RubyGems - bio - Versions diffs - 1.5.0 → 1.5.1 - Mend

bio 1.5.0 → 1.5.1

Files changed (9) hide show

checksums.yaml +4 -4
data/ChangeLog +385 -305
data/RELEASE_NOTES.rdoc +28 -2
data/bioruby.gemspec +1 -1
data/lib/bio/command.rb +40 -2
data/lib/bio/io/ncbirest.rb +26 -24
data/lib/bio/version.rb +2 -2
data/test/network/bio/test_command.rb +17 -0
metadata +3 -3

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data/ChangeLog CHANGED

@@ -1,10 +1,90 @@
+commit 917fe0d0e9910267cd54bf48c2caabe89875a299
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 7 22:00:56 2016 +0900
+    regenerate bioruby.gemspec with rake regemspec
+ bioruby.gemspec | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+commit 1cfa823572742ea46f14420481c10f05fdbce862
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 7 21:51:28 2016 +0900
+    Bio::BIORUBY_EXTRA_VERSION set to nil (Release version)
+ lib/bio/version.rb | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+commit 8c27599ef5b8ee33cd074feadd089de01a8fa8e6
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Sep 7 21:49:20 2016 +0900
+    Added release notes for 1.5.1 release
+ RELEASE_NOTES.rdoc | 26 ++++++++++++++++++++++++++
+ 1 file changed, 26 insertions(+)
+commit 47ada241ad6f3632dbbd77542befb82500b7195e
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Aug 13 08:22:22 2016 +0900
+    Update URLs and use https for NCBI REST web services
+ lib/bio/io/ncbirest.rb | 50 ++++++++++++++++++++++++++------------------------
+ 1 file changed, 26 insertions(+), 24 deletions(-)
+commit 018c2aff1c7813e7b07362ecc8a25db334c0ae95
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Sat Aug 13 08:12:08 2016 +0900
+    New method Bio::Command#start_http_uri(uri) with tests
+     * lib/bio/command.rb: New method Bio::Command#start_http_uri(uri)
+       that supports HTTPS. Note that this method is intended to be
+       called only from BioRuby internals.
+     * lib/bio/command.rb: Bio::Command#post and #post_form are changed
+       to use the start_http_uri().
+     * test/network/bio/test_command.rb: tests for start_http_uri().
+ lib/bio/command.rb               | 42 ++++++++++++++++++++++++++++++++++++++--
+ test/network/bio/test_command.rb | 17 ++++++++++++++++
+ 2 files changed, 57 insertions(+), 2 deletions(-)
+commit 7a5d897ebc45d9ec5357918a42eb2980decf01e4
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jul 2 21:52:17 2015 +0900
+    version changed to 1.5.1-dev (pre-release version of 1.5.1)
+ lib/bio/version.rb | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+commit 8fc4d6c64f6958a352c36b171b00d1f1ff2a2354
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Thu Jul 2 21:47:28 2015 +0900
+    fix English syntax and unexpected word insertion
+ RELEASE_NOTES.rdoc | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+commit 1d165c5def88fdeb8f3beeba1f9e6ab0ce71c2a1
+Author: Naohisa Goto <ng@bioruby.org>
+Date:   Wed Jul 1 17:28:17 2015 +0900
+    BioRuby 1.5.0 is released
+ ChangeLog | 9 +++++++++
+ 1 file changed, 9 insertions(+)
 commit 01ac93ca3b341716c85c571f1194834db0a68e52
 Author: Naohisa Goto <ng@bioruby.org>
 Date:   Wed Jul 1 02:21:26 2015 +0900
     update ChangeLog by rake rechangelog
- ChangeLog |   28 ++++++++++++++++++++++++++++
+ ChangeLog | 28 ++++++++++++++++++++++++++++
  1 file changed, 28 insertions(+)
 commit cac63ff501df6a71afead77175db9fb491c2985b
@@ -13,7 +93,7 @@ Date:   Wed Jul 1 01:31:21 2015 +0900
     .travis.yml: use Ruby 2.1.6 for tar and gem integration tests
- .travis.yml |    8 ++++----
+ .travis.yml | 8 ++++----
  1 file changed, 4 insertions(+), 4 deletions(-)
 commit 5318c99249f34dacc788b82c658ea0e256770db0
@@ -22,8 +102,8 @@ Date:   Wed Jul 1 00:43:39 2015 +0900
     known issues added about new BLAST XML format and BLAST+ text format
- KNOWN_ISSUES.rdoc  |   11 +++++++++++
- RELEASE_NOTES.rdoc |   11 +++++++++++
+ KNOWN_ISSUES.rdoc  | 11 +++++++++++
+ RELEASE_NOTES.rdoc | 11 +++++++++++
  2 files changed, 22 insertions(+)
 commit b61d8df0300ef366539e1154c9a2dac2f1f4ff18
@@ -32,7 +112,7 @@ Date:   Tue Jun 30 23:57:01 2015 +0900
     update ChangeLog with rake rechangelog
- ChangeLog |   47 +++++++++++++++++++++++++++++++++++++++++++++++
+ ChangeLog | 47 +++++++++++++++++++++++++++++++++++++++++++++++
  1 file changed, 47 insertions(+)
 commit 75cf6c31c57239b2e39a171e536ad5dddcaec94a
@@ -41,7 +121,7 @@ Date:   Tue Jun 30 23:56:08 2015 +0900
     regenerate bioruby.gemspec with rake regemspec
- bioruby.gemspec |    1 +
+ bioruby.gemspec | 1 +
  1 file changed, 1 insertion(+)
 commit 608850beb33f3f7333f05307202b766adb350eb9
@@ -50,7 +130,7 @@ Date:   Tue Jun 30 23:54:59 2015 +0900
     description about updating of Ruby's License
- RELEASE_NOTES.rdoc |    9 +++++++++
+ RELEASE_NOTES.rdoc | 9 +++++++++
  1 file changed, 9 insertions(+)
 commit f54bcfc20d20935db4e342e5988c0b7f59c131b3
@@ -59,7 +139,7 @@ Date:   Tue Jun 30 23:16:51 2015 +0900
     BSDL is referred in COPYING and COPYING.ja
- BSDL |   22 ++++++++++++++++++++++
+ BSDL | 22 ++++++++++++++++++++++
  1 file changed, 22 insertions(+)
  create mode 100644 BSDL
@@ -69,8 +149,8 @@ Date:   Tue Jun 30 23:14:42 2015 +0900
     changes of Ruby's License is reflected.
- COPYING    |    4 ++--
- COPYING.ja |   72 ++++++++++++++++++++++++++++++------------------------------
+ COPYING    |  4 ++--
+ COPYING.ja | 72 +++++++++++++++++++++++++++++++-------------------------------
  2 files changed, 38 insertions(+), 38 deletions(-)
 commit 2d9de9a0e2abe7fa9f193e54af0cbfc24bf2c37b
@@ -88,7 +168,7 @@ Date:   Tue Jun 30 22:49:55 2015 +0900
     KNOWN_ISSUES.rdoc: change ruby versions and add descriptions
- KNOWN_ISSUES.rdoc |   14 +++++++++-----
+ KNOWN_ISSUES.rdoc | 14 +++++++++-----
  1 file changed, 9 insertions(+), 5 deletions(-)
 commit 1054106f93b973b5a92f993c5b83b1444f96fffe
@@ -97,8 +177,8 @@ Date:   Tue Jun 30 22:48:51 2015 +0900
     prepare to release BioRuby 1.5.0
- bioruby.gemspec    |    2 +-
- lib/bio/version.rb |    2 +-
+ bioruby.gemspec    | 2 +-
+ lib/bio/version.rb | 2 +-
  2 files changed, 2 insertions(+), 2 deletions(-)
 commit 0f150586904f7e423455615313992ccf77d7e123
@@ -107,7 +187,7 @@ Date:   Tue Jun 30 22:44:58 2015 +0900
     RELEASE_NOTES.rdoc: update many
- RELEASE_NOTES.rdoc |  151 +++++++++++++++++++++++++++++++++++++++++++++-------
+ RELEASE_NOTES.rdoc | 151 ++++++++++++++++++++++++++++++++++++++++++++++-------
  1 file changed, 132 insertions(+), 19 deletions(-)
 commit 2924ca0b977da13d42f232f880fd2df0b2995677
@@ -121,7 +201,7 @@ Date:   Tue Jun 30 21:55:52 2015 +0900
        Thanks to Jose Irizarry who reports and sends suggested fix.
        (https://github.com/bioruby/bioruby/pull/83 )
- lib/bio/db/embl/uniprotkb.rb |    2 +-
+ lib/bio/db/embl/uniprotkb.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 9bf9022007a0ff31a870b1ea08e423aebc487c17
@@ -130,7 +210,7 @@ Date:   Tue Jun 30 18:45:51 2015 +0900
     regenerate bioruby.gemspec with rake regemspec
- bioruby.gemspec |    1 +
+ bioruby.gemspec | 1 +
  1 file changed, 1 insertion(+)
 commit a151e51a44b3dd93e5d075d71954f639eaec339e
@@ -139,7 +219,7 @@ Date:   Tue Jun 30 18:10:55 2015 +0900
     update docs; change recommended Ruby versions
- README.rdoc |    9 ++++++---
+ README.rdoc | 9 ++++++---
  1 file changed, 6 insertions(+), 3 deletions(-)
 commit e86e745c8a6c666c446fe2f9f47818140999e2db
@@ -148,7 +228,7 @@ Date:   Tue Jun 30 18:08:53 2015 +0900
     delete description about SOAP4R
- README.rdoc |    5 -----
+ README.rdoc | 5 -----
  1 file changed, 5 deletions(-)
 commit 7e4bfb6b3757872691487b080bfd87363a4f9480
@@ -161,8 +241,8 @@ Date:   Tue Jun 30 03:22:35 2015 +0900
        that include 'gem "test-unit"' line because test/unit have been
        provided by bundled gem since Ruby 2.2.
- .travis.yml                     |    7 ++++---
- gemfiles/Gemfile.travis-ruby2.2 |    9 +++++++++
+ .travis.yml                     | 7 ++++---
+ gemfiles/Gemfile.travis-ruby2.2 | 9 +++++++++
  2 files changed, 13 insertions(+), 3 deletions(-)
  create mode 100644 gemfiles/Gemfile.travis-ruby2.2
@@ -176,9 +256,9 @@ Date:   Tue Jun 30 02:51:16 2015 +0900
      * Simplify the versioning rules.
      * We will adopt the Semantic Versioning since BioRuby 1.5.1.
- bioruby.gemspec     |    2 +-
- bioruby.gemspec.erb |   21 ++++-----------------
- lib/bio/version.rb  |   17 ++++++++---------
+ bioruby.gemspec     |  2 +-
+ bioruby.gemspec.erb | 21 ++++-----------------
+ lib/bio/version.rb  | 17 ++++++++---------
  3 files changed, 13 insertions(+), 27 deletions(-)
 commit 1a24fb6840932499be833b5ec3bb36184b1334a1
@@ -190,7 +270,7 @@ Date:   Tue Jun 30 02:14:01 2015 +0900
      * Bug fix: update Bio::Hinv::BASE_URI to follow the server URI change.
      * Update official documentation URL.
- lib/bio/io/hinv.rb |    4 ++--
+ lib/bio/io/hinv.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit a9a12fff70ca287aa098d1331a3146e2899cb709
@@ -199,7 +279,7 @@ Date:   Tue Jun 30 02:08:40 2015 +0900
     delete $Id:$ line
- lib/bio/io/hinv.rb |    1 -
+ lib/bio/io/hinv.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 2bfa0f41969003f17c4b894b5279347616c8f187
@@ -208,7 +288,7 @@ Date:   Tue Jun 30 01:58:01 2015 +0900
     delete sections about SOAP4R issues
- KNOWN_ISSUES.rdoc |   12 ------------
+ KNOWN_ISSUES.rdoc | 12 ------------
  1 file changed, 12 deletions(-)
 commit 9dbd83aa00acc5f78b5da68f000c305da9f31b66
@@ -217,9 +297,9 @@ Date:   Tue Jun 30 01:54:16 2015 +0900
     remove commented-out lines of soap4r-ruby1.9
- gemfiles/Gemfile.travis-jruby1.9 |    3 ---
- gemfiles/Gemfile.travis-rbx      |    3 ---
- gemfiles/Gemfile.travis-ruby1.9  |    3 ---
+ gemfiles/Gemfile.travis-jruby1.9 | 3 ---
+ gemfiles/Gemfile.travis-rbx      | 3 ---
+ gemfiles/Gemfile.travis-ruby1.9  | 3 ---
  3 files changed, 9 deletions(-)
 commit 14d2f3e2fa15f94faeff4d28c957f581461eac82
@@ -228,7 +308,7 @@ Date:   Tue Jun 30 01:50:30 2015 +0900
     .travis.yml: update ruby versions, remove ruby 1.9.2
- .travis.yml |    8 ++++----
+ .travis.yml | 8 ++++----
  1 file changed, 4 insertions(+), 4 deletions(-)
 commit 89f9b1fe2332584b5d63b1539b8e470d853478a3
@@ -237,7 +317,7 @@ Date:   Tue Jun 30 00:36:42 2015 +0900
     about removal of Bio::SOAPWSDL, Bio::EBI::SOAP, Bio::HGC::HiGet
- RELEASE_NOTES.rdoc |   20 ++++++++++++++++++++
+ RELEASE_NOTES.rdoc | 20 ++++++++++++++++++++
  1 file changed, 20 insertions(+)
 commit 29516d3d6d2f907f65822bcf4146e95785773a3a
@@ -246,7 +326,7 @@ Date:   Tue Jun 30 00:50:47 2015 +0900
     regenerate bioruby.gemspec with rake regemspec
- bioruby.gemspec |    6 ------
+ bioruby.gemspec | 6 ------
  1 file changed, 6 deletions(-)
 commit 357a1afc5ef457326179142c163968aa5cd94864
@@ -255,7 +335,7 @@ Date:   Tue Jun 30 00:49:42 2015 +0900
     not to load deleted file lib/bio/shell/plugin/soap.rb
- lib/bio/shell.rb |    1 -
+ lib/bio/shell.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 956e475da52ea17f1022493f589489a3e7c06f93
@@ -267,7 +347,7 @@ Date:   Mon Jun 29 23:43:24 2015 +0900
      * deleted lib/bio/shell/plugin/soap.rb because Bio::SOAPWSDL and
        all SOAP client classes in BioRuby are removed.
