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ChangeLog
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ChangeLog
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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