8dec18794c846726733d66c5a22170f5b2c4bb1a Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/6376dd55aa4995769746e556ca719d37f02975d6 6376dd55aa4995769746e556ca719d37f02975d6 2009-12-20T00:55:07-08:00 2009-12-20T00:32:52-08:00 Added README.txt for FASTQ example data. 49988a4e6a28c9e10bf9d04bad2262c58130f0e7 Naohisa Goto ng@bioruby.org 90b97bfbcfb3f7e3d5c28b195bdb9b9c058df887 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/8dec18794c846726733d66c5a22170f5b2c4bb1a 8dec18794c846726733d66c5a22170f5b2c4bb1a 2009-12-14T21:43:53-08:00 2009-12-14T20:51:13-08:00 Newly added unit tests for Bio::KEGG::GLYCAN with test data. 6bb8474441e878e48b45756e7bbd6e3d8ca0e46a Naohisa Goto ng@bioruby.org 443f778795b82a7f572cb8b85d2a8a8b3cea1334 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/90b97bfbcfb3f7e3d5c28b195bdb9b9c058df887 90b97bfbcfb3f7e3d5c28b195bdb9b9c058df887 2009-12-14T20:49:18-08:00 2009-12-14T18:42:39-08:00 Newly added unit test for Bio::KEGG::DRUG with test data. d83e08059c5c8aeee0260456079212b1b23427ef Naohisa Goto ng@bioruby.org 48184d96b989f909ac0effb759cbc4b1ddc98dd1 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/443f778795b82a7f572cb8b85d2a8a8b3cea1334 443f778795b82a7f572cb8b85d2a8a8b3cea1334 2009-12-14T18:38:59-08:00 2009-12-14T18:38:59-08:00 New method Bio::KEGG::DRUG#products * New method Bio::KEGG::DRUG#products. * Improved RDoc. 9f6c14f9e62aec38a873f62200f49e2bfa0a8f23 Naohisa Goto ng@bioruby.org f364ea609f1e01ca5270a5bd7404e0bbf752bc89 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/48184d96b989f909ac0effb759cbc4b1ddc98dd1 48184d96b989f909ac0effb759cbc4b1ddc98dd1 2009-12-10T08:39:55-08:00 2009-12-10T08:36:54-08:00 Methods in Bio::KEGG::Common::* are changed to cache return values in instance variables. 993fb5965685b350116f4f07ac1e8b96b3ec2bd1 Naohisa Goto ng@bioruby.org 096b5fbf6b7ff906203aabf93eb9a0bd56ae9ba2 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/f364ea609f1e01ca5270a5bd7404e0bbf752bc89 f364ea609f1e01ca5270a5bd7404e0bbf752bc89 2009-12-10T08:25:29-08:00 2009-12-10T08:23:42-08:00 Version is changed to 1.4.0-alpha1, and bioruby.gemspec is regenerated. b860a85eaf92ce9580a161151761f6e4d1dd24ac Naohisa Goto ng@bioruby.org 72ed277fe30bb1033cbc16d462f137510afb84e6 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/096b5fbf6b7ff906203aabf93eb9a0bd56ae9ba2 096b5fbf6b7ff906203aabf93eb9a0bd56ae9ba2 2009-12-10T08:22:59-08:00 2009-12-10T08:22:59-08:00 Added documents about Bio::KEGG incompatible changes. 964c621dba110f34bdcd0f221c509d141ab9a10a Naohisa Goto ng@bioruby.org b99fcb39f7c5d2857cbb65283d85ea868ae8561d Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/72ed277fe30bb1033cbc16d462f137510afb84e6 72ed277fe30bb1033cbc16d462f137510afb84e6 2009-12-10T08:21:26-08:00 2009-12-10T08:21:26-08:00 Newly added unit tests for Bio::KEGG::ENZYME with test data. 444450e692dc5b77699b1f0e4e79f55f69827acc Naohisa Goto ng@bioruby.org 2cc9d4e2f28f6b2bbcb8f714f9e2eb144c594fbf Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/b99fcb39f7c5d2857cbb65283d85ea868ae8561d b99fcb39f7c5d2857cbb65283d85ea868ae8561d 2009-12-10T08:09:03-08:00 2009-12-10T08:09:03-08:00 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. caf3e3583d2217f0109d810fa8440063a850c2ef Naohisa Goto ng@bioruby.org a8ceb23bdf19d6649aa4d879cba76a9e3f91d1d4 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/2cc9d4e2f28f6b2bbcb8f714f9e2eb144c594fbf 2cc9d4e2f28f6b2bbcb8f714f9e2eb144c594fbf 2009-12-10T00:02:05-08:00 2009-12-09T23:02:54-08:00 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. 