files changed, 3 insertions(+), 1 deletions(-)

commit 6d4d2e1f37efb1e53091fbc9a0977568996788ff
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Feb 4 16:58:10 2010 +0900

    New unit test for Bio::PAML::Codeml::Report.
    
     * New unit test for Bio::PAML::Codeml::Report and related classes.
       The test code is copied from the examples described in
       lib/bio/appl/paml/codeml/report.rb and modified for the unit test.

 test/unit/bio/appl/paml/codeml/test_report.rb |  253 +++++++++++++++++++++++++
 1 files changed, 253 insertions(+), 0 deletions(-)
 create mode 100644 test/unit/bio/appl/paml/codeml/test_report.rb

commit 8418549811293c3e20b91d4e95da2cb2a282a064
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Feb 4 16:47:37 2010 +0900

    Changes due to the rename to report_single.rb.

 .../bio/appl/paml/codeml/test_report_single.rb     |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 7bfb428da237709b243c8d0e4646bd41710d1519
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Feb 4 16:39:10 2010 +0900

    Renamed codeml/test_report.rb to codeml/test_report_single.rb.
    
     * Renamed test/unit/bio/appl/paml/codeml/test_report.rb to
       test_report_single.rb.

 test/unit/bio/appl/paml/codeml/test_report.rb      |   46 --------------------
 .../bio/appl/paml/codeml/test_report_single.rb     |   46 ++++++++++++++++++++
 2 files changed, 46 insertions(+), 46 deletions(-)
 delete mode 100644 test/unit/bio/appl/paml/codeml/test_report.rb
 create mode 100644 test/unit/bio/appl/paml/codeml/test_report_single.rb

commit 762d38b1564da7d846e3dcd461cf465aa685a1ae
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Tue Jan 12 10:13:35 2010 +0100

    Modified output of Bio::PAML::Codeml::PositiveSites#graph_to_s
    
     * Modified output of Bio::PAML::Codeml::PositiveSites#graph_to_s.
       (Part of commit ea350da85e5db2ba35cb8dd1e86e3d4323ee3fd1.
        Original commit message is:
        HtmlPaml: fixed some missing output
              use real greek omega in output)

 lib/bio/appl/paml/codeml/report.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit f88645cd783b7027950133c0badb0a8da8e4fb95
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Tue Jan 12 09:24:46 2010 +0100

    Codeml: no negative gaps

 lib/bio/appl/paml/codeml/report.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 978b21cf90d0280e6e6c7d6e4fa65c49692bdd69
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 17:31:45 2010 +0100

    Codeml: always raise an error when significance can not be calculated

 lib/bio/appl/paml/codeml/report.rb |   15 ++++++++++-----
 1 files changed, 10 insertions(+), 5 deletions(-)

commit 12b5895f6f1819252d616bb0a38aa88a7828daff
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 17:22:34 2010 +0100

    Codeml: oops

 lib/bio/appl/paml/codeml/report.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit a8ff0a07fdbef72f72103f0bceb9c24a63162fc6
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 17:19:26 2010 +0100

    Codeml: added significance testing for a few model combinations

 lib/bio/appl/paml/codeml/report.rb |   57 +++++++++++++++++++++++++++++++++++-
 1 files changed, 56 insertions(+), 1 deletions(-)

commit 0e11af19450faca3568f89b23d5bd764688f75c0
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 16:24:51 2010 +0100

    Codeml: raise error instead of a 'nil' error when buffer is incomplete

 lib/bio/appl/paml/codeml/report.rb |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit 1cb2aaaa701a1613812dd479201d27c1d7dcf016
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 14:37:52 2010 +0100

    Bio::PAML::Codeml::PositiveSites#graph_to_s gets fill character
    
     * Bio::PAML::Codeml::PositiveSites#graph_to_s gets fill character
       as an argument.
       (Part of commit d67259c9f203dc92c68ad04b4112329a7093a259.
        Original commit message is:
        HtmlPaml: show colors for probabilities of positive selection)

 lib/bio/appl/paml/codeml/report.rb |   15 +++++++++------
 1 files changed, 9 insertions(+), 6 deletions(-)

commit ae5b9cf9ee697cc237c77335b12b57709a0e7a46
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 13:37:52 2010 +0100

    Codeml: return correct buffer

 lib/bio/appl/paml/codeml/report.rb |   10 +++++-----
 1 files changed, 5 insertions(+), 5 deletions(-)

commit 44f2e28c3e0d382505b067ec3c7aa55cbb9f0a38
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 13:10:40 2010 +0100

    Improvement of Bio::PAML::Codeml::PositiveSites#initialize, etc
    
     * Improved target analysis location detection in
       Bio::PAML::Codeml::PositiveSites#initialize.
     * Changed description inside Bio::PAML::Codeml::Report#nb_sites
       and sites methods.
     * This is part of commit e88ff474748b3295a8a4089356d3086638200d64.
       (Original commit message: HtmlPaml: improved output)

 lib/bio/appl/paml/codeml/report.rb |   20 ++++++++++++--------
 1 files changed, 12 insertions(+), 8 deletions(-)

commit ee8973696d0434c591ceaffc580f1aa30fd036f9
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 12:54:40 2010 +0100

    Codeml: fixed doctests

 lib/bio/appl/paml/codeml/report.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit f7bbb0859e28cb51137d0a8f8d962821eb67db91
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 12:51:25 2010 +0100

    New method Bio::PAML::Codeml::PositiveSites#to_s
    
     * New method Bio::PAML::Codeml::PositiveSites#to_s
       (part of the commit 82e933fd1961a2b31873bc37cbf3205adbf0a6de,
        original commit message: HtmlPaml: add facility for color output)

 lib/bio/appl/paml/codeml/report.rb |    6 ++++++
 1 files changed, 6 insertions(+), 0 deletions(-)

commit d4f3dbaf78f623d870a1a76ab1353d786e0fb73b
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 12:34:59 2010 +0100

    Codeml: HtmlPaml: minor tweaks

 lib/bio/appl/paml/codeml/report.rb |    7 ++-----
 1 files changed, 2 insertions(+), 5 deletions(-)

commit 7d41b6acb41c5913622fde127a030f940a432cc5
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 12:19:15 2010 +0100

    Codeml: add short description to positive sites line

 lib/bio/appl/paml/codeml/report.rb |   13 +++++++++++++
 1 files changed, 13 insertions(+), 0 deletions(-)

commit a9d6765b3a5d23be7e8cf59954d67cd2354e5878
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 12:13:55 2010 +0100

    Codeml: fixed bug in graph output

 lib/bio/appl/paml/codeml/report.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit af124dcaa2adb446e273456f8dd0b84aff9b00db
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 11 12:11:00 2010 +0100

    Codeml: added graph_seq, which shows the AA of the first sequence at positive sites

 lib/bio/appl/paml/codeml/report.rb |   11 +++++++++--
 1 files changed, 9 insertions(+), 2 deletions(-)

commit 1924dcd951a9e655726bc1af72626526ed223258
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Fri Jan 8 10:13:37 2010 +0100

    Codeml: added :stopdoc: directive for rdoc

 lib/bio/appl/paml/codeml/report.rb |   21 ++++++++++++---------
 1 files changed, 12 insertions(+), 9 deletions(-)

commit 7b68fd9d785723935f90144f67999fcf74bcc7c0
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Fri Jan 8 10:01:49 2010 +0100

    Codeml: fixed the doctests and added some info.
            all tests pass &

 lib/bio/appl/paml/codeml/report.rb |   43 ++++++++++++++++++++++++-----------
 1 files changed, 29 insertions(+), 14 deletions(-)

commit ce212c507e9e81120e7ad12be6df955e90d0ad33
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Fri Jan 8 09:46:05 2010 +0100

    Codeml: exclude TestFile class from RDoc generated documentation

 lib/bio/appl/paml/codeml/report.rb |    9 ++++++---
 1 files changed, 6 insertions(+), 3 deletions(-)

commit 9d64a70b628cb3cda9cc1576b9966dae242e5230
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Fri Jan 8 09:39:02 2010 +0100

    Codeml: added many comments

 lib/bio/appl/paml/codeml/report.rb |   87 +++++++++++++++++++++++++++++------
 1 files changed, 72 insertions(+), 15 deletions(-)

commit 2b92df64016865a2ab40c93650409cfd67a2a98e
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 4 17:57:32 2010 +0100

    codeml: Added parser for full Bayesian sites
            all tests pass &

 lib/bio/appl/paml/codeml/report.rb |   52 ++++++++++++++++++++++++++++++-----
 1 files changed, 44 insertions(+), 8 deletions(-)

commit 198f0c014f7993fbe22825d0be67e9b1aa19d2de
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 4 17:37:15 2010 +0100

    codeml: show graph

 lib/bio/appl/paml/codeml/report.rb |   46 ++++++++++++++++++++++++++++++++++-
 1 files changed, 44 insertions(+), 2 deletions(-)

commit 0843bb4d79dc4d94a22d79a797a39dc2866222c5
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 4 17:09:27 2010 +0100

    Codeml: added full support for positive selection sites
            doctests + unit tests pass &

 lib/bio/appl/paml/codeml/report.rb |  150 ++++++++++++++++++++++++++++--------
 1 files changed, 118 insertions(+), 32 deletions(-)

commit 1610c5d86cddd53f7f0300d0f7a137daaa61ef94
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 4 12:33:20 2010 +0100

    codeml: added M3 classes

 lib/bio/appl/paml/codeml/report.rb |   28 +++++++++++++++++++++++++---
 1 files changed, 25 insertions(+), 3 deletions(-)

commit efc939fbd300ceb371b342172382cdec9fcc74b7
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Mon Jan 4 12:02:47 2010 +0100

    codeml: adding compatibility layer for single model (old type)
            unit tests pass &

 lib/bio/appl/paml/codeml/report.rb |   44 +++++++++++++++++++++++++++++++-----
 1 files changed, 38 insertions(+), 6 deletions(-)

commit b89990daa3ea26a9f9195ec16044fb2070bcdd1a
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Sun Jan 3 12:34:53 2010 +0100

    Implementation parsing one model - doctests for M0 pass

 lib/bio/appl/paml/codeml/report.rb |   90 ++++++++++++++++++++++++++++++++----
 1 files changed, 81 insertions(+), 9 deletions(-)

commit dce447d3e81e738323e6fb6b2d28324e1fa62e7d
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Sun Jan 3 11:27:54 2010 +0100

    Codeml: use BioTestFile for locating test data in the doctest

 lib/bio/appl/paml/codeml/report.rb |    9 ++++++++-
 1 files changed, 8 insertions(+), 1 deletions(-)

commit 27a7b558d60b7ec127df2c351542433c321704ac
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Sat Jan 2 23:36:47 2010 +0100

    Codeml: split new type report and old type report

 lib/bio/appl/paml/codeml/report.rb |   19 +++++++++++++++----
 1 files changed, 15 insertions(+), 4 deletions(-)

commit 027808e4723ca77af3e15b461ddcc09faf692732
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Sat Jan 2 23:25:22 2010 +0100

    Added example files for PAML codeml dual model runs

 test/data/paml/codeml/models/aa.aln         |   26 ++
 test/data/paml/codeml/models/aa.dnd         |   13 +
 test/data/paml/codeml/models/aa.ph          |   13 +
 test/data/paml/codeml/models/alignment.phy  |   49 ++++
 test/data/paml/codeml/models/results0-3.txt |  312 ++++++++++++++++++++++++
 test/data/paml/codeml/models/results7-8.txt |  340 +++++++++++++++++++++++++++
 6 files changed, 753 insertions(+), 0 deletions(-)
 create mode 100644 test/data/paml/codeml/models/aa.aln
 create mode 100644 test/data/paml/codeml/models/aa.dnd
 create mode 100644 test/data/paml/codeml/models/aa.ph
 create mode 100644 test/data/paml/codeml/models/alignment.phy
 create mode 100644 test/data/paml/codeml/models/results0-3.txt
 create mode 100644 test/data/paml/codeml/models/results7-8.txt

commit 1d35e616ce411bf643ab6dcb7126a6e1aca1e186
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Sat Jan 2 17:04:56 2010 +0100

    Codeml::Report Added new description and reference

 lib/bio/appl/paml/codeml/report.rb |  113 ++++++++++++++++++++++++++++++------
 1 files changed, 96 insertions(+), 17 deletions(-)

commit d21b26044e776fab44dbc95f181afd04b67abe28
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Feb 1 22:31:21 2010 +0900

    Bug fix and Ruby 1.9 support: Bio::Command.call_command_fork etc.
    
     * Bug fix: In Bio::Command.call_command_fork, thread switching is
       disabled in the child process. Thanks to Andrew Grimm who
       reports the bug ([BioRuby] Thread-safety of alignment).
       Note that call_command_fork no longer works in Ruby 1.9 because
       it is changed to use Thread.critical which is removed in Ruby 1.9.
     * Ruby 1.9 support: In Ruby 1.9, Bio::Command.call_command_popen
       bypasses shell execution by passing command-line as an Array,
       which is a new feature added in Ruby 1.9. Now, call_command_popen
       is safe and robust enough with Ruby 1.9.
     * Ruby 1.9 support: In Ruby 1.9, Bio::Command.call_command and
       query_command use call_command_popen and query_command_popen,
       respectively.
     * RDoc for the above and related methods are modified.

 lib/bio/command.rb                  |   80 +++++++++++++++++++++++++++++++----
 test/functional/bio/test_command.rb |    4 ++
 2 files changed, 76 insertions(+), 8 deletions(-)

commit 981dc1c89049bf00e56a9e83ef352cb4c4b45d6a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Feb 2 22:47:36 2010 +0900

    Bug fix: Bio::FastaNumericFormat#to_biosequence bug fix
    
     * Bug fix: New method Bio::FastaNumericFormat#to_biosequence is
       defined to avoid NomethodError occurred in the superclass'es
       method. For the purpose, a new module
       Bio::Sequence::Adapter::FastaNumericFormat is added.
       Thanks to Hiroyuki MISHIMA who reports the bug ([BioRuby] trouble
       on the FASTA.QUAL format (Bio::FastaNumericFormat)).
     * Newly added unit test for Bio::FastaNumericFormat#to_biosequence.

 lib/bio/db/fasta/qual.rb                |   24 ++++++++++++++++++++++++
 lib/bio/db/fasta/qual_to_biosequence.rb |   29 +++++++++++++++++++++++++++++
 lib/bio/sequence/adapter.rb             |    1 +
 test/unit/bio/db/test_qual.rb           |   11 +++++++++--
 4 files changed, 63 insertions(+), 2 deletions(-)
 create mode 100644 lib/bio/db/fasta/qual_to_biosequence.rb

commit 29ed6870e453f54aac2ce9dcb7891186eb01c40d
Author: Ben J Woodcroft <ben@reefedge.sols.uq.edu.au>
Date:   Wed Jan 13 14:38:13 2010 +1000

