8e95f3fb60cd61b2bfad8e66caf03d3ff02a6dca Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/acad9497caf5d737394568e911691fdad11ca091 acad9497caf5d737394568e911691fdad11ca091

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

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

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

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_tmhmm_report.rb. da19a06caf4b7a2b6a989948e4349ade5411f4b9 Naohisa Goto ng@bioruby.org 75f7c8527546f8ea3079f53b90a9b4d8260b4de0 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/dfafb0a2bcec4c0b4cd3640374e151e2039056dc dfafb0a2bcec4c0b4cd3640374e151e2039056dc

2009-11-28T21:59:27-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_targetp_report.rb. 13d09c3bf62fa3d87f86f7667811a722d0fc4a81 Naohisa Goto ng@bioruby.org 8022696295dc296462f73b40cc74ad5259bee387 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/75f7c8527546f8ea3079f53b90a9b4d8260b4de0 75f7c8527546f8ea3079f53b90a9b4d8260b4de0

2009-11-28T21:38:07-08:00

2009-11-28T21:33:28-08:00

Follow-up of the SOSUI server URL change. e2e646f0ca0b2bc7f9b350ef9f0ba96737c4eae4 Naohisa Goto ng@bioruby.org 4acfe7f565039b34a036682912a75f55da808b45 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/8022696295dc296462f73b40cc74ad5259bee387 8022696295dc296462f73b40cc74ad5259bee387

2009-11-28T21:32:11-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_sosui_report.rb. 92cc0cb688c598193b83653ee52dcc94d2a56fe9 Naohisa Goto ng@bioruby.org 4f7bd1b7628d90661d8b557ca854b14cc44fb99c Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/4acfe7f565039b34a036682912a75f55da808b45 4acfe7f565039b34a036682912a75f55da808b45

2009-11-28T21:02:32-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_hmmer_report.rb. 8ec8e3893fb74cb7481d1b8410e2bb71bb4af689 Naohisa Goto ng@bioruby.org c2a72d195189755532e7e206af34d152ab6332d8 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/4f7bd1b7628d90661d8b557ca854b14cc44fb99c 4f7bd1b7628d90661d8b557ca854b14cc44fb99c

2009-11-25T22:59:38-08:00

2009-11-25T22:49:21-08:00

Demo codes in the "if __FILE__ == $0" are removed because they are very short. 8aa11be9a50f5c992de101012fab9b462c607a4a Naohisa Goto ng@bioruby.org 549112fb4dfb5f6b2fe3491fb161887a9f5262ac Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/c2a72d195189755532e7e206af34d152ab6332d8 c2a72d195189755532e7e206af34d152ab6332d8

2009-11-25T22:20:28-08:00

Bug fix: Failure of Bio::Fasta.remote due to the remote site changes. 9247a9c63445f621ee6eb6686565682b74d30f40 Naohisa Goto ng@bioruby.org 0e4ca0db83692fdbbe93e90272a07bcbac89192c Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/549112fb4dfb5f6b2fe3491fb161887a9f5262ac 549112fb4dfb5f6b2fe3491fb161887a9f5262ac

2009-11-25T22:13:10-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_fasta_remote.rb. 29bca4ca378a58c4f9ba1d78b669dd20679f5921 Naohisa Goto ng@bioruby.org c0cf91fe2a9247bc3705b20515f9d4fa14288d5a Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/0e4ca0db83692fdbbe93e90272a07bcbac89192c 0e4ca0db83692fdbbe93e90272a07bcbac89192c

2009-11-25T17:17:47-08:00

Text indents for some comment lines are changed. 12463da3cb9b992f6e76629c3ab8ce7f7deed483 Naohisa Goto ng@bioruby.org 8b8206c1d8ee699185fdd19d3329311c85ee003c Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/c0cf91fe2a9247bc3705b20515f9d4fa14288d5a c0cf91fe2a9247bc3705b20515f9d4fa14288d5a

2009-11-25T17:13:26-08:00

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. 886fb38ec99fa7dea00d0508e6de8c8e2eb5f394 Naohisa Goto ng@bioruby.org ebfeec8243abd4e2f65335fda1ead18efff66897 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/8b8206c1d8ee699185fdd19d3329311c85ee003c 8b8206c1d8ee699185fdd19d3329311c85ee003c

2009-11-25T08:50:06-08:00

Fixed the license line. 7acac0bee9ef52b9261a7b6543d388300c82d339 Naohisa Goto ng@bioruby.org 5a0f8379a374650d12fc88fbbd5b28c38ae96395 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/ebfeec8243abd4e2f65335fda1ead18efff66897 ebfeec8243abd4e2f65335fda1ead18efff66897

2009-11-25T08:41:58-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_ncbi_rest.rb. f11f4adeaa1d341a79a4f10378f2e017b01f37f3 Naohisa Goto ng@bioruby.org c560a5d0ba9d4919dbcca156ea620056dcb8f725 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/5a0f8379a374650d12fc88fbbd5b28c38ae96395 5a0f8379a374650d12fc88fbbd5b28c38ae96395

2009-11-25T08:33:07-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_prosite.rb. 8998e1c83331d096640b6d96db786bdc0cde7f35 Naohisa Goto ng@bioruby.org 1299a55d214784a536ae3cd8bfabdfd61fe1da86 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/c560a5d0ba9d4919dbcca156ea620056dcb8f725 c560a5d0ba9d4919dbcca156ea620056dcb8f725