- lib/bio/shell/plugin/soap.rb |   50 ------------------------------------------
+ lib/bio/shell/plugin/soap.rb | 50 --------------------------------------------
  1 file changed, 50 deletions(-)
  delete mode 100644 lib/bio/shell/plugin/soap.rb
@@ -277,7 +357,7 @@ Date:   Mon Jun 29 23:41:20 2015 +0900
     not to load removed Bio::EBI::SOAP from lib/bio/io/ebisoap.rb
- lib/bio.rb |    4 ----
+ lib/bio.rb | 4 ----
  1 file changed, 4 deletions(-)
 commit d4844b38b5ddaec7ec15b56ef66f6930f0e6cfc0
@@ -289,7 +369,7 @@ Date:   Mon Jun 29 23:38:26 2015 +0900
      * Bio::EBI::SOAP (lib/bio/io/ebisoap.rb) is removed because
        Bio::SOAPWSDL is removed.
- lib/bio/io/ebisoap.rb |  158 -------------------------------------------------
+ lib/bio/io/ebisoap.rb | 158 --------------------------------------------------
  1 file changed, 158 deletions(-)
  delete mode 100644 lib/bio/io/ebisoap.rb
@@ -299,7 +379,7 @@ Date:   Tue Jun 30 00:12:36 2015 +0900
     not to load removed Bio::SOAPWSDL from lib/bio/io/soapwsdl.rb
- lib/bio.rb |    1 -
+ lib/bio.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 03ced6a70973557532517c70dac183775bd11fa7
@@ -314,9 +394,9 @@ Date:   Mon Jun 29 23:59:28 2015 +0900
        well-maintained. Moreover, many SOAP servers have been retired
        (see previous commits). So, we give up maintaining Bio::SOAPWSDL.
- lib/bio/io/soapwsdl.rb               |  119 ----------------------------------
- test/network/bio/io/test_soapwsdl.rb |   53 ---------------
- test/unit/bio/io/test_soapwsdl.rb    |   33 ----------
+ lib/bio/io/soapwsdl.rb               | 119 -----------------------------------
+ test/network/bio/io/test_soapwsdl.rb |  53 ----------------
+ test/unit/bio/io/test_soapwsdl.rb    |  33 ----------
  3 files changed, 205 deletions(-)
  delete mode 100644 lib/bio/io/soapwsdl.rb
  delete mode 100644 test/network/bio/io/test_soapwsdl.rb
@@ -328,7 +408,7 @@ Date:   Mon Jun 29 23:35:38 2015 +0900
     delete old comment-out lines about Bio::DDBJ::XML
- lib/bio.rb |    5 -----
+ lib/bio.rb | 5 -----
  1 file changed, 5 deletions(-)
 commit b995251bf96b8983def36e77bc94d6f0c0f2c78c
@@ -337,7 +417,7 @@ Date:   Mon Jun 29 23:29:47 2015 +0900
     do not load Bio::HGC::HiGet from deleted lib/bio/io/higet.rb
- lib/bio.rb |    4 ----
+ lib/bio.rb | 4 ----
  1 file changed, 4 deletions(-)
 commit 6191020ed1e150f9e70de687375528a899fcf8ef
@@ -346,7 +426,7 @@ Date:   Mon Jun 29 23:27:41 2015 +0900
     remove lib/bio/io/higet.rb because of the server down for a long time
- lib/bio/io/higet.rb |   73 ---------------------------------------------------
+ lib/bio/io/higet.rb | 73 -----------------------------------------------------
  1 file changed, 73 deletions(-)
  delete mode 100644 lib/bio/io/higet.rb
@@ -356,7 +436,7 @@ Date:   Sat Jun 27 02:33:46 2015 +0900
     add/modify about removed features and incompatible changes
- RELEASE_NOTES.rdoc |   71 +++++++++++++++++++++++++++++++++++++++++++++++++---
+ RELEASE_NOTES.rdoc | 71 +++++++++++++++++++++++++++++++++++++++++++++++++++---
  1 file changed, 67 insertions(+), 4 deletions(-)
 commit 1886314d2b8dd7d4b3e86c7b93134facd881127a
@@ -365,7 +445,7 @@ Date:   Sat Jun 27 01:24:36 2015 +0900
     regenerate bioruby.gemspec with rake regemspec
- bioruby.gemspec |    1 -
+ bioruby.gemspec | 1 -
  1 file changed, 1 deletion(-)
 commit 724e9c1c039dcc7fa19fb15de0313218a87f9868
@@ -379,7 +459,7 @@ Date:   Thu Jun 25 23:34:44 2015 +0900
        usually used only for building native extensions. Use gem or
        setup.rb to install BioRuby.
- extconf.rb |    2 --
+ extconf.rb | 2 --
  1 file changed, 2 deletions(-)
  delete mode 100644 extconf.rb
@@ -389,7 +469,7 @@ Date:   Wed Jun 24 22:29:28 2015 +0900
     Ruby 2.3 support: IO#close to closed IO object is allowed without error.
- test/unit/bio/io/flatfile/test_buffer.rb |    8 +++++++-
+ test/unit/bio/io/flatfile/test_buffer.rb | 8 +++++++-
  1 file changed, 7 insertions(+), 1 deletion(-)
 commit 5ea39188ac3cc2609397b2d8864a2019ea6b93d2
@@ -402,8 +482,8 @@ Date:   Fri May 1 23:42:39 2015 +0900
        Thanks to Peter Cock who reports a patch.
        (https://github.com/bioruby/bioruby/issues/101 )
- bioruby.gemspec     |    1 +
- bioruby.gemspec.erb |    1 +
+ bioruby.gemspec     | 1 +
+ bioruby.gemspec.erb | 1 +
  2 files changed, 2 insertions(+)
 commit 2b18ae005a592ea4ae7b632f7e658d4bbf153fd8
@@ -412,8 +492,8 @@ Date:   Fri May 1 23:39:36 2015 +0900
     remove deprecated Gem::Specification#rubyforge_project
- bioruby.gemspec     |    2 +-
- bioruby.gemspec.erb |    2 +-
+ bioruby.gemspec     | 2 +-
+ bioruby.gemspec.erb | 2 +-
  2 files changed, 2 insertions(+), 2 deletions(-)
 commit 3a1d89bde9af44793c850b1cde950e3e3042fb8d
@@ -422,7 +502,7 @@ Date:   Sat Mar 28 01:52:31 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/db/gff.rb |    1 -
+ lib/bio/db/gff.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 165ebf29ba192c7a7e7f1633809d34966c2aeed1
@@ -431,7 +511,7 @@ Date:   Sat Mar 28 01:51:47 2015 +0900
     suppress "character class has duplicated range" warnings
- lib/bio/db/gff.rb |    4 ++--
+ lib/bio/db/gff.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit 715ee5aa3a797737d390365b2c202cc9a0effea5
@@ -440,7 +520,7 @@ Date:   Sat Mar 28 01:37:35 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/appl/sosui/report.rb |    1 -
+ lib/bio/appl/sosui/report.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 71e34938f1228911657ebf00720712a17bc89ea9
@@ -449,7 +529,7 @@ Date:   Sat Mar 28 01:36:44 2015 +0900
     comment out a line to suppress warning: assigned but unused variable - tmh
- lib/bio/appl/sosui/report.rb |    2 +-
+ lib/bio/appl/sosui/report.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit fc518f3826bf60d70ebdbd70acdba512f1462c6f
@@ -458,7 +538,7 @@ Date:   Sat Mar 28 01:34:22 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/db/sanger_chromatogram/chromatogram.rb |    1 -
+ lib/bio/db/sanger_chromatogram/chromatogram.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 516c467dfb245d99c4f7f77e251c77ffc5d274ca
@@ -467,7 +547,7 @@ Date:   Sat Mar 28 01:33:19 2015 +0900
     suppress warning: instance variable @aqual not initialized
- lib/bio/db/sanger_chromatogram/chromatogram.rb |    2 +-
+ lib/bio/db/sanger_chromatogram/chromatogram.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 56d2e472196ba03ba6aa2a2bdf8d3de81272fa15
@@ -476,7 +556,7 @@ Date:   Sat Mar 28 01:30:26 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/db/kegg/module.rb |    1 -
+ lib/bio/db/kegg/module.rb | 1 -
  1 file changed, 1 deletion(-)
 commit fb6b9b6578d08a87c1974e58f6d1f231b4ad52c0
@@ -485,7 +565,7 @@ Date:   Sat Mar 28 01:28:05 2015 +0900
     suppress "instance variable @XXX not initialized" warnings
- lib/bio/db/kegg/module.rb |    8 ++++----
+ lib/bio/db/kegg/module.rb | 8 ++++----
  1 file changed, 4 insertions(+), 4 deletions(-)
 commit 9f70b8d54abd9adbd50d46a3176f23f51af01cc7
@@ -494,7 +574,7 @@ Date:   Sat Mar 28 01:25:50 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/db/kegg/pathway.rb |    1 -
+ lib/bio/db/kegg/pathway.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 3844b9bb69e1f657c9b85bb20a4d209828b78b12
@@ -503,7 +583,7 @@ Date:   Sat Mar 28 01:25:03 2015 +0900
     suppress "instance variable @XXX not initialized" warnings
- lib/bio/db/kegg/pathway.rb |    8 ++++----
+ lib/bio/db/kegg/pathway.rb | 8 ++++----
  1 file changed, 4 insertions(+), 4 deletions(-)
 commit 8d857e246eacb6c9f8fbbceaa2fba7f1211e2b86
@@ -512,7 +592,7 @@ Date:   Sat Mar 28 01:20:13 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/db/fasta/defline.rb |    1 -
+ lib/bio/db/fasta/defline.rb | 1 -
  1 file changed, 1 deletion(-)
 commit aadf285bc9e618b7813b42fd39e0b1966a04385c
@@ -521,7 +601,7 @@ Date:   Sat Mar 28 01:18:43 2015 +0900
     suppress defline.rb:393: warning: character class has duplicated range
- lib/bio/db/fasta/defline.rb |    2 +-
+ lib/bio/db/fasta/defline.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 5297db11eb165885c4f15b914c2132c4122ae5a9
@@ -530,7 +610,7 @@ Date:   Sat Mar 28 01:11:43 2015 +0900
     delete obsolete $Id:$ line
- test/unit/bio/test_db.rb |    1 -
+ test/unit/bio/test_db.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 20381ad45c674c0844a92891cb8ae71edaa6e333
@@ -543,7 +623,7 @@ Date:   Sat Mar 28 01:08:04 2015 +0900
        @tagsize not initialized" when executing Bio::TestDB#test_fetch,
        @tagsize is set in setup.
- test/unit/bio/test_db.rb |    5 ++++-
+ test/unit/bio/test_db.rb | 5 ++++-
  1 file changed, 4 insertions(+), 1 deletion(-)
 commit d194edfc68bc10fde11f2cf014a59113ddc63b24
@@ -552,7 +632,7 @@ Date:   Sat Mar 28 00:59:21 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/data/codontable.rb |    1 -
+ lib/bio/data/codontable.rb | 1 -
  1 file changed, 1 deletion(-)
 commit fac51f540dc7b33cd3ec51f97b5cb1ea587a461e
@@ -561,7 +641,7 @@ Date:   Sat Mar 28 00:57:28 2015 +0900
     suppress warning: instance variable @reverse not initialized
- lib/bio/data/codontable.rb |    2 +-
+ lib/bio/data/codontable.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 4e85315f03e374157f832c8435d0d2f43cd969af
@@ -570,7 +650,7 @@ Date:   Sat Mar 28 00:55:25 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/appl/iprscan/report.rb |    1 -
+ lib/bio/appl/iprscan/report.rb | 1 -
  1 file changed, 1 deletion(-)
 commit dafa7ce62378ff1605a295f8c620eb3a0a4a3c57
@@ -579,7 +659,7 @@ Date:   Sat Mar 28 00:54:37 2015 +0900
     suppress warning: instance variable @ipr_ids not initialized
- lib/bio/appl/iprscan/report.rb |    2 +-
+ lib/bio/appl/iprscan/report.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 52b6073997c1b26fea9d4aae3154b37575944d4d
@@ -588,7 +668,7 @@ Date:   Sat Mar 28 00:50:43 2015 +0900
     suppress "method redefined" warnings and fill RDoc for some methods
- lib/bio/db/phyloxml/phyloxml_elements.rb |   46 +++++++++++++++++++++++-------
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 46 ++++++++++++++++++++++++--------
  1 file changed, 35 insertions(+), 11 deletions(-)
 commit 3d2e99fe993d76d5ece5bdbcd2e9541fa098c4dd
@@ -597,7 +677,7 @@ Date:   Sat Mar 28 00:36:51 2015 +0900
     suppress "instance variable @XXX not initialized" warnings
- lib/bio/db/phyloxml/phyloxml_elements.rb |   88 +++++++++++++++---------------
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 88 ++++++++++++++++----------------
  1 file changed, 44 insertions(+), 44 deletions(-)
 commit 02d4f98eae3934d8ad9c950b41132eb14653fe27
@@ -606,7 +686,7 @@ Date:   Thu Mar 26 20:33:35 2015 +0900
     suppress warning: instance variable @uri not initialized
- lib/bio/db/phyloxml/phyloxml_elements.rb |    2 +-
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 94277712e9dd000c2d9bf5b6ebfd84d0f2fc3b59
@@ -615,7 +695,7 @@ Date:   Thu Mar 26 01:47:45 2015 +0900
     suppress warning: instance variable @format not initialized
- lib/bio/db/fastq.rb |    2 +-
+ lib/bio/db/fastq.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit e61e1071e4bb7dd9ee995c3a7f864c2ef4384edd
@@ -630,7 +710,7 @@ Date:   Thu Mar 26 01:40:33 2015 +0900
      * suppress warning: instance variable @hit_frame not initialized
      * suppress warning: instance variable @query_frame not initialized
- lib/bio/appl/blast/format0.rb |   13 ++++++++++---
+ lib/bio/appl/blast/format0.rb | 13 ++++++++++---
  1 file changed, 10 insertions(+), 3 deletions(-)
 commit 08c458c74a7a34e340e09053cbc0f9c071e27395
@@ -639,7 +719,7 @@ Date:   Thu Mar 26 01:09:16 2015 +0900
     suppress warning: instance variable @pattern not initialized
- lib/bio/appl/blast/format0.rb |    8 ++++++--
+ lib/bio/appl/blast/format0.rb | 8 ++++++--
  1 file changed, 6 insertions(+), 2 deletions(-)
 commit 33d7eed180fd601972724f4b992f1a17c689ef62
@@ -648,7 +728,7 @@ Date:   Thu Mar 26 00:57:02 2015 +0900
     Test bug fix: fix typo of test target method
- test/network/bio/test_command.rb |    2 +-
+ test/network/bio/test_command.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 76a98bce1affac03483c08f803d4314b42a0a3d3
@@ -662,8 +742,8 @@ Date:   Thu Mar 26 00:32:25 2015 +0900
        as String objects. This change also affects Bio::Command.post_form
        and Bio::Command.http_post_form which internally use this method.
