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ChangeLog
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commit 5c88896357e1eff0686ceb06cbec0a7837f85050
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 28 21:55:41 2009 +0900
Preparation for bioruby-1.4.0 release.
lib/bio/version.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
commit 11f56d3d8efc2cf5d9408da865af044fa099b925
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 28 21:52:25 2009 +0900
Added about ChangeLog which is replaced by git-log.
RELEASE_NOTES.rdoc | 5 +++++
1 files changed, 5 insertions(+), 0 deletions(-)
commit 17d5b1825b6c73d710d72903d8710caa9996353a
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 28 20:11:49 2009 +0900
ChangeLog is autogenerated from git log.
* ChangeLog is autogenerated from git log with the following command:
% git log --stat --summary \
3d1dfcc0e13ad582b9c70c7fdde3a89d0bacdc80..HEAD > ChangeLog
ChangeLog | 2306 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 files changed, 2306 insertions(+), 0 deletions(-)
create mode 100644 ChangeLog
commit 02bf77af589ea62df81e9634df6fe949df2fd3ef
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 28 19:25:39 2009 +0900
test_output_size is disabled because it depends on html decorations
test/functional/bio/appl/test_pts1.rb | 6 +++---
1 files changed, 3 insertions(+), 3 deletions(-)
commit 5781fb402e85e73fd47948b4466c8129355b714b
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 28 19:21:21 2009 +0900
The PTS1 Predictor's URL had been changed.
* The PTS1 Predictor's URL had been changed.
* Changed to use @uri instead of @host and @cgi_path.
lib/bio/appl/pts1.rb | 6 ++----
1 files changed, 2 insertions(+), 4 deletions(-)
commit a4e691d913e1ae51eadb1a871efc2c8718ef5587
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 28 18:33:00 2009 +0900
Preparation of ChangeLog autogeneration: old ChangeLog is moved to doc/ChangeLog-before-1.3.1.
ChangeLog | 3961 --------------------------------------------
doc/ChangeLog-before-1.3.1 | 3961 ++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 3961 insertions(+), 3961 deletions(-)
delete mode 100644 ChangeLog
create mode 100644 doc/ChangeLog-before-1.3.1
commit c011604766baa3cdf5ca2f4a776aa67c56460d29
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 28 17:53:51 2009 +0900
Tutorial.rd.html is regenerated.
doc/Tutorial.rd.html | 70 +++++++++++++------------------------------------
1 files changed, 19 insertions(+), 51 deletions(-)
commit 6e2cdd13d61970aa4704475bfb5aefb70719c2e1
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 28 17:42:25 2009 +0900
Added Bio::NCBI.default_email= in the example, and examples using deprecated Bio::PubMed methods are temporarily commented out.
doc/Tutorial.rd | 8 ++++++++
1 files changed, 8 insertions(+), 0 deletions(-)
commit 8e6d5e9baf98be7e58f4dda8b5d043a42149874b
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 28 17:15:09 2009 +0900
Reinserted "==>" for Blast example, and removed duplicated Ruby Ensembl API example.
doc/Tutorial.rd | 25 ++-----------------------
1 files changed, 2 insertions(+), 23 deletions(-)
commit 849edd7e8c5b26923cab47e7f5542948fab2b1fb
Author: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Sun Dec 27 09:49:14 2009 +0100
Tutorial: Added info on how to run rubydoctest
Removed bioruby> prefix for one failing BLAST test
doc/Tutorial.rd | 69 ++++++++++++++++++++++++++++++++++++++----------------
1 files changed, 48 insertions(+), 21 deletions(-)
commit a39fcf0ca1a5265789110f42cc616fc5d3c16414
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 25 12:30:18 2009 +0900
Modified for release notes and fixed typo.
RELEASE_NOTES.rdoc | 29 +++++++++++++++--------------
1 files changed, 15 insertions(+), 14 deletions(-)
commit 3fa8b68f19fc2b6aaf8f54eb10517cc761b2193b
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 25 12:10:34 2009 +0900
Changes following the rename to RELEASE_NOTES.rdoc.
README.rdoc | 2 +-
bioruby.gemspec | 6 +++---
bioruby.gemspec.erb | 2 +-
3 files changed, 5 insertions(+), 5 deletions(-)
commit fd692a1165d368b9bdbe068ea6bf63fd91c9925c
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 25 12:03:41 2009 +0900
Renamed doc/Changes-1.4.rdoc to RELEASE_NOTES.rdoc.