    Bug fix: fixed uniprot GN parsing issue

 lib/bio/db/embl/sptr.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit a3002a79ec012559f5847ba8ebe4faf6e7fa609e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Jan 8 22:14:15 2010 +0900

    Tutorial.rd.html is regenerated.

 doc/Tutorial.rd.html |   29 ++++++++++++++---------------
 1 files changed, 14 insertions(+), 15 deletions(-)

commit 9238c3cb0e8f1156d23a5dfb3ce4e299a91b9f23
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Fri Jan 8 09:04:23 2010 +0100

    Tutorial: removed bad links

 doc/Tutorial.rd |   10 +---------
 1 files changed, 1 insertions(+), 9 deletions(-)

commit 60542fd9863c5fc1240a15cc76f8fa90644a15c8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jan 6 20:38:25 2010 +0900

    Changed header and the depth of loading helper due to the rename.

 test/unit/bio/appl/clustalw/test_report.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 68924e736df76fe3c77d9fe132b6df01fc0621fe
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jan 6 20:34:10 2010 +0900

    Renamed test/unit/bio/db/test_clustalw.rb to test/unit/bio/appl/clustalw/test_report.rb.

 test/unit/bio/appl/clustalw/test_report.rb |   61 ++++++++++++++++++++++++++++
 test/unit/bio/db/test_clustalw.rb          |   61 ----------------------------
 2 files changed, 61 insertions(+), 61 deletions(-)
 create mode 100644 test/unit/bio/appl/clustalw/test_report.rb
 delete mode 100644 test/unit/bio/db/test_clustalw.rb

commit 8368eee50de51f6218ffc7b1bf1aad332702c4ba
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Tue Jan 5 12:54:43 2010 +0100

    Clustal: unit tests according to Naohisa

 lib/bio/appl/clustalw/report.rb   |    6 +++---
 test/unit/bio/db/test_clustalw.rb |   10 +++++-----
 2 files changed, 8 insertions(+), 8 deletions(-)

commit ad525a01fa17052e9b7e9b7f30639c48596552ba
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Tue Jan 5 12:50:17 2010 +0100

    Clustal: unit test uses File.read

 test/unit/bio/db/test_clustalw.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 7ab517e05cc470b9ca57273092599adb8c00dc11
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Tue Jan 5 12:49:21 2010 +0100

    Clustal: unit test, changed class name and copyright header

 test/unit/bio/db/test_clustalw.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 0829ee91a97976eb6671a2feec7edfc524f44b2c
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Tue Jan 5 12:46:37 2010 +0100

    Clustal: Changed [] to get_sequence, with method description
    
     * Clustal: Added copyright.
     * Changed [] to get_sequence, with method description.

 lib/bio/appl/clustalw/report.rb |   12 ++++++++++--
 1 files changed, 10 insertions(+), 2 deletions(-)

commit 3b8968a6b7b98e0f03b0822849594262a8f4ac99
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Sun Dec 27 16:44:30 2009 +0100

    ClustalW: Added [] method to reach sequence + definition

 lib/bio/appl/clustalw/report.rb   |    9 +++++++++
 test/unit/bio/db/test_clustalw.rb |    6 ++----
 2 files changed, 11 insertions(+), 4 deletions(-)

commit 3926fabbcc0636c6e4ed08233af3d647c620cd5b
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Sun Dec 27 16:22:38 2009 +0100

    ClustalW: Add ALN parser unit test

 test/data/clustalw/example1.aln   |   58 ++++++++++++++++++++++++++++++++++
 test/unit/bio/db/test_clustalw.rb |   63 +++++++++++++++++++++++++++++++++++++
 2 files changed, 121 insertions(+), 0 deletions(-)
 create mode 100644 test/data/clustalw/example1.aln
 create mode 100644 test/unit/bio/db/test_clustalw.rb

commit 2ef97f945b122dc279eb0ec0a34a2adb0c5f0cff
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Sat Jan 2 13:24:33 2010 +0100

    Tutorial: Fixed URLs

 doc/Tutorial.rd |   10 +++++-----
 1 files changed, 5 insertions(+), 5 deletions(-)

commit 567ca8b010e15cbea9398ee74c78eae01fc6671d
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Fri Jan 1 12:08:50 2010 +0100

    Tutorial: Added info on gem install

 doc/Tutorial.rd |    9 +++++++--
 1 files changed, 7 insertions(+), 2 deletions(-)

commit 21070ab4928d9c7446d58f3003d43ee6235046aa
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Thu Dec 31 11:41:54 2009 +0100

    Tutorial.rd: Added Naohisa's Ruby replacement for sed conversion

 doc/Tutorial.rd |    6 +++++-
 1 files changed, 5 insertions(+), 1 deletions(-)

commit ebded2364f716fa03b0fdbec9887f807836eb789
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Jan 6 10:59:39 2010 +0900

    Bio::BIORUBY_EXTRA_VERSION is changed to ".5000".

 bioruby.gemspec    |    2 +-
 lib/bio/version.rb |    2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

commit a1bda9088662edec55af0106b4292c39e51c8b7b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 21:56:33 2009 +0900

    BioRuby 1.4.0 is released.

 ChangeLog       |   32 ++++++++++++++++++++++++++++++++
 bioruby.gemspec |    3 ++-
 2 files changed, 34 insertions(+), 1 deletions(-)

commit 5c88896357e1eff0686ceb06cbec0a7837f85050
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 21:55:41 2009 +0900

    Preparation for bioruby-1.4.0 release.

 lib/bio/version.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 11f56d3d8efc2cf5d9408da865af044fa099b925
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 21:52:25 2009 +0900

    Added about ChangeLog which is replaced by git-log.

 RELEASE_NOTES.rdoc |    5 +++++
 1 files changed, 5 insertions(+), 0 deletions(-)

commit 17d5b1825b6c73d710d72903d8710caa9996353a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 20:11:49 2009 +0900

    ChangeLog is autogenerated from git log.
    
     * ChangeLog is autogenerated from git log with the following command:
        % git log --stat --summary \
              3d1dfcc0e13ad582b9c70c7fdde3a89d0bacdc80..HEAD > ChangeLog

 ChangeLog | 2306 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 2306 insertions(+), 0 deletions(-)
 create mode 100644 ChangeLog

commit 02bf77af589ea62df81e9634df6fe949df2fd3ef
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 19:25:39 2009 +0900

    test_output_size is disabled because it depends on html decorations

 test/functional/bio/appl/test_pts1.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit 5781fb402e85e73fd47948b4466c8129355b714b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 19:21:21 2009 +0900

    The PTS1 Predictor's URL had been changed.
    
     * The PTS1 Predictor's URL had been changed.
     * Changed to use @uri instead of @host and @cgi_path.

 lib/bio/appl/pts1.rb |    6 ++----
 1 files changed, 2 insertions(+), 4 deletions(-)

commit a4e691d913e1ae51eadb1a871efc2c8718ef5587
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 18:33:00 2009 +0900

    Preparation of ChangeLog autogeneration: old ChangeLog is moved to doc/ChangeLog-before-1.3.1.

 ChangeLog                  | 3961 --------------------------------------------
 doc/ChangeLog-before-1.3.1 | 3961 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 3961 insertions(+), 3961 deletions(-)
 delete mode 100644 ChangeLog
 create mode 100644 doc/ChangeLog-before-1.3.1

commit c011604766baa3cdf5ca2f4a776aa67c56460d29
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 17:53:51 2009 +0900

    Tutorial.rd.html is regenerated.

 doc/Tutorial.rd.html |   70 +++++++++++++------------------------------------
 1 files changed, 19 insertions(+), 51 deletions(-)

commit 6e2cdd13d61970aa4704475bfb5aefb70719c2e1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 17:42:25 2009 +0900

    Added Bio::NCBI.default_email= in the example, and examples using deprecated Bio::PubMed methods are temporarily commented out.

 doc/Tutorial.rd |    8 ++++++++
 1 files changed, 8 insertions(+), 0 deletions(-)

commit 8e6d5e9baf98be7e58f4dda8b5d043a42149874b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 28 17:15:09 2009 +0900

    Reinserted "==>" for Blast example, and removed duplicated Ruby Ensembl API example.

 doc/Tutorial.rd |   25 ++-----------------------
 1 files changed, 2 insertions(+), 23 deletions(-)

commit 849edd7e8c5b26923cab47e7f5542948fab2b1fb
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date:   Sun Dec 27 09:49:14 2009 +0100

    Tutorial: Added info on how to run rubydoctest
              Removed bioruby> prefix for one failing BLAST test

 doc/Tutorial.rd |   69 ++++++++++++++++++++++++++++++++++++++----------------
 1 files changed, 48 insertions(+), 21 deletions(-)

commit a39fcf0ca1a5265789110f42cc616fc5d3c16414
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 25 12:30:18 2009 +0900

    Modified for release notes and fixed typo.

 RELEASE_NOTES.rdoc |   29 +++++++++++++++--------------
 1 files changed, 15 insertions(+), 14 deletions(-)

commit 3fa8b68f19fc2b6aaf8f54eb10517cc761b2193b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 25 12:10:34 2009 +0900

    Changes following the rename to RELEASE_NOTES.rdoc.

 README.rdoc         |    2 +-
 bioruby.gemspec     |    6 +++---
 bioruby.gemspec.erb |    2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

commit fd692a1165d368b9bdbe068ea6bf63fd91c9925c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 25 12:03:41 2009 +0900

    Renamed doc/Changes-1.4.rdoc to RELEASE_NOTES.rdoc.

 RELEASE_NOTES.rdoc   |  160 ++++++++++++++++++++++++++++++++++++++++++++++++++
 doc/Changes-1.4.rdoc |  160 --------------------------------------------------
 2 files changed, 160 insertions(+), 160 deletions(-)
 create mode 100644 RELEASE_NOTES.rdoc
 delete mode 100644 doc/Changes-1.4.rdoc

commit 0e37f04dd8d34517693fdd4bc27f8bdada7c2f13
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 21:48:52 2009 +0900

    Changed Bio::PhyloXML::Parser.new to open, and regenerated html.

 doc/Tutorial.rd      |   10 ++--
 doc/Tutorial.rd.html |  125 ++++++++++++++++++++++++++++++++++++++++++-------
 2 files changed, 112 insertions(+), 23 deletions(-)

commit aeacbbd425c2e88369c171bd92c60bf8e520a9e5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:26:49 2009 +0900

    bioruby.gemspec is regenerated

 bioruby.gemspec |    8 +++++++-
 1 files changed, 7 insertions(+), 1 deletions(-)

commit 1034205c199a638c359780922293f8b39c467356
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:24:56 2009 +0900

    Version number changed to 1.4.0-rc1

 lib/bio/version.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 04bf2da43f78fbb702b67323f3be1fe3bd2d0351
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:22:41 2009 +0900

    Issues added and modified.

 KNOWN_ISSUES.rdoc |   35 +++++++++++++++++++++++++++++++++--
 1 files changed, 33 insertions(+), 2 deletions(-)

commit f1a76157b009fb0ca94d9a0e0f8a85522c383b19
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:22:19 2009 +0900

    Added news and incompatible changes.

 doc/Changes-1.4.rdoc |  102 ++++++++++++++++++++++++++++++++++++++++++++++++--
 1 files changed, 98 insertions(+), 4 deletions(-)

commit 9c8ef18a20c49f17d5b89aa1db5819b2c8ee9b1d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:10:02 2009 +0900

    Email address for NCBI Entrez is given with Bio::NCBI.default_email=.

 bin/bioruby                           |    5 ++++-
 sample/demo_ncbi_rest.rb              |    2 ++
 sample/demo_pubmed.rb                 |    2 ++
 sample/pmfetch.rb                     |    2 ++
 sample/pmsearch.rb                    |    2 ++
 test/functional/bio/io/test_pubmed.rb |    4 ++++
 6 files changed, 16 insertions(+), 1 deletions(-)

commit 7a7179665694da35ab0970909bfbda9ad1b057da
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 19:09:09 2009 +0900

    Changed autoload hierarchy of Bio::NCBI.

 lib/bio.rb             |   10 ++++++----
 lib/bio/io/ncbisoap.rb |    3 ++-
 2 files changed, 8 insertions(+), 5 deletions(-)

commit f8dc0268d9edf699fd3f0cf18dd55a2b10ec3bcc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 24 18:58:18 2009 +0900

    New singleton methods Bio::NCBI.default_email=, default_tool=, etc.
    
     * New singleton methods Bio::NCBI.default_email=, default_email,
       default_tools=, default_tools, etc., because email and tool
       parameters will be mandatory in Entrez eUtils.
     * Changed to raise error when email or tool is empty. Note that
       default email is nil and library users should always set their
       email address.
     * Default tool name is changed to include $0 and bioruby version ID.
     * Added multi-thread support for Bio::NCBI::REST#ncbi_access_wait.

 lib/bio/io/ncbirest.rb |  161 ++++++++++++++++++++++++++++++++++++++---------
 1 files changed, 130 insertions(+), 31 deletions(-)

commit 2e311dc44290ef6bda48f0bcba09a3c22bf32d9a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 21 22:24:52 2009 +0900

    Description about the incompatible change of Bio::KEGG::REACTION#rpairs.

 doc/Changes-1.4.rdoc |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit d57ace3a89077caae3c681743da4b92d16b90af8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 21 22:17:46 2009 +0900

    Bio::KEGG::R#ACTION#rpairs is changed to return a hash.

 lib/bio/db/kegg/reaction.rb            |   65 ++++++++++++++++++++++++--------
 test/unit/bio/db/kegg/test_reaction.rb |   27 ++++++++++++-
 2 files changed, 74 insertions(+), 18 deletions(-)

commit 60e4c77d184ee81c51668b446518cfbc9256be50
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Dec 21 22:15:44 2009 +0900

    Document bug fix: return value mistake.

 lib/bio/db/kegg/genes.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 6376dd55aa4995769746e556ca719d37f02975d6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Dec 20 17:32:52 2009 +0900

    Added README.txt for FASTQ example data.

 test/data/fastq/README.txt |  109 ++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 109 insertions(+), 0 deletions(-)
 create mode 100644 test/data/fastq/README.txt

commit 8dec18794c846726733d66c5a22170f5b2c4bb1a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Dec 15 13:51:13 2009 +0900

    Newly added unit tests for Bio::KEGG::GLYCAN with test data.

 test/data/KEGG/G00024.glycan         |   47 ++++++
 test/data/KEGG/G01366.glycan         |   18 +++
 test/unit/bio/db/kegg/test_glycan.rb |  260 ++++++++++++++++++++++++++++++++++
 3 files changed, 325 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/G00024.glycan
 create mode 100644 test/data/KEGG/G01366.glycan
 create mode 100644 test/unit/bio/db/kegg/test_glycan.rb

commit 90b97bfbcfb3f7e3d5c28b195bdb9b9c058df887
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Dec 15 11:42:39 2009 +0900