- lib/bio/command.rb            |    2 +-
- test/unit/bio/test_command.rb |    9 +++++----
+ lib/bio/command.rb            | 2 +-
+ test/unit/bio/test_command.rb | 9 +++++----
  2 files changed, 6 insertions(+), 5 deletions(-)
 commit b1612545a7516befd850a6d5925aa73bbaa4b4b0
@@ -672,7 +752,7 @@ Date:   Wed Mar 25 02:36:41 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/io/togows.rb |    1 -
+ lib/bio/io/togows.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 4d5a419cc78ff2a79cff2812adc6f16f286204e8
@@ -681,7 +761,7 @@ Date:   Wed Mar 25 02:35:45 2015 +0900
     delete obsolete $Id:$ line
- test/network/bio/io/test_togows.rb |    1 -
+ test/network/bio/io/test_togows.rb | 1 -
  1 file changed, 1 deletion(-)
 commit a8d2c4cac665b4bb8140df329a9cc1d6e5e2d02d
@@ -690,7 +770,7 @@ Date:   Wed Mar 25 02:35:03 2015 +0900
     delete obsolete $Id:$ line
- test/unit/bio/io/test_togows.rb |    1 -
+ test/unit/bio/io/test_togows.rb | 1 -
  1 file changed, 1 deletion(-)
 commit dd0967db3743789ea5aa48623df8d97f93062694
@@ -699,7 +779,7 @@ Date:   Wed Mar 25 02:33:49 2015 +0900
     test_make_path: add test data using Symbol objects
- test/unit/bio/io/test_togows.rb |    4 +++-
+ test/unit/bio/io/test_togows.rb | 4 +++-
  1 file changed, 3 insertions(+), 1 deletion(-)
 commit e07158a60ca666b5d625408bcf8fa602fd8114a8
@@ -708,7 +788,7 @@ Date:   Wed Mar 25 02:22:31 2015 +0900
     Bio::TogoWS::REST#entry: comma between IDs should NOT be escaped to %2C
- lib/bio/io/togows.rb |   11 +++++++++--
+ lib/bio/io/togows.rb | 11 +++++++++--
  1 file changed, 9 insertions(+), 2 deletions(-)
 commit 98546289b2f2da2dc7f9586fd5e2942da4d8f3a8
@@ -723,7 +803,7 @@ Date:   Wed Mar 25 02:00:17 2015 +0900
        http://togows.org/search/nuccore/Milnesium+tardigradum/2%2C3 fails,
        http://togows.org/search/nuccore/Milnesium+tardigradum/2,3 works fine.
- lib/bio/io/togows.rb |   24 +++++++++++++++++++++---
+ lib/bio/io/togows.rb | 24 +++++++++++++++++++++---
  1 file changed, 21 insertions(+), 3 deletions(-)
 commit 7097f80e315a0a6332e7a76a5bb261649e8dcc1a
@@ -735,7 +815,7 @@ Date:   Wed Mar 25 01:33:26 2015 +0900
      * lib/bio/io/togows.rb: Bug fix: Bio::TogoWS::REST#convert did not work
        because of the spec change of TogoWS REST API.
- lib/bio/io/togows.rb |    7 +++----
+ lib/bio/io/togows.rb | 7 +++----
  1 file changed, 3 insertions(+), 4 deletions(-)
 commit 1a9b1063af4c0b32cd287d4a2c2466343aeddb98
@@ -744,7 +824,7 @@ Date:   Wed Mar 25 01:30:34 2015 +0900
     improve tests for bio/command.rb for methods using http protocol
- test/network/bio/test_command.rb |   67 ++++++++++++++++++++++++++++++++++++--
+ test/network/bio/test_command.rb | 67 ++++++++++++++++++++++++++++++++++++++--
  1 file changed, 65 insertions(+), 2 deletions(-)
 commit c63920e4d8569e3eaef201d4d60fcddfa15f1f34
@@ -753,7 +833,7 @@ Date:   Wed Mar 25 01:30:06 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/command.rb |    1 -
+ lib/bio/command.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 1683edac0e9ecbf819ffcd332a6db2d25c2d596a
@@ -762,7 +842,7 @@ Date:   Wed Mar 25 01:28:28 2015 +0900
     new methods Bio::Command.http_post and Bio::Command.post to post raw data
- lib/bio/command.rb |   61 ++++++++++++++++++++++++++++++++++++++++++++++++++++
+ lib/bio/command.rb | 61 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
  1 file changed, 61 insertions(+)
 commit a40157205282e148bf3a2e43aed1e08d713fb598
@@ -771,7 +851,7 @@ Date:   Tue Mar 24 00:46:23 2015 +0900
     suppress warnings "instance variable @circular not initialized"
- lib/bio/util/restriction_enzyme/range/sequence_range.rb |    4 ++--
+ lib/bio/util/restriction_enzyme/range/sequence_range.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit abcac8de85c9606f6a1879fe9d2ae559911708c9
@@ -780,7 +860,7 @@ Date:   Tue Mar 24 00:29:42 2015 +0900
     delete obsolete $Id:$ line
- test/unit/bio/io/flatfile/test_autodetection.rb |    1 -
+ test/unit/bio/io/flatfile/test_autodetection.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 1b5bf586af238b712a9f640087421fd299376c2d
@@ -789,7 +869,7 @@ Date:   Tue Mar 24 00:28:38 2015 +0900
     suppress warning: assigned but unused variable - length
- test/unit/bio/io/flatfile/test_autodetection.rb |    2 +-
+ test/unit/bio/io/flatfile/test_autodetection.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 5497068d17c2794ab2b6ef1e603e5478a86537c6
@@ -798,7 +878,7 @@ Date:   Tue Mar 24 00:22:54 2015 +0900
     add/modify assertions to suppress "unused variable" warnings
- test/unit/bio/db/genbank/test_genbank.rb |   12 +++++++++---
+ test/unit/bio/db/genbank/test_genbank.rb | 12 +++++++++---
  1 file changed, 9 insertions(+), 3 deletions(-)
 commit d5bafd8b7ee28ab0418b09fd6dd47abcb9eb1ee5
@@ -807,7 +887,7 @@ Date:   Mon Mar 23 23:57:56 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/appl/blast.rb |    1 -
+ lib/bio/appl/blast.rb | 1 -
  1 file changed, 1 deletion(-)
 commit bbd60d1aae7c894f914b7265d2de22fea5eb3faf
@@ -816,7 +896,7 @@ Date:   Mon Mar 23 23:56:42 2015 +0900
     suppress warning: assigned but unused variable - dummy
- lib/bio/appl/blast.rb |    2 +-
+ lib/bio/appl/blast.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 4a91502ccf14ab8655645144120aa97d0c8313a5
@@ -825,7 +905,7 @@ Date:   Mon Mar 23 20:32:59 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/shell/setup.rb |    1 -
+ lib/bio/shell/setup.rb | 1 -
  1 file changed, 1 deletion(-)
 commit c437a4078ff8e2869b9c1ab3543022db373a93c3
@@ -834,7 +914,7 @@ Date:   Mon Mar 23 20:32:20 2015 +0900
     suppress warning: instance variable @mode not initialized
- lib/bio/shell/setup.rb |    2 +-
+ lib/bio/shell/setup.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 8967cf280d5ca8491d57a11e4f3ffab7369c4ea8
@@ -843,7 +923,7 @@ Date:   Mon Mar 23 20:28:50 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/shell/irb.rb |    1 -
+ lib/bio/shell/irb.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 42b5f030067be4bc9c53ccb4c06ccfc5e8d9df03
@@ -852,7 +932,7 @@ Date:   Mon Mar 23 20:28:27 2015 +0900
     change deprecated method File.exists? to File.exist?
- lib/bio/shell/irb.rb |    2 +-
+ lib/bio/shell/irb.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 389ad2f311f161f235db2373aeb2f5500b1ea65f
@@ -861,7 +941,7 @@ Date:   Mon Mar 23 20:27:01 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/shell/interface.rb |    1 -
+ lib/bio/shell/interface.rb | 1 -
  1 file changed, 1 deletion(-)
 commit de5949798d66c16d2b5e2cf8ba7192049ec99c5b
@@ -870,7 +950,7 @@ Date:   Mon Mar 23 20:26:37 2015 +0900
     change deprecated method File.exists? to File.exist?
- lib/bio/shell/interface.rb |    6 +++---
+ lib/bio/shell/interface.rb | 6 +++---
  1 file changed, 3 insertions(+), 3 deletions(-)
 commit c8907059a716a8778e333755c8fb53bb2a0c7158
@@ -879,7 +959,7 @@ Date:   Mon Mar 23 20:24:58 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/shell/core.rb |    1 -
+ lib/bio/shell/core.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 1fe5903f8acd8045d203465a099a45218e7e3891
@@ -888,7 +968,7 @@ Date:   Mon Mar 23 20:24:25 2015 +0900
     change deprecated method File.exists? to File.exist?
- lib/bio/shell/core.rb |   10 +++++-----
+ lib/bio/shell/core.rb | 10 +++++-----
  1 file changed, 5 insertions(+), 5 deletions(-)
 commit 929207c6f186c81f076fab9b1bbbd23c4b966f4e
@@ -897,7 +977,7 @@ Date:   Mon Mar 23 20:20:05 2015 +0900
     delete obsolete $Id:$ line
- test/unit/bio/db/pdb/test_pdb.rb |    1 -
+ test/unit/bio/db/pdb/test_pdb.rb | 1 -
  1 file changed, 1 deletion(-)
 commit e75c57fcd7abc56ba6fcbf1996e491aca890f5b1
@@ -906,7 +986,7 @@ Date:   Mon Mar 23 20:19:30 2015 +0900
     suppress "assigned but unused variable" warnings
- test/unit/bio/db/pdb/test_pdb.rb |   21 ++++++++++++++-------
+ test/unit/bio/db/pdb/test_pdb.rb | 21 ++++++++++++++-------
  1 file changed, 14 insertions(+), 7 deletions(-)
 commit b458301f47322c265fce27efd0ed71443c17d9d7
@@ -915,7 +995,7 @@ Date:   Mon Mar 23 18:34:12 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/shell/plugin/entry.rb |    1 -
+ lib/bio/shell/plugin/entry.rb | 1 -
  1 file changed, 1 deletion(-)
 commit c3f909fe06b82b3cbd4bdcbcdef668fc0727be9d
@@ -924,7 +1004,7 @@ Date:   Mon Mar 23 18:33:30 2015 +0900
     change deprecated method File.exists? to File.exist?
- lib/bio/shell/plugin/entry.rb |    4 ++--
+ lib/bio/shell/plugin/entry.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit 7ba6349c2446aa03b843a2a8fb49505c8f63c6ca
@@ -933,7 +1013,7 @@ Date:   Mon Mar 23 18:20:44 2015 +0900
     change deprecated method File.exists? to File.exist?
- lib/bio/appl/meme/mast.rb |    8 ++++----
+ lib/bio/appl/meme/mast.rb | 8 ++++----
  1 file changed, 4 insertions(+), 4 deletions(-)
 commit e7f78ea3c3fb1b78adcc6ae13f450cf2cda361cd
@@ -942,7 +1022,7 @@ Date:   Mon Mar 23 18:10:27 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/db/phyloxml/phyloxml_writer.rb |    1 -
+ lib/bio/db/phyloxml/phyloxml_writer.rb | 1 -
  1 file changed, 1 deletion(-)
 commit b32eae0050a73bd5a2931c17a6694f494ad00bb2
@@ -951,7 +1031,7 @@ Date:   Mon Mar 23 18:07:54 2015 +0900
     suppress warning: mismatched indentations at 'end' with 'def' at 166
- lib/bio/db/phyloxml/phyloxml_writer.rb |    2 +-
+ lib/bio/db/phyloxml/phyloxml_writer.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit bd735347283ce5d332245d0349186f300800a43f
@@ -960,7 +1040,7 @@ Date:   Sat Mar 21 12:57:03 2015 +0900
     remove duplicated line and suppress Ruby 2.2 warning
- setup.rb |    1 -
+ setup.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 68ad10e178594691c77ba4b97c2449fecf0ac9de
@@ -969,7 +1049,7 @@ Date:   Sat Mar 21 12:50:46 2015 +0900
     Ruby 1.9 support: suppress "shadowing outer local variable" warnings
- setup.rb |   10 +++++-----
+ setup.rb | 10 +++++-----
  1 file changed, 5 insertions(+), 5 deletions(-)
 commit 2343482078aec8373f7a2eb8ed4d7c44119f809c
@@ -978,7 +1058,7 @@ Date:   Sat Mar 21 12:16:45 2015 +0900
     Ruby 2.2 support: Config was renamed to RbConfig
- setup.rb |    2 +-
+ setup.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit d512712745142d6c6ebe9a6ef51c8c4773bd7c2c
@@ -987,7 +1067,7 @@ Date:   Sat Mar 21 11:52:47 2015 +0900
     Ruby 1.9 support: suppress "shadowing outer local variable" warnings
- lib/bio/db/embl/format_embl.rb |    6 +++---
+ lib/bio/db/embl/format_embl.rb | 6 +++---
  1 file changed, 3 insertions(+), 3 deletions(-)
 commit bfa75df9047ab6855c931558f6bf9fdbb1c3c288
@@ -996,7 +1076,7 @@ Date:   Sat Mar 21 11:36:01 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/io/flatfile/buffer.rb |    1 -
+ lib/bio/io/flatfile/buffer.rb | 1 -
  1 file changed, 1 deletion(-)
 commit d6fbaa0c555117ebadd46e284ae357586856102d
@@ -1005,7 +1085,7 @@ Date:   Sat Mar 21 11:35:07 2015 +0900
     Ruby 1.9 support: suppress warning: shadowing outer local variable - fobj
- lib/bio/io/flatfile/buffer.rb |    8 ++++----
+ lib/bio/io/flatfile/buffer.rb | 8 ++++----
  1 file changed, 4 insertions(+), 4 deletions(-)
 commit 0083d3284ec181f4bcc3144f76b12f9d52e3eff6
@@ -1014,7 +1094,7 @@ Date:   Sat Mar 21 11:29:39 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/io/fastacmd.rb |    1 -
+ lib/bio/io/fastacmd.rb | 1 -
  1 file changed, 1 deletion(-)
 commit d4909c0e80e572a639edba07388e430c7f5d6ce8
@@ -1023,7 +1103,7 @@ Date:   Sat Mar 21 11:29:01 2015 +0900
     remove old sample script in "if $0 == __FILE__" block
- lib/bio/io/fastacmd.rb |   15 ---------------
+ lib/bio/io/fastacmd.rb | 15 ---------------
  1 file changed, 15 deletions(-)
 commit 8171162d0a3991d5f0d9a8bccee57250248d6d3d
@@ -1032,7 +1112,7 @@ Date:   Sat Mar 21 11:15:10 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/db/go.rb |    1 -
+ lib/bio/db/go.rb | 1 -
  1 file changed, 1 deletion(-)
 commit ed7c9a5335ef59399f3098311f47b8dec519281a
@@ -1041,7 +1121,7 @@ Date:   Sat Mar 21 11:14:19 2015 +0900
     Ruby 1.9 support: suppress warnings: "shadowing outer local variable - goid"
- lib/bio/db/go.rb |    4 ++--
+ lib/bio/db/go.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit dd543068b046c9a0c2a40159c830c92b680244f1
@@ -1050,7 +1130,7 @@ Date:   Sat Mar 21 11:03:08 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/db/phyloxml/phyloxml_elements.rb |    1 -
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 4c74a6e3aeca30820b0be61e867c9201445542ec
@@ -1059,7 +1139,7 @@ Date:   Sat Mar 21 10:24:40 2015 +0900
     suppress warning: mismatched indentations at 'end' with 'class'
- lib/bio/db/phyloxml/phyloxml_elements.rb |    4 ++--
+ lib/bio/db/phyloxml/phyloxml_elements.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit ee4ffdc748c1f9f45e97ff7f0da8350c5468c333
@@ -1068,7 +1148,7 @@ Date:   Sat Mar 21 10:08:30 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/db/phyloxml/phyloxml_parser.rb |    1 -
+ lib/bio/db/phyloxml/phyloxml_parser.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 46a4edc8729ff836ae28d11f1503c9923275b9f6
@@ -1077,7 +1157,7 @@ Date:   Sat Mar 21 10:00:04 2015 +0900
     Ruby 1.9 support: suppress warning "shadowing outer local variable - flag"
- lib/bio/db/phyloxml/phyloxml_parser.rb |    2 +-
+ lib/bio/db/phyloxml/phyloxml_parser.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit db3552c683edf79adbfa5ed897f5ef91e8417585
@@ -1090,7 +1170,7 @@ Date:   Fri Mar 20 16:33:45 2015 +0900
        return value when giving block.