RELEASE_NOTES.rdoc | 160 ++++++++++++++++++++++++++++++++++++++++++++++++++
doc/Changes-1.4.rdoc | 160 --------------------------------------------------
2 files changed, 160 insertions(+), 160 deletions(-)
create mode 100644 RELEASE_NOTES.rdoc
delete mode 100644 doc/Changes-1.4.rdoc
commit 0e37f04dd8d34517693fdd4bc27f8bdada7c2f13
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 24 21:48:52 2009 +0900
Changed Bio::PhyloXML::Parser.new to open, and regenerated html.
doc/Tutorial.rd | 10 ++--
doc/Tutorial.rd.html | 125 ++++++++++++++++++++++++++++++++++++++++++-------
2 files changed, 112 insertions(+), 23 deletions(-)
commit aeacbbd425c2e88369c171bd92c60bf8e520a9e5
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 24 19:26:49 2009 +0900
bioruby.gemspec is regenerated
bioruby.gemspec | 8 +++++++-
1 files changed, 7 insertions(+), 1 deletions(-)
commit 1034205c199a638c359780922293f8b39c467356
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 24 19:24:56 2009 +0900
Version number changed to 1.4.0-rc1
lib/bio/version.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
commit 04bf2da43f78fbb702b67323f3be1fe3bd2d0351
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 24 19:22:41 2009 +0900
Issues added and modified.
KNOWN_ISSUES.rdoc | 35 +++++++++++++++++++++++++++++++++--
1 files changed, 33 insertions(+), 2 deletions(-)
commit f1a76157b009fb0ca94d9a0e0f8a85522c383b19
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 24 19:22:19 2009 +0900
Added news and incompatible changes.
doc/Changes-1.4.rdoc | 102 ++++++++++++++++++++++++++++++++++++++++++++++++--
1 files changed, 98 insertions(+), 4 deletions(-)
commit 9c8ef18a20c49f17d5b89aa1db5819b2c8ee9b1d
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 24 19:10:02 2009 +0900
Email address for NCBI Entrez is given with Bio::NCBI.default_email=.
bin/bioruby | 5 ++++-
sample/demo_ncbi_rest.rb | 2 ++
sample/demo_pubmed.rb | 2 ++
sample/pmfetch.rb | 2 ++
sample/pmsearch.rb | 2 ++
test/functional/bio/io/test_pubmed.rb | 4 ++++
6 files changed, 16 insertions(+), 1 deletions(-)
commit 7a7179665694da35ab0970909bfbda9ad1b057da
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 24 19:09:09 2009 +0900
Changed autoload hierarchy of Bio::NCBI.
lib/bio.rb | 10 ++++++----
lib/bio/io/ncbisoap.rb | 3 ++-
2 files changed, 8 insertions(+), 5 deletions(-)
commit f8dc0268d9edf699fd3f0cf18dd55a2b10ec3bcc
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 24 18:58:18 2009 +0900
New singleton methods Bio::NCBI.default_email=, default_tool=, etc.
* New singleton methods Bio::NCBI.default_email=, default_email,
default_tools=, default_tools, etc., because email and tool
parameters will be mandatory in Entrez eUtils.
* Changed to raise error when email or tool is empty. Note that
default email is nil and library users should always set their
email address.
* Default tool name is changed to include $0 and bioruby version ID.
* Added multi-thread support for Bio::NCBI::REST#ncbi_access_wait.
lib/bio/io/ncbirest.rb | 161 ++++++++++++++++++++++++++++++++++++++---------
1 files changed, 130 insertions(+), 31 deletions(-)
commit 2e311dc44290ef6bda48f0bcba09a3c22bf32d9a
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 21 22:24:52 2009 +0900
Description about the incompatible change of Bio::KEGG::REACTION#rpairs.
doc/Changes-1.4.rdoc | 6 +++---
1 files changed, 3 insertions(+), 3 deletions(-)
commit d57ace3a89077caae3c681743da4b92d16b90af8
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 21 22:17:46 2009 +0900
Bio::KEGG::R#ACTION#rpairs is changed to return a hash.
lib/bio/db/kegg/reaction.rb | 65 ++++++++++++++++++++++++--------
test/unit/bio/db/kegg/test_reaction.rb | 27 ++++++++++++-
2 files changed, 74 insertions(+), 18 deletions(-)
commit 60e4c77d184ee81c51668b446518cfbc9256be50
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Dec 21 22:15:44 2009 +0900
Document bug fix: return value mistake.
lib/bio/db/kegg/genes.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
commit 6376dd55aa4995769746e556ca719d37f02975d6
Author: Naohisa Goto <ng@bioruby.org>
Date: Sun Dec 20 17:32:52 2009 +0900
Added README.txt for FASTQ example data.
test/data/fastq/README.txt | 109 ++++++++++++++++++++++++++++++++++++++++++++
1 files changed, 109 insertions(+), 0 deletions(-)
create mode 100644 test/data/fastq/README.txt
commit 8dec18794c846726733d66c5a22170f5b2c4bb1a
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Dec 15 13:51:13 2009 +0900
Newly added unit tests for Bio::KEGG::GLYCAN with test data.