    Newly added unit test for Bio::KEGG::DRUG with test data.

 test/data/KEGG/D00063.drug         |  104 +++++++++++++++++++
 test/unit/bio/db/kegg/test_drug.rb |  194 ++++++++++++++++++++++++++++++++++++
 2 files changed, 298 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/D00063.drug
 create mode 100644 test/unit/bio/db/kegg/test_drug.rb

commit 443f778795b82a7f572cb8b85d2a8a8b3cea1334
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Dec 15 11:38:59 2009 +0900

    New method Bio::KEGG::DRUG#products
    
     * New method Bio::KEGG::DRUG#products.
     * Improved RDoc.

 lib/bio/db/kegg/drug.rb |   50 +++++++++++++++++++++++++++++++++++++---------
 1 files changed, 40 insertions(+), 10 deletions(-)

commit 48184d96b989f909ac0effb759cbc4b1ddc98dd1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 11 01:36:54 2009 +0900

    Methods in Bio::KEGG::Common::* are changed to cache return values in instance variables.

 lib/bio/db/kegg/common.rb |   62 ++++++++++++++++++++++++++------------------
 1 files changed, 37 insertions(+), 25 deletions(-)

commit f364ea609f1e01ca5270a5bd7404e0bbf752bc89
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 11 01:23:42 2009 +0900

    Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.

 bioruby.gemspec     |  142 ++++++++++++++++++++++++++++++++++++++++++++++++++-
 bioruby.gemspec.erb |    4 +-
 lib/bio/version.rb  |    4 +-
 3 files changed, 145 insertions(+), 5 deletions(-)

commit 096b5fbf6b7ff906203aabf93eb9a0bd56ae9ba2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 11 01:22:59 2009 +0900

    Added documents about Bio::KEGG incompatible changes.

 doc/Changes-1.4.rdoc |   48 ++++++++++++++++++++++++++++++++++++++++++------
 1 files changed, 42 insertions(+), 6 deletions(-)

commit 72ed277fe30bb1033cbc16d462f137510afb84e6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 11 01:21:26 2009 +0900

    Newly added unit tests for Bio::KEGG::ENZYME with test data.

 test/data/KEGG/1.1.1.1.enzyme        |  935 ++++++++++++++++++++++++++++++++++
 test/unit/bio/db/kegg/test_enzyme.rb |  241 +++++++++
 2 files changed, 1176 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/1.1.1.1.enzyme
 create mode 100644 test/unit/bio/db/kegg/test_enzyme.rb

commit b99fcb39f7c5d2857cbb65283d85ea868ae8561d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Dec 11 01:09:03 2009 +0900

    Changed Bio::KEGG::*#dblinks, pathways, orthologs, genes methods.
    
     * In Bio::KEGG::COMPOUND, DRUG, ENZYME, GLYCAN and ORTHOLOGY, the
       method dblinks is changed to return a Hash. The old methods  are
       renamed to dblinks_as_strings.
     * In Bio::KEGG::COMPOUND, DRUG, ENZYME, GENES, GLYCAN and REACTION,
       the method  pathways is changed to return a Hash. The old methods
       are renamed to pathways_as_strings except for GENES.
     * In Bio::KEGG::ENZYME, GENES, GLYCAN and REACTION, the method
       orthologs is changed to return a Hash. The old methods are renamed
       to orthologs_as_strings.
     * Bio::KEGG::ENZYME#genes and Bio::KEGG::ORTHOLOGY#genes is changed
       to return a Hash. The old methods are renamed to genes_as_strings.
     * Added Bio::KEGG::REACTION#rpairs_as_tokens, older behavior of rpairs.
     * Modules in lib/bio/db/kegg/common.rb are moved uner Bio::KEGG::Common
       namespace.
     * Refactoring.
     * Added documents.
     * Tests modified.

 lib/bio/db/kegg/common.rb              |   40 +++++++++++++++++++++++++------
 lib/bio/db/kegg/compound.rb            |   10 ++++---
 lib/bio/db/kegg/drug.rb                |   27 +++++++++++++++------
 lib/bio/db/kegg/enzyme.rb              |   31 ++++++++++++++++++++----
 lib/bio/db/kegg/genes.rb               |   39 +++++++++++++++++++------------
 lib/bio/db/kegg/glycan.rb              |   22 +++++++++++++++--
 lib/bio/db/kegg/orthology.rb           |   25 +++++++------------
 lib/bio/db/kegg/reaction.rb            |   16 +++++++++---
 test/unit/bio/db/kegg/test_compound.rb |   27 ++++++++++++--------
 test/unit/bio/db/kegg/test_reaction.rb |   13 +++++----
 10 files changed, 170 insertions(+), 80 deletions(-)

commit 2cc9d4e2f28f6b2bbcb8f714f9e2eb144c594fbf
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 10 16:02:54 2009 +0900

    Bio::KEGG::GENES#structure no more adds PDB: prefix.
    
     * Bio::KEGG::GENES#structure no more adds PDB: prefix.
     * Added Bio::KEGG::GENES#structures as an alias of structure.

 lib/bio/db/kegg/genes.rb            |    7 +++----
 test/unit/bio/db/kegg/test_genes.rb |    7 ++++---
 2 files changed, 7 insertions(+), 7 deletions(-)

commit a8ceb23bdf19d6649aa4d879cba76a9e3f91d1d4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Dec 10 15:28:33 2009 +0900

    Refactoring of Bio::KEGG::Orthology#dblinks and genes.
    
     * Refactoring of Bio::KEGG::Orthology#dblinks and genes: no need
       to treat @data because lines_fetch internally does so.

 lib/bio/db/kegg/orthology.rb |   10 ++--------
 1 files changed, 2 insertions(+), 8 deletions(-)

commit 720e0bccdfdc6fac6222cac1a9f05d6e2419896c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 9 16:39:03 2009 +0900

    Changed dummy lines for RDoc.

 lib/bio/db/kegg/compound.rb  |    4 ++--
 lib/bio/db/kegg/orthology.rb |    2 +-
 lib/bio/db/kegg/reaction.rb  |    4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

commit 20f8c03af92e5cfedcb49e8ed9fc6fda2b86e9c9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 9 15:17:39 2009 +0900

    Refactoring of Bio::KEGG::REACTION#orthologs.
    
     * Refactoring of Bio::KEGG::REACTION#orthologs: no need to treat
       @data because lines_fetch internally does so.

 lib/bio/db/kegg/reaction.rb |    5 +----
 1 files changed, 1 insertions(+), 4 deletions(-)

commit b924601bacd643f66b37dd991913e6862df704a9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Dec 6 15:51:03 2009 +0900

    Bio::KEGG::GENES#pathways is changed to return raw lines as an Array of strings.
    
     * Bio::KEGG::GENES#pathways is changed to return raw lines as an
       Array of strings.
     * RDoc is added for Bio::KEGG::GENES.

 lib/bio/db/kegg/genes.rb |   99 ++++++++++++++++++++++++++++++++++++++++++++-
 1 files changed, 96 insertions(+), 3 deletions(-)

commit 4c840dc6a539db1d854b23991269b3e6515f637e
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date:   Wed Dec 2 17:02:00 2009 +0900

    Added test methods.

 test/unit/bio/db/kegg/test_compound.rb |   47 ++++++++++++++++++++++++++++++++
 1 files changed, 47 insertions(+), 0 deletions(-)

commit 105efa1ecd1bc99a54aac32710a97df15035119d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 23:31:07 2009 +0900

    Refactoring: to use lib/bio/db/kegg/common.rb for dblinks_as_hash method.

 lib/bio/db/kegg/orthology.rb |   16 +++++-----------
 1 files changed, 5 insertions(+), 11 deletions(-)

commit c394ead051c3a13ceb534f93816af7ad35be932a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 23:07:23 2009 +0900

    Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash with changing its return value to a hash.
    
     * Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash
       with changing its return value to a hash.
     * The code of the orthologs_as_hash method is moved to
       lib/bio/db/kegg/common.rb.
     * Added new method Bio::KEGG::REACTION#orthologs, copied from
       lib/bio/db/kegg/glycan.rb.

 lib/bio/db/kegg/common.rb              |   18 +++++++++++++++++-
 lib/bio/db/kegg/reaction.rb            |   14 ++++++--------
 sample/demo_kegg_reaction.rb           |    6 ++++--
 test/unit/bio/db/kegg/test_reaction.rb |   12 ++++++++++--
 4 files changed, 37 insertions(+), 13 deletions(-)

commit 4e01fda27166faf066104ab9897904fd46f57123
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 22:48:06 2009 +0900

    Added Bio::KEGG::REACTION#pathways_as_hash and reverted pathways method.
    
     * New method Bio::KEGG::REACTION#pathways_as_hash, using a module
       in lib/bio/db/kegg/common.rb.
     * Bio::KEGG::REACTION#pathways is reverted to return an array of
       string.

 lib/bio/db/kegg/reaction.rb            |   18 +++++++++++-------
 test/unit/bio/db/kegg/test_reaction.rb |    8 +++++++-
 2 files changed, 18 insertions(+), 8 deletions(-)

commit 0c2ce4b8462792d496ab3f58206fdbd47143e280
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 22:35:21 2009 +0900

    New methods Bio::KEGG::COMPOUND#dblinks_as_hash and pathways_as_hash, using modules in lib/bio/db/kegg/common.rb.

 lib/bio/db/kegg/compound.rb            |   14 +++++++++++
 test/unit/bio/db/kegg/test_compound.rb |   38 ++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+), 0 deletions(-)

commit 63df07e030120eb43de22555277529822b072270
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 22:25:20 2009 +0900

    Methods commonly used from Bio::KEGG::* classes.
    
     * Modules containing methods commonly used from Bio::KEGG::* classes.
       The "dblinks_as_hash" method is copied from
       lib/bio/db/kegg/orthology.rb. The "pathways_as_hash" method is
       derived from the dblinks_as_hash and Bio::KEGG::REACTION#pathways
       methods.

 lib/bio/db/kegg/common.rb |   60 +++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 60 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/kegg/common.rb

commit 0e55c6701b09a52356ac55300181ee656773826f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 21:39:06 2009 +0900

    Bio::KEGG::COMPOUND#dblinks is reverted to return an array of string.

 lib/bio/db/kegg/compound.rb            |   11 ++---------
 test/unit/bio/db/kegg/test_compound.rb |    8 +++++++-
 2 files changed, 9 insertions(+), 10 deletions(-)

commit a05adcddf6c7ed67c042f31ecd86848af1ba8a22
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Dec 2 21:13:39 2009 +0900

    Bug fix: fixed a copy-and-paste mistake.

 lib/bio/db/kegg/drug.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 86925f3c80730e3ea3377a23a70cadb3876258c4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Dec 1 21:31:40 2009 +0900

    Bio::KEGG::ORTHOLOGY#dblinks_as_hash should preserve database names.

 doc/Changes-1.4.rdoc                    |    4 ++++
 lib/bio/db/kegg/orthology.rb            |    2 +-
 test/unit/bio/db/kegg/test_orthology.rb |    2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

commit 60847cd2d0701fa38a499578649cb216c93993a2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Dec 1 20:41:51 2009 +0900

    Test class names are changed to avoid potential class name conflict.

 test/unit/bio/db/kegg/test_compound.rb  |    2 +-
 test/unit/bio/db/kegg/test_genes.rb     |    4 ++--
 test/unit/bio/db/kegg/test_orthology.rb |    2 +-
 test/unit/bio/db/kegg/test_reaction.rb  |    2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

commit 2bda62af7a020c22379dd9ec3a42496d2a5b94cb
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date:   Tue Dec 1 04:38:27 2009 +0900

    Added unit tests for Bio::KEGG::ORTHOLOGY.

 test/data/KEGG/K02338.orthology         |  902 +++++++++++++++++++++++++++++++
 test/unit/bio/db/kegg/test_orthology.rb |   50 ++
 2 files changed, 952 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/K02338.orthology
 create mode 100644 test/unit/bio/db/kegg/test_orthology.rb

commit acad9497caf5d737394568e911691fdad11ca091
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 30 21:39:32 2009 +0900

    Changed to use BioRubyTestDataPath instead of __FILE__.

 test/unit/bio/db/kegg/test_compound.rb |    3 +--
 test/unit/bio/db/kegg/test_reaction.rb |    3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

commit 8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 16:37:21 2009 +0900

    Bio::Fastq::QualityScore is renamed to Bio::Sequence::QualityScore.
    
     * Bio::Fastq::QualityScore is renamed to Bio::Sequence::QualityScore.
     * Changes of filenames due to the previous file move.

 lib/bio/db/fasta/format_qual.rb              |   18 ++++++++--------
 lib/bio/db/fastq.rb                          |    7 ++---
 lib/bio/sequence.rb                          |    3 +-
 lib/bio/sequence/quality_score.rb            |   25 +++++++++++------------
 test/unit/bio/sequence/test_quality_score.rb |   28 +++++++++++++-------------
 5 files changed, 40 insertions(+), 41 deletions(-)

commit 2b29654c1d7e927e445e7acdd525835a873c2a2a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 16:15:42 2009 +0900

    lib/bio/db/fastq/quality_score.rb is moved to lib/bio/sequence/. The unit test is also moved.
    