      * Suppress warning "assigned but unused variable - ret"
- lib/bio/db/phyloxml/phyloxml_parser.rb |    1 +
+ lib/bio/db/phyloxml/phyloxml_parser.rb | 1 +
  1 file changed, 1 insertion(+)
 commit 84c2c4e94352cc9cef982d3b505b4f439617e01e
@@ -1099,7 +1179,7 @@ Date:   Fri Mar 20 16:21:49 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/appl/genscan/report.rb |    1 -
+ lib/bio/appl/genscan/report.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 05c55d0aaf1dc130ac04155622ccebb3394fc3c0
@@ -1108,7 +1188,7 @@ Date:   Fri Mar 20 16:21:06 2015 +0900
     Ruby 1.9 support: suppress warning "shadowing outer local variable - i"
- lib/bio/appl/genscan/report.rb |    2 +-
+ lib/bio/appl/genscan/report.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 5edcc1c97ca7c292fa6551509570daf68ac36837
@@ -1117,7 +1197,7 @@ Date:   Fri Mar 20 16:13:57 2015 +0900
     Ruby 1.9 support: suppress warning "shadowing outer local variable - y"
- lib/bio/appl/blast/format0.rb |    2 +-
+ lib/bio/appl/blast/format0.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 813d53a06258244a47784697e8fc95f1f15db8da
@@ -1126,7 +1206,7 @@ Date:   Fri Mar 20 16:03:19 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/io/das.rb |    1 -
+ lib/bio/io/das.rb | 1 -
  1 file changed, 1 deletion(-)
 commit b6ae4a423dd763969c8e18ca6a578fd0600d6159
@@ -1135,7 +1215,7 @@ Date:   Fri Mar 20 16:02:20 2015 +0900
     Ruby 1.9 support: suppress "warning: shadowing outer local variable - e"
- lib/bio/io/das.rb |   80 ++++++++++++++++++++++++++---------------------------
+ lib/bio/io/das.rb | 80 +++++++++++++++++++++++++++----------------------------
  1 file changed, 40 insertions(+), 40 deletions(-)
 commit 7fa75a644167dd8c189f681e29c1cf5f1bf2fe0b
@@ -1144,7 +1224,7 @@ Date:   Fri Mar 20 15:36:00 2015 +0900
     delete obsolete $Id:$ line
- lib/bio/shell/plugin/seq.rb |    1 -
+ lib/bio/shell/plugin/seq.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 051aba1519d71f1205363c4421feb6c06881ab0c
@@ -1158,7 +1238,7 @@ Date:   Fri Mar 20 15:29:02 2015 +0900
        the last part of the string due to a change from Ruby 1.8 to 1.9.
      * Suppress warning message "shadowing outer local variable - i"
- lib/bio/shell/plugin/seq.rb |   12 +++++++-----
+ lib/bio/shell/plugin/seq.rb | 12 +++++++-----
  1 file changed, 7 insertions(+), 5 deletions(-)
 commit a9f2bff92de58c2ab4cefc67e721d3ad69e9de98
@@ -1167,7 +1247,7 @@ Date:   Fri Mar 20 15:09:16 2015 +0900
     Ruby 2.2 support: suppress a "shadowing outer local variable" warning
- lib/bio/alignment.rb |    6 +++---
+ lib/bio/alignment.rb | 6 +++---
  1 file changed, 3 insertions(+), 3 deletions(-)
 commit d0bcc8766d91eb7cacea2a6d5b32b3e0b3c5ce56
@@ -1176,7 +1256,7 @@ Date:   Fri Mar 20 14:31:04 2015 +0900
     delete obsolete $Id:$ line
- test/unit/bio/test_alignment.rb |    1 -
+ test/unit/bio/test_alignment.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 0c8fa8fd558088822a98e11b6fa4bec9b37ebec7
@@ -1188,7 +1268,7 @@ Date:   Fri Mar 20 14:26:38 2015 +0900
      * Ruby 2.2 support: test/unit/bio/test_alignment.rb:
        Suppress warning: duplicated key at line 182 ignored: "t"
- test/unit/bio/test_alignment.rb |    2 +-
+ test/unit/bio/test_alignment.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit ab17c40e1ce492dc924205e8e2f90d31adae4464
@@ -1201,7 +1281,7 @@ Date:   Fri Mar 20 14:18:08 2015 +0900
        Support for test-unit gem bundled in Ruby 2.2.
        See commit log b9488a64abb780c5e9b6cd28e8264bad399fa749 for details.
- test/unit/bio/db/test_fastq.rb |   18 ++++++++++++++----
+ test/unit/bio/db/test_fastq.rb | 18 ++++++++++++++----
  1 file changed, 14 insertions(+), 4 deletions(-)
 commit ea668d73c18e3df33625cba4352ad5f6966e0eb4
@@ -1210,7 +1290,7 @@ Date:   Fri Mar 20 14:03:43 2015 +0900
     delete obsolete $Id:$ line
- test/unit/bio/appl/sim4/test_report.rb |    1 -
+ test/unit/bio/appl/sim4/test_report.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 1abb8d362a0f2443b48923bcccba3d7d0caa1f1d
@@ -1223,7 +1303,7 @@ Date:   Fri Mar 20 13:57:33 2015 +0900
        Support for test-unit gem bundled in Ruby 2.2.
        See commit log b9488a64abb780c5e9b6cd28e8264bad399fa749 for details.
- test/unit/bio/appl/sim4/test_report.rb |   62 +++++++++++++++++++++++---------
+ test/unit/bio/appl/sim4/test_report.rb | 62 +++++++++++++++++++++++++---------
  1 file changed, 46 insertions(+), 16 deletions(-)
 commit b9488a64abb780c5e9b6cd28e8264bad399fa749
@@ -1239,7 +1319,7 @@ Date:   Fri Mar 20 13:13:28 2015 +0900
         are moved to modules and test classes are changed to include
         the modules.
- test/unit/bio/appl/blast/test_report.rb |  156 ++++++++++++++++++++++---------
+ test/unit/bio/appl/blast/test_report.rb | 156 ++++++++++++++++++++++----------
  1 file changed, 110 insertions(+), 46 deletions(-)
 commit febe8bbf614e530f597d7306d33df5f5f4ee6699
@@ -1252,7 +1332,7 @@ Date:   Thu Mar 19 00:55:09 2015 +0900
        Without bio-old-biofetch-emulator, the program exits with error
        message when default BioRuby BioFetch server is specified.
- bin/br_biofetch.rb |   19 +++++++++++++++++++
+ bin/br_biofetch.rb | 19 +++++++++++++++++++
  1 file changed, 19 insertions(+)
 commit 08450e0a35cbf5596dd30238d23aa7a7296c8f67
@@ -1261,7 +1341,7 @@ Date:   Thu Mar 19 00:36:10 2015 +0900
     do not repeat default_url and another_url
- bin/br_biofetch.rb |   14 ++++++++++----
+ bin/br_biofetch.rb | 14 ++++++++++----
  1 file changed, 10 insertions(+), 4 deletions(-)
 commit 8e39d3411405b09cc6ea55ba31e5206536ebf59d
@@ -1274,7 +1354,7 @@ Date:   Wed Mar 18 23:57:59 2015 +0900
        because the old deprecated bioruby biofetch server can be emulated
        by bio-old-biofetch-emulator gem package.
- bin/br_biofetch.rb |   15 ++++++++-------
+ bin/br_biofetch.rb | 15 ++++++++-------
  1 file changed, 8 insertions(+), 7 deletions(-)
 commit 849c38931a64b7ff2ba7ec46a495e65a99a869fb
@@ -1283,8 +1363,8 @@ Date:   Wed Aug 8 09:44:09 2012 +1000
     add FastaFormat#first_name method
- lib/bio/db/fasta.rb            |   17 ++++++++++++++++
- test/unit/bio/db/test_fasta.rb |   42 +++++++++++++++++++++++++++++++++++++++-
+ lib/bio/db/fasta.rb            | 17 +++++++++++++++++
+ test/unit/bio/db/test_fasta.rb | 42 +++++++++++++++++++++++++++++++++++++++++-
  2 files changed, 58 insertions(+), 1 deletion(-)
 commit 888a70508c0392cae89021feba5c4a6a62228a11
@@ -1297,7 +1377,7 @@ Date:   Fri Nov 14 15:08:35 2014 +0900
        https://github.com/bioruby/bioruby/pull/93
        (c4843d65447f6a434da523c9c313f34d025f36f8)
- lib/bio/sequence/compat.rb |    2 +-
+ lib/bio/sequence/compat.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit afc6df190109649e8eb11b2af1184ddfcf5327d3
@@ -1306,7 +1386,7 @@ Date:   Fri Nov 14 14:29:42 2014 +0900
     add documentation when gc_percent is not enough
- lib/bio/sequence/na.rb |    8 ++++++++
+ lib/bio/sequence/na.rb | 8 ++++++++
  1 file changed, 8 insertions(+)
 commit bb63f67f2dfe6dba5c70ada033ca0cc1ecaa7783
@@ -1323,7 +1403,7 @@ Date:   Thu Nov 13 21:43:00 2014 +0900
        fix the issue https://github.com/bioruby/bioruby/issues/75.
        Thanks to Paul Leader who reported the issue and the pull request.
- test/network/bio/io/test_pubmed.rb |   49 ++++++++++++++++++++++++++++++++++++
+ test/network/bio/io/test_pubmed.rb | 49 ++++++++++++++++++++++++++++++++++++++
  1 file changed, 49 insertions(+)
 commit 74edba100da83c27f2edb7a9edc9ec98265a7cff
@@ -1338,7 +1418,7 @@ Date:   Thu Nov 13 12:05:12 2014 +0900
        excess traffic to NCBI.
      * Update RDoc documentation
- lib/bio/io/ncbirest.rb |   48 +++++++++++++++++++++++++++++++++++++++++++-----
+ lib/bio/io/ncbirest.rb | 48 +++++++++++++++++++++++++++++++++++++++++++-----
  1 file changed, 43 insertions(+), 5 deletions(-)
 commit bfe4292c51bba5c4032027c36c35e98f28a9605a
@@ -1353,7 +1433,7 @@ Date:   Thu Nov 13 11:54:53 2014 +0900
        future. To indicate this, show warning message if $VERBOSE is true.
      * Update RDoc documentation
- lib/bio/io/pubmed.rb |  157 ++++++++++++++++++++++++--------------------------
+ lib/bio/io/pubmed.rb | 157 +++++++++++++++++++++++++--------------------------
  1 file changed, 76 insertions(+), 81 deletions(-)
 commit d78173a6eb6d8177e733decc0b8137fac067aa82
@@ -1362,7 +1442,7 @@ Date:   Tue Nov 11 17:41:32 2014 +0900
     remove unused $Id:$ line
- bin/br_biofetch.rb |    1 -
+ bin/br_biofetch.rb | 1 -
  1 file changed, 1 deletion(-)
 commit e29fc5fadbe0dae6528cf49637496dc2df3ec0dc
@@ -1377,7 +1457,7 @@ Date:   Tue Nov 11 17:31:38 2014 +0900
        exits with code 1 (abnormal exit).
      * Usage message is also changed.