test/data/KEGG/G00024.glycan | 47 ++++++
test/data/KEGG/G01366.glycan | 18 +++
test/unit/bio/db/kegg/test_glycan.rb | 260 ++++++++++++++++++++++++++++++++++
3 files changed, 325 insertions(+), 0 deletions(-)
create mode 100644 test/data/KEGG/G00024.glycan
create mode 100644 test/data/KEGG/G01366.glycan
create mode 100644 test/unit/bio/db/kegg/test_glycan.rb
commit 90b97bfbcfb3f7e3d5c28b195bdb9b9c058df887
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Dec 15 11:42:39 2009 +0900
Newly added unit test for Bio::KEGG::DRUG with test data.
test/data/KEGG/D00063.drug | 104 +++++++++++++++++++
test/unit/bio/db/kegg/test_drug.rb | 194 ++++++++++++++++++++++++++++++++++++
2 files changed, 298 insertions(+), 0 deletions(-)
create mode 100644 test/data/KEGG/D00063.drug
create mode 100644 test/unit/bio/db/kegg/test_drug.rb
commit 443f778795b82a7f572cb8b85d2a8a8b3cea1334
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Dec 15 11:38:59 2009 +0900
New method Bio::KEGG::DRUG#products
* New method Bio::KEGG::DRUG#products.
* Improved RDoc.
lib/bio/db/kegg/drug.rb | 50 +++++++++++++++++++++++++++++++++++++---------
1 files changed, 40 insertions(+), 10 deletions(-)
commit 48184d96b989f909ac0effb759cbc4b1ddc98dd1
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 11 01:36:54 2009 +0900
Methods in Bio::KEGG::Common::* are changed to cache return values in instance variables.
lib/bio/db/kegg/common.rb | 62 ++++++++++++++++++++++++++------------------
1 files changed, 37 insertions(+), 25 deletions(-)
commit f364ea609f1e01ca5270a5bd7404e0bbf752bc89
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 11 01:23:42 2009 +0900
Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated.
bioruby.gemspec | 142 ++++++++++++++++++++++++++++++++++++++++++++++++++-
bioruby.gemspec.erb | 4 +-
lib/bio/version.rb | 4 +-
3 files changed, 145 insertions(+), 5 deletions(-)
commit 096b5fbf6b7ff906203aabf93eb9a0bd56ae9ba2
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 11 01:22:59 2009 +0900
Added documents about Bio::KEGG incompatible changes.
doc/Changes-1.4.rdoc | 48 ++++++++++++++++++++++++++++++++++++++++++------
1 files changed, 42 insertions(+), 6 deletions(-)
commit 72ed277fe30bb1033cbc16d462f137510afb84e6
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 11 01:21:26 2009 +0900
Newly added unit tests for Bio::KEGG::ENZYME with test data.
test/data/KEGG/1.1.1.1.enzyme | 935 ++++++++++++++++++++++++++++++++++
test/unit/bio/db/kegg/test_enzyme.rb | 241 +++++++++
2 files changed, 1176 insertions(+), 0 deletions(-)
create mode 100644 test/data/KEGG/1.1.1.1.enzyme
create mode 100644 test/unit/bio/db/kegg/test_enzyme.rb
commit b99fcb39f7c5d2857cbb65283d85ea868ae8561d
Author: Naohisa Goto <ng@bioruby.org>
Date: Fri Dec 11 01:09:03 2009 +0900
Changed Bio::KEGG::*#dblinks, pathways, orthologs, genes methods.
* In Bio::KEGG::COMPOUND, DRUG, ENZYME, GLYCAN and ORTHOLOGY, the
method dblinks is changed to return a Hash. The old methods are
renamed to dblinks_as_strings.
* In Bio::KEGG::COMPOUND, DRUG, ENZYME, GENES, GLYCAN and REACTION,
the method pathways is changed to return a Hash. The old methods
are renamed to pathways_as_strings except for GENES.
* In Bio::KEGG::ENZYME, GENES, GLYCAN and REACTION, the method
orthologs is changed to return a Hash. The old methods are renamed
to orthologs_as_strings.
* Bio::KEGG::ENZYME#genes and Bio::KEGG::ORTHOLOGY#genes is changed
to return a Hash. The old methods are renamed to genes_as_strings.
* Added Bio::KEGG::REACTION#rpairs_as_tokens, older behavior of rpairs.
* Modules in lib/bio/db/kegg/common.rb are moved uner Bio::KEGG::Common
namespace.
* Refactoring.
* Added documents.
* Tests modified.
lib/bio/db/kegg/common.rb | 40 +++++++++++++++++++++++++------
lib/bio/db/kegg/compound.rb | 10 ++++---
lib/bio/db/kegg/drug.rb | 27 +++++++++++++++------
lib/bio/db/kegg/enzyme.rb | 31 ++++++++++++++++++++----
lib/bio/db/kegg/genes.rb | 39 +++++++++++++++++++------------
lib/bio/db/kegg/glycan.rb | 22 +++++++++++++++--
lib/bio/db/kegg/orthology.rb | 25 +++++++------------
lib/bio/db/kegg/reaction.rb | 16 +++++++++---
test/unit/bio/db/kegg/test_compound.rb | 27 ++++++++++++--------
test/unit/bio/db/kegg/test_reaction.rb | 13 +++++----
10 files changed, 170 insertions(+), 80 deletions(-)
commit 2cc9d4e2f28f6b2bbcb8f714f9e2eb144c594fbf
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 10 16:02:54 2009 +0900
Bio::KEGG::GENES#structure no more adds PDB: prefix.