3082958e83624fadb820d3961f3a6a50ccfe8021 Naohisa Goto ng@bioruby.org 720e0bccdfdc6fac6222cac1a9f05d6e2419896c Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/a8ceb23bdf19d6649aa4d879cba76a9e3f91d1d4 a8ceb23bdf19d6649aa4d879cba76a9e3f91d1d4 2009-12-09T22:28:33-08:00 2009-12-09T22:28:33-08:00 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. 992c5bb0f9e18f3d44e55fc14623dbf140d954e3 Naohisa Goto ng@bioruby.org 20f8c03af92e5cfedcb49e8ed9fc6fda2b86e9c9 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/720e0bccdfdc6fac6222cac1a9f05d6e2419896c 720e0bccdfdc6fac6222cac1a9f05d6e2419896c 2009-12-08T23:39:03-08:00 2009-12-08T23:39:03-08:00 Changed dummy lines for RDoc. acd5aaa6d41ffbddcaaa425fb61bb30bf5e7807c Naohisa Goto ng@bioruby.org b924601bacd643f66b37dd991913e6862df704a9 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/20f8c03af92e5cfedcb49e8ed9fc6fda2b86e9c9 20f8c03af92e5cfedcb49e8ed9fc6fda2b86e9c9 2009-12-08T23:37:53-08:00 2009-12-08T22:17:39-08:00 Refactoring of Bio::KEGG::REACTION#orthologs. * Refactoring of Bio::KEGG::REACTION#orthologs: no need to treat @data because lines_fetch internally does so. 2b0b3da92f1e9f388dd45ddf89117bcd95ce3af2 Naohisa Goto ng@bioruby.org 4c840dc6a539db1d854b23991269b3e6515f637e Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/b924601bacd643f66b37dd991913e6862df704a9 b924601bacd643f66b37dd991913e6862df704a9 2009-12-05T22:51:03-08:00 2009-12-05T22:51:03-08:00 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. e4afc678faa4cf36ec388cd4c52cf2c1927137d0 Naohisa Goto ng@bioruby.org 105efa1ecd1bc99a54aac32710a97df15035119d Kozo Nishida kozo-ni@cg05.naist.jp http://github.com/bioruby/bioruby/commit/4c840dc6a539db1d854b23991269b3e6515f637e 4c840dc6a539db1d854b23991269b3e6515f637e 2009-12-02T06:42:34-08:00 2009-12-02T00:02:00-08:00 Added test methods. 89a714e357af585888ada38bc3c76857bdf1e490 Naohisa Goto ng@bioruby.org c394ead051c3a13ceb534f93816af7ad35be932a Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/105efa1ecd1bc99a54aac32710a97df15035119d 105efa1ecd1bc99a54aac32710a97df15035119d 2009-12-02T06:42:23-08:00 2009-12-02T06:31:07-08:00 Refactoring: to use lib/bio/db/kegg/common.rb for dblinks_as_hash method. 92f7ebfcac8aeb76cace536c723fec103da17f6c Naohisa Goto ng@bioruby.org 4e01fda27166faf066104ab9897904fd46f57123 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/c394ead051c3a13ceb534f93816af7ad35be932a c394ead051c3a13ceb534f93816af7ad35be932a 2009-12-02T06:25:40-08:00 2009-12-02T06:07:23-08:00 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. facf980d581f3407fc79ff53115f9261075f05c3 Naohisa Goto ng@bioruby.org 0c2ce4b8462792d496ab3f58206fdbd47143e280 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/4e01fda27166faf066104ab9897904fd46f57123 4e01fda27166faf066104ab9897904fd46f57123 2009-12-02T05:48:06-08:00 2009-12-02T05:48:06-08:00 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. d226ef9fa312d843165aa0a56524b924fabf3c5e Naohisa Goto ng@bioruby.org 63df07e030120eb43de22555277529822b072270 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/0c2ce4b8462792d496ab3f58206fdbd47143e280 0c2ce4b8462792d496ab3f58206fdbd47143e280 2009-12-02T05:35:21-08:00 2009-12-02T05:35:21-08:00 New methods Bio::KEGG::COMPOUND#dblinks_as_hash and pathways_as_hash, using modules in lib/bio/db/kegg/common.rb. c3162daf1cf3ad994bf7f4881dbe9b9065abf1a2 Naohisa Goto ng@bioruby.org 0e55c6701b09a52356ac55300181ee656773826f Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/63df07e030120eb43de22555277529822b072270 63df07e030120eb43de22555277529822b072270 2009-12-02T05:25:20-08:00 2009-12-02T05:25:20-08:00 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. 