- bin/br_biofetch.rb |   15 +++++++--------
+ bin/br_biofetch.rb | 15 +++++++--------
  1 file changed, 7 insertions(+), 8 deletions(-)
 commit 94ecac33e87e444d9fe991340c2d8f3709bc6d90
@@ -1386,7 +1466,7 @@ Date:   Tue Nov 11 17:19:30 2014 +0900
     fix documentation reflecting recent changes of Bio::Fetch
- lib/bio/io/fetch.rb |   33 ++++++++++++++++++++-------------
+ lib/bio/io/fetch.rb | 33 ++++++++++++++++++++-------------
  1 file changed, 20 insertions(+), 13 deletions(-)
 commit 06a9db014614818ef35108928415ef18e8c8ae2c
@@ -1395,7 +1475,7 @@ Date:   Tue Nov 11 16:41:26 2014 +0900
     documentation about incompatible changes of Bio::Fetch
- RELEASE_NOTES.rdoc |   22 ++++++++++++++++++++++
+ RELEASE_NOTES.rdoc | 22 ++++++++++++++++++++++
  1 file changed, 22 insertions(+)
 commit 6d94e949b6d325f27b45b816a8305f828d049ec6
@@ -1409,7 +1489,7 @@ Date:   Tue Nov 11 16:35:50 2014 +0900
      * The BioRuby BioFetch server is deprecated. There is no hope to restart
        the service again. EBI Dbfetch server is an alternative.
- KNOWN_ISSUES.rdoc |    9 ---------
+ KNOWN_ISSUES.rdoc | 9 ---------
  1 file changed, 9 deletions(-)
 commit 699cd3ff136310a551d30e0ddd7fbe66e483b5be
@@ -1418,7 +1498,7 @@ Date:   Tue Nov 11 15:27:11 2014 +0900
     update RDoc documents for Bio::Fetch
- lib/bio/io/fetch.rb |   61 +++++++++++++++++++++++++++++++++------------------
+ lib/bio/io/fetch.rb | 61 +++++++++++++++++++++++++++++++++++------------------
  1 file changed, 40 insertions(+), 21 deletions(-)
 commit c7837f8e5ee2cc1c3085da74567a2b25280bbb8f
@@ -1433,7 +1513,7 @@ Date:   Tue Nov 11 14:48:48 2014 +0900
      * New class method: Bio::Fetch::EBI.query. This can be used as an
        alternative method of deprecated Bio::Fetch.query method.
- lib/bio/io/fetch.rb |   35 ++++++++++++++++++-----------------
+ lib/bio/io/fetch.rb | 35 ++++++++++++++++++-----------------
  1 file changed, 18 insertions(+), 17 deletions(-)
 commit f9048684acaff0fcd00b458a946d5f692706325b
@@ -1450,7 +1530,7 @@ Date:   Tue Nov 11 14:24:22 2014 +0900
        Bio::Fetch.new(Bio::Fetch::EBI::URL) with default database name
        "ena_sequence".
- lib/bio/io/fetch.rb |   36 +++++++++++++++++++++++++++++++++---
+ lib/bio/io/fetch.rb | 36 +++++++++++++++++++++++++++++++++---
  1 file changed, 33 insertions(+), 3 deletions(-)
 commit e8919f4f57fc545ca194bebb08c11159b36071cb
@@ -1459,7 +1539,7 @@ Date:   Tue Nov 11 13:43:28 2014 +0900
     removed unused variables
- lib/bio/io/fetch.rb |    1 -
+ lib/bio/io/fetch.rb | 1 -
  1 file changed, 1 deletion(-)
 commit faec95656b846a7a17cd6a1dbc633dda63cb5b6e
@@ -1468,7 +1548,7 @@ Date:   Tue Nov 11 11:44:00 2014 +0900
     Updated URL of EMBL-EBI Dbfetch
- lib/bio/io/fetch.rb |    2 +-
+ lib/bio/io/fetch.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 85be893655f68aafbf7e13badd20bf7f26cd7328
@@ -1479,7 +1559,7 @@ Date:   Mon Dec 24 12:30:55 2012 -0400
     Use EBI's dbfetch endpoint as default since BioRuby's endpoint has been disabled for a while now.
- lib/bio/io/fetch.rb |    2 +-
+ lib/bio/io/fetch.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 163cc06547beed653e19b8c6e71e829d85f2f99c
@@ -1488,7 +1568,7 @@ Date:   Tue Oct 21 16:42:30 2014 +0900
     Doc bug fix: wrong sample code
- lib/bio/appl/paml/codeml.rb |    4 ++--
+ lib/bio/appl/paml/codeml.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit 97143139d2d4a66366576a8e62518e93fa5afccf
@@ -1500,7 +1580,7 @@ Date:   Tue Oct 21 15:47:52 2014 +0900
      * Bio::Sequence::NA#gc_content, at_content, gc_skew, at_skew: Prevent to
        repeat calculations of total bases.
- lib/bio/sequence/na.rb |   20 ++++++++++++--------
+ lib/bio/sequence/na.rb | 20 ++++++++++++--------
  1 file changed, 12 insertions(+), 8 deletions(-)
 commit b5dbd882e000842fef65e10290b379bfafdddf06
@@ -1514,7 +1594,7 @@ Date:   Tue Oct 21 15:41:13 2014 +0900
        the treatment of "u" and to return 0.0 if there are no bases.
        Reported by ctSkennerton (https://github.com/bioruby/bioruby/issues/73 ).
- lib/bio/sequence/na.rb |   47 +++++++++++++++++++++++++++++++++++++++++++----
+ lib/bio/sequence/na.rb | 47 +++++++++++++++++++++++++++++++++++++++++++----
  1 file changed, 43 insertions(+), 4 deletions(-)
 commit 3ba98d52ce57488e604dd7ac388a874e5b40ae9d
@@ -1523,7 +1603,7 @@ Date:   Tue Aug 12 00:58:38 2014 +0900
     regenerate bioruby.gemspec with rake regemspec
- bioruby.gemspec |   14 ++++++--------
+ bioruby.gemspec | 14 ++++++--------
  1 file changed, 6 insertions(+), 8 deletions(-)
 commit a9724d339582952b40c928beccf91376d4e63315
@@ -1536,7 +1616,7 @@ Date:   Tue Aug 5 19:20:42 2014 +0900
      * Remove links to RubyForge and RAA which have already been closed.
      * Add some words for Ruby 1.9 or later.
- README.rdoc |   24 +++++++++++-------------
+ README.rdoc | 24 +++++++++++-------------
  1 file changed, 11 insertions(+), 13 deletions(-)
 commit 5f3569faaf89ebcd2b2cf9cbe6b3c1f0544b2679
@@ -1545,7 +1625,7 @@ Date:   Wed Mar 5 02:11:07 2014 +0000
     Refactor Bio::AminoAcid#weight: Early return clearer and idiomatic.
- lib/bio/data/aa.rb |   26 ++++++++++++--------------
+ lib/bio/data/aa.rb | 26 ++++++++++++--------------
  1 file changed, 12 insertions(+), 14 deletions(-)
 commit c229a20887fcb6df9a7ba49ad5a23e175056fa8d
@@ -1554,7 +1634,7 @@ Date:   Wed Mar 5 02:02:45 2014 +0000
     Fixed the stack level too deep errors by using Hash#invert.
- lib/bio/data/aa.rb |   18 +-----------------
+ lib/bio/data/aa.rb | 18 +-----------------
  1 file changed, 1 insertion(+), 17 deletions(-)
 commit 08dd928df30f5b39c255f9f70dbed8410d395cdf
@@ -1563,7 +1643,7 @@ Date:   Tue Mar 4 01:22:51 2014 +0000
     Refactored to shorten, remove rescues, and clarify.
- lib/bio/alignment.rb |   19 +++++++------------
+ lib/bio/alignment.rb | 19 +++++++------------
  1 file changed, 7 insertions(+), 12 deletions(-)
 commit 112aa284cb1ebecc1d5de186edf2b385649a7268
@@ -1575,7 +1655,7 @@ Date:   Wed Mar 19 14:48:32 2014 +0900
     * Bug fix: SEQRES serNum digits were extended in PDB v3.2 (2008).
       Thanks to a researcher who reports the patch via email.
- lib/bio/db/pdb/pdb.rb |    4 ++--
+ lib/bio/db/pdb/pdb.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit ecd5e0c86b04aa918b71c859568425fa39ebbde5
@@ -1584,10 +1664,10 @@ Date:   Sat Jan 18 04:22:51 2014 +0900
     suppress "source :rubygems is deprecated" warning
- gemfiles/Gemfile.travis-jruby1.8 |    2 +-
- gemfiles/Gemfile.travis-jruby1.9 |    2 +-
- gemfiles/Gemfile.travis-ruby1.8  |    2 +-
- gemfiles/Gemfile.travis-ruby1.9  |    2 +-
+ gemfiles/Gemfile.travis-jruby1.8 | 2 +-
+ gemfiles/Gemfile.travis-jruby1.9 | 2 +-
+ gemfiles/Gemfile.travis-ruby1.8  | 2 +-
+ gemfiles/Gemfile.travis-ruby1.9  | 2 +-
  4 files changed, 4 insertions(+), 4 deletions(-)
 commit 4bda345fe3de9cf1b64c26f3dca1cb3727c946d0
@@ -1599,8 +1679,8 @@ Date:   Sat Jan 18 04:22:03 2014 +0900
      * gemfiles/Gemfile.travis-rbx: Gemfile for rbx (Rubinius) on Travis-ci
      * .travis.yml is modified to use gemfile/Gemfile.travis-rbx for rbx.
- .travis.yml                 |    4 ++--
- gemfiles/Gemfile.travis-rbx |   16 ++++++++++++++++
+ .travis.yml                 |  4 ++--
+ gemfiles/Gemfile.travis-rbx | 16 ++++++++++++++++
  2 files changed, 18 insertions(+), 2 deletions(-)
  create mode 100644 gemfiles/Gemfile.travis-rbx
@@ -1610,7 +1690,7 @@ Date:   Sat Jan 18 04:13:50 2014 +0900
     .travis.yml: fix mistakes
- .travis.yml |    8 +-------
+ .travis.yml | 8 +-------
  1 file changed, 1 insertion(+), 7 deletions(-)
 commit f0f67f295f05a5e1e30c479621c25498e2c8f6f2
@@ -1625,7 +1705,7 @@ Date:   Sat Jan 18 03:56:54 2014 +0900
        Note that the behavior change is also regarded as a bug in Ruby and
        is fixed. (https://bugs.ruby-lang.org/issues/9340 )
- test/unit/bio/test_pathway.rb |   35 +++++++++++++++++++++++++----------
+ test/unit/bio/test_pathway.rb | 35 +++++++++++++++++++++++++----------
  1 file changed, 25 insertions(+), 10 deletions(-)
 commit e92e09edf5904f51d3e73e61d13fce4159a543c5
@@ -1637,7 +1717,7 @@ Date:   Sat Jan 18 03:32:05 2014 +0900
      * workaround to avoid error in Ruby 1.8.7 and jruby-18mode
        (reference: https://github.com/rubygems/rubygems/pull/763 )
- .travis.yml |    2 ++
+ .travis.yml | 2 ++
  1 file changed, 2 insertions(+)
 commit 655a675096962710896fb458afcac9b5deb1fa5f
@@ -1650,7 +1730,7 @@ Date:   Sat Jan 18 03:22:44 2014 +0900
      * add dependent gems for rbx platforms, described in
        http://docs.travis-ci.com/user/languages/ruby/
- .travis.yml |    7 ++++++-
+ .travis.yml | 7 ++++++-
  1 file changed, 6 insertions(+), 1 deletion(-)
 commit d2f5b882d5e2acf35d0c783a56aa47533b9f2bd5
@@ -1664,7 +1744,7 @@ Date:   Sat Jan 11 03:46:45 2014 +0900
      * Add jruby-18mode
      * Add rbx-2.1.1
- .travis.yml |   32 ++++++++++++++++++++++----------
+ .travis.yml | 32 ++++++++++++++++++++++----------
  1 file changed, 22 insertions(+), 10 deletions(-)
 commit 71991af394b937d35e2bbbc84a21e65ffba7714d
@@ -1681,7 +1761,7 @@ Date:   Thu Jan 9 00:57:25 2014 +0900
      * Remove "exclude" and simplify build matrix.
      * Suggested by agrimm in https://github.com/bioruby/bioruby/pull/91
- .travis.yml |   27 +++++----------------------
+ .travis.yml | 27 +++++----------------------
  1 file changed, 5 insertions(+), 22 deletions(-)
 commit 80966bc875cc6e01978b6c9272f6ddd8f344aa62
@@ -1693,7 +1773,7 @@ Date:   Mon Dec 9 14:57:42 2013 +0100
      * Bug fix: Only do gsub on bio_ref.reference.authors if it exists.
        Fix https://github.com/bioruby/bioruby/issues/89
- lib/bio/db/biosql/sequence.rb |    2 +-
+ lib/bio/db/biosql/sequence.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 3337bbd3be2affcef44202a0c924b3e22dafd856
@@ -1705,7 +1785,7 @@ Date:   Mon Dec 9 14:55:24 2013 +0100
      * Bug fix: Missing require when generating genbank output for BioSQL
        sequence. Partly fix https://github.com/bioruby/bioruby/issues/89
- lib/bio/db/biosql/biosql_to_biosequence.rb |    1 +
+ lib/bio/db/biosql/biosql_to_biosequence.rb | 1 +
  1 file changed, 1 insertion(+)
 commit 1f829ae8e8c89c5c24e7bc7aa8ed5fa25e8ef6c2
@@ -1717,7 +1797,7 @@ Date:   Sat Nov 23 18:17:43 2013 +0900
      * sample/benchmark_clustalw_report.rb: Benchmark parsing speed of
        example1-seqnos.aln in addition to example1.aln.
- sample/benchmark_clustalw_report.rb |   28 ++++++++++++++++++++++------
+ sample/benchmark_clustalw_report.rb | 28 ++++++++++++++++++++++------
  1 file changed, 22 insertions(+), 6 deletions(-)
 commit c5d3e761859fa72c18f9301d84c31070f35e733e
@@ -1726,7 +1806,7 @@ Date:   Tue Sep 17 21:15:56 2013 +1000
     Add benchmark script for Bio::ClustalW::Report.
- sample/benchmark_clustalw_report.rb |   31 +++++++++++++++++++++++++++++++
+ sample/benchmark_clustalw_report.rb | 31 +++++++++++++++++++++++++++++++
  1 file changed, 31 insertions(+)
  create mode 100644 sample/benchmark_clustalw_report.rb
@@ -1742,7 +1822,7 @@ Date:   Sat Nov 23 17:49:54 2013 +0900
      * "$" in the regular expression is changed to "\z". In this context,
        the "$" was intended to be matched with only the end of the string.
- lib/bio/appl/clustalw/report.rb |    4 +++-
+ lib/bio/appl/clustalw/report.rb | 4 +++-
  1 file changed, 3 insertions(+), 1 deletion(-)
 commit 6a78028d4f595ecb5b4600d0f238b07a2d80bdd5
@@ -1756,8 +1836,8 @@ Date:   Sat Nov 23 15:52:15 2013 +0900
      * Bio::TestClustalWReport::TestClustalWReportSeqnos: new test class
        that parses the above data.