* Bio::KEGG::GENES#structure no more adds PDB: prefix.
* Added Bio::KEGG::GENES#structures as an alias of structure.
lib/bio/db/kegg/genes.rb | 7 +++----
test/unit/bio/db/kegg/test_genes.rb | 7 ++++---
2 files changed, 7 insertions(+), 7 deletions(-)
commit a8ceb23bdf19d6649aa4d879cba76a9e3f91d1d4
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Dec 10 15:28:33 2009 +0900
Refactoring of Bio::KEGG::Orthology#dblinks and genes.
* Refactoring of Bio::KEGG::Orthology#dblinks and genes: no need
to treat @data because lines_fetch internally does so.
lib/bio/db/kegg/orthology.rb | 10 ++--------
1 files changed, 2 insertions(+), 8 deletions(-)
commit 720e0bccdfdc6fac6222cac1a9f05d6e2419896c
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Dec 9 16:39:03 2009 +0900
Changed dummy lines for RDoc.
lib/bio/db/kegg/compound.rb | 4 ++--
lib/bio/db/kegg/orthology.rb | 2 +-
lib/bio/db/kegg/reaction.rb | 4 ++--
3 files changed, 5 insertions(+), 5 deletions(-)
commit 20f8c03af92e5cfedcb49e8ed9fc6fda2b86e9c9
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Dec 9 15:17:39 2009 +0900
Refactoring of Bio::KEGG::REACTION#orthologs.
* Refactoring of Bio::KEGG::REACTION#orthologs: no need to treat
@data because lines_fetch internally does so.
lib/bio/db/kegg/reaction.rb | 5 +----
1 files changed, 1 insertions(+), 4 deletions(-)
commit b924601bacd643f66b37dd991913e6862df704a9
Author: Naohisa Goto <ng@bioruby.org>
Date: Sun Dec 6 15:51:03 2009 +0900
Bio::KEGG::GENES#pathways is changed to return raw lines as an Array of strings.
* Bio::KEGG::GENES#pathways is changed to return raw lines as an
Array of strings.
* RDoc is added for Bio::KEGG::GENES.
lib/bio/db/kegg/genes.rb | 99 ++++++++++++++++++++++++++++++++++++++++++++-
1 files changed, 96 insertions(+), 3 deletions(-)
commit 4c840dc6a539db1d854b23991269b3e6515f637e
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date: Wed Dec 2 17:02:00 2009 +0900
Added test methods.
test/unit/bio/db/kegg/test_compound.rb | 47 ++++++++++++++++++++++++++++++++
1 files changed, 47 insertions(+), 0 deletions(-)
commit 105efa1ecd1bc99a54aac32710a97df15035119d
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Dec 2 23:31:07 2009 +0900
Refactoring: to use lib/bio/db/kegg/common.rb for dblinks_as_hash method.
lib/bio/db/kegg/orthology.rb | 16 +++++-----------
1 files changed, 5 insertions(+), 11 deletions(-)
commit c394ead051c3a13ceb534f93816af7ad35be932a
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Dec 2 23:07:23 2009 +0900
Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash with changing its return value to a hash.
* Bio::KEGG::REACTION#orthologies is renamed to orthologs_as_hash
with changing its return value to a hash.
* The code of the orthologs_as_hash method is moved to
lib/bio/db/kegg/common.rb.
* Added new method Bio::KEGG::REACTION#orthologs, copied from
lib/bio/db/kegg/glycan.rb.
lib/bio/db/kegg/common.rb | 18 +++++++++++++++++-
lib/bio/db/kegg/reaction.rb | 14 ++++++--------
sample/demo_kegg_reaction.rb | 6 ++++--
test/unit/bio/db/kegg/test_reaction.rb | 12 ++++++++++--
4 files changed, 37 insertions(+), 13 deletions(-)
commit 4e01fda27166faf066104ab9897904fd46f57123
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Dec 2 22:48:06 2009 +0900
Added Bio::KEGG::REACTION#pathways_as_hash and reverted pathways method.
* New method Bio::KEGG::REACTION#pathways_as_hash, using a module
in lib/bio/db/kegg/common.rb.