     * lib/bio/db/fastq/quality_score.rb is moved to lib/bio/sequence/.
     * test/unit/bio/db/fastq/test_quality_score.rb is moved to
       test/unit/bio/sequence/.
     * The file contents will be modified with the following commit.

 lib/bio/db/fastq/quality_score.rb            |  206 ----------------
 lib/bio/sequence/quality_score.rb            |  206 ++++++++++++++++
 test/unit/bio/db/fastq/test_quality_score.rb |  330 --------------------------
 test/unit/bio/sequence/test_quality_score.rb |  330 ++++++++++++++++++++++++++
 4 files changed, 536 insertions(+), 536 deletions(-)
 delete mode 100644 lib/bio/db/fastq/quality_score.rb
 create mode 100644 lib/bio/sequence/quality_score.rb
 delete mode 100644 test/unit/bio/db/fastq/test_quality_score.rb
 create mode 100644 test/unit/bio/sequence/test_quality_score.rb

commit aa8d49bf31f90dd2796c18ee0aa6291979284ec2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 15:20:36 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_gff1.rb.

 lib/bio/db/gff.rb   |   17 -----------------
 sample/demo_gff1.rb |   49 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 49 insertions(+), 17 deletions(-)
 create mode 100644 sample/demo_gff1.rb

commit 76fffd2d2429346478fb3d8c88cdcd878a1047b1
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 15:06:41 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_tmhmm_report.rb.

 lib/bio/appl/tmhmm/report.rb |   36 ----------------------
 sample/demo_tmhmm_report.rb  |   68 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 68 insertions(+), 36 deletions(-)
 create mode 100644 sample/demo_tmhmm_report.rb

commit dfafb0a2bcec4c0b4cd3640374e151e2039056dc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 14:59:27 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_targetp_report.rb.

 lib/bio/appl/targetp/report.rb |  105 +------------------------------
 sample/demo_targetp_report.rb  |  135 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 136 insertions(+), 104 deletions(-)
 create mode 100644 sample/demo_targetp_report.rb

commit 75f7c8527546f8ea3079f53b90a9b4d8260b4de0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 14:33:28 2009 +0900

    Follow-up of the SOSUI server URL change.

 lib/bio/appl/sosui/report.rb |    6 ++++--
 1 files changed, 4 insertions(+), 2 deletions(-)

commit 8022696295dc296462f73b40cc74ad5259bee387
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 14:32:11 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_sosui_report.rb.

 lib/bio/appl/sosui/report.rb |   53 +------------------------
 sample/demo_sosui_report.rb  |   89 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 90 insertions(+), 52 deletions(-)
 create mode 100644 sample/demo_sosui_report.rb

commit 4acfe7f565039b34a036682912a75f55da808b45
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 29 14:02:32 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_hmmer_report.rb.

 lib/bio/appl/hmmer/report.rb |  100 ----------------------------
 sample/demo_hmmer_report.rb  |  149 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 149 insertions(+), 100 deletions(-)
 create mode 100644 sample/demo_hmmer_report.rb

commit 4f7bd1b7628d90661d8b557ca854b14cc44fb99c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 15:49:21 2009 +0900

    Demo codes in the "if __FILE__ == $0" are removed because they are very short.

 lib/bio/appl/fasta/format10.rb |   14 --------------
 lib/bio/appl/hmmer.rb          |   16 +---------------
 lib/bio/io/flatfile.rb         |    8 +-------
 3 files changed, 2 insertions(+), 36 deletions(-)

commit c2a72d195189755532e7e206af34d152ab6332d8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 15:20:28 2009 +0900

    Bug fix: Failure of Bio::Fasta.remote due to the remote site changes.

 lib/bio/appl/fasta.rb |    5 ++++-
 1 files changed, 4 insertions(+), 1 deletions(-)

commit 549112fb4dfb5f6b2fe3491fb161887a9f5262ac
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 15:13:10 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_fasta_remote.rb.

 lib/bio/appl/fasta.rb       |   18 ---------------
 sample/demo_fasta_remote.rb |   51 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+), 18 deletions(-)
 create mode 100644 sample/demo_fasta_remote.rb

commit 0e4ca0db83692fdbbe93e90272a07bcbac89192c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 10:17:47 2009 +0900

    Text indents for some comment lines are changed.

 sample/demo_blast_report.rb  |    4 ++--
 sample/demo_kegg_compound.rb |    4 ++--
 sample/demo_prosite.rb       |    4 ++--
 sample/demo_sirna.rb         |    4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

commit c0cf91fe2a9247bc3705b20515f9d4fa14288d5a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 10:13:26 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_keggapi.rb.
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_keggapi.rb.
     * Commented out demonstrations of deprecated methods:
       get_neighbors_by_gene, get_similarity_between_genes,
       get_ko_members, get_oc_members_by_gene, get_pc_members_by_gene.
     * Commented out demonstrations of methods internally using
       the deprecated methods: get_all_neighbors_by_gene,
       get_all_oc_members_by_gene, get_all_pc_members_by_gene.

 lib/bio/io/keggapi.rb  |  442 ------------------------------------------
 sample/demo_keggapi.rb |  502 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 502 insertions(+), 442 deletions(-)
 create mode 100644 sample/demo_keggapi.rb

commit 8b8206c1d8ee699185fdd19d3329311c85ee003c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 01:50:06 2009 +0900

    Fixed the license line.

 lib/bio/db/prosite.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit ebfeec8243abd4e2f65335fda1ead18efff66897
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 01:41:58 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_ncbi_rest.rb.

 lib/bio/io/ncbirest.rb   |  101 ------------------------------------
 sample/demo_ncbi_rest.rb |  128 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 128 insertions(+), 101 deletions(-)
 create mode 100644 sample/demo_ncbi_rest.rb

commit 5a0f8379a374650d12fc88fbbd5b28c38ae96395
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 01:33:07 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_prosite.rb.

 lib/bio/db/prosite.rb  |   95 +-------------------------------------
 sample/demo_prosite.rb |  120 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 121 insertions(+), 94 deletions(-)
 create mode 100644 sample/demo_prosite.rb

commit c560a5d0ba9d4919dbcca156ea620056dcb8f725
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 01:14:37 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_psort.rb.

 lib/bio/appl/psort.rb |  111 ---------------------------------------
 sample/demo_psort.rb  |  138 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 138 insertions(+), 111 deletions(-)
 create mode 100644 sample/demo_psort.rb

commit 1299a55d214784a536ae3cd8bfabdfd61fe1da86
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 01:04:29 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_psort_report.rb.
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_psort_report.rb, without any checks.

 lib/bio/appl/psort/report.rb |   46 +---------------------------
 sample/demo_psort_report.rb  |   70 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 71 insertions(+), 45 deletions(-)
 create mode 100644 sample/demo_psort_report.rb

commit a2686fe3c5a93947c94d4602514a62a808c182d5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 00:53:54 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_genscan_report.rb.

 lib/bio/appl/genscan/report.rb |  176 ----------------------------------
 sample/demo_genscan_report.rb  |  202 ++++++++++++++++++++++++++++++++++++++++
 2 files changed, 202 insertions(+), 176 deletions(-)
 create mode 100644 sample/demo_genscan_report.rb

commit 22f662ba69dd2d4a2273562dd7ea921f5cdd84bd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 00:28:01 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_ddbjxml.rb.

 lib/bio/io/ddbjxml.rb  |  182 +-----------------------------------------
 sample/demo_ddbjxml.rb |  212 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 213 insertions(+), 181 deletions(-)
 create mode 100644 sample/demo_ddbjxml.rb

commit ed3b34b6598f632c7b9b3f1a17b42406c19ca32d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 26 00:12:33 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_pubmed.rb.
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_pubmed.rb.
     * Codes using Entrez CGI are disabled in the demo.

 lib/bio/io/pubmed.rb  |   88 -------------------------------------
 sample/demo_pubmed.rb |  116 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 116 insertions(+), 88 deletions(-)
 create mode 100644 sample/demo_pubmed.rb

commit 9e6d720f383e88e247eacab6f0e43f38140a62f2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 23:59:10 2009 +0900

    Demo codes in the "if __FILE__ == $0" are removed.
    
     * Demo codes in the "if __FILE__ == $0" are removed because their
       function have already been moved to sample/demo_blast_report.rb.

 lib/bio/appl/blast/format0.rb |  193 --------------------------------------
 lib/bio/appl/blast/report.rb  |  149 +-----------------------------
 lib/bio/appl/blast/wublast.rb |  208 -----------------------------------------
 3 files changed, 2 insertions(+), 548 deletions(-)

commit bbba2812fa9131d01fc655eb174d84f06facd8b8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 23:49:36 2009 +0900

    New demo code of BLAST parser based on codes in "if __FILE__ ==$0"
    
     * Newly added sample/demo_blast_report.rb, demonstration of
       BLAST parsers  Bio::Blast::Report, Bio::Blast::Default::Report,
       and Bio::Blast::WU::Report. It is based on the demonstration codes
       in the "if __FILE__ == $0" in lib/bio/appl/blast/report.rb,
       lib/bio/appl/blast/format0.rb, and lib/bio/appl/blast/wublast.rb.

 sample/demo_blast_report.rb |  285 +++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 285 insertions(+), 0 deletions(-)
 create mode 100644 sample/demo_blast_report.rb

commit 5235ed15db8d3ba3e59d8dc3bbbcf1b5b9c58281
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 21:57:08 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_das.rb.
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_das.rb.
     * Demo codes using UCSC DAS server is added.
     * Demo using the WormBase DAS server is temporarily disabled because
       it does not work well possibly because of the server trouble.

 lib/bio/io/das.rb  |   44 ----------------------
 sample/demo_das.rb |  105 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 105 insertions(+), 44 deletions(-)
 create mode 100644 sample/demo_das.rb

commit b7b0f7bef0505b9678673e54bb863d4ff7897dd5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 20:58:35 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_taxonomy.rb, although it does not work correctly now.

 lib/bio/db/kegg/taxonomy.rb  |   53 +-----------------------
 sample/demo_kegg_taxonomy.rb |   92 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 93 insertions(+), 52 deletions(-)
 create mode 100644 sample/demo_kegg_taxonomy.rb

commit 23da98ca19fce1f0b487e1f955ef4cd896839590
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 20:11:12 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_reaction.rb.

 lib/bio/db/kegg/reaction.rb  |   16 +----------
 sample/demo_kegg_reaction.rb |   64 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 65 insertions(+), 15 deletions(-)
 create mode 100644 sample/demo_kegg_reaction.rb

commit 9c0bfb857a6b41d8e6a42ff2cbf7b06ca1d38d78
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 19:12:00 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_orthology.rb.

 lib/bio/db/kegg/orthology.rb  |   23 +--------------
 sample/demo_kegg_orthology.rb |   62 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+), 22 deletions(-)
 create mode 100644 sample/demo_kegg_orthology.rb

commit 6f6f1eb3d87dea588ea333708c4d4486ac7136b6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 12:19:26 2009 +0900

    Commented out demo for nonexistent method "bindings".

 sample/demo_kegg_glycan.rb |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 98a6d904058b5af4808f16bcb710d73bd97c9764
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 12:18:31 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_glycan.rb.

 lib/bio/db/kegg/glycan.rb  |   21 -------------
 sample/demo_kegg_glycan.rb |   72 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 72 insertions(+), 21 deletions(-)
 create mode 100644 sample/demo_kegg_glycan.rb

commit d26e835ca9def2287f1050f1b048892e3cafdaa0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 11:49:05 2009 +0900

    Added references.

 lib/bio/db/kegg/genome.rb |    2 ++
 1 files changed, 2 insertions(+), 0 deletions(-)

commit c3c460462481b5b8d6e9441216bcf6370b4890ef
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 11:45:31 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_genome.rb.

 lib/bio/db/kegg/genome.rb  |   42 +------------------------
 sample/demo_kegg_genome.rb |   74 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 75 insertions(+), 41 deletions(-)
 create mode 100644 sample/demo_kegg_genome.rb

commit 0d8e709b66bf18ead5944c27a50eb6cf2c47862f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 11:43:24 2009 +0900

    Added document about downloading sample data.

 sample/demo_kegg_drug.rb |   13 ++++++++++++-
 1 files changed, 12 insertions(+), 1 deletions(-)

commit 0608893198e9bc88521b6c013069d8c7a13bb0e5
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 00:10:48 2009 +0900

    Added documents.

 lib/bio/db/kegg/drug.rb |   15 +++++++++++++++
 1 files changed, 15 insertions(+), 0 deletions(-)

commit 0ecdc1ee0460f16dba1e4cd5ab575c92e1c6b1ac
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 25 00:06:02 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_drug.rb.

 lib/bio/db/kegg/drug.rb  |   18 +--------------
 sample/demo_kegg_drug.rb |   54 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 55 insertions(+), 17 deletions(-)
 create mode 100644 sample/demo_kegg_drug.rb

commit b0c349103f01a26f4741999bd696bf5b1c032e06
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 23:51:13 2009 +0900

    Added documents.

 lib/bio/db/kegg/compound.rb |   10 ++++++++++
 1 files changed, 10 insertions(+), 0 deletions(-)

commit e965b454c553ed9670bc83962a2a9d7c5de49929
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 23:45:15 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_compound.rb.

 lib/bio/db/kegg/compound.rb  |   19 +-------------
 sample/demo_kegg_compound.rb |   57 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 58 insertions(+), 18 deletions(-)
 create mode 100644 sample/demo_kegg_compound.rb

commit 7454db7c8b8ef7202736d311356d4ca350af336f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 23:06:21 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_litdb.rb.

 lib/bio/db/litdb.rb  |   17 +----------------
 sample/demo_litdb.rb |   42 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+), 16 deletions(-)
 create mode 100644 sample/demo_litdb.rb

commit fde284248e013e44184ee2ba7da85e5b83155a69
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 22:57:01 2009 +0900

    Ruby 1.9 support: String#each_line instead of String#each

 lib/bio/db/go.rb |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

commit 8b60099615790fe372b4fde27a391dedc767aab2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 22:53:12 2009 +0900

    Sample code bug fix: fixed method names, and workaround for Zlib error.
    
     * Sample code bug fix: Following method name changes.
     * Workaround for Zlib::DataError.

 sample/demo_go.rb |   13 +++++++++----
 1 files changed, 9 insertions(+), 4 deletions(-)

commit 737fec3db555811d127d2356e5ceef63b0413fb8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 19:47:14 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_go.rb.

 lib/bio/db/go.rb  |   70 +---------------------------------------
 sample/demo_go.rb |   93 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 94 insertions(+), 69 deletions(-)
 create mode 100644 sample/demo_go.rb

commit 8264b15690132d9e766f16d0829bb12cd122b900
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 19:20:52 2009 +0900

    Document bug fix: Changed Bio::Bl2seq to Bio::Blast::Bl2seq in the RDoc.
    