- test/data/clustalw/example1-seqnos.aln     |   58 ++++++++++++++++++++++++++++
- test/unit/bio/appl/clustalw/test_report.rb |   11 ++++++
+ test/data/clustalw/example1-seqnos.aln     | 58 ++++++++++++++++++++++++++++++
+ test/unit/bio/appl/clustalw/test_report.rb | 11 ++++++
  2 files changed, 69 insertions(+)
  create mode 100644 test/data/clustalw/example1-seqnos.aln
@@ -1771,7 +1851,7 @@ Date:   Sat Nov 23 15:35:31 2013 +0900
        filename path.
      * Modify indentes and void lines.
- test/unit/bio/appl/clustalw/test_report.rb |   10 +++-------
+ test/unit/bio/appl/clustalw/test_report.rb | 10 +++-------
  1 file changed, 3 insertions(+), 7 deletions(-)
 commit 8f0bea1d3252d0de9e2d91dc31ef8a9552c2d758
@@ -1786,7 +1866,7 @@ Date:   Sat Nov 23 15:21:38 2013 +0900
      * The test_sequences method is split into two methods
        CommonTestMethods#test_sequence0 and test_sequence1.
- test/unit/bio/appl/clustalw/test_report.rb |   97 +++++++++++++++-------------
+ test/unit/bio/appl/clustalw/test_report.rb | 97 ++++++++++++++++--------------
  1 file changed, 53 insertions(+), 44 deletions(-)
 commit edda65b8fb32c2eee6b0652074981c31aa68b0eb
@@ -1799,7 +1879,7 @@ Date:   Fri Aug 23 23:51:59 2013 +0900
        error. Thanks to nieder (github.com/nieder) who reports the bug.
        (https://github.com/bioruby/bioruby/issues/84)
- test/unit/bio/db/test_phyloxml.rb |    2 +-
+ test/unit/bio/db/test_phyloxml.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 011d6fe5f016408891c5da3143c83e2564ccbf27
@@ -1814,8 +1894,8 @@ Date:   Fri Apr 5 01:13:27 2013 +0900
        * Returns 'false' for non-functional siRNA, as usual.
      * Unit tests are modified to reflect these changes.
- lib/bio/util/sirna.rb            |   92 +++++++++++++++++++++++++++++++-------
- test/unit/bio/util/test_sirna.rb |   44 +++++++++---------
+ lib/bio/util/sirna.rb            | 92 +++++++++++++++++++++++++++++++++-------
+ test/unit/bio/util/test_sirna.rb | 44 +++++++++----------
  2 files changed, 98 insertions(+), 38 deletions(-)
 commit b6e7953108ebf34d61bc79ee4bdae1092cfe339f
@@ -1827,7 +1907,7 @@ Date:   Fri Jun 28 15:40:57 2013 +0900
      * Use Bio::UniProtKB instead of Bio::UniProt.
      * Test class names are also changed from UniProt to UniProtKB.
- test/unit/bio/db/embl/test_uniprotkb_new_part.rb |   22 +++++++++++-----------
+ test/unit/bio/db/embl/test_uniprotkb_new_part.rb | 22 +++++++++++-----------
  1 file changed, 11 insertions(+), 11 deletions(-)
 commit cddd35cf8d64abfff8bd6a8372d019fc4c32848c
@@ -1836,8 +1916,8 @@ Date:   Fri Jun 28 15:26:20 2013 +0900
     rename test/unit/bio/db/embl/test_uniprot_new_part.rb to test_uniprotkb_new_part.rb
- test/unit/bio/db/embl/test_uniprot_new_part.rb   |  208 ----------------------
- test/unit/bio/db/embl/test_uniprotkb_new_part.rb |  208 ++++++++++++++++++++++
+ test/unit/bio/db/embl/test_uniprot_new_part.rb   | 208 -----------------------
+ test/unit/bio/db/embl/test_uniprotkb_new_part.rb | 208 +++++++++++++++++++++++
  2 files changed, 208 insertions(+), 208 deletions(-)
  delete mode 100644 test/unit/bio/db/embl/test_uniprot_new_part.rb
  create mode 100644 test/unit/bio/db/embl/test_uniprotkb_new_part.rb
@@ -1851,7 +1931,7 @@ Date:   Fri Jun 28 15:21:36 2013 +0900
      * Reflect the rename of Bio::UniProtKB from SPTR to UniProtKB.
      * Test class names are also changed.
- test/unit/bio/db/embl/test_uniprotkb.rb |  223 +++++++++++++++----------------
+ test/unit/bio/db/embl/test_uniprotkb.rb | 223 ++++++++++++++++----------------
  1 file changed, 111 insertions(+), 112 deletions(-)
 commit 68494aa862c3495def713e6cad6fc478f223416f
@@ -1872,7 +1952,7 @@ Date:   Fri Jun 28 14:52:08 2013 +0900
     Add autoload of Bio::UniProtKB, and modify comments of deprecated classes.
- lib/bio.rb |   18 ++++++++++--------
+ lib/bio.rb | 18 ++++++++++--------
  1 file changed, 10 insertions(+), 8 deletions(-)
 commit 7c78cb1b275a845e215f9a6da67026836efc5807
@@ -1884,8 +1964,8 @@ Date:   Fri Jun 28 14:28:02 2013 +0900
      * Bio::SwissProt and Bio::TrEMBL are deprecated.
      * Show warning messages when using these classes.
- lib/bio/db/embl/swissprot.rb |   41 ++++++++++++----------------------------
- lib/bio/db/embl/trembl.rb    |   43 +++++++++++++-----------------------------
+ lib/bio/db/embl/swissprot.rb | 41 ++++++++++++-----------------------------
+ lib/bio/db/embl/trembl.rb    | 43 +++++++++++++------------------------------
  2 files changed, 25 insertions(+), 59 deletions(-)
 commit b998ad13849ff7f1d69ed0c640a2e1bafe3fc957
@@ -1894,7 +1974,7 @@ Date:   Fri Jun 28 14:27:36 2013 +0900
     Bio::UniProt is changed to be an alias of Bio::UniProtKB.
- lib/bio/db/embl/uniprot.rb |   41 ++++++++++++-----------------------------
+ lib/bio/db/embl/uniprot.rb | 41 ++++++++++++-----------------------------
  1 file changed, 12 insertions(+), 29 deletions(-)
 commit f46324e2fb6a2bc3e4680c8064dc0fc3d89e6f24
@@ -1907,8 +1987,8 @@ Date:   Fri Jun 28 14:21:56 2013 +0900
      * For older programs which use Bio::SPTR, set Bio::SPTR as an alias of
        Bio::UniProtKB.
- lib/bio/db/embl/sptr.rb      |   20 ++++++
- lib/bio/db/embl/uniprotkb.rb |  147 +++++++++++++++++++++---------------------
+ lib/bio/db/embl/sptr.rb      |  20 ++++++
+ lib/bio/db/embl/uniprotkb.rb | 147 +++++++++++++++++++++----------------------
  2 files changed, 93 insertions(+), 74 deletions(-)
  create mode 100644 lib/bio/db/embl/sptr.rb
@@ -1937,8 +2017,8 @@ Date:   Thu Jun 27 16:36:58 2013 +0900
      * Changed to require genbank.rb only when GenBank is not defined.
        This might reduce the possibility of circular require.
- lib/bio/db/genbank/ddbj.rb   |   11 +++++++++--
- lib/bio/db/genbank/refseq.rb |   14 +++++++++++---
+ lib/bio/db/genbank/ddbj.rb   | 11 +++++++++--
+ lib/bio/db/genbank/refseq.rb | 14 +++++++++++---
  2 files changed, 20 insertions(+), 5 deletions(-)
 commit 118d0bff58b48f69505eef5dcc2f961ac6e0d9de
@@ -1947,7 +2027,7 @@ Date:   Thu Jun 27 16:08:55 2013 +0900
     Remove descriptions about DDBJ Web API (WABI)
- KNOWN_ISSUES.rdoc |    8 --------
+ KNOWN_ISSUES.rdoc | 8 --------
  1 file changed, 8 deletions(-)
 commit fe8f976c7ced4d525a4eabd728269f71326cf001
@@ -1956,7 +2036,7 @@ Date:   Thu Jun 27 13:41:19 2013 +0900
     Remove ddbjsoap method that uses Bio::DDBJ::XML
- lib/bio/shell/plugin/soap.rb |   28 ----------------------------
+ lib/bio/shell/plugin/soap.rb | 28 ----------------------------
  1 file changed, 28 deletions(-)
 commit 54bef3fc48bb48eb198537a9fba6379f33f036cc
@@ -1965,7 +2045,7 @@ Date:   Thu Jun 27 13:39:42 2013 +0900
     Remove Bio::Blast::Remote::DDBJ from the comment line
- test/network/bio/appl/blast/test_remote.rb |    2 +-
+ test/network/bio/appl/blast/test_remote.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit a7c5a656dab1bb8ada6b36ec003a89aec9e26671
@@ -1974,7 +2054,7 @@ Date:   Tue Jun 25 18:34:46 2013 +0900
     Delete sample/demo_ddbjxml.rb which uses Bio::DDBJ::XML
- sample/demo_ddbjxml.rb |  212 ------------------------------------------------
+ sample/demo_ddbjxml.rb | 212 -------------------------------------------------
  1 file changed, 212 deletions(-)
  delete mode 100644 sample/demo_ddbjxml.rb
@@ -1987,10 +2067,10 @@ Date:   Tue Jun 25 18:29:54 2013 +0900
      * Remove Bio::Blast::Remote::DDBJ, Bio::Blast.ddbj and related components
        which use Bio::DDBJ::XML or Bio::DDBJ::REST.
- lib/bio/appl/blast/ddbj.rb                 |  131 ----------------------------
- lib/bio/appl/blast/remote.rb               |    9 --
- test/network/bio/appl/blast/test_remote.rb |   14 ---
- test/network/bio/appl/test_blast.rb        |   12 ---
+ lib/bio/appl/blast/ddbj.rb                 | 131 -----------------------------
+ lib/bio/appl/blast/remote.rb               |   9 --
+ test/network/bio/appl/blast/test_remote.rb |  14 ---
+ test/network/bio/appl/test_blast.rb        |  12 ---
  4 files changed, 166 deletions(-)
  delete mode 100644 lib/bio/appl/blast/ddbj.rb
@@ -2008,11 +2088,11 @@ Date:   Tue Jun 25 16:52:05 2013 +0900
      * Autoload lines in lib/bio/db/genbank/ddbj.rb are removed.
      * Tests are also removed.
- lib/bio/db/genbank/ddbj.rb           |    3 -
- lib/bio/io/ddbjrest.rb               |  344 -------------------------
- lib/bio/io/ddbjxml.rb                |  458 ----------------------------------
- test/network/bio/io/test_ddbjrest.rb |   47 ----
- test/unit/bio/io/test_ddbjxml.rb     |   81 ------
+ lib/bio/db/genbank/ddbj.rb           |   3 -
+ lib/bio/io/ddbjrest.rb               | 344 --------------------------
+ lib/bio/io/ddbjxml.rb                | 458 -----------------------------------
+ test/network/bio/io/test_ddbjrest.rb |  47 ----
+ test/unit/bio/io/test_ddbjxml.rb     |  81 -------
  5 files changed, 933 deletions(-)
  delete mode 100644 lib/bio/io/ddbjrest.rb
  delete mode 100644 lib/bio/io/ddbjxml.rb
@@ -2025,7 +2105,7 @@ Date:   Sat May 25 03:00:08 2013 +0900
     regenerate bioruby.gemspec with rake regemspec
- bioruby.gemspec |    2 --
+ bioruby.gemspec | 2 --
  1 file changed, 2 deletions(-)
 commit 5b90959ab399f961823a7c4453392c75cf971333
@@ -2034,7 +2114,7 @@ Date:   Sat May 25 02:58:50 2013 +0900
     Update files and directories used to create package without git
- bioruby.gemspec.erb |    6 ++++--
+ bioruby.gemspec.erb | 6 ++++--
  1 file changed, 4 insertions(+), 2 deletions(-)
 commit df29f057ded6ac73fbdce7ae04a70ead28f4cc9f
@@ -2047,7 +2127,7 @@ Date:   Sat May 25 02:46:32 2013 +0900
        Because ChangeLog is not rdoc format, rdoc bundled with Ruby 2.0
        raises error during parsing.