* Bio::KEGG::REACTION#pathways is reverted to return an array of
string.
lib/bio/db/kegg/reaction.rb | 18 +++++++++++-------
test/unit/bio/db/kegg/test_reaction.rb | 8 +++++++-
2 files changed, 18 insertions(+), 8 deletions(-)
commit 0c2ce4b8462792d496ab3f58206fdbd47143e280
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Dec 2 22:35:21 2009 +0900
New methods Bio::KEGG::COMPOUND#dblinks_as_hash and pathways_as_hash, using modules in lib/bio/db/kegg/common.rb.
lib/bio/db/kegg/compound.rb | 14 +++++++++++
test/unit/bio/db/kegg/test_compound.rb | 38 ++++++++++++++++++++++++++++++++
2 files changed, 52 insertions(+), 0 deletions(-)
commit 63df07e030120eb43de22555277529822b072270
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Dec 2 22:25:20 2009 +0900
Methods commonly used from Bio::KEGG::* classes.
* Modules containing methods commonly used from Bio::KEGG::* classes.
The "dblinks_as_hash" method is copied from
lib/bio/db/kegg/orthology.rb. The "pathways_as_hash" method is
derived from the dblinks_as_hash and Bio::KEGG::REACTION#pathways
methods.
lib/bio/db/kegg/common.rb | 60 +++++++++++++++++++++++++++++++++++++++++++++
1 files changed, 60 insertions(+), 0 deletions(-)
create mode 100644 lib/bio/db/kegg/common.rb
commit 0e55c6701b09a52356ac55300181ee656773826f
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Dec 2 21:39:06 2009 +0900
Bio::KEGG::COMPOUND#dblinks is reverted to return an array of string.
lib/bio/db/kegg/compound.rb | 11 ++---------
test/unit/bio/db/kegg/test_compound.rb | 8 +++++++-
2 files changed, 9 insertions(+), 10 deletions(-)
commit a05adcddf6c7ed67c042f31ecd86848af1ba8a22
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Dec 2 21:13:39 2009 +0900
Bug fix: fixed a copy-and-paste mistake.
lib/bio/db/kegg/drug.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
commit 86925f3c80730e3ea3377a23a70cadb3876258c4
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Dec 1 21:31:40 2009 +0900
Bio::KEGG::ORTHOLOGY#dblinks_as_hash should preserve database names.
doc/Changes-1.4.rdoc | 4 ++++
lib/bio/db/kegg/orthology.rb | 2 +-
test/unit/bio/db/kegg/test_orthology.rb | 2 +-
3 files changed, 6 insertions(+), 2 deletions(-)
commit 60847cd2d0701fa38a499578649cb216c93993a2
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Dec 1 20:41:51 2009 +0900
Test class names are changed to avoid potential class name conflict.
test/unit/bio/db/kegg/test_compound.rb | 2 +-
test/unit/bio/db/kegg/test_genes.rb | 4 ++--
test/unit/bio/db/kegg/test_orthology.rb | 2 +-
test/unit/bio/db/kegg/test_reaction.rb | 2 +-
4 files changed, 5 insertions(+), 5 deletions(-)
commit 2bda62af7a020c22379dd9ec3a42496d2a5b94cb
Author: Kozo Nishida <kozo-ni@cg05.naist.jp>
Date: Tue Dec 1 04:38:27 2009 +0900
Added unit tests for Bio::KEGG::ORTHOLOGY.
test/data/KEGG/K02338.orthology | 902 +++++++++++++++++++++++++++++++
test/unit/bio/db/kegg/test_orthology.rb | 50 ++
2 files changed, 952 insertions(+), 0 deletions(-)
create mode 100644 test/data/KEGG/K02338.orthology
create mode 100644 test/unit/bio/db/kegg/test_orthology.rb
commit acad9497caf5d737394568e911691fdad11ca091
Author: Naohisa Goto <ng@bioruby.org>
Date: Mon Nov 30 21:39:32 2009 +0900
Changed to use BioRubyTestDataPath instead of __FILE__.
test/unit/bio/db/kegg/test_compound.rb | 3 +--
test/unit/bio/db/kegg/test_reaction.rb | 3 +--
2 files changed, 2 insertions(+), 4 deletions(-)
commit 8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca
Author: Naohisa Goto <ng@bioruby.org>
Date: Sun Nov 29 16:37:21 2009 +0900
Bio::Fastq::QualityScore is renamed to Bio::Sequence::QualityScore.
* Bio::Fastq::QualityScore is renamed to Bio::Sequence::QualityScore.
* Changes of filenames due to the previous file move.
lib/bio/db/fasta/format_qual.rb | 18 ++++++++--------
lib/bio/db/fastq.rb | 7 ++---
lib/bio/sequence.rb | 3 +-
lib/bio/sequence/quality_score.rb | 25 +++++++++++------------
test/unit/bio/sequence/test_quality_score.rb | 28 +++++++++++++-------------
5 files changed, 40 insertions(+), 41 deletions(-)
commit 2b29654c1d7e927e445e7acdd525835a873c2a2a
Author: Naohisa Goto <ng@bioruby.org>
Date: Sun Nov 29 16:15:42 2009 +0900
lib/bio/db/fastq/quality_score.rb is moved to lib/bio/sequence/. The unit test is also moved.