2eeaaee5aa383e89e77c4923ccf11276b69055b3 Naohisa Goto ng@bioruby.org a05adcddf6c7ed67c042f31ecd86848af1ba8a22 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/0e55c6701b09a52356ac55300181ee656773826f 0e55c6701b09a52356ac55300181ee656773826f 2009-12-02T04:51:27-08:00 2009-12-02T04:39:06-08:00 Bio::KEGG::COMPOUND#dblinks is reverted to return an array of string. dfa6fd8b5e039b668a6ddc4be85f3a9b7eeb432a Naohisa Goto ng@bioruby.org 86925f3c80730e3ea3377a23a70cadb3876258c4 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/a05adcddf6c7ed67c042f31ecd86848af1ba8a22 a05adcddf6c7ed67c042f31ecd86848af1ba8a22 2009-12-02T04:13:39-08:00 2009-12-02T04:13:39-08:00 Bug fix: fixed a copy-and-paste mistake. e08277fe3141d92702bd2d2795610c43a5443893 Naohisa Goto ng@bioruby.org 60847cd2d0701fa38a499578649cb216c93993a2 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/86925f3c80730e3ea3377a23a70cadb3876258c4 86925f3c80730e3ea3377a23a70cadb3876258c4 2009-12-01T04:31:40-08:00 2009-12-01T04:31:40-08:00 Bio::KEGG::ORTHOLOGY#dblinks_as_hash should preserve database names. 0a096ea9c4e3b356631e8e36df6153cb0a72fc53 Naohisa Goto ng@bioruby.org 2bda62af7a020c22379dd9ec3a42496d2a5b94cb Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/60847cd2d0701fa38a499578649cb216c93993a2 60847cd2d0701fa38a499578649cb216c93993a2 2009-12-01T03:41:51-08:00 2009-12-01T03:41:51-08:00 Test class names are changed to avoid potential class name conflict. db33e8b1b25b947aa18bd1d101f7710c965f2e82 Naohisa Goto ng@bioruby.org acad9497caf5d737394568e911691fdad11ca091 Kozo Nishida kozo-ni@cg05.naist.jp http://github.com/bioruby/bioruby/commit/2bda62af7a020c22379dd9ec3a42496d2a5b94cb 2bda62af7a020c22379dd9ec3a42496d2a5b94cb 2009-12-01T03:34:32-08:00 2009-11-30T11:38:27-08:00 Added unit tests for Bio::KEGG::ORTHOLOGY. 17dac4e9122991e4b93dbb8e3da743e76df34430 Naohisa Goto ng@bioruby.org 8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/acad9497caf5d737394568e911691fdad11ca091 acad9497caf5d737394568e911691fdad11ca091 2009-11-30T04:39:32-08:00 2009-11-30T04:39:32-08:00 Changed to use BioRubyTestDataPath instead of __FILE__. c738dec47999febdfe3ec76c00c5890343855882 Naohisa Goto ng@bioruby.org 2b29654c1d7e927e445e7acdd525835a873c2a2a Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca 8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca 2009-11-28T23:37:21-08:00 2009-11-28T23:37:21-08:00 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. 71a54ef545e24e8d4d27ff0e5c427f08e10a2ab2 Naohisa Goto ng@bioruby.org aa8d49bf31f90dd2796c18ee0aa6291979284ec2 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/2b29654c1d7e927e445e7acdd525835a873c2a2a 2b29654c1d7e927e445e7acdd525835a873c2a2a 2009-11-28T23:24:57-08:00 2009-11-28T23:15:42-08:00 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. d2489d6aa171e6014217d5e1f743e6caf38e09cf Naohisa Goto ng@bioruby.org 76fffd2d2429346478fb3d8c88cdcd878a1047b1 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/aa8d49bf31f90dd2796c18ee0aa6291979284ec2 aa8d49bf31f90dd2796c18ee0aa6291979284ec2 2009-11-28T22:20:36-08:00 2009-11-28T22:20:36-08:00 Demo codes in the "if __FILE__ == $0" are moved to sample/demo_gff1.rb. 8942f676d8fa4025809b96cc5854fbd13ffa5923 Naohisa Goto ng@bioruby.org dfafb0a2bcec4c0b4cd3640374e151e2039056dc Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/76fffd2d2429346478fb3d8c88cdcd878a1047b1 76fffd2d2429346478fb3d8c88cdcd878a1047b1 2009-11-28T22:06:41-08:00 2009-11-28T22:06:41-08:00 Demo codes in the "if __FILE__ == $0" are moved to sample/demo_tmhmm_report.rb. da19a06caf4b7a2b6a989948e4349ade5411f4b9 Naohisa Goto ng@bioruby.org