- bioruby.gemspec.erb |    4 ++--
+ bioruby.gemspec.erb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit 930a5fcf5e38ae2bdfeee62eed9a46db1c519fae
@@ -2060,7 +2140,7 @@ Date:   Thu Apr 4 17:29:33 2013 +0900
     * warning: assigned but unused variable
- lib/bio/util/contingency_table.rb |    2 --
+ lib/bio/util/contingency_table.rb | 2 --
  1 file changed, 2 deletions(-)
 commit 490b3f7ca3b987c1a17852b641aad3125fc565cd
@@ -2073,7 +2153,7 @@ Date:   Thu Apr 4 17:28:30 2013 +0900
     * warning: assigned but unused variable
- lib/bio/tree.rb |    4 ++--
+ lib/bio/tree.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit c024fb972edb52e213165149273fc7ac4bec2f6e
@@ -2082,7 +2162,7 @@ Date:   Thu May 16 21:26:44 2013 +0900
     Refactoring to suppress "warning: assigned but unused variable"
- lib/bio/pathway.rb |    2 +-
+ lib/bio/pathway.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit b3b2a268d6118307eed88fce1d805a61c6fb843d
@@ -2095,7 +2175,7 @@ Date:   Thu Apr 4 17:18:44 2013 +0900
     * warning: assigned but unused variable
- lib/bio/db/transfac.rb |    2 +-
+ lib/bio/db/transfac.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit dd8abf1f95af4a70cf0b86b0e719e3dcfd8abecf
@@ -2104,7 +2184,7 @@ Date:   Thu May 16 21:13:34 2013 +0900
     Refactoring to suppress warnings "assigned but unused variable"
- lib/bio/db/nexus.rb |    5 +++--
+ lib/bio/db/nexus.rb | 5 +++--
  1 file changed, 3 insertions(+), 2 deletions(-)
 commit b37512fb8028cf30bb2f813928aed49a5b39dce3
@@ -2117,7 +2197,7 @@ Date:   Thu Apr 4 17:15:59 2013 +0900
     * warning: assigned but unused variable
- lib/bio/db/kegg/reaction.rb |    2 +-
+ lib/bio/db/kegg/reaction.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit a81fca3b1247ae4a3e05bfa912c8181efdfca81b
@@ -2130,7 +2210,7 @@ Date:   Thu Apr 4 17:15:09 2013 +0900
     * warning: assigned but unused variable
- lib/bio/db/go.rb |    6 +++---
+ lib/bio/db/go.rb | 6 +++---
  1 file changed, 3 insertions(+), 3 deletions(-)
 commit 69b0c433e76faffba6a48dfc38dcc2b1444ce2b7
@@ -2143,7 +2223,7 @@ Date:   Thu Apr 4 17:13:24 2013 +0900
     * warning: assigned but unused variable
- lib/bio/db/gff.rb |    2 +-
+ lib/bio/db/gff.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 88c214fe3183c161cda94a3a4cda442b3a769965
@@ -2152,7 +2232,7 @@ Date:   Thu May 9 23:46:28 2013 +0900
     add a dummy line to suppress "warning: assigned but unused variable"
- lib/bio/db/embl/sptr.rb |    1 +
+ lib/bio/db/embl/sptr.rb | 1 +
  1 file changed, 1 insertion(+)
 commit 1ead12f9c951a983c6775f79ca1b6944f95a61b9
@@ -2161,7 +2241,7 @@ Date:   Thu May 9 23:41:54 2013 +0900
     Refactoring to suppress warnings "assigned but unused variable"
- lib/bio/db/embl/embl.rb |    7 ++++---
+ lib/bio/db/embl/embl.rb | 7 ++++---
  1 file changed, 4 insertions(+), 3 deletions(-)
 commit 8d0eb5105eb2f419f5b4f4fbb191b8fb2032664b
@@ -2174,7 +2254,7 @@ Date:   Thu Apr 4 17:01:27 2013 +0900
     * warning: assigned but unused variable
- lib/bio/appl/paml/common.rb |    2 +-
+ lib/bio/appl/paml/common.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit c6cf0d2e2a3a0b9062f9464dba0e363f460d04e4
@@ -2183,7 +2263,7 @@ Date:   Thu May 9 23:27:54 2013 +0900
     suppress warning "assigned but unused variable"
- lib/bio/appl/paml/codeml/report.rb |    1 +
+ lib/bio/appl/paml/codeml/report.rb | 1 +
  1 file changed, 1 insertion(+)
 commit 8834d50544b03a92a3ca816704b179e4333d1dfc
@@ -2196,7 +2276,7 @@ Date:   Thu Apr 4 16:59:18 2013 +0900
     * warning: assigned but unused variable
- lib/bio/appl/meme/mast/report.rb |    2 +-
+ lib/bio/appl/meme/mast/report.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit fe51a49ee68c41a3ce0c48c39db6e8a28d1689ee
@@ -2209,7 +2289,7 @@ Date:   Thu Apr 4 16:57:44 2013 +0900
     * warning: assigned but unused variable
- lib/bio/appl/blast/report.rb |    2 +-
+ lib/bio/appl/blast/report.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 622497ff309412fb986c5315d55d41c3ca48d362
@@ -2222,7 +2302,7 @@ Date:   Thu Apr 4 17:25:29 2013 +0900
     * warning: mismatched indentations at ...
- lib/bio/map.rb |    2 +-
+ lib/bio/map.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 3ea6bcaf229fd1a71a0192253cc47e817bb64b82
@@ -2235,7 +2315,7 @@ Date:   Thu Apr 4 18:05:04 2013 +0900
     * warning: assigned but unused variable
- test/unit/bio/appl/blast/test_report.rb |    2 --
+ test/unit/bio/appl/blast/test_report.rb | 2 --
  1 file changed, 2 deletions(-)
 commit 178ca9e5244cc3aa7f0507c7d5528bb57b0858be
@@ -2248,7 +2328,7 @@ Date:   Thu Apr 4 18:03:46 2013 +0900
     * warning: assigned but unused variable
- test/unit/bio/appl/bl2seq/test_report.rb |    1 -
+ test/unit/bio/appl/bl2seq/test_report.rb | 1 -
  1 file changed, 1 deletion(-)
 commit b8a5c1cb9f54d9199200b406f77e8152eef96f02
@@ -2261,7 +2341,7 @@ Date:   Thu May 9 21:20:10 2013 +0900
        and reverse_complement methods. This change also aims to suppress
        "assigned but unused variable" warnings.
- test/unit/bio/sequence/test_na.rb |    4 +++-
+ test/unit/bio/sequence/test_na.rb | 4 +++-
  1 file changed, 3 insertions(+), 1 deletion(-)
 commit bd8fc9b197c54c108d74fea9161c8f0dd3b041fc
@@ -2274,7 +2354,7 @@ Date:   Thu Apr 4 17:59:09 2013 +0900
     * warning: assigned but unused variable
- test/unit/bio/io/flatfile/test_splitter.rb |    2 +-
+ test/unit/bio/io/flatfile/test_splitter.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 0a87c9e265c4560453faf84fc009b60319c75416
@@ -2287,7 +2367,7 @@ Date:   Thu Apr 4 17:57:51 2013 +0900
     * warning: assigned but unused variable
- test/unit/bio/db/test_phyloxml_writer.rb |    4 ++--
+ test/unit/bio/db/test_phyloxml_writer.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit 95b2614eb32eb12428df29360d0c1f146f39a469
@@ -2296,7 +2376,7 @@ Date:   Thu May 9 20:56:43 2013 +0900
     Comment out some lines to suppress "unused variable" warnings
- test/unit/bio/db/test_gff.rb |    4 ++--
+ test/unit/bio/db/test_gff.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit b8917841559fbd506c73fdf374a8097f23a1bc37
@@ -2309,7 +2389,7 @@ Date:   Thu Apr 4 17:51:11 2013 +0900
      * Note that the sequence in TestSPTRUniProtRel7_6#test_10000aa is
        a fragment of human p53 protein, and is not related with Q09165.
- test/unit/bio/db/embl/test_sptr.rb |    3 ---
+ test/unit/bio/db/embl/test_sptr.rb | 3 ---
  1 file changed, 3 deletions(-)
 commit 6b46d324a545f509bbd238ae7ec009d586469314
@@ -2322,7 +2402,7 @@ Date:   Thu Apr 4 17:45:47 2013 +0900
     * warning: assigned but unused variable
- test/unit/bio/db/embl/test_embl_rel89.rb |    1 -
+ test/unit/bio/db/embl/test_embl_rel89.rb | 1 -
  1 file changed, 1 deletion(-)
 commit f36eeb0107e7a8315c66888ec8292ed33bd959cc
@@ -2335,7 +2415,7 @@ Date:   Thu Apr 4 17:45:21 2013 +0900
     * warning: assigned but unused variable
- test/unit/bio/db/embl/test_embl.rb |    1 -
+ test/unit/bio/db/embl/test_embl.rb | 1 -
  1 file changed, 1 deletion(-)
 commit a1a2ad9b963d9bb2da8d07ae7b182bd339bea88e
@@ -2348,7 +2428,7 @@ Date:   Thu Apr 4 17:36:59 2013 +0900
     * warning: mismatched indentations at ...
- test/unit/bio/sequence/test_dblink.rb |    2 +-
+ test/unit/bio/sequence/test_dblink.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 345a8eb4408ca241c13c410a578490c905eb7391
@@ -2361,7 +2441,7 @@ Date:   Thu Apr 4 17:36:21 2013 +0900
     * warning: mismatched indentations at ...
- test/unit/bio/db/test_phyloxml.rb |   58 ++++++++++++++++++-------------------
+ test/unit/bio/db/test_phyloxml.rb | 58 +++++++++++++++++++--------------------
  1 file changed, 29 insertions(+), 29 deletions(-)
 commit ae8c7a6705a30c0c18c57df9869979a968aa63ac
@@ -2374,7 +2454,7 @@ Date:   Thu Apr 4 17:35:07 2013 +0900
     * warning: mismatched indentations at ...
- test/unit/bio/db/genbank/test_genbank.rb |    2 +-
+ test/unit/bio/db/genbank/test_genbank.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 872d8954e1351251fbace20e331035251ae5f806
@@ -2387,7 +2467,7 @@ Date:   Thu Apr 4 17:33:23 2013 +0900
     * warning: mismatched indentations at ...
- test/unit/bio/appl/test_blast.rb |    4 ++--
+ test/unit/bio/appl/test_blast.rb | 4 ++--
  1 file changed, 2 insertions(+), 2 deletions(-)
 commit bd973e084695c4d777c8ecf6d566788838158165
@@ -2396,7 +2476,7 @@ Date:   Wed Mar 27 03:03:49 2013 +0900
     .travis.yml: rbx-18mode is moved to allow_failures
- .travis.yml |    8 +++++---
+ .travis.yml | 8 +++++---
  1 file changed, 5 insertions(+), 3 deletions(-)
 commit 63e93faba74a8143a0be9595fdf87329f3015745
@@ -2405,7 +2485,7 @@ Date:   Tue Mar 26 20:20:11 2013 +1100
     Squash warning in alignment.rb: assigned but unused variable - oldkeys
- lib/bio/alignment.rb |    1 -
+ lib/bio/alignment.rb | 1 -
  1 file changed, 1 deletion(-)
 commit bd735d6f9d6edfd1550a4279167ac06b372f847a
@@ -2414,7 +2494,7 @@ Date:   Tue Mar 26 20:14:46 2013 +1100
     Squash warning in alignment.rb: assigned but unused variable - lines
- lib/bio/alignment.rb |    2 +-
+ lib/bio/alignment.rb | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit 3e7b27f96a901a3abfc338572f98d60a9e3be498
@@ -2423,7 +2503,7 @@ Date:   Tue Mar 26 19:44:49 2013 +1100
     Squash warning in defline.rb: assigned but unused variable - idtype
- lib/bio/db/fasta/defline.rb |    1 -
+ lib/bio/db/fasta/defline.rb | 1 -
  1 file changed, 1 deletion(-)
 commit aafc03330fa79243cfa4097d356a7c304ddb7980
@@ -2435,11 +2515,11 @@ Date:   Sat Feb 16 21:22:55 2013 +0900
     * /\w/ including /\d/
     * /\s/ including [/\r/, /\t/, /\n/]
- lib/bio/appl/blast/format0.rb |    2 +-
- lib/bio/db/embl/common.rb     |    2 +-
- lib/bio/db/embl/embl.rb       |    2 +-
- lib/bio/db/embl/sptr.rb       |    2 +-
- lib/bio/db/gff.rb             |    2 +-
+ lib/bio/appl/blast/format0.rb | 2 +-
+ lib/bio/db/embl/common.rb     | 2 +-
+ lib/bio/db/embl/embl.rb       | 2 +-
+ lib/bio/db/embl/sptr.rb       | 2 +-
+ lib/bio/db/gff.rb             | 2 +-
  5 files changed, 5 insertions(+), 5 deletions(-)
 commit 623ad4011fa8b56f3c9f50a859d1fa26f6570700
@@ -2452,7 +2532,7 @@ Date:   Fri Jan 11 16:41:12 2013 +0900
      * To avoid potential XSS in old MSIE which ignores content-type,
        always do CGI.escapeHTML for parameters in error messages
- sample/biofetch.rb |   91 ++++++++++++++++++++++++++++++++++++----------------
+ sample/biofetch.rb | 91 +++++++++++++++++++++++++++++++++++++-----------------
  1 file changed, 63 insertions(+), 28 deletions(-)
 commit 03d48c43f1de7ebc9104b9aa972f226774a0bf49
@@ -2465,7 +2545,7 @@ Date:   Fri Jan 11 15:32:05 2013 +0900
        available formats for each database. Database entries are not cached.
      * charset=utf-8 in CGI header.
- sample/biofetch.rb |  110 +++++++++++++++++++++++++++++++++++++++++-----------
+ sample/biofetch.rb | 110 ++++++++++++++++++++++++++++++++++++++++++-----------
  1 file changed, 87 insertions(+), 23 deletions(-)
 commit 114d29d4bdfc328f5e91adee9bea465622248e0d
@@ -2474,7 +2554,7 @@ Date:   Fri Jan 11 09:10:08 2013 +0900
     remove excess double quotations in html part
- sample/biofetch.rb |    8 ++++----
+ sample/biofetch.rb | 8 ++++----
  1 file changed, 4 insertions(+), 4 deletions(-)
 commit 949311648b92d51a2596f896fdae8d74ac0608a3
@@ -2483,7 +2563,7 @@ Date:   Fri Jan 11 08:59:18 2013 +0900
     add magic comment: coding utf-8
- sample/biofetch.rb |    1 +
+ sample/biofetch.rb | 1 +
  1 file changed, 1 insertion(+)
 commit 4ae509273134c5deca7910847063ed07c56150db
@@ -2501,7 +2581,7 @@ Date:   Thu Jan 10 23:27:09 2013 +0900
      * New constans SCRIPT_NAME and BASE_URL for easy customizing.
      * Many changes. See "git diff" for details.
- sample/biofetch.rb |  265 ++++++++++++++++++++++++++--------------------------
+ sample/biofetch.rb | 265 ++++++++++++++++++++++++++---------------------------
  1 file changed, 131 insertions(+), 134 deletions(-)
 commit bc98bc54c59be98425d66c64b19a3b9612993beb
@@ -2510,7 +2590,7 @@ Date:   Thu Jan 10 15:17:42 2013 +0900
     Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
- gemfiles/Gemfile.travis-ruby1.9 |    1 +
+ gemfiles/Gemfile.travis-ruby1.9 | 1 +
  1 file changed, 1 insertion(+)
 commit dfe54b2fbe303f56a868404173fe346724b7aa4a
@@ -2519,8 +2599,8 @@ Date:   Thu Jan 10 14:06:45 2013 +0900
     Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
- gemfiles/Gemfile.travis-jruby1.8 |    1 +
- gemfiles/Gemfile.travis-jruby1.9 |    1 +
+ gemfiles/Gemfile.travis-jruby1.8 | 1 +
+ gemfiles/Gemfile.travis-jruby1.9 | 1 +
  2 files changed, 2 insertions(+)
 commit f07ec6ac326d51c055496983abba54afd00c35d4
@@ -2529,7 +2609,7 @@ Date:   Thu Jan 10 01:38:00 2013 +0900
     Add 'gem "rdoc"' to avoid "ERROR: 'rake/rdoctask' is obsolete..."