* lib/bio/db/fastq/quality_score.rb is moved to lib/bio/sequence/.
* test/unit/bio/db/fastq/test_quality_score.rb is moved to
test/unit/bio/sequence/.
* The file contents will be modified with the following commit.
lib/bio/db/fastq/quality_score.rb | 206 ----------------
lib/bio/sequence/quality_score.rb | 206 ++++++++++++++++
test/unit/bio/db/fastq/test_quality_score.rb | 330 --------------------------
test/unit/bio/sequence/test_quality_score.rb | 330 ++++++++++++++++++++++++++
4 files changed, 536 insertions(+), 536 deletions(-)
delete mode 100644 lib/bio/db/fastq/quality_score.rb
create mode 100644 lib/bio/sequence/quality_score.rb
delete mode 100644 test/unit/bio/db/fastq/test_quality_score.rb
create mode 100644 test/unit/bio/sequence/test_quality_score.rb
commit aa8d49bf31f90dd2796c18ee0aa6291979284ec2
Author: Naohisa Goto <ng@bioruby.org>
Date: Sun Nov 29 15:20:36 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_gff1.rb.
lib/bio/db/gff.rb | 17 -----------------
sample/demo_gff1.rb | 49 +++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 49 insertions(+), 17 deletions(-)
create mode 100644 sample/demo_gff1.rb
commit 76fffd2d2429346478fb3d8c88cdcd878a1047b1
Author: Naohisa Goto <ng@bioruby.org>
Date: Sun Nov 29 15:06:41 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_tmhmm_report.rb.
lib/bio/appl/tmhmm/report.rb | 36 ----------------------
sample/demo_tmhmm_report.rb | 68 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 68 insertions(+), 36 deletions(-)
create mode 100644 sample/demo_tmhmm_report.rb
commit dfafb0a2bcec4c0b4cd3640374e151e2039056dc
Author: Naohisa Goto <ng@bioruby.org>
Date: Sun Nov 29 14:59:27 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_targetp_report.rb.
lib/bio/appl/targetp/report.rb | 105 +------------------------------
sample/demo_targetp_report.rb | 135 ++++++++++++++++++++++++++++++++++++++++
2 files changed, 136 insertions(+), 104 deletions(-)
create mode 100644 sample/demo_targetp_report.rb
commit 75f7c8527546f8ea3079f53b90a9b4d8260b4de0
Author: Naohisa Goto <ng@bioruby.org>
Date: Sun Nov 29 14:33:28 2009 +0900
Follow-up of the SOSUI server URL change.
lib/bio/appl/sosui/report.rb | 6 ++++--
1 files changed, 4 insertions(+), 2 deletions(-)
commit 8022696295dc296462f73b40cc74ad5259bee387
Author: Naohisa Goto <ng@bioruby.org>
Date: Sun Nov 29 14:32:11 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_sosui_report.rb.
lib/bio/appl/sosui/report.rb | 53 +------------------------
sample/demo_sosui_report.rb | 89 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 90 insertions(+), 52 deletions(-)
create mode 100644 sample/demo_sosui_report.rb
commit 4acfe7f565039b34a036682912a75f55da808b45
Author: Naohisa Goto <ng@bioruby.org>
Date: Sun Nov 29 14:02:32 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_hmmer_report.rb.
lib/bio/appl/hmmer/report.rb | 100 ----------------------------
sample/demo_hmmer_report.rb | 149 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 149 insertions(+), 100 deletions(-)
create mode 100644 sample/demo_hmmer_report.rb
commit 4f7bd1b7628d90661d8b557ca854b14cc44fb99c
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 15:49:21 2009 +0900
Demo codes in the "if __FILE__ == $0" are removed because they are very short.
lib/bio/appl/fasta/format10.rb | 14 --------------
lib/bio/appl/hmmer.rb | 16 +---------------
lib/bio/io/flatfile.rb | 8 +-------
3 files changed, 2 insertions(+), 36 deletions(-)
commit c2a72d195189755532e7e206af34d152ab6332d8
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 15:20:28 2009 +0900
Bug fix: Failure of Bio::Fasta.remote due to the remote site changes.
lib/bio/appl/fasta.rb | 5 ++++-
1 files changed, 4 insertions(+), 1 deletions(-)
commit 549112fb4dfb5f6b2fe3491fb161887a9f5262ac
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 15:13:10 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_fasta_remote.rb.
lib/bio/appl/fasta.rb | 18 ---------------
sample/demo_fasta_remote.rb | 51 +++++++++++++++++++++++++++++++++++++++++++
2 files changed, 51 insertions(+), 18 deletions(-)
create mode 100644 sample/demo_fasta_remote.rb
commit 0e4ca0db83692fdbbe93e90272a07bcbac89192c
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 10:17:47 2009 +0900
Text indents for some comment lines are changed.
sample/demo_blast_report.rb | 4 ++--
sample/demo_kegg_compound.rb | 4 ++--
sample/demo_prosite.rb | 4 ++--
sample/demo_sirna.rb | 4 ++--
4 files changed, 8 insertions(+), 8 deletions(-)
commit c0cf91fe2a9247bc3705b20515f9d4fa14288d5a
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 10:13:26 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_keggapi.rb.