     * Document bug fix: Changed Bio::Bl2seq to Bio::Blast::Bl2seq
       in the RDoc.
     * Modified copyright line.

 lib/bio/appl/bl2seq/report.rb |   18 +++++++++---------
 1 files changed, 9 insertions(+), 9 deletions(-)

commit c572ff022fee43505355608f0a0e3ba2181e87e2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 19:17:04 2009 +0900

    Bug fix: Failed to read Bio::Blast::Bl2seq::Report data by using Bio::FlatFile.

 lib/bio/appl/bl2seq/report.rb |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit 4f6b080623442dfcc5864e2aefde7e53ace068e8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 19:15:11 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_bl2seq_report.rb.

 lib/bio/appl/bl2seq/report.rb |  194 +------------------------------------
 sample/demo_bl2seq_report.rb  |  220 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 221 insertions(+), 193 deletions(-)
 create mode 100644 sample/demo_bl2seq_report.rb

commit 2f03e8757383e0d1a26c0f6942c74a30f3b26d90
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 18:24:43 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_genbank.rb.
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_genbank.rb, and modified as below.
        * To get sequences from the NCBI web service.
        * By default, arguments are sequence IDs (accession numbers).
        * New option "--files" (or "-files", "--file", or "-file") to
          read sequences from file(s).

 lib/bio/db/genbank/genbank.rb |   87 +--------------------------
 sample/demo_genbank.rb        |  132 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 133 insertions(+), 86 deletions(-)
 create mode 100644 sample/demo_genbank.rb

commit a2981c28fdb629a655c71c920f6588f8b80aff06
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 15:06:50 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_aaindex.rb.

 lib/bio/db/aaindex.rb  |   39 +---------------------------
 sample/demo_aaindex.rb |   67 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 68 insertions(+), 38 deletions(-)
 create mode 100644 sample/demo_aaindex.rb

commit b741d17ec5c5ac234bab35b8716fee072635de1a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 24 12:45:43 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_sirna.rb
    
     * Demo codes in the "if __FILE__ == $0" are moved to
       sample/demo_sirna.rb, and modified for reading normal sequence
       files instead of a raw sequence.

 lib/bio/util/sirna.rb |   24 +------------------
 sample/demo_sirna.rb  |   63 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 64 insertions(+), 23 deletions(-)
 create mode 100644 sample/demo_sirna.rb

commit 7cc778e78bc63ef73796ee15d6f0db8d6967aefe
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 23:00:42 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_pathway.rb.

 lib/bio/pathway.rb     |  171 -----------------------------------------
 sample/demo_pathway.rb |  196 ++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 196 insertions(+), 171 deletions(-)
 create mode 100644 sample/demo_pathway.rb

commit 7e5510587abc0b50b6851f005a3236bf9dc79d08
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 22:49:13 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_locations.rb.

 lib/bio/location.rb      |   73 ----------------------------------
 sample/demo_locations.rb |   99 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 99 insertions(+), 73 deletions(-)
 create mode 100644 sample/demo_locations.rb

commit f1c02666f4b11d5cf208d6beb592d8ac962ce2da
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 22:35:50 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_codontable.rb.

 lib/bio/data/codontable.rb |   96 +-----------------------------------
 sample/demo_codontable.rb  |  119 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 120 insertions(+), 95 deletions(-)
 create mode 100644 sample/demo_codontable.rb

commit c11a7793f85faf3d66d630833c38358ffa34a698
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 16:35:16 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_nucleicacid.rb.

 lib/bio/data/na.rb         |   27 +-----------------------
 sample/demo_nucleicacid.rb |   49 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+), 26 deletions(-)
 create mode 100644 sample/demo_nucleicacid.rb

commit de41b67c3f65baa0f122689b2e9f479d8a247934
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 16:25:05 2009 +0900

    Demo codes in the "if __FILE__ == $0" are moved to sample/demo_aminoacid.rb.

 lib/bio/data/aa.rb       |   78 +-----------------------------------
 sample/demo_aminoacid.rb |  101 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 102 insertions(+), 77 deletions(-)
 create mode 100644 sample/demo_aminoacid.rb

commit e652dd44ecb6b6dad652e33a398f92bb8373e7dd
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 16:12:48 2009 +0900

    Added an error message about encoding in Ruby 1.9.1

 KNOWN_ISSUES.rdoc |    3 ++-
 1 files changed, 2 insertions(+), 1 deletions(-)

commit 003133b0d4e2234c27927c9d10b75185c354102e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 23 15:52:21 2009 +0900

    changed recommended Ruby version

 README.rdoc |    4 ++--
 1 files changed, 2 insertions(+), 2 deletions(-)

commit 408483d36b713678361cecf6c77ff7a2098f71fc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 22 17:07:37 2009 +0900

    added information about doc/Changes-1.4.rdoc

 README.rdoc |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit ef342933839e8c6cef9883045fcaf468aff5da23
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 22 16:50:55 2009 +0900

    In PhyloXML support, added a link to GNOME Libxml2 and fixed RDoc syntax.

 README.rdoc |    6 ++++--
 1 files changed, 4 insertions(+), 2 deletions(-)

commit 0237ef42d60c7a76cadf8ea78f4251bcfe89c95f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 19 09:43:15 2009 +0900

    Ruby 1.9 support: String#each_line instead of String#each

 lib/bio/appl/meme/mast/report.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit ec935ea9b19415bf3325bcc0763fbc22f3c71a3d
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 19 09:40:49 2009 +0900

    The "libpath magic" is replaced by loading helper routine.

 test/unit/bio/appl/meme/mast/test_report.rb |   11 ++++++-----
 test/unit/bio/appl/meme/test_mast.rb        |   11 ++++++-----
 test/unit/bio/appl/meme/test_motif.rb       |    8 +++++---
 3 files changed, 17 insertions(+), 13 deletions(-)

commit 3f65eeb503f3b2ef866cab4c73d2d700ca572835
Author: Adam Kraut <adamnkraut@gmail.com>
Date:   Tue Mar 17 19:41:31 2009 -0400

    Added basic support for MEME/MAST applications

 lib/bio/appl/meme/mast.rb                   |  156 +++++++++++++++++++++++++++
 lib/bio/appl/meme/mast/report.rb            |   91 ++++++++++++++++
 lib/bio/appl/meme/motif.rb                  |   48 ++++++++
 test/data/meme/mast.out                     |   13 +++
 test/data/meme/meme.out                     |    3 +
 test/unit/bio/appl/meme/mast/test_report.rb |   45 ++++++++
 test/unit/bio/appl/meme/test_mast.rb        |  102 +++++++++++++++++
 test/unit/bio/appl/meme/test_motif.rb       |   36 ++++++
 8 files changed, 494 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/appl/meme/mast.rb
 create mode 100644 lib/bio/appl/meme/mast/report.rb
 create mode 100644 lib/bio/appl/meme/motif.rb
 create mode 100644 test/data/meme/db
 create mode 100644 test/data/meme/mast
 create mode 100644 test/data/meme/mast.out
 create mode 100644 test/data/meme/meme.out
 create mode 100644 test/unit/bio/appl/meme/mast/test_report.rb
 create mode 100644 test/unit/bio/appl/meme/test_mast.rb
 create mode 100644 test/unit/bio/appl/meme/test_motif.rb

commit 3862f54fda0caec2a07e563a1f8a11913baca2e3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 18 20:29:56 2009 +0900

    New version of PhyloXML schema, version 1.10.
    
     * Upgraded to New version of PhyloXML schema, version 1.10,
       developed by Christian M Zmasek.

 lib/bio/db/phyloxml/phyloxml.xsd | 1155 +++++++++++++++++++-------------------
 1 files changed, 582 insertions(+), 573 deletions(-)

commit 45ffd9228d513b3dbf29e1011c6a6689a8bd1b08
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 18 00:26:44 2009 +0900

    Newly added sample script to test big PhyloXML data
    
     * Newly added a sample script to test big PhyloXML data based on
       Diana Jaunzeikare's work.
       (http://github.com/latvianlinuxgirl/bioruby/blob/
       20627fc5a443d6c2e3dc73ed50e9c578ffcbc330/
       test/unit/bio/db/test_phyloxml_big.rb).

 sample/test_phyloxml_big.rb |  205 +++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 205 insertions(+), 0 deletions(-)
 create mode 100644 sample/test_phyloxml_big.rb

commit 828a8971e057919b80508cf29fd9518828b74a2f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 17 23:54:37 2009 +0900

    Speed up of Bio::Tree#children and parent: caching node's parent.
    
     * For speed up of Bio::Tree#children and parent, internal cache of
       the parent for each node is added. The cache is automatically
       cleared when the tree is modified. Note that the cache can only
       be accessed from inside Bio::Tree.
     * Bio::Tree#parent is changed to directly raise IndexError when
       both of the root specified in the argument and preset in the
       tree are nil (previously, the same error is raised in the path
       method which is internally called from the parent method).
     * Bio::Tree#path is changed not to call bfs_shortest_path if the
       node1 and node2 are adjacent.

 lib/bio/tree.rb |   75 +++++++++++++++++++++++++++++++++++++++++++++++++++---
 1 files changed, 70 insertions(+), 5 deletions(-)

commit 75862212e6bb807a570338e39e19d527219b6f13
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 22:11:15 2009 +0900

    Documented incompatible changes of Bio::KEGG::COMPOUND and Bio::KEGG:REACTION.

 doc/Changes-1.4.rdoc |   10 ++++++++++
 1 files changed, 10 insertions(+), 0 deletions(-)

commit c74cfabd6414c8b50db0251739f967accd90773f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 21:20:42 2009 +0900

    Ruby compatibility issue: Enumerable#each_slice(4).each does not work in Ruby 1.8.5.

 lib/bio/db/kegg/reaction.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit e6a920e401a2b06c355174ccdc9b993a38f9d7ec
Author: Mitsuteru Nakao <mitsuteru.nakao@gmail.com>
Date:   Wed Jul 22 22:50:22 2009 +0900

    Added new method Bio::KEGG::GENES#structure with the unit tests.

 lib/bio/db/kegg/genes.rb            |   12 ++++++++++++
 test/unit/bio/db/kegg/test_genes.rb |   25 +++++++++++++++++++++++++
 2 files changed, 37 insertions(+), 0 deletions(-)

commit 9fee0c133d069348857014410983f682e468c1c7
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 21:04:02 2009 +0900

    The "libpath magic" is replaced by loading helper routine.

 test/unit/bio/db/kegg/test_compound.rb |    6 ++++--
 test/unit/bio/db/kegg/test_reaction.rb |    6 ++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

commit 1199330eab95b8434303e92c5f792818e96db814
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date:   Sat Nov 14 09:03:50 2009 +0900

    Newly added unit tests for Bio::KEGG::COMPOUND and Bio::KEGG::REACTION
    
     * Newly added unit tests for Bio::KEGG::COMPOUND and
       Bio::KEGG::REACTION with test data. (Note that this is a
       combination of several commits made by Kozo Nishida,
       merged from git://github.com/kozo2/bioruby.git ).

 test/data/KEGG/C00025.compound         |  102 ++++++++++++++++++++++++++++++++
 test/data/KEGG/R00006.reaction         |   14 ++++
 test/unit/bio/db/kegg/test_compound.rb |   49 +++++++++++++++
 test/unit/bio/db/kegg/test_reaction.rb |   57 ++++++++++++++++++
 4 files changed, 222 insertions(+), 0 deletions(-)
 create mode 100644 test/data/KEGG/C00025.compound
 create mode 100644 test/data/KEGG/R00006.reaction
 create mode 100644 test/unit/bio/db/kegg/test_compound.rb
 create mode 100644 test/unit/bio/db/kegg/test_reaction.rb

commit 1b47640665d4332bafd9e9709628ee9722f1f3f4
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date:   Sat Nov 14 09:03:50 2009 +0900

    Bio::KEGG::COMPOUND#dblinks changed to return hash list
    
     * Bio::KEGG::COMPOUND#dblinks is changed to return hash list (array
       containing hashes).

 lib/bio/db/kegg/compound.rb |   11 +++++++++--
 1 files changed, 9 insertions(+), 2 deletions(-)

commit 2aa43a0aa765ee4502923c2102e352826a9a7abd
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date:   Sat Nov 14 07:29:19 2009 +0900

    Bio::KEGG:REACTION#rpair and pathways changed to return hash list, and added orthologies method.
    
     * New method: Bio::KEGG:REACTION#orthologies
     * Bio::KEGG:REACTION#rpair and pathways are changed to return hash
       list (array containing hashes).

 lib/bio/db/kegg/reaction.rb |   33 ++++++++++++++++++++++++++++++---
 1 files changed, 30 insertions(+), 3 deletions(-)

commit a82f5d228370beeeb397be07e07394652fd7837e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 20:03:19 2009 +0900

    Changed not to modify given argument

 lib/bio/util/restriction_enzyme/single_strand.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit ff10d5540759a5e7eaaa71da020d95170b98e007
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 19:50:08 2009 +0900

    Newly added a document for incompatible and/or important changes of the new release version.
    
     * Newly added a document for incompatible and/or important changes
       of the new release version.
     * Added description about Bio::RestrictionEnzyme validation is
       disabled (although very small change).

 doc/Changes-1.4.rdoc |   16 ++++++++++++++++
 1 files changed, 16 insertions(+), 0 deletions(-)
 create mode 100644 doc/Changes-1.4.rdoc

commit 629e537f90e0825fadeec2e0207f8caddfbed59a
Author: trevor <>
Date:   Sat Sep 19 11:03:23 2009 -0500

    speed-up serial calls to RestrictionEnzyme

 lib/bio/db/rebase.rb                               |    2 +-
 lib/bio/util/restriction_enzyme/single_strand.rb   |    3 +-
 .../util/restriction_enzyme/test_single_strand.rb  |   24 ++++++++++---------
 .../test_single_strand_complement.rb               |   24 ++++++++++---------
 4 files changed, 29 insertions(+), 24 deletions(-)

commit 9b55a92d5300294bef7b624d0f9aa3edd3e8d7fc
Author: trevor <>
Date:   Sat Sep 19 10:46:21 2009 -0500

    speed-up rebase library

 lib/bio/db/rebase.rb |    9 ++++-----
 1 files changed, 4 insertions(+), 5 deletions(-)

commit 4aaa24b3fc3cf2d1f7cf8b6d974d2115958b5a1b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 15:08:31 2009 +0900

    Ruby 1.9 support: Array#to_s is changed to join('')

 lib/bio/db/sanger_chromatogram/scf.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 1cf924b81150545e807169144aeaca6a75f9731c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Mon Nov 16 12:59:10 2009 +0900

    Ruby 1.9 support: Array#nitems (counts the number of non-nil elements) is removed in 1.9.
    
     * Ruby 1.9 support: Array#nitems (counts the number of non-nil
       elements) is removed in Ruby 1.9. In scf.rb, it seems that
       nil would never be included in the array, and simply replaced
       by Array#size.

 lib/bio/db/sanger_chromatogram/scf.rb |    8 ++++----
 1 files changed, 4 insertions(+), 4 deletions(-)

commit a95994d9cfbf4fc89fa716358ac5b92d42a1307b
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 15 19:23:12 2009 +0900

    Bug fix: error when quality_scores are larger than the sequence length, and added a require line.
    