2009-11-25T08:14:37-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_psort.rb. 02e948647e705a76f000dbc335d4cebc0eddb5e3 Naohisa Goto ng@bioruby.org a2686fe3c5a93947c94d4602514a62a808c182d5 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/1299a55d214784a536ae3cd8bfabdfd61fe1da86 1299a55d214784a536ae3cd8bfabdfd61fe1da86

2009-11-25T08:04:29-08:00

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. 7cfdc0cabf6fba1e5e7ab09b1052872678359292 Naohisa Goto ng@bioruby.org 22f662ba69dd2d4a2273562dd7ea921f5cdd84bd Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/a2686fe3c5a93947c94d4602514a62a808c182d5 a2686fe3c5a93947c94d4602514a62a808c182d5

2009-11-25T07:53:54-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_genscan_report.rb. 190f10d2af0f36ffb6d7a78a354580df7064cfc0 Naohisa Goto ng@bioruby.org ed3b34b6598f632c7b9b3f1a17b42406c19ca32d Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/22f662ba69dd2d4a2273562dd7ea921f5cdd84bd 22f662ba69dd2d4a2273562dd7ea921f5cdd84bd

2009-11-25T07:28:01-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_ddbjxml.rb. cf8c67ce07d8e047a9264747eaf7b79b7d48bc6c Naohisa Goto ng@bioruby.org 9e6d720f383e88e247eacab6f0e43f38140a62f2 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/ed3b34b6598f632c7b9b3f1a17b42406c19ca32d ed3b34b6598f632c7b9b3f1a17b42406c19ca32d

2009-11-25T07:13:56-08:00

2009-11-25T07:12:33-08:00

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. c255c2a5cced6e9db7d43821b62dd19b8afe2102 Naohisa Goto ng@bioruby.org bbba2812fa9131d01fc655eb174d84f06facd8b8 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/9e6d720f383e88e247eacab6f0e43f38140a62f2 9e6d720f383e88e247eacab6f0e43f38140a62f2

2009-11-25T07:01:00-08:00

2009-11-25T06:59:10-08:00

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. 3cc8e6f4522c4a0139973fc4a56de48138781ebc Naohisa Goto ng@bioruby.org 5235ed15db8d3ba3e59d8dc3bbbcf1b5b9c58281 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/bbba2812fa9131d01fc655eb174d84f06facd8b8 bbba2812fa9131d01fc655eb174d84f06facd8b8

2009-11-25T06:49:36-08:00

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. 7f51e1b253502aae4c3bce966b412c5bee86d0dd Naohisa Goto ng@bioruby.org b7b0f7bef0505b9678673e54bb863d4ff7897dd5 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/5235ed15db8d3ba3e59d8dc3bbbcf1b5b9c58281 5235ed15db8d3ba3e59d8dc3bbbcf1b5b9c58281

2009-11-25T05:01:04-08:00

2009-11-25T04:57:08-08:00

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. 3bfeebcaa2242797a9e2a8b6bcd75243940d678b Naohisa Goto ng@bioruby.org 23da98ca19fce1f0b487e1f955ef4cd896839590 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/b7b0f7bef0505b9678673e54bb863d4ff7897dd5 b7b0f7bef0505b9678673e54bb863d4ff7897dd5

2009-11-25T03:58:35-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_taxonomy.rb, although it does not work correctly now. d981719613ba7e3020d5b91f9942d0dfb5ff8341 Naohisa Goto ng@bioruby.org 9c0bfb857a6b41d8e6a42ff2cbf7b06ca1d38d78 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/23da98ca19fce1f0b487e1f955ef4cd896839590 23da98ca19fce1f0b487e1f955ef4cd896839590

2009-11-25T03:17:10-08:00

2009-11-25T03:11:12-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_reaction.rb. ce17701357f0dd41e4314e63fdc9bbc1114904fe Naohisa Goto ng@bioruby.org 6f6f1eb3d87dea588ea333708c4d4486ac7136b6 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/9c0bfb857a6b41d8e6a42ff2cbf7b06ca1d38d78 9c0bfb857a6b41d8e6a42ff2cbf7b06ca1d38d78

2009-11-25T02:12:00-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_orthology.rb. a8edf2e2836e609e9c94711db1b7c1e583bdc729 Naohisa Goto ng@bioruby.org 98a6d904058b5af4808f16bcb710d73bd97c9764 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/6f6f1eb3d87dea588ea333708c4d4486ac7136b6 6f6f1eb3d87dea588ea333708c4d4486ac7136b6

2009-11-24T19:19:26-08:00

Commented out demo for nonexistent method "bindings". 94657b22108cc97f931dec3baecc564cda64a471 Naohisa Goto ng@bioruby.org d26e835ca9def2287f1050f1b048892e3cafdaa0 Naohisa Goto ng@bioruby.org http://github.com/bioruby/bioruby/commit/98a6d904058b5af4808f16bcb710d73bd97c9764 98a6d904058b5af4808f16bcb710d73bd97c9764

2009-11-24T19:18:31-08:00

Demo codes in the "if __FILE__ == $0" are moved to sample/demo_kegg_glycan.rb. f5830f6ea8fbd29fc917174d0c20775e0e72e9f2 Naohisa Goto ng@bioruby.org