* Demo codes in the "if __FILE__ == $0" are moved to
sample/demo_keggapi.rb.
* Commented out demonstrations of deprecated methods:
get_neighbors_by_gene, get_similarity_between_genes,
get_ko_members, get_oc_members_by_gene, get_pc_members_by_gene.
* Commented out demonstrations of methods internally using
the deprecated methods: get_all_neighbors_by_gene,
get_all_oc_members_by_gene, get_all_pc_members_by_gene.
lib/bio/io/keggapi.rb | 442 ------------------------------------------
sample/demo_keggapi.rb | 502 ++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 502 insertions(+), 442 deletions(-)
create mode 100644 sample/demo_keggapi.rb
commit 8b8206c1d8ee699185fdd19d3329311c85ee003c
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 01:50:06 2009 +0900
Fixed the license line.
lib/bio/db/prosite.rb | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
commit ebfeec8243abd4e2f65335fda1ead18efff66897
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 01:41:58 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_ncbi_rest.rb.
lib/bio/io/ncbirest.rb | 101 ------------------------------------
sample/demo_ncbi_rest.rb | 128 ++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 128 insertions(+), 101 deletions(-)
create mode 100644 sample/demo_ncbi_rest.rb
commit 5a0f8379a374650d12fc88fbbd5b28c38ae96395
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 01:33:07 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_prosite.rb.
lib/bio/db/prosite.rb | 95 +-------------------------------------
sample/demo_prosite.rb | 120 ++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 121 insertions(+), 94 deletions(-)
create mode 100644 sample/demo_prosite.rb
commit c560a5d0ba9d4919dbcca156ea620056dcb8f725
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 01:14:37 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_psort.rb.
lib/bio/appl/psort.rb | 111 ---------------------------------------
sample/demo_psort.rb | 138 +++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 138 insertions(+), 111 deletions(-)
create mode 100644 sample/demo_psort.rb
commit 1299a55d214784a536ae3cd8bfabdfd61fe1da86
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 01:04:29 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_psort_report.rb.
* Demo codes in the "if __FILE__ == $0" are moved to
sample/demo_psort_report.rb, without any checks.
lib/bio/appl/psort/report.rb | 46 +---------------------------
sample/demo_psort_report.rb | 70 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 71 insertions(+), 45 deletions(-)
create mode 100644 sample/demo_psort_report.rb
commit a2686fe3c5a93947c94d4602514a62a808c182d5
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 00:53:54 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_genscan_report.rb.
lib/bio/appl/genscan/report.rb | 176 ----------------------------------
sample/demo_genscan_report.rb | 202 ++++++++++++++++++++++++++++++++++++++++
2 files changed, 202 insertions(+), 176 deletions(-)
create mode 100644 sample/demo_genscan_report.rb
commit 22f662ba69dd2d4a2273562dd7ea921f5cdd84bd
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 00:28:01 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_ddbjxml.rb.
lib/bio/io/ddbjxml.rb | 182 +-----------------------------------------
sample/demo_ddbjxml.rb | 212 ++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 213 insertions(+), 181 deletions(-)
create mode 100644 sample/demo_ddbjxml.rb
commit ed3b34b6598f632c7b9b3f1a17b42406c19ca32d
Author: Naohisa Goto <ng@bioruby.org>
Date: Thu Nov 26 00:12:33 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_pubmed.rb.
* Demo codes in the "if __FILE__ == $0" are moved to
sample/demo_pubmed.rb.
* Codes using Entrez CGI are disabled in the demo.
lib/bio/io/pubmed.rb | 88 -------------------------------------
sample/demo_pubmed.rb | 116 +++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 116 insertions(+), 88 deletions(-)
create mode 100644 sample/demo_pubmed.rb
commit 9e6d720f383e88e247eacab6f0e43f38140a62f2
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 23:59:10 2009 +0900
Demo codes in the "if __FILE__ == $0" are removed.
* Demo codes in the "if __FILE__ == $0" are removed because their
function have already been moved to sample/demo_blast_report.rb.
lib/bio/appl/blast/format0.rb | 193 --------------------------------------
lib/bio/appl/blast/report.rb | 149 +-----------------------------
lib/bio/appl/blast/wublast.rb | 208 -----------------------------------------
3 files changed, 2 insertions(+), 548 deletions(-)
commit bbba2812fa9131d01fc655eb174d84f06facd8b8
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 23:49:36 2009 +0900
New demo code of BLAST parser based on codes in "if __FILE__ ==$0"
* Newly added sample/demo_blast_report.rb, demonstration of
BLAST parsers Bio::Blast::Report, Bio::Blast::Default::Report,
and Bio::Blast::WU::Report. It is based on the demonstration codes
in the "if __FILE__ == $0" in lib/bio/appl/blast/report.rb,
lib/bio/appl/blast/format0.rb, and lib/bio/appl/blast/wublast.rb.
sample/demo_blast_report.rb | 285 +++++++++++++++++++++++++++++++++++++++++++
1 files changed, 285 insertions(+), 0 deletions(-)
create mode 100644 sample/demo_blast_report.rb
commit 5235ed15db8d3ba3e59d8dc3bbbcf1b5b9c58281
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 21:57:08 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_das.rb.