     * Bug fix: error when sequence.quality_scores are larger than
       the sequence length.
     * Added a require line.

 lib/bio/db/fasta/format_qual.rb |    5 ++++-
 1 files changed, 4 insertions(+), 1 deletions(-)

commit c5aafca19b58b1651080e81699b7020cd3fd3f47
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Nov 15 19:21:49 2009 +0900

    Newly added unit tests for Bio::Sequence::Format::Formatter::Fasta_numeric and Qual.

 test/unit/bio/db/fasta/test_format_qual.rb |  346 ++++++++++++++++++++++++++++
 1 files changed, 346 insertions(+), 0 deletions(-)
 create mode 100644 test/unit/bio/db/fasta/test_format_qual.rb

commit 6e24170e29d2576ff69b18eaadc94e9769b8612a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Nov 14 02:41:13 2009 +0900

    Newly added Bio::Sequence::Format::Formatter::Qual and Fasta_numeric, formatter for Qual format and FastaNumericFormat.

 lib/bio/db/fasta/format_qual.rb |  201 +++++++++++++++++++++++++++++++++++++++
 lib/bio/sequence/format.rb      |    7 ++
 2 files changed, 208 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/fasta/format_qual.rb

commit 6959fd359040b6ca9570111d515118dc2d472029
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Nov 14 02:19:17 2009 +0900

    Split quality score methods in Bio::Fastq::FormatData into separete modules
    
     * Quality score calculation methods in Bio::Fastq::FormatData in
       lib/bio/db/fastq.rb is splitted into separate modules
       Bio::Fastq::QualityScore::Converter, Phred, and Solexa
       in lib/bio/db/fastq/quality_score.rb.
     * Unit tests for Bio::Fastq::QualityScore::* are newly added
       in test/unit/bio/db/fastq/test_quality_score.rb.
     * Possible bug fix: probability should be 0 <= p <= 1.

 lib/bio/db/fastq.rb                          |  112 +--------
 lib/bio/db/fastq/quality_score.rb            |  206 ++++++++++++++++
 test/unit/bio/db/fastq/test_quality_score.rb |  330 ++++++++++++++++++++++++++
 3 files changed, 544 insertions(+), 104 deletions(-)
 create mode 100644 lib/bio/db/fastq/quality_score.rb
 create mode 100644 test/unit/bio/db/fastq/test_quality_score.rb

commit 98f7703c28f0c2c34e4fe1631de227e20b9666c3
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 23:48:19 2009 +0900

    When no error_probabilities in the sequence and quality_score_type is nil, Fastq formatter implicitly assumes that the quality_score_type is :phred.
    
     * When no error_probabilities in the sequence and
       quality_score_type is nil, Fastq formatter implicitly assumes
       that the quality_score_type is :phred.
     * Bug fix: fixed typo in lib/bio/db/fastq/format_fastq.rb.

 lib/bio/db/fastq/format_fastq.rb |    5 ++++-
 lib/bio/sequence.rb              |    3 +++
 2 files changed, 7 insertions(+), 1 deletions(-)

commit f85a6aee9827bc573dcb735f4a1a1827926cc66c
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 23:29:19 2009 +0900

    Bug fix: fixed typo for Bio::Sequence#quality_score_type.

 lib/bio/sequence.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit d81a611d7c7c46a789b86e99cebe064ba559e3e0
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 20:42:12 2009 +0900

    Splitting lib/bio/db/fasta.rb: FastaNumericFormat is moved to a new file, etc.
    
     * Splitting lib/bio/db/fasta.rb as follows:
        * Bio::FastaNumericFormat is moved to lib/bio/db/fasta/qual.rb.
        * Demo codes in the "if __FILE__ == $0" are moved to
          sample/demo_fastaformat.rb.
     * Unit tests for Bio::FastaNumericFormat are moved from
       test/unit/bio/db/test_fasta.rb to test/unit/bio/db/test_qual.rb.
     * lib/bio.rb is also modified for the autoload.
     * Bug fix: fixed incorrect autoload path for Bio::FastaDefline.

 lib/bio.rb                     |    4 +-
 lib/bio/db/fasta.rb            |  135 +---------------------------------------
 lib/bio/db/fasta/qual.rb       |  102 ++++++++++++++++++++++++++++++
 sample/demo_fastaformat.rb     |  105 +++++++++++++++++++++++++++++++
 test/unit/bio/db/test_fasta.rb |   43 -------------
 test/unit/bio/db/test_qual.rb  |   63 +++++++++++++++++++
 6 files changed, 273 insertions(+), 179 deletions(-)
 create mode 100644 lib/bio/db/fasta/qual.rb
 create mode 100644 sample/demo_fastaformat.rb
 create mode 100644 test/unit/bio/db/test_qual.rb

commit c70bed5c3f828c94084fdeabe255fbb3930097d0
Author: Andrew Grimm <andrew.j.grimm@gmail.com>
Date:   Sun Aug 16 19:49:38 2009 +1000

    Removed use of uninitialized variable in FastaNumericFormat.

 lib/bio/db/fasta.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit ce6dcc344a3d7beec544d7164308dd97bafa8a19
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 13:04:11 2009 +0900

    User data type should be stored as is, even if unknown data type.

 lib/bio/db/sanger_chromatogram/abif.rb |    3 ++-
 1 files changed, 2 insertions(+), 1 deletions(-)

commit ca96e59f151c2e10b5cd8c0690b8297979e52036
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 12:50:59 2009 +0900

    Removed Bio::Abif#method_missing and added alternative method
    
     * Removed Bio::Abif#method_missing, because method_missing can
       hide many errors related to method calls e.g. method name typo,
       and it is not suitable for only getting data.
     * New method Bio::Abif#data is added to get data (alternative of
       the method_missing).

 lib/bio/db/sanger_chromatogram/abif.rb |   19 ++++++++++++-------
 1 files changed, 12 insertions(+), 7 deletions(-)

commit 8b0da27523998cb9a9df07f5e907cda6e3cef0dc
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 12:04:41 2009 +0900

    removed a non-ascii character in comment

 lib/bio/db/sanger_chromatogram/chromatogram.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 55c1a180fec97338bae8e3c5b5d5ceec64aed0f6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Nov 13 12:02:53 2009 +0900

    Bug fix: Bio::SangerChromatogram#complement fails when the object is frozen.

 lib/bio/db/sanger_chromatogram/chromatogram.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 4e7d8b0ba304d1ff01364fad68035f7ec9463fb9
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 12 22:23:47 2009 +0900

    fixed a typo in a copyright line

 test/unit/bio/util/test_sirna.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit f376124112d23ba9b0491dbd427d328edc81d872
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Nov 12 22:05:37 2009 +0900

    The "libpath magic" in tests are replaced by the load of helper routine.
    
     * In all unit tests, the "libpath magic" are replaced by the load
       of helper routine.
     * Changed to use a constant BioRubyTestDataPath for generating test
       data file path.
     * Some "require" lines are modified.
     * "File.open(...).read" in some tests are replaced by "File.read(...)".
     * Header comment lines of some tests with wrong filename and/or
       class/module name information are fixed.

 test/functional/bio/appl/test_pts1.rb              |    6 ++++--
 test/functional/bio/io/test_ensembl.rb             |    7 ++++---
 test/functional/bio/io/test_pubmed.rb              |    8 +++++---
 test/functional/bio/io/test_soapwsdl.rb            |    9 +++++----
 test/functional/bio/io/test_togows.rb              |    9 +++++----
 test/functional/bio/sequence/test_output_embl.rb   |   10 ++++++----
 test/functional/bio/test_command.rb                |   10 +++++-----
 test/runner.rb                                     |    8 +++++---
 test/unit/bio/appl/bl2seq/test_report.rb           |    9 +++++----
 test/unit/bio/appl/blast/test_ncbioptions.rb       |    6 ++++--
 test/unit/bio/appl/blast/test_report.rb            |    9 +++++----
 test/unit/bio/appl/blast/test_rpsblast.rb          |    9 +++++----
 test/unit/bio/appl/gcg/test_msf.rb                 |   10 +++++-----
 test/unit/bio/appl/genscan/test_report.rb          |   17 ++++++++---------
 test/unit/bio/appl/hmmer/test_report.rb            |    9 +++++----
 test/unit/bio/appl/iprscan/test_report.rb          |   11 ++++++-----
 test/unit/bio/appl/mafft/test_report.rb            |   11 ++++++-----
 test/unit/bio/appl/paml/codeml/test_rates.rb       |    9 +++++----
 test/unit/bio/appl/paml/codeml/test_report.rb      |    9 +++++----
 test/unit/bio/appl/paml/test_codeml.rb             |    9 +++++----
 test/unit/bio/appl/sim4/test_report.rb             |    9 +++++----
 test/unit/bio/appl/sosui/test_report.rb            |   11 ++++++-----
 test/unit/bio/appl/targetp/test_report.rb          |    8 +++++---
 test/unit/bio/appl/test_blast.rb                   |    9 +++++----
 test/unit/bio/appl/test_fasta.rb                   |    6 ++++--
 test/unit/bio/appl/test_pts1.rb                    |    6 ++++--
 test/unit/bio/appl/tmhmm/test_report.rb            |   11 ++++++-----
 test/unit/bio/data/test_aa.rb                      |    8 +++++---
 test/unit/bio/data/test_codontable.rb              |    9 +++++----
 test/unit/bio/data/test_na.rb                      |    8 +++++---
 test/unit/bio/db/biosql/tc_biosql.rb               |    6 +++++-
 test/unit/bio/db/embl/test_common.rb               |    6 ++++--
 test/unit/bio/db/embl/test_embl.rb                 |   12 ++++++------
 test/unit/bio/db/embl/test_embl_rel89.rb           |   12 ++++++------
 test/unit/bio/db/embl/test_embl_to_bioseq.rb       |   15 +++++++--------
 test/unit/bio/db/embl/test_sptr.rb                 |   14 ++++++--------
 test/unit/bio/db/embl/test_uniprot.rb              |   11 ++++++-----
 test/unit/bio/db/kegg/test_genes.rb                |    8 +++++---
 test/unit/bio/db/pdb/test_pdb.rb                   |    6 ++++--
 test/unit/bio/db/sanger_chromatogram/test_abif.rb  |    3 ++-
 test/unit/bio/db/sanger_chromatogram/test_scf.rb   |    3 ++-
 test/unit/bio/db/test_aaindex.rb                   |   12 ++++++------
 test/unit/bio/db/test_fasta.rb                     |    8 +++++---
 test/unit/bio/db/test_fastq.rb                     |   10 +++++-----
 test/unit/bio/db/test_gff.rb                       |    6 ++++--
 test/unit/bio/db/test_lasergene.rb                 |   12 +++++++-----
 test/unit/bio/db/test_medline.rb                   |    6 ++++--
 test/unit/bio/db/test_newick.rb                    |   12 ++++++------
 test/unit/bio/db/test_nexus.rb                     |    6 ++++--
 test/unit/bio/db/test_phyloxml.rb                  |   14 +++++++-------
 test/unit/bio/db/test_phyloxml_writer.rb           |   15 +++++++--------
 test/unit/bio/db/test_prosite.rb                   |   11 ++++++-----
 test/unit/bio/db/test_rebase.rb                    |    8 +++++---
 test/unit/bio/db/test_soft.rb                      |   13 +++++++------
 test/unit/bio/io/flatfile/test_autodetection.rb    |   13 ++++++-------
 test/unit/bio/io/flatfile/test_buffer.rb           |   11 ++++++-----
 test/unit/bio/io/flatfile/test_splitter.rb         |    8 ++++----
 test/unit/bio/io/test_ddbjxml.rb                   |    7 ++++---
 test/unit/bio/io/test_ensembl.rb                   |    8 +++++---
 test/unit/bio/io/test_fastacmd.rb                  |    7 ++++---
 test/unit/bio/io/test_flatfile.rb                  |   11 ++++++-----
 test/unit/bio/io/test_soapwsdl.rb                  |    7 ++++---
 test/unit/bio/io/test_togows.rb                    |    6 ++++--
 test/unit/bio/sequence/test_aa.rb                  |    8 +++++---
 test/unit/bio/sequence/test_common.rb              |    6 ++++--
 test/unit/bio/sequence/test_compat.rb              |    6 ++++--
 test/unit/bio/sequence/test_dblink.rb              |    8 +++++---
 test/unit/bio/sequence/test_na.rb                  |    6 ++++--
 test/unit/bio/shell/plugin/test_seq.rb             |    8 +++++---
 test/unit/bio/test_alignment.rb                    |    8 +++++---
 test/unit/bio/test_command.rb                      |    7 ++++---
 test/unit/bio/test_db.rb                           |    8 +++++---
 test/unit/bio/test_feature.rb                      |    6 ++++--
 test/unit/bio/test_location.rb                     |    6 ++++--
 test/unit/bio/test_map.rb                          |    8 +++++---
 test/unit/bio/test_pathway.rb                      |    6 ++++--
 test/unit/bio/test_reference.rb                    |    6 ++++--
 test/unit/bio/test_sequence.rb                     |    8 +++++---
 test/unit/bio/test_shell.rb                        |    8 +++++---
 test/unit/bio/test_tree.rb                         |   12 ++++++------
 .../analysis/test_calculated_cuts.rb               |    6 ++++--
 .../restriction_enzyme/analysis/test_cut_ranges.rb |    6 ++++--
 .../analysis/test_sequence_range.rb                |    6 ++++--
 .../double_stranded/test_aligned_strands.rb        |    6 ++++--
 .../double_stranded/test_cut_location_pair.rb      |    6 ++++--
 .../test_cut_location_pair_in_enzyme_notation.rb   |    6 ++++--
 .../double_stranded/test_cut_locations.rb          |    6 ++++--
 .../test_cut_locations_in_enzyme_notation.rb       |    6 ++++--
 .../test_cut_locations_in_enzyme_notation.rb       |    6 ++++--
 .../bio/util/restriction_enzyme/test_analysis.rb   |    6 ++++--
 .../bio/util/restriction_enzyme/test_cut_symbol.rb |    6 ++++--
 .../restriction_enzyme/test_double_stranded.rb     |    6 ++++--
 .../util/restriction_enzyme/test_single_strand.rb  |    6 ++++--
 .../test_single_strand_complement.rb               |    6 ++++--
 .../restriction_enzyme/test_string_formatting.rb   |    6 ++++--
 test/unit/bio/util/test_color_scheme.rb            |    8 +++++---
 test/unit/bio/util/test_contingency_table.rb       |    8 +++++---
 test/unit/bio/util/test_restriction_enzyme.rb      |    6 ++++--
 test/unit/bio/util/test_sirna.rb                   |    8 +++++---
 99 files changed, 479 insertions(+), 343 deletions(-)

commit f4fa0a5edc6ff6fc35577d84bda86363014a57a4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 11 17:04:43 2009 +0900

    test_chromatogram.rb is splitted into test_abif.rb and test_scf.rb

 test/unit/bio/db/sanger_chromatogram/test_abif.rb  |   75 +++++++++++++++
 .../db/sanger_chromatogram/test_chromatogram.rb    |  101 --------------------
 test/unit/bio/db/sanger_chromatogram/test_scf.rb   |   97 +++++++++++++++++++
 3 files changed, 172 insertions(+), 101 deletions(-)
 create mode 100644 test/unit/bio/db/sanger_chromatogram/test_abif.rb
 delete mode 100644 test/unit/bio/db/sanger_chromatogram/test_chromatogram.rb
 create mode 100644 test/unit/bio/db/sanger_chromatogram/test_scf.rb

commit d9cc613273cadc7f9fdfe2bafbd933efb1f403ca
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Nov 11 17:01:37 2009 +0900

    Newly added unit test helper routine which aims to replace the libpath magic

 test/bioruby_test_helper.rb |   61 +++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 61 insertions(+), 0 deletions(-)
 create mode 100644 test/bioruby_test_helper.rb

commit 10e76db2a8ec37bde541157d0735303b4ca8b3b8
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Nov 10 20:59:01 2009 +0900

    Bio::SangerChromatogram#to_s is renamed to sequence_string.

 lib/bio/db/sanger_chromatogram/chromatogram.rb |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

commit 0ec2c2f38c4b4a3e451841dc32540dfa10743bc2
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 30 22:49:19 2009 +0900

    Renamed/moved files/directories following the rename of class names.
    