- gemfiles/Gemfile.travis-ruby1.8 |    1 +
+ gemfiles/Gemfile.travis-ruby1.8 | 1 +
  1 file changed, 1 insertion(+)
 commit 4221d52055087f85daa1c23349d10ecdb4d01a31
@@ -2538,7 +2618,7 @@ Date:   Thu Jan 10 01:27:03 2013 +0900
     Ruby 2.0 support: Set script encoding to US-ASCII for gff.rb.
- lib/bio/db/gff.rb |    1 +
+ lib/bio/db/gff.rb | 1 +
  1 file changed, 1 insertion(+)
 commit 1526df8273e9d2283fd4a921d4cf8c0c664fe71c
@@ -2557,8 +2637,8 @@ Date:   Thu Jan 10 00:41:51 2013 +0900
     updated doc/Tutorial.rd.html and doc/Tutorial.rd.ja.html
- doc/Tutorial.rd.html    |   19 ++---
- doc/Tutorial.rd.ja.html |  202 +++++++++++++----------------------------------
+ doc/Tutorial.rd.html    |  19 ++---
+ doc/Tutorial.rd.ja.html | 202 ++++++++++++++----------------------------------
  2 files changed, 63 insertions(+), 158 deletions(-)
 commit 8db12935a9cc15bae92bdb7183476cfea9e1f819
@@ -2567,7 +2647,7 @@ Date:   Thu Jan 10 00:38:18 2013 +0900
     Set html title when generating tutorial html
- Rakefile |    3 ++-
+ Rakefile | 3 ++-
  1 file changed, 2 insertions(+), 1 deletion(-)
 commit 644d438decceb072475877a749435fba543ff8ea
@@ -2576,7 +2656,7 @@ Date:   Fri Jan 4 03:19:00 2013 +0900
     regenerate bioruby.gemspec with rake regemspec
- bioruby.gemspec |    6 ------
+ bioruby.gemspec | 6 ------
  1 file changed, 6 deletions(-)
 commit 54dc9b9f68ee2de9ee005a772ce000277a073d97
@@ -2591,7 +2671,7 @@ Date:   Fri Jan 4 02:35:01 2013 +0900
        the new API seems to lack color_pathway_by_objects that returns
        image URL. Moreover, there is no one-by-one API migration guide.
- sample/psortplot_html.rb |  214 ----------------------------------------------
+ sample/psortplot_html.rb | 214 -----------------------------------------------
  1 file changed, 214 deletions(-)
  delete mode 100644 sample/psortplot_html.rb
@@ -2601,8 +2681,8 @@ Date:   Fri Jan 4 02:34:05 2013 +0900
     Remove descriptions about KEGG API and Bio::KEGG::API.
- doc/Tutorial.rd    |    6 ---
- doc/Tutorial.rd.ja |  106 +---------------------------------------------------
+ doc/Tutorial.rd    |   6 ---
+ doc/Tutorial.rd.ja | 106 +----------------------------------------------------
  2 files changed, 1 insertion(+), 111 deletions(-)
 commit 3ca725dc1e07f794344c9fcae43d4972ed2895da
@@ -2611,7 +2691,7 @@ Date:   Fri Jan 4 02:33:09 2013 +0900
     Remove description about KEGG API and Bio::KEGG::API.
- README.rdoc |    6 ++----
+ README.rdoc | 6 ++----
  1 file changed, 2 insertions(+), 4 deletions(-)
 commit d4568788069f2d998a78ad72b1d906aae13e85f4
@@ -2620,8 +2700,8 @@ Date:   Thu Jan 3 23:55:58 2013 +0900
     Remove KEGG API plugin of BioRuby Shell, due to the removal of Bio::KEGG::API.
- lib/bio/shell.rb                |    1 -
- lib/bio/shell/plugin/keggapi.rb |  181 ---------------------------------------
+ lib/bio/shell.rb                |   1 -
+ lib/bio/shell/plugin/keggapi.rb | 181 ----------------------------------------
  2 files changed, 182 deletions(-)
  delete mode 100644 lib/bio/shell/plugin/keggapi.rb
@@ -2631,7 +2711,7 @@ Date:   Thu Jan 3 23:52:36 2013 +0900
     Delete autoload lines for removed Bio::KEGG::API
- lib/bio.rb |    4 ----
+ lib/bio.rb | 4 ----
  1 file changed, 4 deletions(-)
 commit b56ec0984d5001c3a4d3b4f0ba8fbbbf79835747
@@ -2666,7 +2746,7 @@ Date:   Mon Oct 1 21:11:14 2012 +0900
        Thanks to Edward Rice who reports the bug. (Bug #3385)
        (https://redmine.open-bio.org/issues/3385)
- lib/bio/appl/blast/format0.rb |   38 +++++++++++++++++++-------------------
+ lib/bio/appl/blast/format0.rb | 38 +++++++++++++++++++-------------------
  1 file changed, 19 insertions(+), 19 deletions(-)
 commit 9f2f682ec6624ff356bea7aca76365ba95d33549
@@ -2675,7 +2755,7 @@ Date:   Fri Sep 7 16:50:44 2012 +0900
     add an env line to be recognized in allow_failures
- .travis.yml |    1 +
+ .travis.yml | 1 +
  1 file changed, 1 insertion(+)
 commit fead6dda526081db09c56c2262f111338b7d8cd7
@@ -2684,7 +2764,7 @@ Date:   Fri Sep 7 16:08:57 2012 +0900
     environment variable TESTOPTS=-v for verbose output of rake test
- .travis.yml |   22 ++++++++++++++--------
+ .travis.yml | 22 ++++++++++++++--------
  1 file changed, 14 insertions(+), 8 deletions(-)
 commit 3de19895140502898c77fc83d9ad6fae47331763
@@ -2699,7 +2779,7 @@ Date:   Thu Sep 6 18:17:22 2012 +0900
        normally be avoided unless it is really necessary. Alternatively,
        use Bio::Shell.xxxxx (xxxxx is a method name).
- lib/bio.rb |   13 -------------
+ lib/bio.rb | 13 -------------
  1 file changed, 13 deletions(-)
 commit a358584c4a76be6a38ab38a18e6dc66840030450
@@ -2708,7 +2788,7 @@ Date:   Thu Sep 6 16:48:51 2012 +0900
     Delete autoload line of a removed class Bio::NCBI::SOAP.
- lib/bio/io/ncbirest.rb |    1 -
+ lib/bio/io/ncbirest.rb | 1 -
  1 file changed, 1 deletion(-)
 commit 340d665775b862da638e4d12751b84d2ccd83e82
@@ -2717,7 +2797,7 @@ Date:   Thu Sep 6 16:47:03 2012 +0900
     Delete autoload lines of removed classes.
- lib/bio.rb |    4 ----
+ lib/bio.rb | 4 ----
  1 file changed, 4 deletions(-)
 commit c7c29a672b38d2182cf4afc9a970b854af1149a7
@@ -2726,7 +2806,7 @@ Date:   Thu Sep 6 16:43:25 2012 +0900
     regenerate bioruby.gemspec with rake regemspec
- bioruby.gemspec |    3 ---
+ bioruby.gemspec | 3 ---
  1 file changed, 3 deletions(-)
 commit 09bb4b8a8b7e01a36dbe0cf44a5c2a6a6b5750f1
@@ -2735,7 +2815,7 @@ Date:   Thu Sep 6 16:23:17 2012 +0900
     Remove Bio::Shell#ncbisoap which uses removed Bio::NCBI::SOAP.
- lib/bio/shell/plugin/soap.rb |    9 ---------
+ lib/bio/shell/plugin/soap.rb | 9 ---------
  1 file changed, 9 deletions(-)
 commit a5e46acdaf06568bea6cb773200bbf3881b5670e
@@ -2744,7 +2824,7 @@ Date:   Thu Sep 6 16:02:32 2012 +0900
     Remove issues about removed classes Bio::NCBI::SOAP and Bio::KEGG::Taxonomy
- KNOWN_ISSUES.rdoc |   10 ----------
+ KNOWN_ISSUES.rdoc | 10 ----------
  1 file changed, 10 deletions(-)
 commit 529815acb1b57486bd506b81eec6be80277cbae7
@@ -2763,8 +2843,8 @@ Date:   Wed Sep 5 11:33:27 2012 +0900
      * Deleted files: lib/bio/db/kegg/taxonomy.rb,
        sample/demo_kegg_taxonomy.rb
- lib/bio/db/kegg/taxonomy.rb  |  280 ------------------------------------------
- sample/demo_kegg_taxonomy.rb |   92 --------------
+ lib/bio/db/kegg/taxonomy.rb  | 280 -------------------------------------------
+ sample/demo_kegg_taxonomy.rb |  92 --------------
  2 files changed, 372 deletions(-)
  delete mode 100644 lib/bio/db/kegg/taxonomy.rb
  delete mode 100644 sample/demo_kegg_taxonomy.rb
@@ -2782,7 +2862,7 @@ Date:   Wed Sep 5 11:26:00 2012 +0900
        needed, that seems very difficult. The alternative is Bio::NCBI::REST,
        REST client class for the NCBI EUtil web services.
- lib/bio/io/ncbisoap.rb |  156 ------------------------------------------------
+ lib/bio/io/ncbisoap.rb | 156 -------------------------------------------------
  1 file changed, 156 deletions(-)
  delete mode 100644 lib/bio/io/ncbisoap.rb
@@ -2792,7 +2872,7 @@ Date:   Tue Sep 4 11:13:47 2012 +0900
     regenerate bioruby.gemspec with rake regemspec
- bioruby.gemspec |   10 ++++------
+ bioruby.gemspec | 10 ++++------
  1 file changed, 4 insertions(+), 6 deletions(-)
 commit e929d5d23a9b489ef42f30b33959f059baf1e185
@@ -2801,7 +2881,7 @@ Date:   Tue Sep 4 11:09:36 2012 +0900
     Remove issues about removed classes Bio::Ensembl and Bio::DBGET.
- KNOWN_ISSUES.rdoc |   16 ----------------
+ KNOWN_ISSUES.rdoc | 16 ----------------
  1 file changed, 16 deletions(-)
 commit 550a5440490012f73b6d38d84238cd498f2ebb02
@@ -2817,9 +2897,9 @@ Date:   Tue Sep 4 10:57:20 2012 +0900
      * Deleted files: lib/bio/io/ensembl.rb,
        test/network/bio/io/test_ensembl.rb, test/unit/bio/io/test_ensembl.rb.
- lib/bio/io/ensembl.rb               |  229 ----------------------------------
- test/network/bio/io/test_ensembl.rb |  230 -----------------------------------
- test/unit/bio/io/test_ensembl.rb    |  111 -----------------
+ lib/bio/io/ensembl.rb               | 229 -----------------------------------
+ test/network/bio/io/test_ensembl.rb | 230 ------------------------------------
+ test/unit/bio/io/test_ensembl.rb    | 111 -----------------
  3 files changed, 570 deletions(-)
  delete mode 100644 lib/bio/io/ensembl.rb
  delete mode 100644 test/network/bio/io/test_ensembl.rb
@@ -2835,8 +2915,8 @@ Date:   Tue Sep 4 10:47:52 2012 +0900
        discontinued about 8 years ago.
      * Remove lib/bio/io/dbget.rb and sample/dbget.
- lib/bio/io/dbget.rb |  194 ---------------------------------------------------
- sample/dbget        |   37 ----------
+ lib/bio/io/dbget.rb | 194 ----------------------------------------------------
+ sample/dbget        |  37 ----------
  2 files changed, 231 deletions(-)
  delete mode 100644 lib/bio/io/dbget.rb
  delete mode 100755 sample/dbget
@@ -2852,7 +2932,7 @@ Date:   Thu Aug 23 00:25:43 2012 +0900
        For the changes before 1.4.2, see doc/ChangeLog-before-1.4.2.
        For the changes before 1.3.1, see doc/ChangeLog-before-1.3.1.
- ChangeLog |   61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ ChangeLog | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  1 file changed, 61 insertions(+)
  create mode 100644 ChangeLog
@@ -2862,7 +2942,7 @@ Date:   Thu Aug 23 00:25:07 2012 +0900
     Rakefile: Update hardcoded git tag name for updating of ChangeLog.
- Rakefile |    2 +-
+ Rakefile | 2 +-
  1 file changed, 1 insertion(+), 1 deletion(-)
 commit b10c7ad2db24d88726ffb8c63078baa217aeac43
@@ -2883,7 +2963,7 @@ Date:   Thu Aug 23 00:18:50 2012 +0900
     ChangeLog updated: add log about 1.4.3 release.
- ChangeLog |    9 +++++++++
+ ChangeLog | 9 +++++++++
  1 file changed, 9 insertions(+)
 commit 5e88ccbe0fefdd4d57f144aaf9073f5e7d93281c
@@ -2892,7 +2972,7 @@ Date:   Thu Aug 23 00:16:25 2012 +0900
     New RELEASE_NOTES.rdoc for the next release version.
- RELEASE_NOTES.rdoc |   47 +++++++++++++++++++++++++++++++++++++++++++++++
+ RELEASE_NOTES.rdoc | 47 +++++++++++++++++++++++++++++++++++++++++++++++
  1 file changed, 47 insertions(+)
  create mode 100644 RELEASE_NOTES.rdoc
@@ -2902,8 +2982,8 @@ Date:   Thu Aug 23 00:12:40 2012 +0900
     Renamed RELEASE_NOTES.rdoc to doc/RELEASE_NOTES-1.4.3.rdoc
- RELEASE_NOTES.rdoc           |  204 ------------------------------------------
- doc/RELEASE_NOTES-1.4.3.rdoc |  204 ++++++++++++++++++++++++++++++++++++++++++
+ RELEASE_NOTES.rdoc           | 204 -------------------------------------------
+ doc/RELEASE_NOTES-1.4.3.rdoc | 204 +++++++++++++++++++++++++++++++++++++++++++
  2 files changed, 204 insertions(+), 204 deletions(-)
  delete mode 100644 RELEASE_NOTES.rdoc
  create mode 100644 doc/RELEASE_NOTES-1.4.3.rdoc
@@ -2914,6 +2994,6 @@ Date:   Thu Aug 23 00:00:15 2012 +0900
     Bio::BIORUBY_EXTRA_VERSION set to ".5000" (unstable version).
- bioruby.gemspec    |    2 +-
- lib/bio/version.rb |    2 +-
+ bioruby.gemspec    | 2 +-
+ lib/bio/version.rb | 2 +-
  2 files changed, 2 insertions(+), 2 deletions(-)