* Demo codes in the "if __FILE__ == $0" are moved to
sample/demo_das.rb.
* Demo codes using UCSC DAS server is added.
* Demo using the WormBase DAS server is temporarily disabled because
it does not work well possibly because of the server trouble.
lib/bio/io/das.rb | 44 ----------------------
sample/demo_das.rb | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 105 insertions(+), 44 deletions(-)
create mode 100644 sample/demo_das.rb
commit b7b0f7bef0505b9678673e54bb863d4ff7897dd5
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 20:58:35 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_taxonomy.rb, although it does not work correctly now.
lib/bio/db/kegg/taxonomy.rb | 53 +-----------------------
sample/demo_kegg_taxonomy.rb | 92 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 93 insertions(+), 52 deletions(-)
create mode 100644 sample/demo_kegg_taxonomy.rb
commit 23da98ca19fce1f0b487e1f955ef4cd896839590
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 20:11:12 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_reaction.rb.
lib/bio/db/kegg/reaction.rb | 16 +----------
sample/demo_kegg_reaction.rb | 64 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 65 insertions(+), 15 deletions(-)
create mode 100644 sample/demo_kegg_reaction.rb
commit 9c0bfb857a6b41d8e6a42ff2cbf7b06ca1d38d78
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 19:12:00 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_orthology.rb.
lib/bio/db/kegg/orthology.rb | 23 +--------------
sample/demo_kegg_orthology.rb | 62 +++++++++++++++++++++++++++++++++++++++++
2 files changed, 63 insertions(+), 22 deletions(-)
create mode 100644 sample/demo_kegg_orthology.rb
commit 6f6f1eb3d87dea588ea333708c4d4486ac7136b6
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 12:19:26 2009 +0900
Commented out demo for nonexistent method "bindings".
sample/demo_kegg_glycan.rb | 4 ++--
1 files changed, 2 insertions(+), 2 deletions(-)
commit 98a6d904058b5af4808f16bcb710d73bd97c9764
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 12:18:31 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_glycan.rb.
lib/bio/db/kegg/glycan.rb | 21 -------------
sample/demo_kegg_glycan.rb | 72 ++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 72 insertions(+), 21 deletions(-)
create mode 100644 sample/demo_kegg_glycan.rb
commit d26e835ca9def2287f1050f1b048892e3cafdaa0
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 11:49:05 2009 +0900
Added references.
lib/bio/db/kegg/genome.rb | 2 ++
1 files changed, 2 insertions(+), 0 deletions(-)
commit c3c460462481b5b8d6e9441216bcf6370b4890ef
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 11:45:31 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_genome.rb.
lib/bio/db/kegg/genome.rb | 42 +------------------------
sample/demo_kegg_genome.rb | 74 ++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 75 insertions(+), 41 deletions(-)
create mode 100644 sample/demo_kegg_genome.rb
commit 0d8e709b66bf18ead5944c27a50eb6cf2c47862f
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 11:43:24 2009 +0900
Added document about downloading sample data.
sample/demo_kegg_drug.rb | 13 ++++++++++++-
1 files changed, 12 insertions(+), 1 deletions(-)
commit 0608893198e9bc88521b6c013069d8c7a13bb0e5
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 00:10:48 2009 +0900
Added documents.
lib/bio/db/kegg/drug.rb | 15 +++++++++++++++
1 files changed, 15 insertions(+), 0 deletions(-)
commit 0ecdc1ee0460f16dba1e4cd5ab575c92e1c6b1ac
Author: Naohisa Goto <ng@bioruby.org>
Date: Wed Nov 25 00:06:02 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_drug.rb.
lib/bio/db/kegg/drug.rb | 18 +--------------
sample/demo_kegg_drug.rb | 54 ++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 55 insertions(+), 17 deletions(-)
create mode 100644 sample/demo_kegg_drug.rb
commit b0c349103f01a26f4741999bd696bf5b1c032e06
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Nov 24 23:51:13 2009 +0900
Added documents.
lib/bio/db/kegg/compound.rb | 10 ++++++++++
1 files changed, 10 insertions(+), 0 deletions(-)
commit e965b454c553ed9670bc83962a2a9d7c5de49929
Author: Naohisa Goto <ng@bioruby.org>
Date: Tue Nov 24 23:45:15 2009 +0900
Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_compound.rb.
lib/bio/db/kegg/compound.rb | 19 +-------------