     * renamed: lib/bio/db/chromatogram.rb ->
                lib/bio/db/sanger_chromatogram/chromatogram.rb
     * renamed: lib/bio/db/chromatogram/abi.rb ->
                lib/bio/db/sanger_chromatogram/abif.rb
     * renamed: lib/bio/db/chromatogram/scf.rb ->
                lib/bio/db/sanger_chromatogram/scf.rb
     * renamed: lib/bio/db/chromatogram/chromatogram_to_biosequence.rb ->
                lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb
     * renamed: test/unit/bio/db/test_chromatogram.rb ->
                test/unit/bio/db/sanger_chromatogram/test_chromatogram.rb
     * renamed: test/data/chromatogram/test_chromatogram_abi.ab1 ->
                test/data/sanger_chromatogram/test_chromatogram_abif.ab1
     * renamed: test/data/chromatogram/*.scf ->
                test/data/sanger_chromatogram/*.scf

 lib/bio/db/chromatogram.rb                         |  133 -------------
 lib/bio/db/chromatogram/abi.rb                     |  114 -----------
 .../db/chromatogram/chromatogram_to_biosequence.rb |   32 ---
 lib/bio/db/chromatogram/scf.rb                     |  210 --------------------
 lib/bio/db/sanger_chromatogram/abif.rb             |  114 +++++++++++
 lib/bio/db/sanger_chromatogram/chromatogram.rb     |  133 +++++++++++++
 .../chromatogram_to_biosequence.rb                 |   32 +++
 lib/bio/db/sanger_chromatogram/scf.rb              |  210 ++++++++++++++++++++
 test/data/chromatogram/test_chromatogram_abi.ab1   |  Bin 228656 -> 0 bytes
 .../data/chromatogram/test_chromatogram_scf_v2.scf |  Bin 47503 -> 0 bytes
 .../data/chromatogram/test_chromatogram_scf_v3.scf |  Bin 47503 -> 0 bytes
 .../sanger_chromatogram/test_chromatogram_abif.ab1 |  Bin 0 -> 228656 bytes
 .../test_chromatogram_scf_v2.scf                   |  Bin 0 -> 47503 bytes
 .../test_chromatogram_scf_v3.scf                   |  Bin 0 -> 47503 bytes
 .../db/sanger_chromatogram/test_chromatogram.rb    |  101 ++++++++++
 test/unit/bio/db/test_chromatogram.rb              |  101 ----------
 16 files changed, 590 insertions(+), 590 deletions(-)
 delete mode 100644 lib/bio/db/chromatogram.rb
 delete mode 100644 lib/bio/db/chromatogram/abi.rb
 delete mode 100644 lib/bio/db/chromatogram/chromatogram_to_biosequence.rb
 delete mode 100644 lib/bio/db/chromatogram/scf.rb
 create mode 100644 lib/bio/db/sanger_chromatogram/abif.rb
 create mode 100644 lib/bio/db/sanger_chromatogram/chromatogram.rb
 create mode 100644 lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb
 create mode 100644 lib/bio/db/sanger_chromatogram/scf.rb
 delete mode 100644 test/data/chromatogram/test_chromatogram_abi.ab1
 delete mode 100644 test/data/chromatogram/test_chromatogram_scf_v2.scf
 delete mode 100644 test/data/chromatogram/test_chromatogram_scf_v3.scf
 create mode 100644 test/data/sanger_chromatogram/test_chromatogram_abif.ab1
 create mode 100644 test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf
 create mode 100644 test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf
 create mode 100644 test/unit/bio/db/sanger_chromatogram/test_chromatogram.rb
 delete mode 100644 test/unit/bio/db/test_chromatogram.rb

commit 49bfe319e535c8414be32b47c07fe5204a24b398
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 30 22:02:08 2009 +0900

    Renamed Chromatogram to SangerChromatogram and Abi to Abif, and preparation of filename changes.
    
     * Renamed Chromatogram to SangerChromatogram because the word
       "chromatogram" may be used by various experimental methods
       other than the Sanger chromatogram.
     * Renamed Abi to Abif because Applied Biosystems who determined
       the file format says that its name is ABIF.
     * Preparation of changing filenames. However, filenames are
       not really changed now because of recording history of file
       contents modification. The paths shown in the "require" lines
       and test data paths may not be existed now.

 lib/bio.rb                                         |    6 ++--
 lib/bio/db/chromatogram.rb                         |   24 +++++++-------
 lib/bio/db/chromatogram/abi.rb                     |   15 +++++----
 .../db/chromatogram/chromatogram_to_biosequence.rb |   10 +++---
 lib/bio/db/chromatogram/scf.rb                     |   15 +++++----
 lib/bio/sequence/adapter.rb                        |    3 +-
 test/unit/bio/db/test_chromatogram.rb              |   32 ++++++++++---------
 7 files changed, 57 insertions(+), 48 deletions(-)

commit 6c020440663214014973ae8e5007ce2d31d8d45e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 24 00:44:47 2009 +0900

    New class method Bio::PhyloXML::Parser.open(filename) and API change of new(), etc.
    
     * New class methods to create parser object from various data
       source are added: Bio::PhyloXML::Parser.open(filename),
       for_io(io), open_uri(uri).
     * API change of Bio::PhyloXML::Parser.new(). Now, new(filename)
       is deprecated and it can only take a XML-formatted string.
     * Tests are added and modified to reflect the above changes.
     * test/unit/bio/db/test_phyloxml_writer.rb: avoid using WeakRef
       for temporary directory maintenance.

 lib/bio/db/phyloxml/phyloxml_parser.rb   |  224 +++++++++++++++++++++++++++---
 lib/bio/db/phyloxml/phyloxml_writer.rb   |    4 +-
 test/unit/bio/db/test_phyloxml.rb        |  178 ++++++++++++++++++++++--
 test/unit/bio/db/test_phyloxml_writer.rb |   70 +++++-----
 4 files changed, 408 insertions(+), 68 deletions(-)

commit fca5e800fc051a38ac6d25652c684fdd4f9bff14
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 23 15:13:25 2009 +0900

    Rearrangement of require and autoload so as to correctly load PhyloXML classes

 lib/bio.rb                               |   11 +++++++----
 lib/bio/db/phyloxml/phyloxml_elements.rb |   16 +++++++++++++++-
 lib/bio/db/phyloxml/phyloxml_parser.rb   |   11 ++++++-----
 lib/bio/db/phyloxml/phyloxml_writer.rb   |    5 ++++-
 test/unit/bio/db/test_phyloxml.rb        |    5 -----
 test/unit/bio/db/test_phyloxml_writer.rb |    3 ---
 6 files changed, 32 insertions(+), 19 deletions(-)

commit a291af62ef262ee04f3a0e1b6415d4e256c56a94
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Oct 23 00:08:44 2009 +0900

    Fixed argument order of assert_equal(expected, actual), etc.
    
     * Test bug fix: Argument order of assert_equal must be
       assert_equal(expected, actual).
     * assert_instance_of() instead of assert_equal() in
       TestPhyloXML1#test_init.
     * Removed some commented-out tests which may not be needed.

 test/unit/bio/db/test_phyloxml.rb        |  295 +++++++++++++++---------------
 test/unit/bio/db/test_phyloxml_writer.rb |    8 +-
 2 files changed, 147 insertions(+), 156 deletions(-)

commit 152304dc9809102f56a2f1779c59111f84b9cd02
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 17 01:40:49 2009 +0900

    Improvement of tests for Bio::Fastq and related classes.

 test/unit/bio/db/test_fastq.rb |  372 ++++++++++++++++++++++++++--------------
 1 files changed, 245 insertions(+), 127 deletions(-)

commit 61556223a469a5f8b1bb4f343eca92c88c66cb9a
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 17 01:38:52 2009 +0900

    FASTQ output support is added to Bio::Sequence.

 lib/bio/db/fastq/format_fastq.rb |  172 ++++++++++++++++++++++++++++++++++++++
 lib/bio/sequence/format.rb       |    9 ++
 2 files changed, 181 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/fastq/format_fastq.rb

commit ea4203ebb7ca268a5b6d6c50aeb63ed0eed5a803
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 17 01:32:50 2009 +0900

    New attributes for genome sequencer data are added to Bio::Sequence.
    
     * New attributes for genome sequencer data are added to
       Bio::Sequence class: quality_scores, quality_scores_type,
       error_probabilities.

 lib/bio/sequence.rb |   13 +++++++++++++
 1 files changed, 13 insertions(+), 0 deletions(-)

commit fce158b2194519081361e12c170882ec2e87fc5e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Oct 17 01:13:27 2009 +0900

    New methods Bio::Fastq#to_biosequence, etc. and improvement of tolerance for overflows
    
     * Bio::Fastq#to_biosequence is newly added.
     * New methods: Bio::Fastq#seq, entry_id, quality_score_type.
     * Default behavior of Bio::Fastq::FormatData#scores2str is changed
       not to raise error but to truncate saturated values.
     * Improvement of tolerance for overflows, and preventing to calculate
       log of negative number.

 lib/bio/db/fastq.rb                      |  105 ++++++++++++++++++++++++++++--
 lib/bio/db/fastq/fastq_to_biosequence.rb |   40 +++++++++++
 lib/bio/sequence/adapter.rb              |    1 +
 3 files changed, 139 insertions(+), 7 deletions(-)
 create mode 100644 lib/bio/db/fastq/fastq_to_biosequence.rb

commit 0f189974d2027cecee575b27e969de7f62508309
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Oct 13 21:41:58 2009 +0900

    Avoid using Numeric#fdiv because it can only be used in Ruby 1.8.7 or later

 lib/bio/db/fastq.rb            |    6 +++---
 test/unit/bio/db/test_fastq.rb |   10 +++++-----
 2 files changed, 8 insertions(+), 8 deletions(-)

commit 42999fc6230e52c4f241f411d299db941196f62e
Author: Naohisa Goto <ng@bioruby.org>
Date:   Tue Oct 13 21:30:25 2009 +0900

    Bio::Fastq#qualities is renamed to quality_scores.
    
     * Bio::Fastq#qualities is renamed to Bio::Fastq#quality_scores, and
       the original method name is changed to be an alias of the new name.

 lib/bio/db/fastq.rb            |   16 +++++++++-------
 test/unit/bio/db/test_fastq.rb |   30 +++++++++++++++---------------
 2 files changed, 24 insertions(+), 22 deletions(-)

commit cc0ee2169f298046c5e55fcbadfeaac01f6bf704
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Oct 11 19:19:18 2009 +0900

    Newly added unit tests for Bio::Fastq with test data
    
     * Newly added unit tests for Bio::Fastq with test data. The test data
       is created by P.J.A. Cock et al., and is also used in Biopython and
       BioPerl.

 test/data/fastq/error_diff_ids.fastq               |   20 +
 test/data/fastq/error_double_qual.fastq            |   22 +
 test/data/fastq/error_double_seq.fastq             |   22 +
 test/data/fastq/error_long_qual.fastq              |   20 +
 test/data/fastq/error_no_qual.fastq                |   20 +
 test/data/fastq/error_qual_del.fastq               |   20 +
 test/data/fastq/error_qual_escape.fastq            |   20 +
 test/data/fastq/error_qual_null.fastq              |  Bin 0 -> 610 bytes
 test/data/fastq/error_qual_space.fastq             |   21 +
 test/data/fastq/error_qual_tab.fastq               |   21 +
 test/data/fastq/error_qual_unit_sep.fastq          |   20 +
 test/data/fastq/error_qual_vtab.fastq              |   20 +
 test/data/fastq/error_short_qual.fastq             |   20 +
 test/data/fastq/error_spaces.fastq                 |   20 +
 test/data/fastq/error_tabs.fastq                   |   21 +
 test/data/fastq/error_trunc_at_plus.fastq          |   19 +
 test/data/fastq/error_trunc_at_qual.fastq          |   19 +
 test/data/fastq/error_trunc_at_seq.fastq           |   18 +
 test/data/fastq/error_trunc_in_plus.fastq          |   19 +
 test/data/fastq/error_trunc_in_qual.fastq          |   20 +
 test/data/fastq/error_trunc_in_seq.fastq           |   18 +
 test/data/fastq/error_trunc_in_title.fastq         |   17 +
 .../fastq/illumina_full_range_as_illumina.fastq    |    8 +
 .../data/fastq/illumina_full_range_as_sanger.fastq |    8 +
 .../data/fastq/illumina_full_range_as_solexa.fastq |    8 +
 .../illumina_full_range_original_illumina.fastq    |    8 +
 test/data/fastq/longreads_as_illumina.fastq        |   40 ++
 test/data/fastq/longreads_as_sanger.fastq          |   40 ++
 test/data/fastq/longreads_as_solexa.fastq          |   40 ++
 test/data/fastq/longreads_original_sanger.fastq    |  120 ++++
 test/data/fastq/misc_dna_as_illumina.fastq         |   16 +
 test/data/fastq/misc_dna_as_sanger.fastq           |   16 +
 test/data/fastq/misc_dna_as_solexa.fastq           |   16 +
 test/data/fastq/misc_dna_original_sanger.fastq     |   16 +
 test/data/fastq/misc_rna_as_illumina.fastq         |   16 +
 test/data/fastq/misc_rna_as_sanger.fastq           |   16 +
 test/data/fastq/misc_rna_as_solexa.fastq           |   16 +
 test/data/fastq/misc_rna_original_sanger.fastq     |   16 +
 .../data/fastq/sanger_full_range_as_illumina.fastq |    8 +
 test/data/fastq/sanger_full_range_as_sanger.fastq  |    8 +
 test/data/fastq/sanger_full_range_as_solexa.fastq  |    8 +
 .../fastq/sanger_full_range_original_sanger.fastq  |    8 +
 .../data/fastq/solexa_full_range_as_illumina.fastq |    8 +
 test/data/fastq/solexa_full_range_as_sanger.fastq  |    8 +
 test/data/fastq/solexa_full_range_as_solexa.fastq  |    8 +
 .../fastq/solexa_full_range_original_solexa.fastq  |    8 +
 test/data/fastq/wrapping_as_illumina.fastq         |   12 +
 test/data/fastq/wrapping_as_sanger.fastq           |   12 +
 test/data/fastq/wrapping_as_solexa.fastq           |   12 +
 test/data/fastq/wrapping_original_sanger.fastq     |   24 +
 test/unit/bio/db/test_fastq.rb                     |  711 ++++++++++++++++++++
 51 files changed, 1652 insertions(+), 0 deletions(-)
 create mode 100644 test/data/fastq/error_diff_ids.fastq
 create mode 100644 test/data/fastq/error_double_qual.fastq
 create mode 100644 test/data/fastq/error_double_seq.fastq
 create mode 100644 test/data/fastq/error_long_qual.fastq
 create mode 100644 test/data/fastq/error_no_qual.fastq
 create mode 100644 test/data/fastq/error_qual_del.fastq
 create mode 100644 test/data/fastq/error_qual_escape.fastq
 create mode 100644 test/data/fastq/error_qual_null.fastq
 create mode 100644 test/data/fastq/error_qual_space.fastq
 create mode 100644 test/data/fastq/error_qual_tab.fastq
 create mode 100644 test/data/fastq/error_qual_unit_sep.fastq
 create mode 100644 test/data/fastq/error_qual_vtab.fastq
 create mode 100644 test/data/fastq/error_short_qual.fastq
 create mode 100644 test/data/fastq/error_spaces.fastq
 create mode 100644 test/data/fastq/error_tabs.fastq
 create mode 100644 test/data/fastq/error_trunc_at_plus.fastq
 create mode 100644 test/data/fastq/error_trunc_at_qual.fastq
 create mode 100644 test/data/fastq/error_trunc_at_seq.fastq
 create mode 100644 test/data/fastq/error_trunc_in_plus.fastq
 create mode 100644 test/data/fastq/error_trunc_in_qual.fastq
 create mode 100644 test/data/fastq/error_trunc_in_seq.fastq
 create mode 100644 test/data/fastq/error_trunc_in_title.fastq
 create mode 100644 test/data/fastq/illumina_full_range_as_illumina.fastq
 create mode 100644 test/data/fastq/illumina_full_range_as_sanger.fastq
 create mode 100644 test/data/fastq/illumina_full_range_as_solexa.fastq
 create mode 100644 test/data/fastq/illumina_full_range_original_illumina.fastq
 create mode 100644 test/data/fastq/longreads_as_illumina.fastq
 create mode 100644 test/data/fastq/longreads_as_sanger.fastq
 create mode 100644 test/data/fastq/longreads_as_solexa.fastq
 create mode 100644 test/data/fastq/longreads_original_sanger.fastq
 create mode 100644 test/data/fastq/misc_dna_as_illumina.fastq
 create mode 100644 test/data/fastq/misc_dna_as_sanger.fastq
 create mode 100644 test/data/fastq/misc_dna_as_solexa.fastq
 create mode 100644 test/data/fastq/misc_dna_original_sanger.fastq
 create mode 100644 test/data/fastq/misc_rna_as_illumina.fastq
 create mode 100644 test/data/fastq/misc_rna_as_sanger.fastq
 create mode 100644 test/data/fastq/misc_rna_as_solexa.fastq
 create mode 100644 test/data/fastq/misc_rna_original_sanger.fastq
 create mode 100644 test/data/fastq/sanger_full_range_as_illumina.fastq
 create mode 100644 test/data/fastq/sanger_full_range_as_sanger.fastq
 create mode 100644 test/data/fastq/sanger_full_range_as_solexa.fastq
 create mode 100644 test/data/fastq/sanger_full_range_original_sanger.fastq
 create mode 100644 test/data/fastq/solexa_full_range_as_illumina.fastq
 create mode 100644 test/data/fastq/solexa_full_range_as_sanger.fastq
 create mode 100644 test/data/fastq/solexa_full_range_as_solexa.fastq
 create mode 100644 test/data/fastq/solexa_full_range_original_solexa.fastq
 create mode 100644 test/data/fastq/wrapping_as_illumina.fastq
 create mode 100644 test/data/fastq/wrapping_as_sanger.fastq
 create mode 100644 test/data/fastq/wrapping_as_solexa.fastq
 create mode 100644 test/data/fastq/wrapping_original_sanger.fastq
 create mode 100644 test/unit/bio/db/test_fastq.rb

commit 951d8f7303a5c28783a2c8b25c9fb347730c1a8f
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Oct 11 19:10:15 2009 +0900

    Bio::Fastq API changed.
    
     * Bio::Fastq API changed. Removed methods: phred_quality, solexa_quality.
       New methods: qualities, error_probabilities, format, format=,
       validate_format.
     * New exception classes Bio::Fastq::Error::* for errors.
     * Internal structure is also changed. Internal only classes
       Bio::Fastq::FormatData::* which store parameters for format variants.

 lib/bio/db/fastq.rb |  519 +++++++++++++++++++++++++++++++++++++++++++++++++--
 1 files changed, 501 insertions(+), 18 deletions(-)

commit 9bb7f6ca762c615e50d98c35b60982a4caeea323
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 25 23:36:13 2009 +0900

    Bug fix: infinite loop in Bio::Fastq.new. Thanks to Hiroyuki Mishima for reporting the bug.

 lib/bio/db/fastq.rb |   16 ++++++++++------
 1 files changed, 10 insertions(+), 6 deletions(-)

commit fca6aa5333a95db4dc87e8fc814bd028d5720de4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Mar 20 11:52:33 2009 +0900

    Added file format autodetection for Bio::Fastq

 lib/bio/io/flatfile/autodetection.rb |    6 ++++++
 1 files changed, 6 insertions(+), 0 deletions(-)

commit 1ba21545e7d49ae8b775fbed7a4e92b1daa54ac6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Mar 20 11:48:59 2009 +0900

    Added autoload for Bio::Fastq

 lib/bio.rb |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)

commit 380b99106d4c7955b9d07ee8668b53d384c974f4
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Mar 19 17:07:25 2009 +0900

    Newly added FASTQ format parser (still a prototype)

 lib/bio/db/fastq.rb |  162 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 files changed, 162 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/fastq.rb

commit 2c5df2a5f1b5ae1ea9e61c1dccc8bcd2f496f6ce
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Sep 20 19:08:55 2009 +0900

    Removed "require 'rubygems'".

 lib/bio/db/phyloxml/phyloxml_parser.rb |    2 --
 1 files changed, 0 insertions(+), 2 deletions(-)

commit 67818d2550e5d53eeee0f3d710f66f7506fb8127
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sat Sep 19 17:06:21 2009 +0900

    Use Bio::PubMed.esearch and efetch, etc.
    
     * Changed to use Bio::PubMed.esearch and efetch instead of
       deprecated methods.
     * Regular expression for extracting option is changed.

 sample/pmfetch.rb  |   15 +++++++++++----
 sample/pmsearch.rb |   17 +++++++++++++----
 2 files changed, 24 insertions(+), 8 deletions(-)

commit 0c95889bf69e3140b5f09ade1203d50136aee014
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 18 17:58:17 2009 +0900

    Changed to use temporary directory when writing a file, etc.
    
      * To avoid unexpected file corruption and possibly security risk,
        changed to use temporary directory when writing files. The
        temporary directory is normally removed when all tests end.
        To prevent removing the directory, set environment variable
        BIORUBY_TEST_DEBUG.
      * To avoid test class name conflict, TestPhyloXMLData is renamed
        to TestPhyloXMLWriterData.
      * Added a new test to check existence of libxml-ruby, and removed
        code to raise error when it is not found. The code of the new
        test is completely the same as of in test_phyloxml.rb, but it
        is added for the purpose when test_phyloxml_writer.rb is called
        independently.

 test/unit/bio/db/test_phyloxml_writer.rb |  161 +++++++++++++++++++++---------
 1 files changed, 112 insertions(+), 49 deletions(-)

commit 520d0f5ed535f621aed60b71d8765a99e97306a6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Sun Sep 20 18:34:19 2009 +0900

    Newly added internal-only class Bio::Command::Tmpdir to handle temporary directory
    
     * Newly added internal-only class Bio::Command::Tmpdir to handle
       temporary directory. It is BioRuby library internal use only.
     * Bio::Command.mktmpdir is changed to be completely compatible
       with Ruby 1.9.x's Dir.mktmpdir.

 lib/bio/command.rb                  |  104 +++++++++++++++++++++++++++++++---
 test/functional/bio/test_command.rb |   49 ++++++++++++++++
 2 files changed, 143 insertions(+), 10 deletions(-)

commit c813b60ae62f44d9688b21d47c84e4b7083547e6
Author: Naohisa Goto <ng@bioruby.org>
Date:   Fri Sep 18 17:55:14 2009 +0900

    Added new test to check existence of libxml-ruby, instead of raising error.

 test/unit/bio/db/test_phyloxml.rb |   30 ++++++++++++++++++++----------
 1 files changed, 20 insertions(+), 10 deletions(-)

commit 1b71dd9624640f3f775baab360eef0be92a86677
Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
Date:   Fri Sep 18 21:43:18 2009 -0400

    Renamed output files generated by phyloxml_writer unit tests.

 test/unit/bio/db/test_phyloxml_writer.rb |   13 ++++++++++---
 1 files changed, 10 insertions(+), 3 deletions(-)

commit f8e138cb9e28996f1024fa9cf7c68c8f08603941
Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
Date:   Fri Sep 18 21:33:35 2009 -0400

    Added ncbi_taxonomy_mollusca_short.xml test file

 .../data/phyloxml/ncbi_taxonomy_mollusca_short.xml |   65 ++++++++++++++++++++
 1 files changed, 65 insertions(+), 0 deletions(-)
 create mode 100644 test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml

commit be1be310b7581928581cde24303fe2e16c04e82f
Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
Date:   Fri Sep 18 21:29:20 2009 -0400

    Made the code compactible with libxml-ruby 1.1.3 (previous was 0.9.4) version.

 lib/bio/db/phyloxml/phyloxml_elements.rb |   58 +++++++++++++++---------------
 lib/bio/db/phyloxml/phyloxml_parser.rb   |   10 ++++-
 lib/bio/db/phyloxml/phyloxml_writer.rb   |    8 +++--
 3 files changed, 42 insertions(+), 34 deletions(-)

commit a3441afd5650069a5ada64b202a0714e8723e911
Author: Diana Jaunzeikare <latvianlinuxgirl@gmail.com>
Date:   Tue May 26 00:55:47 2009 -0400

    Newly added PhyloXML support written by Diana Jaunzeikare.
    
     * Newly added PhyloXML support written by Diana Jaunzeikare.
       It have been written during the Google Summer of Code 2009
       "Implementing phyloXML support in BioRuby", mentored by
       Christian Zmasek et al. with NESCent. For details of development,
       see git://github.com/latvianlinuxgirl/bioruby.git and BioRuby
       mailing list archives.
     * This is a combination of 119 commits. The last commit date was
       Mon Aug 17 10:30:10 2009 -0400.

 README.rdoc                              |    3 +
 doc/Tutorial.rd                          |  120 ++-
 lib/bio.rb                               |    6 +
 lib/bio/db/phyloxml/phyloxml.xsd         |  573 ++++++++
 lib/bio/db/phyloxml/phyloxml_elements.rb | 1160 +++++++++++++++++
 lib/bio/db/phyloxml/phyloxml_parser.rb   |  767 +++++++++++
 lib/bio/db/phyloxml/phyloxml_writer.rb   |  223 ++++
 test/data/phyloxml/apaf.xml              |  666 ++++++++++
 test/data/phyloxml/bcl_2.xml             | 2097 ++++++++++++++++++++++++++++++
 test/data/phyloxml/made_up.xml           |  144 ++
 test/data/phyloxml/phyloxml_examples.xml |  415 ++++++
 test/unit/bio/db/test_phyloxml.rb        |  619 +++++++++
 test/unit/bio/db/test_phyloxml_writer.rb |  258 ++++
 13 files changed, 7050 insertions(+), 1 deletions(-)
 create mode 100644 lib/bio/db/phyloxml/phyloxml.xsd
 create mode 100644 lib/bio/db/phyloxml/phyloxml_elements.rb
 create mode 100644 lib/bio/db/phyloxml/phyloxml_parser.rb
 create mode 100644 lib/bio/db/phyloxml/phyloxml_writer.rb
 create mode 100644 test/data/phyloxml/apaf.xml
 create mode 100644 test/data/phyloxml/bcl_2.xml
 create mode 100644 test/data/phyloxml/made_up.xml
 create mode 100644 test/data/phyloxml/phyloxml_examples.xml
 create mode 100644 test/unit/bio/db/test_phyloxml.rb
 create mode 100644 test/unit/bio/db/test_phyloxml_writer.rb

commit fd8281f03423ddf23f7d409863b4df647f1b1564
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 9 21:08:15 2009 +0900

    Newly added Chromatogram classes contributed by Anthony Underwood.
    
     * Newly added Chromatogram classes contributed by Anthony Underwood.
       See git://github.com/aunderwo/bioruby.git for details of development
       before this merge.

 lib/bio.rb                                         |    3 +
 lib/bio/db/chromatogram.rb                         |  133 +++++++++++++
 lib/bio/db/chromatogram/abi.rb                     |  111 +++++++++++
 .../db/chromatogram/chromatogram_to_biosequence.rb |   32 +++
 lib/bio/db/chromatogram/scf.rb                     |  207 ++++++++++++++++++++
 lib/bio/sequence/adapter.rb                        |    1 +
 test/data/chromatogram/test_chromatogram_abi.ab1   |  Bin 0 -> 228656 bytes
 .../data/chromatogram/test_chromatogram_scf_v2.scf |  Bin 0 -> 47503 bytes
 .../data/chromatogram/test_chromatogram_scf_v3.scf |  Bin 0 -> 47503 bytes
 test/unit/bio/db/test_chromatogram.rb              |   99 ++++++++++
 10 files changed, 586 insertions(+), 0 deletions(-)
 create mode 100644 lib/bio/db/chromatogram.rb
 create mode 100644 lib/bio/db/chromatogram/abi.rb
 create mode 100644 lib/bio/db/chromatogram/chromatogram_to_biosequence.rb
 create mode 100644 lib/bio/db/chromatogram/scf.rb
 create mode 100644 test/data/chromatogram/test_chromatogram_abi.ab1
 create mode 100644 test/data/chromatogram/test_chromatogram_scf_v2.scf
 create mode 100644 test/data/chromatogram/test_chromatogram_scf_v3.scf
 create mode 100644 test/unit/bio/db/test_chromatogram.rb

commit 78f9463b764687401ff4a7480c1383c5594e5133
Author: Naohisa Goto <ng@bioruby.org>
Date:   Thu Sep 10 12:38:25 2009 +0900

    Bio::BIORUBY_EXTRA_VERSION is changed to ".5000".

 bioruby.gemspec    |    2 +-
 lib/bio/version.rb |    2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

commit e731c6e52bc9a672e4546eeca4f2d2d968bdba09
Author: Naohisa Goto <ng@bioruby.org>
Date:   Wed Sep 2 15:24:00 2009 +0900

    BioRuby 1.3.1 is released.
    
    ChangeLog is modified, and bioruby.gemspec is regenerated.

 ChangeLog       |   11 +++++++++++
 bioruby.gemspec |    2 +-
 2 files changed, 12 insertions(+), 1 deletions(-)